bluuebunny/crossref_metadata_2025 huggingface dataset:
Problematizing the user in user-centered production: A new media lab meets its audiences
Authors: Ross Philippe
Published: December 2010

With the widespread implementation of ‘participatory’, ‘user-led’, and ‘user-centered’ principles in both the practice and study of technology production, it has become commonplace to treat users as partners in design. This paper is critical of that trend, arguing that the users of a technology in development must first be treated as objects rather than agents of social construction. It draws from a case study of a publicly funded British production-research laboratory in educational new media that was carried out during its first year of existence. The case study highlights some of the tensions and contradictions between the discourse and practice of user-centered design during an uncertain period in a project. By extending Callon’s concept of problematization to include the putative users of technologies in development, this study shows how producers distinguish and mediate between users and partners; how they sustain the notion that there is a group of users ‘out there’ whose existence and requirements can be substantiated prior to the creation of specific technical choices; and how user involvement in and of itself is used for the strategic purpose of enticing partners and asserting their control over the production process. By doing so, the paper affords insight into the practitioners’ belief in the need to gain ever more refined knowledge of specific users, and their recourse to their own experience as a necessary alternative.
Skin-Derived Tenocyte-like Cells for the Treatment of Patellar Tendinopathy
Authors: Clarke Andrew W. , Alyas Faisal , Morris Tim , Robertson Claire J. , Bell Jonathan , Connell David A.
Published: December 2010

Background: Recent research of lateral elbow tendinopathy has led to the use of laboratory-amplified tenocyte-like cells.

Hypothesis: Ultrasound-guided injection of autologous skin-derived tendon-like cells are effective compared with other injectable therapies for the treatment of refractory patellar tendinosis.

Study Design: Randomized controlled trial; Level of evidence, 1.

Methods: From 60 patellar tendons in 46 patients with refractory patellar tendinopathy, a 4-mm skin biopsy was sampled to grow tenocyte-like collagen-producing cells. Patients were allocated into 2 groups: (1) injection with laboratory-prepared, amplified collagen-producing cells derived from dermal fibroblasts and suspended in autologous plasma from centrifuged autologous whole blood or (2) injection with autologous plasma alone. Injections were made into the sites of hypoechogenicity, intrasubstance tears, and fibrillar discontinuity within the patellar tendon. The Victorian Institute of Sport Assessment (VISA) score was used to assess pain, severity, and functional disability. Ultrasound was performed to assess structural and blood flow changes, evaluating 4 criteria: tendon thickness, hypoechogenicity, intrasubstance tears, and neovascularity.

Results: In the cell group, mean VISA scores improved from 44 ± 15 before treatment to 75 ± 17 at 6 months; in the plasma group, from 50 ± 18 to 70 ± 14. Estimated average difference between groups was 8.1, a significantly higher score in the cell group. Patients treated with collagen-producing cells also had significantly faster improvement and a highly significant effect of treatment, with the difference between groups estimated as 2.5 per unit increase in [Formula: see text]. One patient treated with cell therapy had a late rupture and progressed to surgery; histopathology showed normal tendon structure.

Conclusion: Ultrasound-guided injection of autologous skin-derived tendon-like cells can be safely used in the short term to treat patellar tendinopathy, with faster response of treatment and significantly greater improvement in pain and function than with plasma alone.
Alive and Well? The ‘Surveillance Society’ and the Coalition
Authors: Bellamy Christine
Published: December 2010

The new Coalition government in the UK seems to be determined to reverse the ‘surveillance society’ which many observers claimed to have emerged under the previous Labour government. This short article reviews the reasons why the ‘surveillance society’ became a major issue in the last years of the New Labour government, and, in the light of recent policy statements, questions whether the libertarian thrust of the Coalition’s political programme can, in practice, be carried through consistently into departments’ policies.
Consciousness
Authors: Robinson Daniel N.
Published: December 2010

Reductive strategies are especially ill suited to the nature and study of consciousness. The major result of conventional modes of inquiry is the enlargement of the list of correlates, none of which alone or in combination recovers the phenomenon itself.
The Acculturated Brain
Authors: Gergen Kenneth J.
Published: December 2010

Recent decades have been marked by a steadily increasing emphasis on neural determinants of behavior. Concerns with socio-cultural processes have simultaneously been diminished. Given the significance of this shift toward a cortical explanation of human behavior—in terms of both the direction of research in psychology and the implications of this research for social practices and policy—critical reflection is essential. In particular, when significant conceptual flaws are brought into focus, we find good reason to reconsider the significance of socio-cultural process. And, when we take into account major vistas of neuropsychological research, the conclusion becomes evident that not only is human action unintelligible in terms of neural activity, but the brain primarily functions in the service of cultural process. To be sure, cortical functioning may both enable and limit human activity. However, given the enormous variation in human conduct, and the dependency of such conduct on the generation of cultural meaning, the most promising conclusion, both for research and for societal practice, is to view the brain chiefly as an instrument for achieving socially originated ends. This is not to argue against inquiry into brain functioning, but to be more judicious about the domains of its utility, and critical in terms of what it offers for understanding human action.
Personal Reflections on Theory and Psychology
Authors: Gigerenzer Gerd
Published: December 2010

