bluuebunny/crossref_metadata_2025 huggingface dataset:
DRIMM-Synteny: decomposing genomes into evolutionary conserved segments
Authors: Pham Son K. , Pevzner Pavel A.
Published: August 2010

Motivation: The rapidly increasing set of sequenced genomes highlights the importance of identifying the synteny blocks in multiple and/or highly duplicated genomes. Most synteny block reconstruction algorithms use genes shared over all genomes to construct the synteny blocks for multiple genomes. However, the number of genes shared among all genomes quickly decreases with the increase in the number of genomes.

Results: We propose the Duplications and Rearrangements In Multiple Mammals (DRIMM)-Synteny algorithm to address this bottleneck and apply it to analyzing genomic architectures of yeast, plant and mammalian genomes. We further combine synteny block generation with rearrangement analysis to reconstruct the ancestral preduplicated yeast genome.

Contact:  kspham@cs.ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ICPS: an integrative cancer profiler system
Authors: Zhang Xin-yu , Shi Lin , Liu Yan , Tian Feng , Zhao Hai-tao , Miao Xiao-ping , Huang Ming-lie , Zhu Xiao-yan
Published: August 2010

Founded upon the database of 570 public signatures, ICPS is a web-based application to obtain biomarker profiles among 11 common cancers by integrating genomic alterations with transcription signatures on the basis of a previously developed integrative pipeline. ICPS supports both public data and user's in-house data, and performs meta-analysis at a cancer subtype level by combining heterogeneous datasets. Finally, ICPS returns the robust gene signature containing potential cancer biomarkers that may be useful to carcinogenesis study and clinical cancer diagnosis.

Availability:  http://server.bioicps.org

Contact:  zhxy@mail.tsinghua.edu.cn; zxy-dcs@mail.tsinghua.edu.cn
Deep and wide digging for binding motifs in ChIP-Seq data
Authors: Kulakovskiy I. V. , Boeva V. A. , Favorov A. V. , Makeev V. J.
Published: August 2010

Summary: ChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of thousands of DNA segments with base-specific coverage values. We present a new version of our DNA motif discovery software ChIPMunk adapted for ChIP-Seq data. ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences. Comparison with traditional (MEME) or ChIP-Seq-oriented (HMS) motif discovery tools shows that ChIPMunk identifies the correct motifs with the same or better quality but works dramatically faster.

Availability and implementation: ChIPMunk is freely available within the ru_genetika Java package: http://line.imb.ac.ru/ChIPMunk. Web-based version is also available.

Contact:  ivan.kulakovskiy@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Discriminating between Posidonia oceanica meadows and sand substratum using multibeam sonar
Authors: Di Maida Germana , Tomasello Agostino , Luzzu Filippo , Scannavino Antonino , Pirrotta Maria , Orestano Carla , Calvo Sebastiano
Published: August 2010

Di Maida, G., Tomasello, A., Luzzu, F., Scannavino, A., Pirrotta, M., Orestano, C., and Calvo, S. 2011. Discriminating between Posidonia oceanica meadows and sand substratum using multibeam sonar. – ICES Journal of Marine Science, 68: 12–19. High-resolution, multibeam sonar (MBS) (455 kHz) was used to identify two typologies of seabed 8 m deep: Posidonia oceanica meadow and sandy substratum. The results showed that the heterogeneity of the architecture of the P. oceanica canopy and the relatively simple morphology of a sandy substratum can be detected easily by statistical indices such as standard deviation or range-of-beam depth. Based on these indices, an automated classification was performed for seabed mapping. The overall classification accuracy was as high as 99 and 98% in October and January, respectively. The probability that P. oceanica in situ was omitted on the map was <7%, whereas the probability that an area classified as P. oceanica on the map did not correspond to the seagrass in situ was consistently negligible. Based on these results, high-resolution MBS can be considered to be an accurate tool for mapping P. oceanica and sand substrata, and its discriminating power seems to be independent of season (autumn or winter).
Predictors of Recovery After Conservative Treatment of AO-Type A Thoracolumbar Spine Fractures Without Neurological Deficit
Authors: Vorlat Peter , Leirs Geert , Tajdar Farhad , Hulsmans Heinz , De Boeck Hugo , Vaes Peter
Published: August 2010

Study Design.

Prospective, correlational, exploratory, clinical research.

Objective.

To identify the factors determining a patient's recovery after conservative treatment of compression fractures of the thoracolumbar spine.

Summary of Background Data.

The reported results of compression fractures are poor. These results are not influenced by the severity of compression, the fracture site, or the residual deformity. Otherwise, the factors that determine a patient's recovery are unknown.

Methods.

In 48 conservatively treated patients the preinjury versus the 12-month follow-up differences (Δ) in back pain (visual analogue scale for pain), Oswestry disability index (ODI), and the Greenough and Fraser low back outcome scale were prospectively recorded. For these differences and for time lost from work and satisfaction, multiple linear regressions with combinations of 16 factors were performed.

Results.

