bluuebunny/crossref_metadata_2025 huggingface dataset:
Retraction of van den Bos and Stapel (2008)
Authors: van den Bos Arne , Stapel Diederik A.
Published: October 2008

The following article from issue 4, 2008 is being retracted: Van den Bos, A., and Stapel, D. (2008). The impact of comprehension versus self-enhancement goals on group perception. Social Psychology, 39, 222-230, doi 10.1027/1864-9335.39.4.222 . This retraction follows the results of an investigation by the Rector Magnificus of the Tilburg University into the work of Diederik Stapel. Three Committees examined Diederik Stapel’s places of employment: The Levelt Committee (Tilburg University), the Noort Committee (University of Groningen), and the Drenth Committee (University of Amsterdam). They concluded that the findings of, and data collected by, Stapel could not be confirmed. In the case of the above article, the Noort Committee (University of Groningen) reported the following (see https://www.commissielevelt.nl ): “– Data collection was managed by Mr. Stapel and results were handed over for further analysis to the first author. – There are strong indications that the data in this paper were manipulated and faked: duplicate cases, and strange (inconsistent) correlation structures between variables within different conditions. – Mr. Stapel did declare that he is not sure about the character (fraudulent or not) of this article.” The Noort Committee therefore requested the retraction of this article. Diederik Stapel’s co-author Arne van den Bos stated that he was unaware of Stapel’s actions and was not involved in the collection of the data in question.
Do Shy People Prefer to Send E-Mail?
Authors: Hertel Guido , Schroer Joachim , Batinic Bernad , Naumann Sonja
Published: October 2008

Personality aspects are largely neglected in existing models of media preferences. Based on a functional approach, it is hypothesized that media preferences are affected by Extraversion and Neuroticism particularly in situations that correspond to the motivational implications of these traits. The results of a questionnaire study (N = 228) on preferences for communication media with varying levels of media richness (face-to-face conversation, e-mail) revealed Extraversion and Neuroticism as significant predictors of media preferences. Moreover, these effects were mediated by the motivational manifestations of these traits in social situations (i.e., social skills, social anxiety). Finally, the effects were moderated by the potential threat of a communication situation, showing significant trait effects particularly in social conflicts.
Sea ice drift in the Arctic since the 1950s
Authors: Hakkinen Sirpa , Proshutinsky Andrey , Ashik Igor
Published: October 2008

Sea ice drift data (from Russian North Pole stations, various ice camps, and the International Arctic Buoy Program) and surface wind stress data from the NCAR/NCEP Reanalysis are analyzed to determine their long‐term trends and causality. The study finds that both parameters (ice drift and wind stress) show gradual acceleration over last 50 years. Significant positive trends are present in both winter and summer data. The major cause of observed positive trends is increasing Arctic storm activity over the Transpolar Drift Stream caused by a shift of storm tracks toward higher latitudes. It is speculated, with some observational evidence, that the increased stirring of the ocean by winds could hasten the transition of the Arctic toward a weakly stratified ocean with a potential for deep convection and a new sink for atmospheric CO2.
Impact of a shrinking Arctic ice cover on marine primary production
Authors: Arrigo Kevin R. , van Dijken Gert , Pabi Sudeshna
Published: October 2008

Loss of Arctic sea ice has accelerated recently, culminating in a 2007 summer minimum ice extent that was 23% below the previous low. To quantify the impact of this unprecedented loss of ice on marine primary production, we have coupled satellite‐derived sea ice, SST, and chlorophyll to a primary production algorithm parameterized for Arctic waters. Annual primary production in the Arctic has increased yearly by an average of 27.5 Tg C yr−1 since 2003 and by 35 Tg C yr−1 between 2006 and 2007. 30% of this increase is attributable to decreased minimum summer ice extent and 70% to a longer phytoplankton growing season. Should these trends continue, additional loss of ice during Arctic spring could boost productivity >3‐fold above 1998–2002 levels, potentially altering marine ecosystem structure and the degree of pelagic‐benthic coupling. Changes in carbon export could in turn modify benthic denitrification on the vast continental shelves.
Gregorian calendar bias in monthly temperature databases
Authors: Cerveny Randall S. , Svoma Bohumil M. , Balling Robert C. , Vose Russell S.
Published: October 2008