Psychology’s most important task is to integrate the various extant patchworks of theories into overarching theories. Theory integration is a longstanding concern in biology, economics, or physics, but not in psychology. We teach our students how to test theories, not the art of theory construction in the first place. As a consequence, in some parts of psychology, theories have become replaced by surrogates, such as circular restatements of the phenomenon, one-word explanations, and lists of general dichotomies. Moving backwards from existing models to labels is an odd event in science, which typically progresses in the opposite direction. Theory construction should be taught in graduate school, and editors of major journals should encourage submissions that make advances in theory integration.
The Powers of Emptiness
Authors: Hook Derek
Published: December 2010

Foucault is often considered to be the commensurate theorist of power. His late work provides an impressive array of concepts that enables a multi-dimensional analysis of the historical, material, and discursive facets of power. What is missing from this approach, however, is the factor of passionate attachments, or what we might term the sublime motivations that underlie any regime of control. Lacan’s ethical thought prioritizes precisely the issue of the sublime, and, more to the point, the process of sublimation which establishes an effective “short-circuit” between socially valorized objects and direct drive satisfactions of individuals. Key here is the notion of das Ding, the place of the absent object of primordial satisfaction that generates libidinal enjoyment and draws the subject toward the pinnacle of social valorization. Lacan thus shows us what Foucault cannot theorize. That is to say, if sublimation consists of a relation to the real of das Ding, then it cannot be limited in the terms of its activation to the powers of discursive domain alone; it remains a self-initiating and self-regulating form of power.
Salbutamol misuse or abuse with fatal outcome: A case-report
Authors: Boucher Alexandra , Payen Christine , Garayt Christelle , Ibanez Hervé , Dieny Anne , Doche Christophe , Chuniaud Christine , Descotes Jacques
Published: December 2010

Salbutamol is a short-acting agonist of the β2 adrenergic receptors sometimes misused or abused, which can result in various cardiovascular adverse effects. We report one case of fatal salbutamol misuse or abuse in a 36-year-old poorly controlled female asthmatic patient with a past medical history of alcoholism and a recent smoking cessation. She died shortly after hospital admission following acute dyspnea and sudden collapse at home. Toxicological analyses evidenced salbutamol overdose, and necropsy showed acute lung edema and marked dysplasia of the right ventricle and revealed the patient was pregnant. The involvement of an initial disorder of the ventricular rhythm leading to cardiac failure is suggested by the presence of several combined pro-arrhythmogenic factors, such as arrhythmogenic right ventricle dysplasia, hypoxemia related to bronchospasm and salbutamol overdose.
Identification of liver proteins and their roles associated with carbon tetrachloride-induced hepatotoxicity
Authors: Wong Leo Lap Yan , Fan Sheung Tat , Man Kwan , Sit Wai-Hung , Jiang Ping Ping , Jor Irene Wing-Yan , Lee Carol Yee-Ki , Ling Wai Lim , Tam Kin Tung , Wan Jennifer Man-Fan
Published: December 2010

Carbon tetrachloride (CCl4) is a common hepatotoxin used in experimental models to elicit liver injury. To identify the proteins involved in CCl4-induced hepatotoxicity, two-dimensional gel electrophoresis was employed followed by mass spectrometry - mass spectrometry (MS/MS) to study the differentially expressed proteins during CCl4exposure in the Fischer 344 rat liver proteome for 5 weeks. Ten spots with notable changes between the Control and CCl4groups were successfully identified. Among them, four proteins with significant up-regulation, namely calcium-binding protein 1, protein disulfide isomerase, mitochondrial aldehyde dehydrogenase precursor, and, glutathione-S-transferase mu1 and six proteins with significant down-regulation, namely catechol- O-methyltransferase, hemoglobin-alpha-2-chain, hemopexin precursor, methionine sulfoxide reductase A, catalase and carbonic anhydrase 3, were identified. The data indicates that CCl4causes hepatotoxicity by depleting oxygen radical scavengers in the hepatocytes. In this rat model, we profiled hepatic proteome alterations in response to CCl4intoxication. The findings should facilitate understanding of the mechanism of CCl4-induced liver injury.
Protective role of melatonin in myocardial oxidative damage induced by mercury in murine model
Authors: Jindal Mitali , Garg Gobind Rai , Mediratta Pramod Kumari , Fahim Mohammad
Published: December 2010

