bluuebunny/crossref_metadata_2025 huggingface dataset:
The global wood market, wood resource productivity and price trends: an examination with special attention to China
Authors: AJANI JUDITH
Published: January 2011

Global wood consumption trends are reviewed in the context of framing a coherent forest policy in the era of climate change. Over the period 1980 to 2007, global wood consumption has been essentially stagnant, increasing by only 0.4% per year. In contrast over the same period, global consumption of wood products increased steadily, paper by an average 3.2% per annum and solid wood products (sawn timber and wood panels) by 0.8% per annum. Wood saving explains these significantly different growth trajectories in unprocessed wood and processed wood products. Wood saving strategies include recycling paper (in particular), investing in higher yielding pulp technologies, substituting reconstituted wood panels for sawn timber and plywood and growing high pulp-yielding trees in a plantation regime. China's rapidly growing wood products industry has lifted wood saving to a new high. Consistent with the theory of induced innovation, China has so far avoided triggering a global wood shortage and associated wood price increases through a progression of strategies: successful pre-emptive price negotiations, increased use of recycled paper, adoption of high-yielding pulp technologies, substitution of reconstituted wood panels for sawn timber and tree planting substituting for natural forest supply. If China's current wood saving strategies were emulated worldwide, through increased use of recycled paper in particular, and to a lesser extent, substitution of reconstituted wood panels for sawn timber and plywood, the already low growth in global wood consumption would flatten further and perhaps start to decline. These economic realities in the wood products industry align positively with the interlinked imperatives of biodiversity conservation and carbon storage in natural forests, if wood-saving is converted to forest-saving.
A decision tree to help determine the best timing and antiretroviral strategy in HIV-infected patients
Authors: PIROTH L. , FOURNEL I. , MAHY S. , YAZDANPANAH Y. , REY D. , RABAUD C. , FALLER J. P. , HOEN B. , FARDEHEB M. , QUANTIN C. , CHAVANET P. , BINQUET C.
Published: January 2011

Optimal antiretroviral strategies for HIV-infected patients still need to be established. To this end a decision tree including different antiretroviral strategies that could be adopted for HIV-infected patients was built. A 10-year follow-up was simulated by using transitional probabilities estimated from a large cohort using a time-homogeneous Markov model. The desired outcome was for patients to maintain a CD4 cell count of >500 cells/mm3without experiencing AIDS or death. For patients with a baseline HIV viral load ⩾5 log10copies/ml, boosted protease inhibitor-based immediate highly active antiretroviral therapy (HAART) allowed them to spend 12% more time with CD4 ⩾500/mm3than did delayed HAART (6·40vs. 5·69 and 5·57vs. 4·90 years for baseline CD4 ⩾500 and 350–499/mm3, respectively). In patients with a baseline HIV viral load ⩽3·5 log10copies/ml, delayed HAART performed better than immediate HAART (6·43vs. 6·26 and 5·95vs. 5·18 for baseline CD4 ⩾500 and 350–499/mm3, respectively). Immediate HAART is beneficial in patients with a baseline HIV viral load ⩾5 log10copies/ml, whereas deferred HAART appears to be the best option for patients with CD4 ⩾350/mm3and baseline HIV viral load <3·5 log10copies/ml.
“What's Wrong with Being Sexy?” Why Political Science Needs to Get Serious about Sexuality
Authors: Doan Alesha E.
Published: January 2011

From the infamous blue dress to lewd gesturing under an airport bathroom stall, the scandalous coupling of sex and politics generates a lot of buzz. Political pundits inevitably find themselves on the media frontlines, ruminating on the impact of a particular impropriety, its implications for the dishonored politician's career, and his or her ability to effectively perform his or her job. Comedians gather some of their greatest material from the collision of sex and politics. Their jokes and send-ups, however, are not limited to sexual scandal. Tina Fey's impersonation of Sarah Palin catapultedSaturday Night Live(SNL) to the top of the Nielson ratings map in 2008. The nation collectively busted a gut watching the mock “nonpartisan” television announcement featuring Sarah Palin (dressed in a brightly colored skirt suit and punctuating her statements with emotive winks or cutesy giggles) and Hillary Clinton (sporting a drab pantsuit and underscoring her statements with firm nods or a clenched fist pounding the podium) as they denounced the role that sexism played in the presidential campaign.
Gay, Straight, or Questioning? Sexuality and Political Science
Authors: Smith Charles Anthony
Published: January 2011

In August of 2009, the American Psychological Association adopted the report of its Task Force on Appropriate Therapeutic Responses to Sexual Orientation and urged mental health professionals to avoid telling their patients that sexual orientation can be changed (APA 2009a). The report examined the efficacy of “conversion therapies”—also called “reparative therapies”—wherein the patient and therapist attempt to change the sexual orientation of the patient from gay or lesbian to heterosexual. The report is over 160 pages and examines over 80 peer-reviewed, published studies spanning five decades of research. Despite the heft of the report, the findings are briefly and well summarized by the chair of the task force, Judith M. Glassgold, Psy.D.: “Contrary to the claims of sexual orientation change advocates and practitioners, there is insufficient evidence to support the use of psychological interventions to change sexual orientation” (APA 2009b). Of course, this conclusion is a given among all but minor fringe elements in the lesbian, gay, bisexual, or transgender (LGBT) community or among this community's friends and affiliates. While sexuality collectively seems to present itself along a scale, it seems for individuals to become fixed at some point along that scale. The APA report provides a useful framework for considering the role of sexuality in political science and raises several important questions for political science as both an endeavor and a discipline.
Networking Networkers: An Initial Exploration of the Patterns of Collaboration among the Members of a New Community in Political Science
Authors: Berardo Ramiro
Published: January 2011