In this study we address a systematic bias in climate records that manifests due to the establishment of the Gregorian calendar system and exerts a statistically significant effect on monthly and seasonal temperature records. The addition of one extra day in February normally every fourth year produces a significant seasonal drift in the monthly values of that year in four major temperature datasets used in climate change analysis. The addition of a ‘leap year day’ for the Northern Hemisphere creates statistically significantly colder months of July to December and, to a lesser degree warmer months of February to June than correspondingly common (non‐leap year) months. The discovery of such a fundamental bias in four major temperature datasets used in climate analysis (and likely present in any dataset displaying strong annual cycles, e.g., U.S. streamflow data) indicates the continued need for detailed scrutiny of climate records for such biases.
Estimating the potential for methane clathrate instability in the 1%‐CO2 IPCC AR‐4 simulations
Authors: Lamarque Jean‐François
Published: October 2008

The recent work of Reagan and Moridis (2007) has shown that even a limited warming of 1 K over 100 years can lead to clathrate destabilization, leading to a significant flux of methane into the ocean water, at least for shallow deposits. Here we study the potential for methane clathrate destabilization by identifying the 100‐year temperature increase in the available IPCC (Intergovernmental Panel on Climate Change) AR‐4 1%‐CO2 increase per year (up to doubling over pre‐industrial conditions, which occurs after 70 years) simulations. Depending on assumptions made on the possible locations (in this case, only depth) of methane clathrates and on temperature dependence, our calculation leads to an estimated model‐mean release of methane at the bottom of the ocean of approximately 560‐2140 Tg(CH4)/year; as no actual geographical distribution of methane clathrates is considered here, these flux estimates must be viewed as upper bound estimates. Using an observed 1% ratio to estimate the amount of methane reaching the atmosphere, our analysis leads to a relatively small methane flux of approximately 5–21 Tg(CH4)/year, with an estimated inter‐model standard deviation of approximately 30%. The role of sea‐level rise by 2100 will be to further stabilize methane clathrates, albeit to a small amount as the sea‐level rise is expected to be less than a few meters.
Deuterium excess record from a small Arctic ice cap
Authors: Divine D. V. , Isaksson E. , Pohjola V. , Meijer H. , van de Wal R. S. W. , Martma T. , Moore J. , Sjögren B. , Godtliebsen F.
Published: October 2008

In this paper we present a deuterium excess (d) record from an ice core drilled on a small ice cap in Svalbard in 1997. The core site is located at Lomonosovfonna at 1255 m asl, and the analyzed time series spans the period 1400–1990 A.D. The record shows pronounced multidecadal to centennial‐scale variations coherent with sea surface temperature changes registered in the subtropical to southern middle‐latitude North Atlantic during the instrumental period. We interpret the negative trend in the deuterium excess during the 1400s and 1500s as an indication of cooling in the North Atlantic associated with the onset of the Little Ice Age. Consistently positive anomalies of d after 1900, peaking at about 1950, correspond with well‐documented contemporary warming. Yet the maximum values of deuterium excess during 1900–1990 are not as high as in the early part of the record (pre‐1550). This suggests that the sea surface temperatures during this earlier period of time in the North Atlantic to the south of approximately 45°N were at least comparable with those registered in the 20th century before the end of the 1980s. We examine the potential for a cold bias to exist in the deuterium excess record due to increased evaporation from the local colder sources of moisture having isotopically cold signature. It is argued that despite a recent oceanic warming, the contribution from this local moisture to the Lomonosovfonna precipitation budget is still insufficient to interfere with the isotopic signal from the primary moisture region in the midlatitude North Atlantic.
Comprehensive principles of quantitative hydrogeology established by Darcy (1856) and Dupuit (1857)
Authors: Ritzi Robert W. , Bobeck Patricia
Published: October 2008

Henry Darcy and Jules Dupuit were born 1 year apart, were classmates during their undergraduate and graduate education in civil engineering, and were colleagues in the French corps of civil engineers, with overlapping appointments as inspector general in the early 1850s. At that time Darcy turned over, to Dupuit, his position as Director of Water and Bridges in Paris and the research on pipe flow he had begun there in 1849. In these pipe flow experiments, Darcy discovered what he referred to as a “law” of fluid mechanics, which is that above a certain velocity threshold, the head loss is proportional to velocity squared, and below that threshold, the head loss is linearly proportional to velocity. During the remainder of their careers, Darcy and Dupuit applied this law with their collective, extensive, prior knowledge of fluid mechanics, geology, aquifers, wells, and springs to quantitative studies of fluid flow in the subsurface (and also in pipes, aqueducts, rivers, and sand filters). Two monographs by Darcy (1856) and Dupuit (1857) are mutually cited retrospectives on much of this research, submitted at nearly the same time, to the same Corps des Ponts et Chaussées publisher, near the end of their careers. Between these two monographs, many of the fundamentals of quantitative hydrogeology were established, including the equation for groundwater motion, average linear velocity, average travel time, effective hydraulic conductivity for layered heterogeneity, conservation of mass in confined and unconfined flow, the nature of the regional pieziometric surface, porous flow versus flow through discrete fractures and karst conduits, the equation for a cone of depression around flowing wells, superposition of the effects of multiple wells, and capture zone geometries of wells within a regional flow field.
Validation of a Parent‐proxy, Obesity‐specific Quality‐of‐life Measure: Sizing Them Up
Authors: Modi Avani C. , Zeller Meg H.
Published: October 2008