This study was designed to investigate the electrophysiological, hemodynamic and biochemical parameters of mercuric chloride and methylmercury exposure on cardiovascular functions and its modulation by melatonin in vivo. Wistar albino rats were divided into six group containing 10 animals each. Mercuric chloride (3.75 µM/L) in drinking water and methylmercury (0.5 mg/kg/day) through gavage, given for 1 month, induced a statistically significant increase ( p < 0.001) in left ventricular end diastolic pressure, blood and cardiac tissue mercury content and myocardial lipid peroxides compared to control. Significant attenuation ( p < 0.05) of baroreflex sensitivity and depletion of myocardial endogenous antioxidants ( p < 0.001) viz. Reduced glutathione (GSH) and superoxide dismutase (SOD) were also found in the mercury-exposed groups as compared to control group. Mercury exposure followed by subacute treatment with melatonin (4 µg/mL/day) in drinking water for 1 month significantly lowered ( p < 0.01) left ventricular end diastolic pressure and lipid peroxide levels and increased baroreceptor sensitivity ( p < 0.001) and also levels of GSH and SOD ( p < 0.001) as compared to mercury-exposed rats. The results of our study provide clear evidence that elevated oxidative stress and altered baroreflex mechanisms caused by mercury intoxication may be the contributing factors responsible for impairment of cardiovascular functions and melatonin may exhibit cardioprotective property against subacute heavy metal intoxication and enhance the antioxidant defense against mercury-induced oxidative myocardial injury in rats.
The endothelium: an interface between autoimmunity and atherosclerosis in systemic lupus erythematosus?
Authors: Narshi CB , Giles IP , Rahman A
Published: December 2010

Patients with systemic lupus erythematosus (SLE) have an increased risk of developing cardiovascular disease (CVD). Traditional risk factors fail to fully explain all of this increased risk. As atherosclerosis is recognized as a chronic inflammatory disease, it has been advocated that persistent inflammatory activity in patients with SLE is the principal mechanism that promotes accelerated atherogenesis. Autoantibodies in SLE might contribute to the pathogenesis of atherosclerosis by causing injury to the endothelium and altering the metabolism of lipoproteins involved in atherogenesis. Circulating immune complexes and anti-endothelial cell antibodies can induce expression of a proinflammatory and proadhesive endothelial cell phenotype. Similarly, antiphospholipid antibodies (aPL) may directly activate the endothelium or, via cross-reactivity with other antigens, interfere with lipoprotein metabolism. Antibodies to oxidized low-density lipoprotein (anti-oxLDL) rise with anti-double-stranded DNA antibody titres, complement activation and disease activity scores in patients with SLE. Both clinical and in vitro studies, however, have yielded conflicting results regarding the role of anti-oxLDL and aPL antibodies in CVD. Elevated levels of antibodies to high-density lipoprotein (HDL) and apolipoprotein A1 (the principal protein fraction of HDL) are found in patients with coronary ischaemia. Titres of these antibodies are significantly higher in SLE patients with persistent inflammatory disease and correlate inversely with activity of paraoxonase, a key enzyme that gives HDL its anti-oxidant properties. This review summarizes the evidence that autoantibodies in SLE might contribute to the pathogenesis of atherosclerosis by causing injury to the endothelium and altering the metabolism of lipoproteins involved in atherogenesis.
The prognosis of severe lupus nephritis based on the Modification of Diet in Renal Disease (MDRD) Study estimated glomerular filtration rate
Authors: Patel SB , Korbet SM , Lewis EJ
Published: December 2010

The level of renal function at biopsy is predictive of outcome in patients with severe lupus nephritis (SLN). While renal function has been based on serum creatinine (SCr) alone, measuring the estimated glomerular filtration rate (eGFR) utilizing the Modification of Diet in Renal Disease (MDRD) Study equation has been found to be more accurate. The MDRD eGFR (ml/min/1.73 m2) at biopsy was calculated in 86 patients with SLN and patients were categorized based on eGFR: ≥60 (33 pts), 59–30 (33 pts) and <30 (20 pts). An eGFR was <60 in 18% of patients with a normal SCr. After 120 ± 65 months of follow-up, attainment of a complete remission (76% versus 30% versus 10%, p < 0.0001) and patient survival without end-stage renal disease (ESRD; 10 year survival: 85% versus 45% versus 14%, p < 0.0001 overall) was highest in patients with an eGFR ≥60 and lowest in those with an eGFR <30. The long-term prognosis for patients with severe lupus nephritis and an eGFR ≥60 was extremely good. Since the prognosis for patients with an eGFR <60 was poor even in those patients with a normal SCr, renal function is more accurately determined by the MDRD eGFR.
Not just the Games? Power, protest and politics at the Olympics
Authors: Cottrell M. Patrick , Nelson Travis
Published: December 2010

This article conducts a theoretical and empirical analysis of political protest activity surrounding the modern Olympic Games. Although the Olympics are certainly among the world’s most prominent and recognized events, they have seldom been explored from a political perspective within the mainstream International Relations and transnational protest literatures. We argue, however, that the Olympics provide a theoretically interesting context in which to examine political contention in International Relations in large part because they provide such a unique opportunity structure for a range of actors to exercise power in pursuit of their goals. The article presents an original dataset of all protest occurring between 1896 and 2008 and uses these data to show that not only has Olympic political contention grown substantially over time, but it also has evolved in interesting ways in terms of the particular actors engaged in contention, the tactics they use, and the resistance they face. Furthermore, we suggest that the study of the Olympics has important implications for understanding the power and power limitations of those actors (including transnational advocacy networks, international institutions, and sovereign states) participating in Olympic protest.
Technical considerations for lower limb multidetector computed tomographic angiography
Authors: Keeling Aoife N , Farrelly Cormac , Carr James C , Yaghmai Vahid
Published: December 2010