A number of indicators signal a growing interest in the study of political phenomena from a network perspective in the United States, such as the growing number of published articles with a network focus in the discipline's top-tier journals and the creation of a new Political Networks section of the APSA in 2008. Yet another notable indicator is the organization of a new annual conference financially supported by the National Science Foundation—the Political Networks conference. The meeting not only brings together scholars who study networks in political science, but also fosters collaboration across disciplines by encouraging participation of non–political scientists with the goal of achieving more comprehensive answers to questions that cannot be properly answered within the confines of individual disciplines.
Obama's Local Connection: Racial Conflict or Solidarity
Authors: Liu Baodong
Published: January 2011

Local elections in the past four decades have provided valuable data for political scientists to test various hypotheses concerning racial relations in the United States. Past research has shown, for example, that the elections of African American candidates to powerful offices in urban America are closely related to the changing racial demographics of cities (Browning, Marshall, and Tabb 2003). More specifically, racial polarization in a city's mayoral election tends to be at a maximum when whites and blacks each compose about 50% of the city's population. On the other hand, a biracial coalition between whites and blacks led by a charismatic black candidate is more likely to win elections when blacks become a clear majority of the city population (Liu and Vanderleeuw 2007). One remaining question that has increasingly drawn attention from scholars is the condition under which amultiracialcoalition may be successfully formed.
Thirty Years of Reform and Opening Up: Teaching International Relations in China
Authors: McMahon Patrice C. , Zou Yue
Published: January 2011

In 1978, Deng Xiaoping declared that China's future depended on gaige kaifang (reform and opening up to the West). By any standard, China has reformed its economic system and prospered handsomely by integrating into the world economy. With less fanfare, China has taken steps to restructure its political system and committed substantial resources to harmonizing relations with its neighbors. Given these changes, China's insular tradition, and Communist government, this article considers how the country's reemergence has impacted the teaching of international relations (IR) at Chinese universities. Using primary and secondary sources, including university Web sites written in Chinese and English, and about a dozen semi-structured interviews conducted in Beijing and Xi'an, this study concludes that although China has become actively engaged in IR and the internationalization of universities is evident, the government has yet to endorse fully the importance of IR as a discipline, and universities have not systematically adopted the theoretical toolbox developed outside of China to describe, explain, and predict behavior in IR.
Polling on a Budget: Implementing Telephone Surveys in Introductory and Advanced American Politics Courses
Authors: Williamson Jonathan
Published: January 2011

Research suggests that student learning is enhanced when students are engaged through active learning strategies. In studying public opinion and polling, challenges include the provision of meaningful active learning environments when resources are limited. In this article, I discuss the design and implementation of telephone surveys as a teaching tool for use in introductory American politics as well as upper-level public opinion courses. I emphasize polling situations in which there are limited resources or no established survey research center is available. Topics include student involvement in survey design and implementation, logistics, and budgeting. Student satisfaction with participation in the survey process is also discussed.
ASHER ARIAN
Authors: Gelb Joyce , Shamir Michael , Kuperman Ranan
Published: January 2011

Asher Arian, one of Israel's most prominent political scientists, died on July 6 after a long illness, a four-year battle with cancer. He was 71. Asher Arian was a leading political scientist both in Israel and the United States.
ROBERT V. DANIELS
Authors: Hoffmann Erik P.
Published: January 2011

Robert V. (“Bill”) Daniels died in Burlington, Vermont, on March 28, 2010, at the age of 84. He was a distinguished scholar and teacher at the University of Vermont for more than three decades, a respected administrator in various university positions, a president of the American Association for the Advancement of Slavic Studies, and an elected state senator in the Vermont legislature for nearly a decade. He authored two dozen books on themes of fundamental importance, mostly on revolution and modernization, power and authority, leadership and opposition, participation and bureaucracy, representation and communication, and ideology and culture in the Soviet Union.
C. NEAL TATE
Authors: Booth John , Geer John , Seligson Mitch
Published: January 2011

C. Neal Tate, born October 17, 1943, passed away September 13, 2009, in Nashville, Tennessee. At the time of his death, Neal was the Alexander Heard Distinguished Service Professor, professor of political science, and professor of law at Vanderbilt University, where he had also served as chair of the political science department since 2003. He had previously served on the faculty of the University of North Texas from 1970 through 2003. With a deep sense of sadness, his colleagues and friends at both institutions say goodbye to a beloved friend, teacher, and colleague. Neal's passing has been a great loss for many people around the country and around the world. His contributions were many, and while we will no longer have the benefit of his kindness, keen intellect, and fine sense of humor, we will continue to benefit from his many legacies.
The 2011 Annual Meeting Panel Allocations
Authors: Hauck Robert J-P.
Published: January 2011