At 1 year, patients with an income-insurance were 9% (P = 0.096) more disabled than those without. They reported a 15% less favorable global outcome and 27% less participation. Smokers were 13% (P = 0.010) more disabled and 11% (P = 0.044) less satisfied. With each increase of the AO-fracture type from A1 to A3 the disability was 8% worse. Patients with pre-existent chronic low back pain (CLBP) returned two points (on a visual analogue scale [VAS] pain total of 10) more closely (P = 0.041) to their preinjury pain level than those without but were 21% (P = 0.001) less satisfied. Our model offers an explanation for more than 25% of the variability of ΔODI and of the satisfaction. For sick leave, no significant predictors were found.

Conclusion.

Smoking and insurance status are the strongest negative predictors for recovery. LBP patients returned more closely to their preinjury back pain level, but were less satisfied. The AO fracture type had a marked influence on disability, the sagittal deformity had not. The time lost from work did not depend on patient or injury-related factors.

Level of Evidence: N/A
Left Ventricular Giant Pseudoaneurysm
Authors: Filizcan Uğur , Cetemen Sebnem , Soylu Ozer , Bicer Mehmet , Aydogan Hakki , Eren Ergin
Published: August 2010

Left ventricular (LV) pseudoaneurysm is a rare complication of myocardial infarction. It may also occur as a complication of mitral valve surgery, chest trauma, and bacterial endocarditis. It forms when a cardiac rupture contains adherent pericardium or scar tissue and is typically located on the posterior or inferior LV wall. Pseudoaneurysms have a propensity to spontaneous rupture; hence, immediate surgical intervention is the treatment of choice for LV pseudoaneurysms diagnosed in the first months after myocardial infarction. The management of chronic LV pseudoaneurysms is still a subject of debate.
Lung Hernia after Video-Assisted Thoracoscopic Lobectomy
Authors: Johnson Caitlyn , Weksler Benny
Published: August 2010

Lung hernias are rare and are most commonly secondary to blunt or penetrating trauma. Few cases have been reported after video-assisted thoracoscopic surgery and only one case after video-assisted thoracoscopic surgery lobectomy. We report a case of lung hernia after video-assisted, thoracoscopic, right upper lobectomy. The hernia was demonstrated by computerized tomography and repaired by minimally invasive techniques. We believe that the combination of removal of a large lung specimen and the presence of emphysema may predispose to lung herniation after thoracoscopic lobectomy. Thoracic surgeons should be aware of this possible complication.
Advantages of Sutureless Aortic Valve in a Patient with Unsuspected Pheochromocytoma
Authors: Soon Jia-Lin , Gibson Fiona A. M. , Janas Shirley , Pillai Ravi
Published: August 2010

We describe a 60-year-old man who underwent elective aortic valve replacement and concurrent single graft coronary artery bypass surgery with acute intraoperative hypertension. The early suspicion of a pheochromocytoma and immediate aggressive pharmacologic intervention are discussed. Expeditious surgery contributed to the good outcome. It is possible that the short implant time of the sutureless valve may have been beneficial, but this is speculative. The management of an undiagnosed pheochromocytoma presenting during general anesthesia is reviewed.
Suppression of the Vacuolar Invertase Gene Prevents Cold-Induced Sweetening in Potato
Authors: Bhaskar Pudota B. , Wu Lei , Busse James S. , Whitty Brett R. , Hamernik Andy J. , Jansky Shelley H. , Buell C. Robin , Bethke Paul C. , Jiang Jiming
Published: August 2010

Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to prevent sprouting, minimize disease losses, and supply consumers and the processing industry with high-quality tubers throughout the year. Unfortunately, cold storage triggers an accumulation of reducing sugars in tubers. High-temperature processing of these tubers results in dark-colored, bitter-tasting products. Such products also have elevated amounts of acrylamide, a neurotoxin and potential carcinogen. We demonstrate that silencing the potato vacuolar acid invertase gene VInv prevents reducing sugar accumulation in cold-stored tubers. Potato chips processed from VInv silencing lines showed a 15-fold acrylamide reduction and were light in color even when tubers were stored at 4°C. Comparable, low levels of VInv gene expression were observed in cold-stored tubers from wild potato germplasm stocks that are resistant to cold-induced sweetening. Thus, both processing quality and acrylamide problems in potato can be controlled effectively by suppression of the VInv gene through biotechnology or targeted breeding.
Purification, crystallization and preliminary crystallographic analysis of the catalytic domain of the extracellular cellulase CBHI fromTrichoderma harzianum
Authors: Colussi Francieli , Textor Larissa C. , Serpa Viviane , Maeda Roberto Nobuyuki , Pereira Nei , Polikarpov Igor
Published: August 2010

The filamentous fungusTrichoderma harzianumhas a considerable cellulolytic activity that is mediated by a complex of enzymes which are essential for the hydrolysis of microcrystalline cellulose. These enzymes were produced by the induction ofT. harzianumwith microcrystalline cellulose (Avicel) under submerged fermentation in a bioreactor. The catalytic core domain (CCD) of cellobiohydrolase I (CBHI) was purified from the extracellular extracts and submitted to robotic crystallization. Diffraction-quality CBHI CCD crystals were grown and an X-ray diffraction data set was collected under cryogenic conditions using a synchrotron-radiation source.
Cloning, expression, purification, crystallization and preliminary crystallographic analysis of 5-aminolaevulinic acid dehydratase fromBacillus subtilis
Authors: Lu Qianda , Ma Jinming , Rong Hui , Fan Jun , Yuan Ye , Li Kuai , Gao Yongxiang , Zhang Xiao , Teng Maikun , Niu Liwen
Published: August 2010