Multidetector computed tomography (MDCT) enables imaging of the entire arterial tree non-invasively. Optimal technical considerations for performing MDCT angiography (MDCTA) are essential for accurate diagnosis and atherosclerotic disease stratification. This review article focuses on the various technical aspects necessary for peripheral computed tomographic angiography (CTA) acquisition. Common clinical indications for peripheral MDCTA and the latest scan protocols are described. The essential issue of radiation dose reduction is discussed, along with methods of optimal contrast bolus detection and delivery. Post-processing techniques are also presented. Previously, digital subtraction angiography was the only established reliable imaging technique to quantify atherosclerotic disease load; however, MDCTA may now challenge this old gold standard, along with other non-invasive techniques such as magnetic resonance angiography (MRA).
(De)Financialization and Crisis in Eastern Europe
Authors: Gabor Daniela
Published: December 2010

This paper investigates how financialization pressures in Eastern Europe shaped vulnerabilities to the 2007 global deleveraging and to what extent policy responses to crisis have sought to reinforce or delink from financialization. It explores the technical devices underpinning financialization, linked to the dominance of carry-trade strategies in foreign-owned banks and nonresident investors, validated by a set of central bank practices that changed the relationship between wholesale money markets and currency markets. Three distinct periods in the timeline of crisis show that central bank interventions were crucial in resuscitating financialization and that attempts to re-embed finance cannot be successful if public debt dynamics are neglected.
The Financial Crisis of 2007–09 and Emerging Countries: The Political Economy Analysis of Central Banks in the Brazilian and Korean Economies
Authors: Painceira Juan Pablo
Published: December 2010

Insofar as the global crisis of 2007–09 can be understood as a fully-fledged crisis of the financialization era, it has presented new challenges for central banks. However, this paper argues that the central banks' interventions in key middle income countries (Brazil and Korea) have reinforced the main characteristics of financialization and have been different from their previous foreign exchange crisis of the late 1990s. The key reasons for this sharp contrast in central bank interventions can be found in the origins of the recent crisis — in developed financial markets — which is different from the previous one which originated in emerging markets. Furthermore, the higher level of financial integration of both economies in relation to the late 1990s is a more important factor. The Korean and Brazilian experiences show that liquidity management by central banks has been conditioned by international capital flows, and more importantly they have reinforced this trend through their operations in spite of differences in the dynamics of capital flows, in their timing of reserve accumulation and in their level of financial integration.
Limited clinical relevance of imaging techniques in the follow-up of patients with advanced chronic lymphocytic leukemia: results of a meta-analysis
Authors: Eichhorst Barbara F. , Fischer Kirsten , Fink Anna-Maria , Elter Thomas , Wendtner Clemens M. , Goede Valentin , Bergmann Manuela , Stilgenbauer Stephan , Hopfinger Georg , Ritgen Matthias , Bahlo Jasmin , Busch Raymonde , Hallek Michael ,   for the German CLL Study Group (GCLLSG)
Published: December 2010

The clinical value of imaging is well established for the follow-up of many lymphoid malignancies but not for chronic lymphocytic leukemia (CLL). A meta-analysis was performed with the dataset of 3 German CLL Study Group phase 3 trials (CLL4, CLL5, and CLL8) that included 1372 patients receiving first-line therapy for CLL. Response as well as progression during follow-up was reassessed according to the National Cancer Institute Working Group1996 criteria. A total of 481 events were counted as progressive disease during treatment or follow-up. Of these, 372 progressions (77%) were detected by clinical symptoms or blood counts. Computed tomography (CT) scans or ultrasound were relevant in 44 and 29 cases (9% and 6%), respectively. The decision for relapse treatment was determined by CT scan or ultrasound results in only 2 of 176 patients (1%). CT scan results had an impact on the prognosis of patients in complete remission only after the administration of conventional chemotherapy but not after chemoimmunotherapy. In conclusion, physical examination and blood count remain the methods of choice for staging and clinical follow-up of patients with CLL as recommended by the International Workshop on Chronic Lymphocytic Leukemia 2008 guidelines. These trials are registered at http://www.isrctn.org as ISRCTN 75653261 and ISRCTN 36294212 and at http://www.clinicaltrials.gov as NCT00281918.
GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells
Authors: Yu Shuyang , Cui Kairong , Jothi Raja , Zhao Dong-Mei , Jing Xuefang , Zhao Keji , Xue Hai-Hui
Published: December 2010