The process by which panels are allocated among program committee divisions and related groups may appear to be arcane. It needn't be. In the late fall of the year preceding the next Annual Meeting, each division or group organizer receives a panel allocation and a detailed explanation of how the size of the allocation was determined. The following paragraphs detail the process by which the 2011 panel allocations were determined.
Postmortems of the 2010 Midterm Election Forecasts: Forecasting House Seats from Generic Congressional Polls: A Post-Mortem
Authors: Bafumi Joseph , Erikson Robert S. , Wlezien Christopher
Published: January 2011

Based on information available in July, we predicted that the Republicans would receive 52.9% of the total House vote and end up holding 229 seats, gaining control from the Democrats in the process (Bafumi, Erikson, and Wlezien 2010b). Our national vote forecast proved to be nearly correct, undershooting the actual Republican share (53.8%) by slightly less than one percentage point. Our seat forecast was a little less accurate. Although we did foresee the House changing hands, we did not predict such a large Republican windfall in seats—we forecast a “mere” swing of 50 seats, which was short of the actual outcome by about 13 seats. The Republican seat total of 242, however, was well within the 95% confidence interval (199 to 259).
Postmortems of the 2010 Midterm Election Forecasts: Assessing The 2010 State Legislative Election Forecasting Models
Authors: Klarner Carl
Published: January 2011

This brief note reports the accuracy of my two forecasts for the 2010 state legislative elections, one made on July 22 and reported in the October 2010 issue of this journal (the “PS model”; Klarner 2010a), and the other made on September 18 and reported in the October issue of Forum: A Journal of Applied Research in Contemporary Politics (i.e., the “Forum model”; Klarner 2010b). Both models used presidential approval, the state of the economy, and midterm loss as national-level predictor variables, while the later forecast also used Gallup's generic ballot question asking respondents which party they would vote for in the upcoming U.S. House election. The PS model predicted the Republicans would pick up 11 chambers, while the Forum model forecast a 15-chamber pickup. In actuality, the Republicans picked up 21 chambers, in contrast to the average 3.2-net chamber shift in party control toward one party or the other from 1962 to 2008. While both forecasts understated the extent of the Republican wave, the July forecast especially did. Overall, the Forum forecast did a good job of predicting the Republican wave, calling about three-fourths of its magnitude.
Limits to biodiversity cycles from a unified model of mass-extinction events
Authors: Feulner Georg
Published: January 2011

Episodes of species mass extinction dramatically affected the evolution of life on Earth, but their causes remain a source of debate. Even more controversy surrounds the hypothesis of periodicity in the fossil record, with conflicting views still being published in the scientific literature, often even based on the same state-of-the-art datasets. From an empirical point of view, limitations of the currently available data on extinctions and possible causes remain an important issue. From a theoretical point of view, it is likely that a focus on single extinction causes and strong periodic forcings has strongly contributed to this controversy. Here I show that if there is a periodic extinction signal at all, it is much more likely to result from a combination of a comparatively weak periodic cause and various random factors. Tests of this unified model of mass extinctions on the available data show that the model is formally better than a model with random extinction causes only. However, the contribution of the periodic component is small compared to factors such as impacts or volcanic eruptions.
Genomic tools and germplasm diversity for chickpea improvement
Authors: Upadhyaya Hari D. , Thudi Mahendar , Dronavalli Naresh , Gujaria Neha , Singh Sube , Sharma Shivali , Varshney Rajeev K.
Published: January 2011

Chickpea is the third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years, specialized germplasm subsets such as global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources such as molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), diversity arrays technology (DArT) and transcript sequences, e.g. expressed sequence tags, short transcript reads, have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that the use of genomic resources and specialized germplasm subsets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, trait mapping and allele mining for resistance to biotic and abiotic stresses and for agronomic traits. Advent of the next generation sequencing technologies coupled with advances in bioinformatics offers the possibility of undertaking large-scale sequencing of germplasm accessions so that modern breeding approaches such as genomic selection and breeding by design can be realized in near future for chickpea improvement.
Optical switch probes and optical lock-in detection (OLID) imaging microscopy: high-contrast fluorescence imaging within living systems
Authors: Yan Yuling , Marriott M. Emma , Petchprayoon Chutima , Marriott Gerard
Published: January 2011

Few to single molecule imaging of fluorescent probe molecules can provide information on the distribution, dynamics, interactions and activity of specific fluorescently tagged proteins during cellular processes. Unfortunately, these imaging studies are made challenging in living cells because of fluorescence signals from endogenous cofactors. Moreover, related background signals within multi-cell systems and intact tissue are even higher and reduce signal contrast even for ensemble populations of probe molecules. High-contrast optical imaging within high-background environments will therefore require new ideas on the design of fluorescence probes, and the way their fluorescence signals are generated and analysed to form an image. To this end, in the present review we describe recent studies on a new family of fluorescent probe called optical switches, with descriptions of the mechanisms that underlie their ability to undergo rapid and reversible transitions between two distinct states. Optical manipulation of the fluorescent and non-fluorescent states of an optical switch probe generates a modulated fluorescence signal that can be isolated from a larger unmodulated background by using OLID (optical lock-in detection) techniques. The present review concludes with a discussion on select applications of synthetic and genetically encoded optical switch probes and OLID microscopy for high-contrast imaging of specific proteins and membrane structures within living systems.
The multiple facets of the Golgi reassembly stacking proteins
Authors: Vinke Fabian P. , Grieve Adam G. , Rabouille Catherine
Published: January 2011