The aims of the present study were to develop and validate a new obesity‐specific, parent‐proxy measure of health‐related quality of life (HRQOL), Sizing Them Up. Participants included 220 obese youth (Mage = 11.6 years, 68% female, 53% African American, MBMI = 36.7) and their primary caregivers (88% mothers). Primary caregivers completed a demographics questionnaire and two HRQOL measures: Sizing Them Up (obesity‐specific) and PedsQL (generic). Youth height and weight were measured. Psychometric evaluation of Sizing Them Up was completed by conducting a factor analysis and determining internal consistency coefficients, test‐retest reliability, convergent and discriminant validity, predictive validity, responsiveness to change, and minimal clinically important difference (MCID) scores. Sizing Them Up is a 22‐item measure with six scales (i.e., Emotional Functioning, Physical Functioning, Teasing/Marginalization, Positive Social Attributes, Mealtime Challenges, and School Functioning) that account for 66% of the variance. The measure also includes an Adolescent Developmental Adaptation module. Sizing Them Up had internal consistency coefficients ranging from 0.59 to 0.91 and test‐retest reliabilities ranging from 0.57 to 0.80. Validity was demonstrated by significant relations between a majority of Sizing Them Up scales and BMI z‐scores. Sizing Them Up also demonstrated good convergent validity with other HRQOL measures and responsiveness to change related to weight loss for adolescents who had undergone bariatric surgery. Overall, Sizing Them Up is a reliable and valid parent‐proxy measure of obesity‐specific HRQOL that can be used in both clinical and research settings.
The FTO Gene and Obesity in a Large Eastern European Population Sample: The HAPIEE Study
Authors: Hubacek Jaroslav A. , Bohuslavova Romana , Kuthanova Lada , Kubinova Ruzena , Peasey Anne , Pikhart Hynek , Marmot Michael G. , Bobak Martin
Published: October 2008

Variants in the FTO (oxoglutarate‐dependent nucleic acid demethylase) gene have been associated with the BMI determination in Western European and North American populations. To widen the geographical coverage of the FTO studies, we have analyzed the association between the FTO gene variant rs17817449 (G>C) and obesity in a Slavic Eastern European population. A total of 3,079 males and 3,602 females 45–69 years old were randomly selected from population registers of seven Czech cities. We examined three indices of obesity: BMI (kg/m2), waist circumference, and waist‐to‐hip ratio (WHR). The FTO rs17817449 variant was significantly associated with BMI both in males (GG 28.7 ± 4.1; GT 28.3 ± 3.9; TT 28.0 ± 3.9; P = 0.003) and females (GG 28.7 ± 5.2; GT 28.2 ± 5.1; TT 27.2 ± 4.9; P < 0.001); the associations were not affected by adjustment for age, smoking, socioeconomic status, and physical activity. The FTO variant was also associated with waist circumference (difference between GG and TT was 1.1 cm (P = 0.043) in men and 2.4 cm (P < 0.001) in women) but this relationship disappeared after adjustment for BMI. Similarly, BMI explained the weak association of FTO with WHR and C‐reactive protein. FTO was not associated with plasma total and high‐density lipoprotein cholesterol, triglycerides, blood glucose, and blood pressure. These results confirm that in a Slavic population the FTO variant is strongly associated with BMI but not with other risk factors.
Quality Food, Public Procurement, and Sustainable Development: The School Meal Revolution in Rome
Authors: Sonnino Roberta
Published: October 2008

In the last decade the concept of quality has been widely used to describe the dynamics that have been shaping the agrifood system. Despite differences in research focus and approach, scholars agree that quality is the outcome of a contingent and so far underresearched process of negotiation that entails and determines relations of power in the food chain. To understand the nature and implications of the relationship between quality and power in the food sector, this paper focuses on the recent ‘quality revolution’ implemented in the school meals system in Rome. Based on the analysis of documentary material and qualitative data collected through formal and informal interviews, the paper examines the process through which city authorities have integrated different (and at times contrasting) quality conventions. The analysis shows that procurement policies such as those implemented in Rome have the power to create an ‘economy of quality’ that can deliver the economic, environmental, and social benefits of sustainable development.
The Paradoxes of Personhood: Banal Multiculturalism and Racial–Ethnic Identification among Latina and Armenian Girls at a Los Angeles High School
Authors: Thomas Mary E
Published: October 2008