Maintaining a steady pool of self-renewing hematopoietic stem cells (HSCs) is critical for sustained production of multiple blood lineages. Many transcription factors and molecules involved in chromatin and epigenetic modifications have been found to be critical for HSC self-renewal and differentiation; however, their interplay is less understood. The transcription factor GA binding protein (GABP), consisting of DNA-binding subunit GABPα and transactivating subunit GABPβ, is essential for lymphopoiesis as shown in our previous studies. Here we demonstrate cell-intrinsic, absolute dependence on GABPα for maintenance and differentiation of hematopoietic stem/progenitor cells. Through genome-wide mapping of GABPα binding and transcriptomic analysis of GABPα-deficient HSCs, we identified Zfx and Etv6 transcription factors and prosurvival Bcl-2 family members including Bcl-2, Bcl-XL, and Mcl-1 as direct GABP target genes, underlying its pivotal role in HSC survival. GABP also directly regulates Foxo3 and Pten and hence sustains HSC quiescence. Furthermore, GABP activates transcription of DNA methyltransferases and histone acetylases including p300, contributing to regulation of HSC self-renewal and differentiation. These systematic analyses revealed a GABP-controlled gene regulatory module that programs multiple aspects of HSC biology. Our studies thus constitute a critical first step in decoding how transcription factors are orchestrated to regulate maintenance and multipotency of HSCs.
Evidence for the cure of HIV infection by CCR5Δ32/Δ32 stem cell transplantation
Authors: Allers Kristina , Hütter Gero , Hofmann Jörg , Loddenkemper Christoph , Rieger Kathrin , Thiel Eckhard , Schneider Thomas
Published: December 2010

HIV entry into CD4+ cells requires interaction with a cellular receptor, generally either CCR5 or CXCR4. We have previously reported the case of an HIV-infected patient in whom viral replication remained absent despite discontinuation of antiretroviral therapy after transplantation with CCR5Δ32/Δ32 stem cells. However, it was expected that the long-lived viral reservoir would lead to HIV rebound and disease progression during the process of immune reconstitution. In the present study, we demonstrate successful reconstitution of CD4+ T cells at the systemic level as well as in the gut mucosal immune system after CCR5Δ32/Δ32 stem cell transplantation, while the patient remains without any sign of HIV infection. This was observed although recovered CD4+ T cells contain a high proportion of activated memory CD4+ T cells, ie, the preferential targets of HIV, and are susceptible to productive infection with CXCR4-tropic HIV. Furthermore, during the process of immune reconstitution, we found evidence for the replacement of long-lived host tissue cells with donor-derived cells, indicating that the size of the viral reservoir has been reduced over time. In conclusion, our results strongly suggest that cure of HIV has been achieved in this patient.
Ribonucleotide reduction - horizontal transfer of a required function spans all three domains
Authors: Lundin Daniel , Gribaldo Simonetta , Torrents Eduard , Sjöberg Britt-Marie , Poole Anthony M
Published: December 2010

Background

Ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of DNA. The reaction is catalysed by ribonucleotide reductases (RNRs), an ancient enzyme family comprised of three classes. Each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class I RNRs have been identified in archaeal genomes, and classes II and III likewise appear rare across eukaryotes. In this study, we examine whether this distribution is best explained by presence of all three classes in the Last Universal Common Ancestor (LUCA), or by horizontal gene transfer (HGT) of RNR genes. We also examine to what extent environmental factors may have impacted the distribution of RNR classes.

Results

Our phylogenies show that the Last Eukaryotic Common Ancestor (LECA) possessed a class I RNR, but that the eukaryotic class I enzymes are not directly descended from class I RNRs in Archaea. Instead, our results indicate that archaeal class I RNR genes have been independently transferred from bacteria on two occasions. While LECA possessed a class I RNR, our trees indicate that this is ultimately bacterial in origin. We also find convincing evidence that eukaryotic class I RNR has been transferred to the Bacteroidetes, providing a stunning example of HGT from eukaryotes back to Bacteria. Based on our phylogenies and available genetic and genomic evidence, class II and III RNRs in eukaryotes also appear to have been transferred from Bacteria, with subsequent within-domain transfer between distantly-related eukaryotes. Under the three-domains hypothesis the RNR present in the last common ancestor of Archaea and eukaryotes appears, through a process of elimination, to have been a dimeric class II RNR, though limited sampling of eukaryotes precludes a firm conclusion as the data may be equally well accounted for by HGT.

Conclusions

Horizontal gene transfer has clearly played an important role in the evolution of the RNR repertoire of organisms from all three domains of life. Our results clearly show that class I RNRs have spread to Archaea and eukaryotes via transfers from the bacterial domain, indicating that class I likely evolved in the Bacteria. However, against the backdrop of ongoing transfers, it is harder to establish whether class II or III RNRs were present in the LUCA, despite the fact that ribonucleotide reduction is an essential cellular reaction and was pivotal to the transition from RNA to DNA genomes. Instead, a general pattern of ongoing horizontal transmission emerges wherein environmental and enzyme operational constraints, especially the presence or absence of oxygen, are likely to be major determinants of the RNR repertoire of genomes.
Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered european eel
Authors: Coppe Alessandro , Pujolar Jose Martin , Maes Gregory E , Larsen Peter F , Hansen Michael M , Bernatchez Louis , Zane Lorenzo , Bortoluzzi Stefania
Published: December 2010

Background

Once highly abundant, the European eel (Anguilla anguilla L.; Anguillidae; Teleostei) is considered to be critically endangered and on the verge of extinction, as the stock has declined by 90-99% since the 1980s. Yet, the species is poorly characterized at molecular level with little sequence information available in public databases.