The mammalian GRASPs (Golgi reassembly stacking proteins) GRASP65 and GRASP55 were first discovered more than a decade ago as factors involved in the stacking of Golgi cisternae. Since then, orthologues have been identified in many different organisms and GRASPs have been assigned new roles that may seem disconnected. In vitro, GRASPs have been shown to have the biochemical properties of Golgi stacking factors, but the jury is still out as to whether they act as such in vivo. In mammalian cells, GRASP65 and GRASP55 are required for formation of the Golgi ribbon, a structure which is fragmented in mitosis owing to the phosphorylation of a number of serine and threonine residues situated in its C-terminus. Golgi ribbon unlinking is in turn shown to be part of a mitotic checkpoint. GRASP65 also seems to be the key target of signalling events leading to re-orientation of the Golgi during cell migration and its breakdown during apoptosis. Interestingly, the Golgi ribbon is not a feature of lower eukaryotes, yet a GRASP homologue is present in the genome of Encephalitozoon cuniculi, suggesting they have other roles. GRASPs have no identified function in bulk anterograde protein transport along the secretory pathway, but some cargo-specific trafficking roles for GRASPs have been discovered. Furthermore, GRASP orthologues have recently been shown to mediate the unconventional secretion of the cytoplasmic proteins AcbA/Acb1, in both Dictyostelium discoideum and yeast, and the Golgi bypass of a number of transmembrane proteins during Drosophila development. In the present paper, we review the multiple roles of GRASPs.
A human pathology-related mutation prevents import of an aminoacyl-tRNA synthetase into mitochondria
Authors: Messmer Marie , Florentz Catherine , Schwenzer Hagen , Scheper Gert C. , van der Knaap Marjo S. , Maréchal-Drouard Laurence , Sissler Marie
Published: January 2011

Mutations in the nuclear gene coding for the mitochondrial aspartyl-tRNA synthetase, a key enzyme for mitochondrial translation, are correlated with leukoencephalopathy. A Ser45 to Gly45 mutation is located in the predicted targeting signal of the protein. We demonstrate in the present study, by in vivo and in vitro approaches, that this pathology-related mutation impairs the import process across mitochondrial membranes.
Time-resolved FT-IR Spectroscopy of Membrane Proteins
Authors: Radu Ionela , Schleeger Michael , Nack Melanie , Heberle Joachim
Published: January 2011

Time-resolved Fourier transform infrared spectroscopy (FT-IR) offers distinct advantages concerning restrictions pertinent to biomolecules. In particular, it is possible to monitor the temporal evolution of the reaction mechanism of complex machineries as membrane proteins, where other techniques encounter significant experimental difficulties. Here, we present the classical principles and experimental realizations of time-resolved FT-IR spectroscopy together with recent developments employed in our laboratory. Examples from applications to retinal proteins are reviewed that underline the impact of time-resolved FT-IR spectroscopy on the understanding of protein reactions on the level of single bonds.
Femtosecond Fluorescence Upconversion Investigations on the Excited-State Photophysics of Curcumin
Authors: Kee Tak W. , Adhikary Ramkrishna , Carlson Philip J. , Mukherjee Prasun , Petrich Jacob W.
Published: January 2011

The demonstration of curcumin as a photodynamic therapy agent has generated a high level of interest in understanding the photoinduced chemical and physical properties of this naturally occurring, yellow-orange medicinal compound. Important photophysical processes that may be related to photodynamic therapy effects including excited-state intramolecular hydrogen atom transfer (ESIHT) occur within the femtosecond to picosecond time scales. Femtosecond fluorescence upconversion spectroscopy has sufficient time resolution to resolve and investigate these important photophysical processes. In this review, recent advances in using femtosecond fluorescence upconversion to reveal ultrafast solvation and ESIHT of curcumin are presented. The excited-state photophysics of curcumin has been investigated in alcohols and micellar solutions. The results of curcumin in methanol and ethylene glycol reveal the presence of two decay components in the excited-state kinetics with time scales of 12–20 ps and ∼100 ps. Similarly, in a micellar solution, biphasic kinetics are present with the fast decay component having a time constant of 3–8 ps, the slow decay component 50–80 ps. Deuteration of curcumin in both media leads to a pronounced isotope effect in the slow decay component, which suggests that ESIHT is an important photophysical process on this time scale. The results of multiwavelength fluorescence upconversion studies show that the fast component in the excited-state kinetics is due to ultrafast solvation. These advances form a part of the continuing efforts to elucidate the photodynamic therapy properties of curcumin.
High-throughput ectopic expression screen for tamoxifen resistance identifies an atypical kinase that blocks autophagy
Authors: Gonzalez-Malerva Laura , Park Jaehong , Zou Lihua , Hu Yanhui , Moradpour Zahra , Pearlberg Joseph , Sawyer Jacqueline , Stevens Hallam , Harlow Ed , LaBaer Joshua
Published: January 2011