5-Aminolaevulinic acid dehydratase (ALAD), a crucial enzyme in the biosynthesis of tetrapyrrole, catalyses the condensation of two 5-aminolaevulinic acid (ALA) molecules to form porphobilinogen (PBG). The gene encoding ALAD was amplified from genomic DNA ofBacillus subtilisand the protein was overexpressed inEscherichia colistrain BL21 (DE3). The protein was purified and crystallized with an additional MGSSHHHHHHSSGLVPRGSH– tag at the N-terminus of the target protein. Diffraction-quality single crystals were obtained by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected at a resolution of 2.7 Å.
Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of a human condensin SMC2 hinge domain with short coiled coils
Authors: Kawahara Kazuki , Nakamura Shota , Katsu Yasuhiro , Motooka Daisuke , Hosokawa Yuki , Kojima Yukiko , Matsukawa Keiko , Takinowaki Hiroto , Uchiyama Susumu , Kobayashi Yuji , Fukui Kiichi , Ohkubo Tadayasu
Published: August 2010

In higher eukaryotes, the condensin complex, which mainly consists of two structural maintenance of chromosomes (SMC) subunits, SMC2 (CAP-E) and SMC4 (CAP-C), plays a critical role in the formation of higher order chromosome structures during mitosis. Biochemical and electron-microscopic studies have revealed that the SMC2 and SMC4 subunits dimerize through the interaction of their hinge domains, forming a characteristic V-shaped heterodimer. However, the details of their function are still not fully understood owing to a lack of structural information at the atomic level. In this study, the human SMC2 hinge domain with short coiled coils was cloned, expressed, purified and crystallized in the orthorhombic space groupC222 in native and SeMet-derivatized forms. Because of the poor diffraction properties of these crystals, the mutant Leu68→SeMet was designed and crystallized in order to obtain the experimental phases. The SeMet-derivatized crystals of the mutant belonged to space groupP3212, with unit-cell parametersa=b= 128.8,c = 91.4 Å. The diffraction data obtained from a crystal that diffracted to 2.4 Å resolution were suitable for SAD phasing.
Crystallization and preliminary X-ray analysis of the major peanut allergen Ara h 1 core region
Authors: Cabanos Cerrone , Urabe Hiroyuki , Masuda Taro , Tandang-Silvas Mary Rose , Utsumi Shigeru , Mikami Bunzo , Maruyama Nobuyuki
Published: August 2010

Peanuts contain some of the most potent food allergens known to date. Ara h 1 is one of the three major peanut allergens. As a first step towards three-dimensional structure elucidation, recombinant Ara h 1 core region was cloned, expressed inEscherichia coliand purified to homogeneity. Crystals were obtained using 0.1 Msodium citrate pH 5.6, 0.1 MNaCl, 15% PEG 400 as precipitant. The crystals diffracted to 2.25 Å resolution using synchrotron radiation and belonged to the monoclinic space groupC2, with unit-cell parametersa= 156.521,b= 88.991,c= 158.971 Å, β = 107.144°. Data were collected at the BL-38B1 station of SPring-8 (Hyogo, Japan).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of the catalytic domain of a hyperthermostable endo-1,4-β-D-mannanase fromThermotoga petrophilaRKU-1
Authors: Santos Camila Ramos , Squina Fabio Marcio , Navarro Andreia Meza , Ruller Roberto , Prade Rolf , Murakami Mario Tyago
Published: August 2010

Endo-1,4-β-D-mannanases play key roles in seed germination and fruit ripening and have recently received much attention owing to their potential applications in the food, detergent and kraft pulp industries. In order to delineate their structural determinants for specificity and stability, X-ray crystallographic investigations combined with detailed functional studies are being performed. In this work, crystals of the catalytic domain of a hyperthermostable endo-1,4-β-D-mannanase fromThermotoga petrophilaRKU-1 were obtained from three different conditions, resulting in two crystalline forms. Crystals from conditions with phosphate or citrate salts as precipitant (CryP) belonged to space groupP212121, with unit-cell parametersa= 58.76,b= 87.99,c= 97.34 Å, while a crystal from a condition with ethanol as precipitant (CryE) belonged to space groupI212121, with unit-cell parametersa= 91.03,b= 89.97,c= 97.89 Å. CryP and CryE diffracted to resolutions of 1.40 and 1.45 Å, respectively.
Growth and differentiation of the developing limb bud from the perspective of chondrogenesis
Authors: Shimizu Hirohito , Yokoyama Shigetoshi , Asahara Hiroshi
Published: August 2010