Results

The first European eel transcriptome was obtained by 454 FLX Titanium sequencing of a normalized cDNA library, produced from a pool of 18 glass eels (juveniles) from the French Atlantic coast and two sites in the Mediterranean coast. Over 310,000 reads were assembled in a total of 19,631 transcribed contigs, with an average length of 531 nucleotides. Overall 36% of the contigs were annotated to known protein/nucleotide sequences and 35 putative miRNA identified.

Conclusions

This study represents the first transcriptome analysis for a critically endangered species. EeelBase, a dedicated database of annotated transcriptome sequences of the European eel is freely available at http://compgen.bio.unipd.it/eeelbase. Considering the multiple factors potentially involved in the decline of the European eel, including anthropogenic factors such as pollution and human-introduced diseases, our results will provide a rich source of data to discover and identify new genes, characterize gene expression, as well as for identification of genetic markers scattered across the genome to be used in various applications.
Brazilian Plasmodium falciparum isolates: investigation of candidate polymorphisms for artemisinin resistance before introduction of artemisinin-based combination therapy
Authors: Gama Bianca E , de Oliveira Natália K Almeida , de Souza José M , Santos Fátima , de Carvalho Leonardo JM , Melo Yonne FC , Rosenthal Philip J , Daniel-Ribeiro Cláudio T , Ferreira-da-Cruz Maria de Fátima
Published: December 2010

Background

This study was performed to better understand the genetic diversity of known polymorphisms in pfatpase6 and pfmdr1 genes before the introduction of ACT in Brazil, in order to get a genotypic snapshot of Plasmodium falciparum parasites that may be used as baseline reference for future studies.

Methods

Parasites from P. falciparum samples collected in 2002, 2004 and 2006-2007 were genotyped using PCR and DNA sequencing at codons 86, 130, 184, 1034, 1042, 1109 and 1246 for pfmdr1 gene, and 243, 263, 402, 431, 623, 630, 639, 683, 716, 776, 769 and 771 for pfatpase6 gene.

Results

A pfmdr1 haplotype NEF/CDVY was found in 97% of the samples. In the case of pfatpase6, four haplotypes, wild-type (37%), 630 S (35%), 402 V (5%) and double-mutant 630 S + 402 V (23%), were detected.

Conclusion

Although some polymorphism in pfmdr1 and pfatpase6 were verified, no reported haplotypes in both genes that may mediate altered response to ACT was detected before the introduction of this therapy in Brazil. Thus, the haplotypes herein described can be very useful as a baseline reference of P. falciparum populations without ACT drug pressure.
Kalman estimator- and general linear model-based on-line brain activation mapping by near-infrared spectroscopy
Authors: Hu Xiao-Su , Hong Keum-Shik , Ge Shuzhi S , Jeong Myung-Yung
Published: December 2010

Background

Near-infrared spectroscopy (NIRS) is a non-invasive neuroimaging technique that recently has been developed to measure the changes of cerebral blood oxygenation associated with brain activities. To date, for functional brain mapping applications, there is no standard on-line method for analysing NIRS data.

Methods

In this paper, a novel on-line NIRS data analysis framework taking advantages of both the general linear model (GLM) and the Kalman estimator is devised. The Kalman estimator is used to update the GLM coefficients recursively, and one critical coefficient regarding brain activities is then passed to at-statistical test. Thet-statistical test result is used to update a topographic brain activation map. Meanwhile, a set of high-pass filters is plugged into the GLM to prevent very low-frequency noises, and an autoregressive (AR) model is used to prevent the temporal correlation caused by physiological noises in NIRS time series. A set of data recorded in finger tapping experiments is studied using the proposed framework.

Results

The obtained results suggest that the method can effectively track the task related brain activation areas, and prevent the noise distortion in the estimation while the experiment is running. Thereby, the potential of the proposed method for real-time NIRS-based brain imaging was demonstrated.

Conclusions

This paper presents a novel on-line approach for analysing NIRS data for functional brain mapping applications. This approach demonstrates the potential of a real-time-updating topographic brain activation map.
The practical application of 2D inversion to marine controlled-source electromagnetic data
Authors: Weitemeyer Karen , Gao Guozhong , Constable Steven , Alumbaugh David
Published: December 2010

An algorithm is presented for the inversion of marine controlled-source electromagnetic (CSEM) data that uses a 2D finite difference (FD) forward driver. This code is demonstrated by inverting a CSEM data set collected at Hydrate Ridge, Oregon, consisting of 25 seafloor sites recording a [Formula: see text] transmission frequency. The sites are located across a bathymetric high, with variations in water depth of [Formula: see text] along the [Formula: see text] profile. To model this complex seafloor bathymetry accurately, the FD grid was designed by careful benchmarking using a different 2D finite element (FE) forward code. A comparison of the FE and FD forward model solutions verifies that no features in the inversion are due to inaccuracies of the FD grid. The inversion includes the local seawater conductivity–depth profile as recorded by the transmitter’s conductivity–temperature-depth gauge, because seawater conductivity is known to have a significant effect on the CSEM responses. An apparent resistivity pseudosection of the CSEM data resembles the 2D inversion in general appearance. However, the inversion provides depth and geometric control of features that cannot be provided by the pseudosection and eliminates artifacts generated from the pseudosection projection.
A simple model for squirt-flow dispersion and attenuation in fluid-saturated granular rocks
Authors: Gurevich Boris , Makarynska Dina , de Paula Osni Bastos , Pervukhina Marina
Published: December 2010