Resistance to tamoxifen in breast cancer patients is a serious therapeutic problem and major efforts are underway to understand underlying mechanisms. Resistance can be either intrinsic or acquired. We derived a series of subcloned MCF7 cell lines that were either highly sensitive or naturally resistant to tamoxifen and studied the factors that lead to drug resistance. Gene-expression studies revealed a signature of 67 genes that differentially respond to tamoxifen in sensitive vs. resistant subclones, which also predicts disease-free survival in tamoxifen-treated patients. High-throughput cell-based screens, in which >500 human kinases were independently ectopically expressed, identified 31 kinases that conferred drug resistance on sensitive cells. One of these, HSPB8, was also in the expression signature and, by itself, predicted poor clinical outcome in one cohort of patients. Further studies revealed that HSPB8 protected MCF7 cells from tamoxifen and blocked autophagy. Moreover, silencing HSBP8 induced autophagy and caused cell death. Tamoxifen itself induced autophagy in sensitive cells but not in resistant ones, and tamoxifen-resistant cells were sensitive to the induction of autophagy by other drugs. These results may point to an important role for autophagy in the sensitivity to tamoxifen.
Heterotrimeric kinesin-II is necessary and sufficient to promote different stepwise assembly of morphologically distinct bipartite cilia inDrosophilaantenna
Authors: Jana Swadhin C. , Girotra Mukul , Ray Krishanu
Published: January 2011

Structurally diverse sensory cilia have evolved from primary cilia, a microtubule-based cellular extension engaged in chemical and mechanical sensing and signal integration. The diversity is often associated with functional specialization. The olfactory receptor neurons in Drosophila, for example, express three distinct bipartite cilia displaying different sets of olfactory receptors on them. Molecular description underlying their assembly and diversification is still incomplete. Here, we show that the branched and the slender olfactory cilia develop in two distinct step-wise patterns through the pupal stages before the expression of olfactory receptor genes in olfactory neurons. The process initiates with a thin procilium growth from the dendrite apex, followed by volume increment in successive stages. Mutations in the kinesin-II subunit genes either eliminate or restrict the cilia growth as well as tubulin entry into the developing cilia. Together with previous results, our results here suggest that heterotrimeric kinesin-II is the primary motor engaged in all type-I sensory cilia assembly in Drosophila and that the cilia structure diversity is achieved through additional transports supported by the motor during development.
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
Authors: Hao Xiaolin , Jiang Rui , Chen Ting
Published: January 2011

Motivation: With the advancements of next-generation sequencing technology, it is now possible to study samples directly obtained from the environment. Particularly, 16S rRNA gene sequences have been frequently used to profile the diversity of organisms in a sample. However, such studies are still taxed to determine both the number of operational taxonomic units (OTUs) and their relative abundance in a sample.

Results: To address these challenges, we propose an unsupervised Bayesian clustering method termed Clustering 16S rRNA for OTU Prediction (CROP). CROP can find clusters based on the natural organization of data without setting a hard cut-off threshold (3%/5%) as required by hierarchical clustering methods. By applying our method to several datasets, we demonstrate that CROP is robust against sequencing errors and that it produces more accurate results than conventional hierarchical clustering methods.

Availability and Implementation: Source code freely available at the following URL: http://code.google.com/p/crop-tingchenlab/, implemented in C++ and supported on Linux and MS Windows.

Contact:  tingchen@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles
Authors: Wang Yejun , Zhang Qing , Sun Ming-an , Guo Dianjing
Published: January 2011

Motivation: Bacterial type III secreted (T3S) effectors are delivered into host cells specifically via type III secretion systems (T3SSs), which play important roles in the interaction between bacteria and their hosts. Previous computational methods for T3S protein prediction have only achieved limited accuracy, and distinct features for effective T3S protein prediction remain to be identified.

Results: In this work, a distinctive N-terminal position-specific amino acid composition (Aac) feature was identified for T3S proteins. A large portion (∼50%) of T3S proteins exhibit distinct position-specific Aac features that can tolerate position shift. A classifier, BPBAac, was developed and trained using Support Vector Machine (SVM) based on the Aac feature extracted using a Bi-profile Bayes model. We demonstrated that the BPBAac model outperformed other implementations in classification of T3S and non-T3S proteins, giving an average sensitivity of ∼90.97% and an average selectivity of ∼97.42% in a 5-fold cross-validation evaluation. The model was also robust when a small-size training dataset was used. The fact that the position-specific Aac feature is commonly found in T3S proteins across different bacterial species gives this model wide application. To demonstrate the model's application, a genome-wide prediction of T3S effector proteins was performed for Ralstonia solanacearum, an important plant pathogenic bacterium, and a number of putative candidates were identified using this model.

Availability: An R package of BPBAac tool is freely downloadable from: http://biocomputer.bio.cuhk.edu.hk/softwares/BPBAac.