Limb skeletal elements develop from a cartilage template, which is formed by the process termed chondrogenesis. This process is crucial in determining the shape and size of definitive bones in vertebrates. During chondrogenesis, aggregated mesenchymal cells undergo a highly organized process of proliferation and maturation along with secretion of extracellular matrix followed by programmed cell death and replacement by bone. The molecular mechanisms underlying this sophisticated process have been extensively studied. It has been demonstrated that several transcription factors such as Sox genes and Runx genes are indispensable for the major steps in chondrogenesis. Additionally, a number of signaling molecules including Bmps, Fgfs and Ihh/PTHrP are known to regulate chondrogenesis through highly coordinated interactions. This review is meant to provide an overview of the current knowledge of chondrogenesis with particular emphasis on the cellular and molecular aspects.
New Foundations for Imperative Logic I: Logical Connectives, Consistency, and Quantifiers*
Authors: Vranas Peter B. M.
Published: August 2010

Imperatives cannot be true or false, so they are shunned by logicians. And yet imperatives can be combined by logical connectives: “kiss me and hug me” is theconjunctionof “kiss me” with “hug me”. This example may suggest that declarative and imperative logic are isomorphic: just as the conjunction of two declaratives istrueexactly if both conjuncts are true, the conjunction of two imperatives issatisfiedexactly if both conjuncts are satisfied—what more is there to say? Much more, I argue. “If you love me, kiss me”, aconditionalimperative, mixes a declarative antecedent (“you love me”) with an imperative consequent (“kiss me”); it issatisfiedif you love and kiss me,violatedif you love but don't kiss me, andavoidedif you don't love me. So we need a logic ofthree‐valued imperatives whichmixesdeclaratives with imperatives. I develop such a logic.
Frankfurt's Argument against Alternative Possibilities: Looking Beyond the Examples1
Authors: McKenna Michael
Published: August 2010

Harry Frankfurt dramatically shaped the debates over freedom and responsibility by arguing that the sort of freedom germane to responsibility does not involve the freedom to do otherwise. His argument turns upon an example meant to disprove the Principle of Alternative Possibilities:

 A person is morally responsible for what she has done only if she could have done otherwise.

Debate over Frankfurt's argument has turned almost exclusively on the success of the example meant to defeat it. But there is more to Frankfurt's argument than the example in question, and this is not widely recognized. Inattention to these other aspects of Frankfurt's argument has distorted the force of it. In this paper I shall explore avenues for both refuting and advancing Frankfurt's argument that look beyond the examples. These further considerations invite us to think in broader terms about moral responsibility's nature and the sort of freedom required for it.
A Third Way in Metaethics
Authors: Schroeter Laura , Schroeter François
Published: August 2010

What does it take to count as competent with the meaning of a thin evaluative predicate like ‘is the right thing to do’? According to minimalists like Allan Gibbard and Ralph Wedgwood, competent speakers must simply use the predicate to express their own motivational states. According to analytic descriptivists like Frank Jackson, Philip Pettit and Christopher Peacocke, competent speakers must grasp a particular criterion for identifying the property picked out by the term. Both approaches face serious difficulties. We suggest that these difficulties derive from a shared background assumption that competence conditions must be explained in terms of a determinate conceptual role. We propose a new way of characterizing competence with evaluative terms: what's required for competence is participation in a shared epistemic practice with a term. Our approach, we argue, better explains the nature of evaluative inquiry and the extent of disagreement about evaluative questions.
Chicken, Eggs, and Speciation1
Authors: Matthen Mohan
Published: August 2010

Standard biological and philosophical treatments assume that dramatic genotypic or phenotypic change constitutes instantaneous speciation, and that barring such saltation, speciation is gradual evolutionary change in individual properties. Both propositions appear to be incongruent with standard theoretical perspectives on species themselves, since these perspectives are (a) non‐pheneticist, and (b) tend to disregard intermediate cases. After reviewing certain key elements of such perspectives, it is proposed that species‐membership is mediated by membership in a population. Species‐membership depends, therefore, not on intrinsic characteristics of an organism, but on relationship of an organism to others. A new definition of speciation is proposed in the spirit of this proposal. This definition implies that dramatic change is neither necessary nor sufficient for speciation. It also implies, surprisingly, that an organism can change species during its lifetime.
Why Experience Told Me Nothing about Transparency1
Authors: Molyneux Bernard
Published: August 2010

The transparency argument concludes that we're directly aware of external properties and not directly aware of the properties of experience. Focusing on the presentation used by Michael Tye (2002) I contend that the argument requires experience to have content that it cannot plausibly have. I attribute the failure to a faulty account of the transparency phenomenon and conclude by suggesting an alternative understanding that is independently plausible, is not an error‐theory and yet renders the transparency of experience compatible with mental‐paint style views.
Experts, Semantic and Epistemic
Authors: Goldberg Sanford
Published: August 2010

In this paper I argue that the tendency to defer in matters semantic is rationalized by our reliance on the say‐so of others for much of what we know about the world. The result, I contend, is a new and distinctly epistemic source of support for the doctrine of attitude anti‐individualism.
The Financialization of Urban Redevelopment
Authors: Rutland Ted
Published: August 2010