A major cause of seismic attenuation in fluid-saturated rocks is the flow of the pore fluid induced by the passing wave. At sonic and ultrasonic frequencies, attenuation appears to be dominated by the local (pore-scale) flow between pores of different shapes and orientations. A simple squirt flow model is developed in which all of the parameters can be independently measured or estimated from measurements. The pore space of the rock is assumed to consist of stiff porosity and compliant (or soft) pores present at grain contacts. The effect of isotropically distributed compliant pores is modeled by considering pressure relaxation in a disk-shaped gap between adjacent grains. This derivation gives the complex and frequency-dependent effective bulk and shear moduli of a rock, in which the compliant pores are liquid saturated and stiff pores are dry. The resulting squirt model is consistent with Gassmann’s and Mavko–Jizba equations at low and high frequencies, respectively. The magnitude of attenuation and dispersion given by the model is directly related to the variation of dry bulk modulus with pressure and is relatively independent of fluid properties.
Vax2 regulates retinoic acid distribution and cone opsin expression in the vertebrate eye
Authors: Alfano Giovanna , Conte Ivan , Caramico Tiziana , Avellino Raffaella , Arnò Benedetta , Pizzo Maria Teresa , Tanimoto Naoyuki , Beck Susanne C. , Huber Gesine , Dollé Pascal , Seeliger Mathias W. , Banfi Sandro
Published: December 2010

Vax2 is an eye-specific homeobox gene, the inactivation of which in mouse leads to alterations in the establishment of a proper dorsoventral eye axis during embryonic development. To dissect the molecular pathways in which Vax2 is involved, we performed a transcriptome analysis of Vax2–/– mice throughout the main stages of eye development. We found that some of the enzymes involved in retinoic acid (RA) metabolism in the eye show significant variations of their expression levels in mutant mice. In particular, we detected an expansion of the expression domains of the RA-catabolizing enzymes Cyp26a1 and Cyp26c1, and a downregulation of the RA-synthesizing enzyme Raldh3. These changes determine a significant expansion of the RA-free zone towards the ventral part of the eye. At postnatal stages of eye development, Vax2 inactivation led to alterations of the regional expression of the cone photoreceptor genes Opn1sw (S-Opsin) and Opn1mw (M-Opsin), which were significantly rescued after RA administration. We confirmed the above described alterations of gene expression in the Oryzias latipes (medaka fish) model system using both Vax2 gain- and loss-of-function assays. Finally, a detailed morphological and functional analysis of the adult retina in mutant mice revealed that Vax2 is necessary for intraretinal pathfinding of retinal ganglion cells in mammals. These data demonstrate for the first time that Vax2 is both necessary and sufficient for the control of intraretinal RA metabolism, which in turn contributes to the appropriate expression of cone opsins in the vertebrate eye.
Choice of random rather than imprinted X inactivation in female embryonic stem cell-derived extra-embryonic cells
Authors: Murakami Kazuhiro , Araki Kimi , Ohtsuka Satoshi , Wakayama Teruhiko , Niwa Hitoshi
Published: December 2010

In female mammals, one of two X chromosomes is epigenetically inactivated for gene dosage compensation, known as X inactivation (Xi). Inactivation occurs randomly in either the paternal or maternal X chromosome in all embryonic cell lineages, designated as random Xi. By contrast, in extra-embryonic cell lineages, which are segregated from somatic cell lineages in pre-implantation development, the paternal X chromosome is selectively inactivated, known as imprinted Xi. Although it is speculated that erasure of the imprinted mark on either the maternal or paternal X chromosome in somatic cell lineages might change the mode of Xi from imprinted to random, it is not known when this event is completed in development. Here, we tested the mode of Xi during the differentiation of female mouse embryonic stem (ES) cells derived from the inner cell mass (ICM) of blastocyst-stage embryos toward trophectoderm (TE) and primitive endoderm (PrE) lineages induced by artificial activation of transcription factor genes Cdx2 and Gata6, respectively. We found that random Xi occurs in both TE and PrE cells. Moreover, cloned embryos generated by the transfer of nuclei from the female ES cells showed random Xi in TE, suggesting the complete erasure of all X imprints for imprinted Xi in ICM-derived ES cells.
Environmental differences in substrate mechanics do not affect sprinting performance in sand lizards (Uma scoparia and Callisaurus draconoides)
Authors: Korff Wyatt L. , McHenry Matthew J.
Published: December 2010