In the spring of 2005, numerous racially motivated, large-scale fights broke out in Los Angeles, California, high schools, from the San Fernando Valley to south Los Angeles. Most of the fighting occurred between youth who identify as ethnic–racial minorities, like Latinos, African-Americans, and Armenians. Just after one such fight involving several hundred students, which quickly became known as a ‘race riot’ at the school, I conducted a series of interviews with teenage girls asking them what they thought of this outburst of ethnic–racial violence, in their valley school's case between Latinos and Armenians. In the research, girls detailed to me their postracial attitudes (typified by such ideals as ‘race doesn't matter, we are all the same’), but their narratives evidenced extreme racial–ethnic segregation and their own racist sentiments. In this paper, I explore this contradiction and focus on how girls articulate multicultural and humanist ideals to situate themselves as antiracists. However, concurrently, I argue that the girls' racialized resentments of others illustrate their profound and wounded investments in difference. The girls' narratives and identities also indicate why multicultural attempts to foster respect of diversity in this urban high school have failed.
Cities and Regions: Problems and Potentials
Authors: Parr John B
Published: October 2008

The central concern is with the nature of cities and regions and the vagueness that appears to have enveloped each of these terms. Consideration is initially given to the ‘built city’ and how this perspective on the city may be extended in several ways. There follows an examination of the region, with a brief exploration of the classification proposed by Meyer, involving homogeneous, nodal, and policy regions. Attention then turns to two distinctive regional forms (the city-region and the polycentric urban region), each of which has recently become the focus of interest. The two regional forms are examined in terms of spatial structure and interaction patterns, with attention given to particular aspects of economic development. Finally, there is a discussion of the problems of identifying regional forms and the difficulties of interpretation.
Towards an Amphibious Anthropology: Water and Peter Sloterdijk
Authors: ten Bos René
Published: October 2008

In the paper Peter Sloterdijk is portrayed as a philosopher of elements who tries to correct the traditional philosophical reliance on earth by focusing on the elements air and water. The paper discusses the role that the latter element plays in Sloterdijk's philosophy. It is argued that it is crucial to understand this role in order to come to grips with what Sloterdijk himself has referred to as his ‘amphibious’ anthropology. The human animal does not prefer one element but switches from one element to the other.
Investigations of Human EEG Response to Viewing Fractal Patterns
Authors: Hagerhall Caroline M , Laike Thorbjörn , Taylor Richard P , Küller Marianne , Küller Rikard , Martin Theodore P
Published: October 2008

Owing to the prevalence of fractal patterns in natural scenery and their growing impact on cultures around the world, fractals constitute a common feature of our daily visual experiences, raising an important question: what responses do fractals induce in the observer? We monitored subjects' EEG while they were viewing fractals with different fractal dimensions, and the results show that significant effects could be found in the EEG even by employing relatively simple silhouette images. Patterns with a fractal dimension of 1.3 elicited the most interesting EEG, with the highest alpha in the frontal lobes but also the highest beta in the parietal area, pointing to a complicated interplay between different parts of the brain when experiencing this pattern.
Location of the Auditory Egocentre in the Blind and Normally Sighted
Authors: Sukemiya Haru , Nakamizo Sachio , Ono Hiroshi
Published: October 2008

We estimated the location of the auditory egocentre in congenitally blind, late-onset blind, and normally sighted participants, using a revised auditory version of Howard and Templeton's method. The mean location of the auditory egocentre of the congenitally blind participants was found to be close to the midpoint of the interaural axis or the centre of head rotation. It was significantly different from those in the normally sighted and late-onset blind participants, whose mean location of the auditory egocentre was close to the midpoint of the interocular axis or visual egocentre.
Spatial Attention Can Modulate Unconscious Orientation Processing
Authors: Bahrami Bahador , Carmel David , Walsh Vincent , Rees Geraint , Lavie Nilli
Published: October 2008

It has recently been suggested that visual spatial attention can only affect consciously perceived events. We measured the effects of sustained spatial attention on orientation-selective adaptation to gratings, rendered invisible by prolonged interocular suppression. Spatial attention augmented the orientation-selective adaptation to invisible adaptor orientation. The effect of attention was clearest for test stimuli at peri-threshold, intermediate contrast levels, suggesting that previous negative results were due to assessing orientation discrimination at maximum contrast. On the basis of these findings we propose a constrained hypothesis for the difference between neuronal mechanisms of spatial attention in the presence versus absence of awareness.
A Functional Explanation for the Effects of Visual Exposure on Preference
Authors: Changizi Mark A , Shimojo Shinsuke
Published: October 2008