Spurred by the conviction that not only financial capital but also changes in finance and changes in its relations with non‐financial activities have immense and complicated consequences for ongoing processes of urban redevelopment, this article puts the presently separate financialization and urban redevelopment literatures in conversation. The article begins with a review of the financialization literature, outlining and evaluating four different approaches to the topic and seeking to consider what, if anything, they might have to offer to an area of inquiry that has long considered finance to be a central concern. The second section examines how financial capital has been analyzed in the urban redevelopment literature since the pioneering work of David Harvey in the 1970s. The final section examines how financialization has played out in the medium‐sized port city of Halifax, Nova Scotia. Drawing on interviews with financiers and property developments, as well as secondary research materials, the study describes how a recent urban design process in Halifax enlisted urban images and ideas to rewrite development regulations, eliminate popular political involvement in the development approvals process, and lever open the downtown landscape to the whims of worldwide financial markets. The essay concludes that studies of urban redevelopment would indeed gain something by engaging with the financialization literature, so long as the former continue to attend not just to financial capital but also to the material and ideological mechanisms through which property is continually reproduced as a financial asset.
Hydrogeomorphic Processes in Temperate and Tropical Forests: Effects of Land Use and Scale
Authors: Sidle Roy C.
Published: August 2010

The science of hydrogeomorphology has evolved during the past few decades to include not only the coupling of hydrologic and geomorphic processes but also the spatial and temporal interactions of these processes. Bioclimatic factors play an important role in determining which hydrologic and geomorphic processes dominate in various environments and how these processes evolve and distribute in time and space. Herein, sediment production and transport are discussed as examples of important hydrogeomorphic phenomena at different spatial and temporal scales in the context of climate, forest cover, hydrology, and geomorphic setting. Examples are presented that illustrate the dominant hydrogeomorphic processes in steep (typical slope gradients >30°) humid tropical and temperate forests. Landslides contribute substantial sediment loads to streams, particularly in steep temperate forest terrain; however, the timing between the mass wasting event on the hillslope and the delivery and mobilization of the sediment in the channel can be highly variable. Linkages between surface erosion on hillslopes and sediment response in streams are more direct if connected pathways exist. The connectivity of sediment sources with flow pathways in catchments can be greatly enhanced by land uses (particularly unpaved roads and trails) that compact and disturb soils and redistribute water onto susceptible landforms.
Spatio‐Temporal Attributes of Pandemic and Epidemic Diseases
Authors: Bossak Brian H. , Welford Mark R.
Published: August 2010

Human‐to‐human transmissible pandemics, most notably the Medieval Black Death and Spanish Flu of 1918, have historically resulted in the world’s greatest mortality events. Today, as global transportation networks move people rapidly around the world, there are few barriers to emergent diseases. The mystery of the next great pandemic is not if, but rather when and where it will emerge. Therefore, understanding basic epidemiological attributes of infection, and the highly variable matrix of political, economic, and cultural attributes which affect micro‐scale disease transmission, is now more critical than ever. An emergent disease has the capacity to become a deadly global pandemic if optimized for infectivity, lethality, and environmental persistence. Lacking optimization in any one of these broad attributes can lead to a disease that is technically a pandemic with high infectivity, yet exhibits low lethality, such as Swine Flu (H1N1). In addition, a disease could emerge with very high lethality, yet which does not persist in the environment very long outside of a host, nor kills slow enough to allow for a large amount of secondary infections to occur from contact with a primary infected host, similar to the Ebola virus in Sub‐Saharan Africa. The spatial dynamics of emergent diseases is also affected by socioeconomic processes such as the built environment, migration, poverty, race, ethnicity, and gender relationships. Yet even with so many variables present, super‐spreading events, whereby a few infected individuals secondarily infect a high number of susceptible individuals, can rapidly transmit infectious diseases across very heterogeneous spaces. Today’s global social networks and connectivity are leading toward an enhanced potential for pandemic infections and greater disease virulence as a bio‐evolutionary consequence toward pathogenic success.
Climate Change Impacts in Alpine Environments
Authors: Grabherr Georg , Gottfried Michael , Pauli Harald
Published: August 2010

Alpine ecosystems (alpine tundra) occur at a range of air density, water availability and seasonality worldwide on the treeless high terrain of mountains. They vary along geographic scales: boreal dwarf‐shrub heaths, temperate sedge heaths, subtropical dwarf shrubs and tussock grasslands, and tropical giant forblands. Along local topographic gradients plant cover changes from windswept dwarf‐shrub heath, to dense grass‐sedge heath, to snowbank vegetation. These cold and relatively little exploited alpine ecosystems, nonetheless, are among those where climate warming impacts are forecast to be pronounced and detectable early on. We first review alpine life conditions and organism traits as a background to understanding climate impact related processes. Next, we provide an account of how alpine flora and vegetation have been impacted by recently observed climate change. Finally, a global network for long‐term monitoring of climate‐induced changes of vegetation and biodiversity in alpine environments is described.
Neoliberalism and Geography: Expansions, Variegations, Formations
Authors: Springer Simon
Published: August 2010