Running performance depends on a mechanical interaction between the feet of an animal and the substrate. This interaction may differ between two species of sand lizard from the Mojave Desert that have different locomotor morphologies and habitat distributions. Uma scorparia possesses toe fringes and inhabits dunes, whereas the closely related Callisaurus draconoides lacks fringes and is found on dune and wash habitats. The present study evaluated whether these distribution patterns are related to differential locomotor performance on the fine sand of the dunes and the course sand of the wash habitat. We measured the kinematics of sprinting and characterized differences in grain size distribution and surface strength of the soil in both habitats. Although wash sand had a surface strength (15.4±6.2 kPa) that was more than three times that of dune sand (4.7±2.1 kPa), both species ran with similar sprinting performance on the two types of soil. The broadly distributed C. draconoides ran with a slightly (22%) faster maximum speed (2.2±0.2 m s–1) than the dune-dwelling U. scorparia (1.8±0.2 m s–1) on dune sand, but not on wash sand. Furthermore, there were no significant differences in maximum acceleration or the time to attain maximum speed between species or between substrates. These results suggest that differences in habitat distribution between these species are not related to locomotor performance and that sprinting ability is dominated neither by environmental differences in substrate nor the presence of toe fringes.
Visualizing a set of olfactory sensory neurons responding to a bile salt
Authors: Døving Kjell B. , Hansson Kenth-Arne , Backström Tobias , Hamdani El Hassan
Published: December 2010

In the present study, we exposed the olfactory epithelia of crucian carp, Carassius carassius, and brown trout, Salmo trutta, to dextran coupled with Alexa dyes together with odorants. Dye uptake was severely reduced after pre-exposure to nocodazole, an inhibitor of microtubule polymerization that impairs endocytosis, supporting the hypothesis that odour-activated olfactory receptor molecules undergo endocytosis. Application of the bile acid taurolithocholate, a potent and specific odorant for fish, resulted in the labelling of a sparse (less than 3%) cell population with the typical morphology of ciliated sensory neurons (CSNs) – long dendrites and cell somata deep in the sensory epithelium. The dye was distributed throughout the sensory neuron, also revealing axons and target glomeruli. Stained axons redistribute at the entrance of the olfactory bulb and terminate in two small target areas, a dorsal and a medial one. These results are consistent with the notion that taurolithocholate is detected specifically by a few ciliated sensory neurons. Application of the olfactory epithelium of brown trout to bile acid stained cells with the appearance of CSNs. Application of an alarm agonist, hypxanthine-3-N-oxide, to crucian carp olfactory organ caused staining of another set of sensory neurons. Furthermore, our results show that odour-induced uptake of a dye can serve to identify the subtype of olfactory sensory neurons responding to a particular odorant, and to pinpoint the target regions of these neurons in the olfactory bulb as a first step to elucidating the neuronal network responding to a particular odour.
State-dependent physiological maintenance in a long-lived ectotherm, the painted turtle (Chrysemys picta)
Authors: Schwanz Lisa , Warner Daniel A. , McGaugh Suzanne , Di Terlizzi Roberta , Bronikowski Anne
Published: December 2010

Energy allocation among somatic maintenance, reproduction and growth varies not only among species, but among individuals according to states such as age, sex and season. Little research has been conducted on the somatic (physiological) maintenance of long-lived organisms, particularly ectotherms such as reptiles. In this study, we examined sex differences and age- and season-related variation in immune function and DNA repair efficiency in a long-lived reptile, the painted turtle (Chrysemys picta). Immune components tended to be depressed during hibernation, in winter, compared with autumn or spring. Increased heterophil count during hibernation provided the only support for winter immunoenhancement. In juvenile and adult turtles, we found little evidence for senescence in physiological maintenance, consistent with predictions for long-lived organisms. Among immune components, swelling in response to phytohemagglutinin (PHA) and control injection increased with age, whereas basophil count decreased with age. Hatchling turtles had reduced basophil counts and natural antibodies, indicative of an immature immune system, but demonstrated higher DNA repair efficiency than older turtles. Reproductively mature turtles had reduced lymphocytes compared with juvenile turtles in the spring, presumably driven by a trade-off between maintenance and reproduction. Sex had little influence on physiological maintenance. These results suggest that components of physiological maintenance are modulated differentially according to individual state and highlight the need for more research on the multiple components of physiological maintenance in animals of variable states.
Flowers help bees cope with uncertainty: signal detection and the function of floral complexity
Authors: Leonard Anne S. , Dornhaus Anna , Papaj Daniel R.
Published: December 2010

Plants often attract pollinators with floral displays composed of visual, olfactory, tactile and gustatory stimuli. Since pollinators' responses to each of these stimuli are usually studied independently, the question of why plants produce multi-component floral displays remains relatively unexplored. Here we used signal detection theory to test the hypothesis that complex displays reduce a pollinator's uncertainty about the floral signal. Specifically, we asked whether one component of the floral display, scent, improved a bee's certainty about the value of another component, color hue. We first trained two groups of bumble bees (Bombus impatiens Cresson) to discriminate between rewarding and unrewarding artificial flowers of slightly different hues in the presence vs absence of scent. In a test phase, we presented these bees with a gradient of floral hues and assessed their ability to identify the hue rewarded during training. We interpreted the extent to which bees' preferences were biased away from the unrewarding hue (‘peak shift’) as an indicator of uncertainty in color discrimination. Our data show that the presence of an olfactory signal reduces uncertainty regarding color: not only was color learning facilitated on scented flowers but also bees showed a lower amount of peak shift in the presence of scent. We explore potential mechanisms by which scent might reduce uncertainty about color, and discuss the broader significance of our results for our understanding of signal evolution.