Contact:  djguo@cuhk.edu.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
T-box-mediated control of the anabolic proline biosynthetic genes of Bacillus subtilis
Authors: Brill Jeanette , Hoffmann Tamara , Putzer Harald , Bremer Erhard
Published: January 2011

Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ–ProA–ProH route is responsible for the production of proline as an osmoprotectant, and the ProB–ProA–ProI route provides proline for protein synthesis. We show here that the transcription of the anabolic proBA and proI genes is controlled in response to proline limitation via a T-box-mediated termination/antitermination regulatory mechanism, a tRNA-responsive riboswitch. Primer extension analysis revealed mRNA leader transcripts of 270 and 269 nt for the proBA and proI genes, respectively, both of which are synthesized from SigA-type promoters. These leader transcripts are predicted to fold into two mutually exclusive secondary mRNA structures, forming either a terminator or an antiterminator configuration. Northern blot analysis allowed the detection of both the leader and the full-length proBA and proI transcripts. Assessment of the level of the proBA transcripts revealed that the amount of the full-length mRNA species strongly increased in proline-starved cultures. Genetic studies with a proB–treA operon fusion reporter strain demonstrated that proBA transcription is sensitively tied to proline availability and is derepressed as soon as cellular starvation for proline sets in. Both the proBA and the proI leader sequences contain a CCU proline-specific specifier codon prone to interact with the corresponding uncharged proline-specific tRNA. By replacing the CCU proline specifier codon in the proBA T-box leader with UUC, a codon recognized by a Phe-specific tRNA, we were able to synthetically re-engineer the proline-specific control of proBA transcription to a control that was responsive to starvation for phenylalanine.
Familial concordance for age at menarche: analyses from the Breakthrough Generations Study
Authors: Morris Danielle H. , Jones Michael E. , Schoemaker Minouk J. , Ashworth Alan , Swerdlow Anthony J.
Published: January 2011

Morris DH, Jones ME, Schoemaker MJ, Ashworth A, Swerdlow AJ. Familial concordance for age at menarche: analyses from the Breakthrough Generations Study. Paediatric and Perinatal Epidemiology 2011; 25: 306–311.

Age at menarche is correlated within families, but estimates of the heritability of menarcheal age have a wide range (0.45–0.95). We examined the familial resemblance for age at menarche and the extent to which this is due to genetic and shared environmental factors. Between 2003 and 2010 data were retrospectively collected by questionnaire from participants within the UK‐based Breakthrough Generations Study. These analyses included 25 970 female participants aged 16–98 with at least one female relative who was also a study participant. A woman's menarche was significantly delayed for each yearly increase in the menarcheal age of her monozygotic twin (average increase = 7.2 months, P < 0.001), dizygotic twin (average increase = 3.0 months, P = 0.03), older sister (average increase = 3.3 months, P < 0.001), mother (average increase = 3.4 months, P < 0.001), maternal grandmother (average increase = 1.5 months, P = 0.04), maternal aunt (average increase = 1.4 months, P < 0.001) and paternal aunt (average increase = 3.0 months, P < 0.001). There was not a significant association between the menarcheal ages of half‐sister pairs or of paternal grandmother–granddaughter pairs, based on small numbers. Heritability was estimated as 0.57 [95% confidence interval 0.53, 0.61]. Shared environmental factors did not have an effect in the model. In conclusion, approximately half of the variation in age at menarche was attributable to additive genetic effects with the remainder attributable to non‐shared environmental effects.
Fabric and formation of grapestone concretions within an unusual ancient methane seep system (Eocene, Bulgaria)
Authors: De Boever Eva , Birgel Daniel , Muchez Philippe , Peckmann Jörn , Dimitrov Lyubomir , Swennen Rudy
Published: January 2011

Terra Nova, 23, 56–61, 2011

Authigenic carbonates at methane seeps provide valuable information on the evolution of seepage dynamics. In this study, we report on an unusual type of 13C‐depleted [δ13C: −44.8‰ to −8.3‰V‐PDB (Vienna PeeDee Belemnite)] calcite‐cemented grapestone concretion composed of small spheroidal nodules, <0.1–15 cm across, associated with an ancient seep setting in Eocene marine sediments (Pobiti Kamani area, NE Bulgaria). Field observations suggest that the nodules started to grow close to the ancient sea floor and apparently were agitated by fluid flow, promoting their spheroidal shape. The precipitation of calcite between sand grains started at multiple closely spaced nucleation sites, induced by locally elevated calcite supersaturation in response to anaerobic microbial consumption of ascending methane. Consecutive nodule growth continued deeper in the sediment, with the formation of dark and light concentric bands surrounding one or more nodule cores. The occurrence of similar grapestone concretions at seeps might indicate changing redox conditions at the seep site.
Rabbit antithymocyte induction and dosing in deceased donor renal transplant recipients over 60 yr of age
Authors: Patel Samir J. , Knight Richard J. , Suki Wadi N. , Abdellatif Abdul , Duhart Benjamin T. , Krauss Amy G. , Mannan Saurabh , Nezakatgoo Nosratollah , Osama Gaber A.
Published: January 2011

Patel SJ, Knight RJ, Suki WN, Abdellatif A, Duhart BT, Krauss AG, Mannan S, Nezakatgoo N, Gaber AO. Rabbit antithymocyte induction and dosing in deceased donor renal transplant recipients over 60 yr of age. Clin Transplant 2011: 25: E250–E256. © 2011 John Wiley & Sons A/S.

Abstract:  Background:  Antithymocyte globulin (rATG) is a commonly used induction agent in renal transplantation; however, data in older kidney recipients are limited.