The pervasiveness of neoliberalism within the field of human geography is remarkable, especially when we consider its virtual absence from the literature less than a decade ago. While the growing attention afforded to neoliberalism among geographers is new, the phenomenon of neoliberalism is not. This paper traces the intellectual history of neoliberalism and its expansions across various institutional frameworks and geographical settings. I review the primary contributions geographers have made to the literature, and specifically their recognition for neoliberalism’s variegations within existing political economic matrixes and institutional frameworks. Contra the prevailing view of neoliberalism as a pure and static end‐state, geographical inquiry illuminates neoliberalism as a dynamic and unfolding process. The concept of ‘neoliberalization’ is thus seen as more appropriate to geographical theorizations insofar as it recognizes neoliberalism’s hybridized and mutated forms as it travels around our world. I also consider some of the most salient ways that neoliberalism has been theorized among human geographers. In particular, I highlight understandings of neoliberalism as a hegemonic ideology, as a policy‐based approach to state reform, and as a particular logic of governmentality, arguing that while there are significant differences between these various formations, it may also be important to work beyond methodological, epistemological, and ontological divides in the larger interest of social justice.
Chinese Spatial Inequalities and Spatial Policies
Authors: Dunford Michael , Li Li
Published: August 2010

In the last fifty years Chinese spatial inequalities have expanded in phases of industrial expansion and contracted in phases favourable to agriculture. Since 1985 real per capita disposable income and real per capita expenditure have increased rapidly in all parts of China. The increases were however much greater (i) in areas on the east coast than in the centre, northeast and west creating widening macro‐territorial inequalities, (ii) in some provinces rather than others increasing inter‐provincial inequalities and (iii) in urban areas rather than rural areas. These imbalances have seen the adoption of a succession of policies designed initially to promote a more equilibrated model of co‐ordinated national development and more recently a more sustainable and more equitable development path consistent with the more recent emphasis on the goal of harmonious development. This paper examines the evolution and impact of these trends in inequality and policy initiatives paying attention to a variety of geographical scales.
The Business of Temporary Staffing: A Developing Research Agenda
Authors: Coe Neil M. , Jones Katharine , Ward Kevin
Published: August 2010

This paper offers a critical review of the existing literatures on temporary staffing. It argues that while research on both client firm rationales and the experiences and characteristics of temporary agency workers are relatively well advanced, work that explores the temporary staffing industry and its own strategies and expansionary logics is still in its infancy. This is a significant oversight given the increasingly widespread influence of this particular form of labour market intermediary. Grounded in recent work in economic geography, the paper maps a future research agenda.
NGOs in Microfinance: Learning from the Past, Accepting Limitations, and Moving Forward
Authors: Baruah Bipasha
Published: August 2010

Over the past three decades, microfinance has become an extremely popular and populist development intervention. The Grameen Bank and its founder, Dr. Muhammad Yunus, were awarded the 2006 Nobel Peace Prize and the Global Microcredit Summit in Halifax, Nova Scotia set itself the goal of lending to 175 million people around the world by 2015. Despite such global enthusiasm, the limitations of microfinance are gradually being acknowledged even by its most vociferous proponents. The vast majority of NGOs in microfinance not only face tremendous challenges in balancing outreach and financial sustainability, but there is also growing evidence of their failure to make an aggregate impact on poverty reduction. At the same time, there is evidence that NGOs can – even without offering credit or savings programs – play extremely important roles in areas such as poverty relief, marketing, enterprise development, innovation, and social intermediation. This article looks at strategies NGOs in microfinance can use to meet their social justice goals without becoming completely seduced by commercial values or being lured away from their major objective of serving the poor. As a development methodology, microfinance is firmly embedded within a neo‐liberal framework that seeks to increase poor people’s access to financial resources without really challenging the entrenched status quo of unequal power relations between different groups of people. The continued popularity of microfinance should not foreclose the possibility of more creative and complex engagement with inequality as well as for more boldly original visions and innovative solutions to promote human dignity and social justice.
More than Visiting Hours: Maintaining Ties Between Incarcerated Mothers and Their Children
Authors: Michalsen Venezia , Flavin Jeanne , Krupat Tanya
Published: August 2010

The majority of people in America’s prisons are the parents of minor children. Incarcerated mothers, in particular, were likely to have been a part of their children’s lives before their imprisonment, and most will soon be returning to the community and to their children. Research has shown that it is in the best interests of the mothers and the children to maintain a relationship across the prison bars. In this article, we use the example of New York State to show how institutional policies and structures can impede or encourage efforts to maintain ties between women and their children and why demonstrating support for family ties must extend well beyond having visiting hours.
Social Movements Through the Gender Lens
Authors: Yulia Zemlinskaya
Published: August 2010

Although it is widely acknowledged that many aspects of social life are gendered, only relatively recently have feminist researchers begun to address the ‘gender blindness’ of the social movement theory. Integrating findings from multiple studies, the article considers how gender affects social movement dynamics. It is argued that gender exerts pervasive influence on every aspect of social movement activities. The patterns of mobilisation, political and cultural opportunities, framing process and intra‐movement dynamics are all gendered. It is argued that although ample evidence demonstrates that protest is gendered, we do not yet know whether there is any general pattern of influence of gender on social movements, a pattern that enables a systematic explanation of the effects of gender on social movement dynamics. In conclusion, I will examine the reasons for this and suggest avenues for research.
Expanding Horizons of Risk in Criminology
Authors: Anderson Leon , Brown Michelle
Published: August 2010

Few topics in the social sciences have witnessed as dramatic an increase in scholarly attention over the past two decades as the topic of risk. In this essay we examine sociological approaches to risk in criminological research and theory. After briefly describing the concept of risk in classical and neoclassical criminology, we turn our attention to three emerging social science perspectives on risk, those associated with the scholarship on risk society, edgework, and governmentality. We examine the new directions that these emerging ``risk paradigms'' open for criminological theory and research, including new perspectives on the motivation for criminal risk‐taking, the organization of policing and criminal justice systems, and public and political responses to crime. We conclude by reviewing critiques of the scholarship associated with the new risk paradigms and by suggesting promising future directions for criminological research seeking to advance these perspectives.
Under One Roof: A Review of Research on Intergenerational Coresidence and Multigenerational Households in the United States
Authors: Keene Jennifer Reid , Batson Christie D.
Published: August 2010

What motivates adult children, parents, and even grandchildren to live together? To answer this question, we review the sociological and social gerontological research on multigenerational households and families. We first provide a snapshot of multigenerational coresidence in the US and then discuss the primary theoretical perspectives used to explain these patterns: exchange theory, altruism, and norms and obligations. Structural conditions including economic crises tend to facilitate adult children moving in with parents (often with dependent children in tow), while spousal loss and declining health act as catalysts for parents moving in with adult children. Furthermore, economic struggles often facilitate the formation of grandparent‐headed families where the middle generation parents may or may not be present. We suggest that the current economic recession and housing crises will have profound effects on multigenerational households and may also encourage more coresidence. Changes in social welfare policies, increases in coresident grandparenting, and changes in the racial and ethnic composition of the US also have implications for multigenerational households’ economic and social security.
Family Genealogy: A Sociological Imagination Reveals Intersectional Relations
Authors: Hackstaff Karla B.
Published: August 2010

This article depicts everyday family genealogy as a vehicle for the sociological imagination that links personal biography to social–historical contexts across generations. As genealogists construct current from past identities, they engage a sociological imagination that potentially enables them to grasp how intersectionality – gender, race, ethnic, sexuality, nation, class, and age relations – is articulated through history. The key aims here are: (1) to provide background conditions behind the growth of genealogy; (2) to reveal how doing and studying family genealogy engages a sociological imagination that can be a vehicle for perceiving theintersectionalunderpinnings of social memories. Genealogy can be seen as a political practice where race‐class‐gender within social memories can contribute to diverse stories from new standpoints in American history.
Predetonation probability of a fission-bomb core
Authors: Reed B. Cameron
Published: August 2010

An undergraduate-level derivation of the probability that a uranium or plutonium fission bomb will suffer an uncontrolled predetonation due to neutrons liberated in spontaneous fissions in the fissile material is developed. Consistent with what was learned by Los Alamos bomb designers during World War II, it is shown why uncontrolled predetonation was not a problem for a U-235 bomb of the Little Boy “gun” design but necessitated development of implosion engineering for the Pu-239 Trinity and Fat Man bombs where the cores were contaminated with highly spontaneously fissile Pu-240.
Determining the eccentricity of the Moon’s orbit without a telescope
Authors: Krisciunas Kevin
Published: August 2010

Prior to the invention of the telescope many astronomers worked out models of the motion of the Moon to predict the position of the Moon in the sky. These geometrical models implied a certain range of distances of the Moon from Earth. Ptolemy’s most quoted model predicted that the Moon was nearly twice as far away at apogee than at perigee. Measurements of the angular size of the Moon were within the capabilities of pretelescopic astronomers. Such measurements could have helped refine the models of the motion of the Moon, but hardly anyone seems to have made any measurements that have come down to us. We use a piece of cardboard with a small hole in it which slides up and down a yardstick to show that it is possible to determine the eccentricity ϵ≈0.039±0.006 of the Moon’s orbit. A typical measurement uncertainty of the Moon’s angular size is ±0.8 arc min. Because the Moon’s angular size ranges from 29.4 to 33.5 arc min, carefully taken naked eye data are accurate enough to demonstrate periodic variations of the Moon’s angular size.
Simple thermodynamics of jet engines
Authors: Patrício Pedro , Tavares José M.
Published: August 2010

We use the first and second laws of thermodynamics to analyze the behavior of an ideal jet engine. Simple analytical expressions for the thermal efficiency, the overall efficiency, and the reduced thrust are derived. We show that the thermal efficiency depends only on the compression ratio r and on the velocity of the aircraft. The other two performance measures depend also on the ratio of the temperature at the turbine to the inlet temperature in the engine, T3/Ti. An analysis of these expressions shows that it is not possible to choose an optimal set of values of r and T3/Ti that maximize both the overall efficiency and thrust. We study how irreversibilities in the compressor and the turbine decrease the overall efficiency of jet engines and show that this effect is more pronounced for smaller T3/Ti.
The step-harmonic potential
Authors: Rizzi L. , Piattella O. F. , Cacciatori S. L. , Gorini V.
Published: August 2010

We analyze the behavior of a quantum system described by a one-dimensional asymmetric potential consisting of a step plus a harmonic barrier. We solve the eigenvalue equation by the integral representation method, which allows us to classify the independent solutions as equivalence classes of homotopic paths in the complex plane. We then consider the propagation of a wave packet reflected by the harmonic barrier and obtain an expression for the interaction time as a function of the peak energy. For high energies we recover the classical half-period limit.
The weight of a falling chain, revisited
Authors: Hamm Eugenio , Géminard Jean-Christophe
Published: August 2010