Methods:  We reviewed charts of 301 deceased donor renal transplants who received a protocol consisting of 3–7 doses of rATG and triple maintenance therapy. Outcomes of patients >60 yr of age (n = 45) were compared to those aged 18–59 yr (n = 256).

Results:  Older recipients had more diabetics, were more likely to receive expanded criteria donor kidneys (p < 0.01), and over 30% were sensitized. Recipients >60 received less cumulative rATG (4.6 vs. 5.1 mg/kg; p < 0.01). Three‐yr acute rejection was lower in the >60 group (2% vs. 16%, p < 0.01) although glomerular filtration rates were similar between groups. Actuarial graft survival was similar; however, patient survival in the >60 group at three yr was lower (80% vs. 95%; p = 0.02). Specifically, patients >60 with delayed graft function and rATG cumulative dosing >6 mg/kg had a survival of <50% by two yr.

Conclusion:  Recipients over 60 yr receiving rATG induction have acceptable renal function and a low risk of rejection; however, reduced survival was noted among those receiving >6 mg/kg. These data suggest that when used, lower cumulative dosages of rATG are preferable in the older recipient.
Examination of glucose transporter‐1, transforming growth factor‐β and neuroglobin immunoreactivity in the orbitofrontal cortex in late‐life depression
Authors: Khundakar Ahmad , Morris Christopher , Slade Janet , Thomas Alan J.
Published: January 2011

Aims:  This study immunohistochemically examined the orbitofrontal cortex for three possible candidates in hypoxic/ischemic signaling: the cytokine transforming growth factor‐β, the glucose transporter‐1 and the neuron‐specific oxygen‐binding protein neuroglobin.

Methods:  Post‐mortem tissue from 20 depressed and 20 non‐depressed individuals was obtained and the expression of the three proteins was analyzed using image analysis software.

Results:  No significant changes were found in transforming growth factor‐β or neuroglobin in the orbitofrontal cortex between depressed and non‐depressed individuals. There was, however, a trend towards a reduction in glucose transporter‐1 in the depressed group.

Conclusions:  This study does not clearly support the hypothesis that hypoxic/ischemic processes are behind the pathological deficits in the frontal‐subcortical circuitry associated with depression and therefore does not provide evidence to support the ‘vascular depression’ hypothesis.
Magnetic resonance imaging of the brain in children and young people with cerebral palsy: who reports matters?
Authors: HORRIDGE KAREN A , JOHNSTON JESSICA , PHATAK VISHAKHA , GUADAGNO ALISON
Published: January 2011

Retrospective case note audits were undertaken of children with clinically diagnosed cerebral palsy known to paediatricians and physiotherapists in Sunderland (UK). Evidence of brain magnetic resonance imaging (MRI) was recorded, including expert opinions requested, in order to quantify the perceived mismatch between local, general radiological and regional, specialist neuroradiological reporting, towards ensuring the best possible yield to inform clinical practice and accurate information‐sharing with families. One hundred and ninety‐seven out of 214 (92%) had documented neuroimaging; 111 out of 197 (56.3%) were dual reported. Only 34 out of 111 reports were concordant overall. Sixty per cent of brain MRI reported as normal locally, were found not to be normal on specialist review. Clinicians requesting brain MRI in children with disordered development must be mindful of the expertise of those reporting. Those based in district settings must network closely with specialists in expert centres, if disabled children and young people are to receive equitable care of the highest standard.
A new genus and species of nothrotheriid sloth (Xenarthra, Tardigrada, Nothrotheriidae) from the Late Miocene (Huayquerian) of Peru
Authors: DE IULIIS GERARDO , GAUDIN TIMOTHY J. , VICARS MATTHEW J.
Published: January 2011

Abstract: The nothrotheriine sloth from riverbank deposits of the Río Acre region of Peru in western Amazonia was originally assigned toNothropus priscusBurmeister, 1882. Although relatively complete, with essentially the pes unknown, its description was accompanied only by limited information on its cranial remains. The remains of this sloth, actually of late Miocene age, were extensively prepared. Subsequent analysis indicates that its original assignment is incorrect and that it belongs to a new genus and species, which is distinguished from other nothrotheriines by the following (among other) features: notably domed braincase; depressed, narrow snout; lack of parietal/alisphenoid contact; ulna with prominently projecting anconeal process; distal position of femoral greater trochanter; medial articular condyle of femur butts against patellar trochlea. Phylogenetic analysis places the new genus and species as sister group to the (Pronothrotherium(Nothrotheriops + Nothrotherium)) clade.
Three distinct but rare kovalevisargid flies from the Jurassic Daohugou biota, China (Insecta, Diptera, Brachycera, Kovalevisargidae)
Authors: ZHANG JUNFENG
Published: January 2011