A vertically hanging chain is released from rest and falls due to gravity on a scale pan. We discuss the various experimental and theoretical aspects of this classic problem. Careful time-resolved force measurements allow us to determine the differences between the idealized problem and its implementation in the laboratory. We observe that, in spite of the upward force exerted by the pan on the chain, the free end at the top falls faster than a freely falling body. Because a real chain exhibits a finite minimum radius of curvature, the contact at the bottom results in a tensional force, which pulls the falling part downward.
Student experiences of virtual reality: A case study in learning special relativity
Authors: McGrath Dominic , Wegener Margaret , McIntyre Timothy J. , Savage Craig , Williamson Michael
Published: August 2010

A teaching package has been developed centered around a relativistic virtual reality. It introduces concepts of special relativity to students in a gamelike environment where users experience the effects of traveling at near light speeds. From this perspective, space and time are significantly different from that experienced in everyday life. We explore how students worked with this environment and how they used this experience in their study of special relativity. Students found the simulation to be a positive learning experience and described the subject area as being less abstract after its use. Students were more capable of correctly answering concept questions relating to special relativity, and a small but measurable improvement was observed in the final exam.
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria
Authors: Hazen Terry C. , Dubinsky Eric A. , DeSantis Todd Z. , Andersen Gary L. , Piceno Yvette M. , Singh Navjeet , Jansson Janet K. , Probst Alexander , Borglin Sharon E. , Fortney Julian L. , Stringfellow William T. , Bill Markus , Conrad Mark E. , Tom Lauren M. , Chavarria Krystle L. , Alusi Thana R. , Lamendella Regina , Joyner Dominique C. , Spier Chelsea , Baelum Jacob , Auer Manfred , Zemla Marcin L. , Chakraborty Romy , Sonnenthal Eric L. , D’haeseleer Patrik , Holman Hoi-Ying N. , Osman Shariff , Lu Zhenmei , Van Nostrand Joy D. , Deng Ye , Zhou Jizhong , Mason Olivia U.
Published: August 2010

Diving into Deep Water

The Deepwater Horizon oil spill in the Gulf of Mexico was one of the largest oil spills on record. Its setting at the bottom of the sea floor posed an unanticipated risk as substantial amounts of hydrocarbons leaked into the deepwater column. Three separate cruises identified and sampled deep underwater hydrocarbon plumes that existed in May and June, 2010—before the well head was ultimately sealed.

Camilli
et al.

(p.
201
; published online 19 August) used an automated underwater vehicle to assess the dimensions of a stabilized, diffuse underwater plume of oil that was 22 miles long and estimated the daily quantity of oil released from the well, based on the concentration and dimensions of the plume.

Hazen
et al.

(p.
204
; published online 26 August) also observed an underwater plume at the same depth and found that hydrocarbon-degrading bacteria were enriched in the plume and were breaking down some parts of the oil. Finally,

Valentine
et al.

(p.
208
; published online 16 September) found that natural gas, including propane and ethane, were also present in hydrocarbon plumes. These gases were broken down quickly by bacteria, but primed the system for biodegradation of larger hydrocarbons, including those comprising the leaking crude oil. Differences were observed in dissolved oxygen levels in the plumes (a proxy for bacterial respiration), which may reflect differences in the location of sampling or the aging of the plumes.
A Biosynthetic Alternative to Human Donor Tissue for Inducing Corneal Regeneration: 24-Month Follow-Up of a Phase 1 Clinical Study
Authors: Fagerholm Per , Lagali Neil S. , Merrett Kimberley , Jackson W. Bruce , Munger Rejean , Liu Yuwen , Polarek James W. , Söderqvist Monica , Griffith May
Published: August 2010

A biosynthetic cornea is stably integrated with host tissues for 2 years after implantation and produces nerve regeneration and vision improvement.
Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS): A Multiorgan Antiviral T Cell Response
Authors: Picard Damien , Janela Baptiste , Descamps Vincent , D’Incan Michel , Courville Philippe , Jacquot Serge , Rogez Sylvie , Mardivirin Laurent , Moins-Teisserenc Hélène , Toubert Antoine , Benichou Jacques , Joly Pascal , Musette Philippe
Published: August 2010

A dangerous drug reaction may be caused by a severe immune response to reactivated resident herpes viruses.
Ferroportin and Iron Regulation in Breast Cancer Progression and Prognosis
Authors: Pinnix Zandra K. , Miller Lance D. , Wang Wei , D’Agostino Ralph , Kute Tim , Willingham Mark C. , Hatcher Heather , Tesfay Lia , Sui Guangchao , Di Xiumin , Torti Suzy V. , Torti Frank M.
Published: August 2010

An iron efflux pump is a pivotal protein in breast cancer biology and a strong and independent predictor of breast cancer prognosis.
Advancing Science, Promoting Peace
Authors: Agre Peter C. , Turekian Vaughan
Published: August 2010

Despite political differences, scientific diplomacy can help to bridge disparate cultures.