Abstract:  Three nearly complete male specimens of kovalevisargid flies are described as Kovalevisargus macropterus sp. nov., K. brachypterus sp. nov. and Kerosargus sororius sp. nov. (family Kovalevisargidae) from the Callovian–Oxfordian Daohugou biota in Inner Mongolia, China. These extend the range of the family Kovalevisargidae outside of Central Asia for the first time, reveal new morphological details about kovalevisargid flies and offer new evidence for the biostratigraphic correlation of nonmarine sedimentary strata of both the Karabastau and Daohugou Formations. Close similarities in the composition of insect taxa from both entomofaunas imply not only the geological age but also the sedimentary environment at that time being the same, or nearly so. Familial and generic diagnoses of kovalevisargid flies are supplemented based on information derived from these new species.
NP‐313, 2‐acetylamino‐3‐chloro‐1,4‐naphthoquinone, a novel antithrombotic agent with dual inhibition of thromboxane A2synthesis and calcium entry
Authors: Kuo Heng‐Lan , Lien Jin‐Cherng , Chang Chien‐Hsin , Chung Ching‐Hu , Kuo Sheng‐Chu , Hsu Chun‐Chieh , Peng Hui‐Chin , Huang Tur‐Fu
Published: January 2011

BACKGROUND AND PURPOSE

1,4‐Naphthoquinones exhibit antiplatelet activity bothin vivoandin vitro. In the present study, we investigated the antiplatelet effect of a novel naphthoquinone derivative NP‐313, 2‐acetylamino‐3‐chloro‐1,4‐naphthoquinone and its mechanism of action.

EXPERIMENTAL APPROACH

We measured platelet aggregation, Ca2+mobilization, thromboxane B2 formation and P‐selectin expression and examined several enzymatic activities. Furthermore, we used the irradiated mesenteric venules in fluorescein sodium–treated mice to monitor the antithrombotic effect of NP‐313in vivo.

KEY RESULTS

NP‐313 concentration‐dependently inhibited human platelet aggregation induced by collagen, arachidonic acid, thapsigargin, thrombin and A23187. NP‐313 also inhibited P‐selectin expression, thromboxane B2formation and [Ca2+]ielevation in platelets stimulated by thrombin and collagen. NP‐313 at 10 µM inhibited cyclooxygenase, thromboxane A2synthase, and protein kinase Cα, whereas it did not affect phospholipase A2or phospholipase C activity. In the presence of indomethacin and an adenosine 5‐diphosphate scavenger, NP‐313 concentration‐dependently inhibited thrombin‐ and A23187‐induced [Ca2+]iincrease through its inhibitory effects on Ca2+influx, rather than blocking Ca2+release from intracellular stores. NP‐313 also inhibited thapsigargin‐mediated Ca2+influx through store‐operated calcium channel but had no effect on Ca2+influx through store‐independent calcium channel evoked by the diacylglycerol analogue 1‐oleoyl‐2‐acetyl‐sn‐glycerol. Nevertheless, it had little effect on cyclic AMP and cyclic GMP levels. Also, intravenously administered NP‐313 dose‐dependently inhibited the thrombus occlusion of the irradiated mesenteric vessels of fluorescein‐pretreated mice.

CONCLUSIONS AND IMPLICATIONS

Taken together, these results indicate that NP‐313 exerts its antithrombotic activity through dual inhibition of thromboxane A2synthesis and Ca2+influx through SOCC.
Transcriptional activation of the anchoring protein SAP97 by heat shock factor (HSF)‐1 stabilizes Kv1.5 channels in HL‐1 cells
Authors: Ting YK , Morikawa K , Kurata Y , Li P , Bahrudin U , Mizuta E , Kato M , Miake J , Yamamoto Y , Yoshida A , Murata M , Inoue T , Nakai A , Shiota G , Higaki K , Nanba E , Ninomiya H , Shirayoshi Y , Hisatome I
Published: January 2011

BACKGROUND AND PURPOSEThe expression of voltage‐dependent K+channels (Kv) 1.5 is regulated by members of the heat shock protein (Hsp) family. We examined whether the heat shock transcription factor 1 (HSF‐1) and its inducer geranylgeranylacetone (GGA) could affect the expression of Kv1.5 channels and its anchoring protein, synapse associated protein 97 (SAP97).

EXPERIMENTAL APPROACHTransfected mouse atrial cardiomyocytes (HL‐1 cells) and COS7 cells were subjected to luciferase reporter gene assay and whole‐cell patch clamp. Protein and mRNA extracts were subjected to Western blot and quantitative real‐time polymerase chain reaction.

KEY RESULTSHeat shock of HL‐1 cells induced expression of Hsp70, HSF‐1, SAP97 and Kv1.5 proteins. These effects were reproduced by wild‐type HSF‐1. Both heat shock and expression of HSF‐1, but not the R71G mutant, increased the SAP97 mRNA level. Small interfering RNA (siRNA) against SAP97 abolished HSF‐1‐induced increase of Kv1.5 and SAP97 proteins. A luciferase reporter gene assay revealed that the SAP97 promoter region (from −919 to −740) that contains heat shock elements (HSEs) was required for this induction. Suppression of SIRT1 function either by nicotinamide or siRNA decreased the level of SAP97 mRNA. SIRT1 activation by resveratrol had opposing effects. A treatment of the cells with GGA increased the level of SAP97 mRNA, Kv1.5 proteins and IKurcurrent, which could be modified with either resveratrol or nicotinamide.

CONCLUSIONS AND IMPLICATIONSHSF‐1 induced transcription of SAP97 through SIRT1‐dependent interaction with HSEs; the increase in SAP97 resulted in stabilization of Kv1.5 channels. These effects were mimicked by GGA.