Visual exposure to an object can modulate an observer's degree of preference for it, initially enhancing preference (a ‘familiarity preference’ regime), and eventually lowering it again (a ‘novelty preference’ regime). Here we investigate whether there may be a functional advantage to modulating preference in this way. We put forth the simple hypothesis that degree of preference for an object of type X is the brain's estimate of the expected utility of acting to obtain X. In the light of this view of what preferences fundamentally represent, we are able to explain the ‘exposure effect’ and many of the connected phenomena.
Generation and regulation of human CD4
+
IL-17-producing T cells in ovarian cancer
Authors: Miyahara Yoshihiro , Odunsi Kunle , Chen Wenhao , Peng Guangyong , Matsuzaki Junko , Wang Rong-Fu
Published: October 2008

Despite the important role of Th17 cells in the pathogenesis of many autoimmune diseases, their prevalence and the mechanisms by which they are generated and regulated in cancer remain unclear. Here, we report the presence of a high percentage of CD4
+
Th17 cells at sites of ovarian cancer, compared with a low percentage of Th17 cells in peripheral blood mononuclear cells from healthy donors and cancer patients. Analysis of cytokine production profiles revealed that ovarian tumor cells, tumor-derived fibroblasts, and antigen-presenting cells (APCs) secreted several key cytokines including IL-1β, IL-6, TNF-α and TGF-β, which formed a cytokine milieu that regulated and expanded human IL-17-producing T-helper (Th17) cells. We further show that IL-1β was critically required for the differentiation and expansion of human Th17 cells, whereas IL-6 and IL-23 may also play a role in the expansion of memory Th17 cells, even though IL-23 levels are low or undetectable in ovarian cancer. Further experiments demonstrated that coculture of naïve or memory CD4
+
T cells with tumor cells, APCs, or both could generate high percentages of Th17 cells. Treatment with anti-IL-1 alone or a combination of anti-IL-1 and anti-IL-6 reduced the ability of tumor cells to expand memory Th17 cells. Thus, we have identified a set of key cytokines secreted by ovarian tumor cells and tumor-associated APCs that favor the generation and expansion of human Th17 cells. These findings should accelerate efforts to define the function of this important subset of CD4
+
T cells in the human immune response to cancer.
Circumspect descent prevails in solving random constraint satisfaction problems
Authors: Alava Mikko , Ardelius John , Aurell Erik , Kaski Petteri , Krishnamurthy Supriya , Orponen Pekka , Seitz Sakari
Published: October 2008

We study the performance of stochastic local search algorithms for random instances of the
K
-satisfiability (
K
-SAT) problem. We present a stochastic local search algorithm, ChainSAT, which moves in the energy landscape of a problem instance by never going upwards in energy. ChainSAT is a focused algorithm in the sense that it focuses on variables occurring in unsatisfied clauses. We show by extensive numerical investigations that ChainSAT and other focused algorithms solve large
K
-SAT instances almost surely in linear time, up to high clause-to-variable ratios α; for example, for
K
= 4 we observe linear-time performance well beyond the recently postulated clustering and condensation transitions in the solution space. The performance of ChainSAT is a surprise given that by design the algorithm gets trapped into the first local energy minimum it encounters, yet no such minima are encountered. We also study the geometry of the solution space as accessed by stochastic local search algorithms.
Mg
2+
-sensing mechanism of Mg
2+
transporter MgtE probed by molecular dynamics study
Authors: Ishitani Ryuichiro , Sugita Yuji , Dohmae Naoshi , Furuya Noritaka , Hattori Motoyuki , Nureki Osamu
Published: October 2008

Proper regulation of the intracellular ion concentration is essential to maintain life and is achieved by ion transporters that transport their substrates across the membrane in a strictly regulated manner. MgtE is a Mg
2+
transporter that may function in the homeostasis of the intracellular Mg
2+
concentration. A recent crystallographic study revealed that its cytosolic domain undergoes a Mg
2+
-dependent structural change, which is proposed to gate the ion-conducting pore passing through the transmembrane domain. However, the dynamics of Mg
2+
sensing, i.e., how MgtE responds to the change in the intracellular Mg
2+
concentration, remained elusive. Here we performed molecular dynamics simulations of the MgtE cytosolic domain. The simulations successfully reproduced the structural changes of the cytosolic domain upon binding or releasing Mg
2+
, as well as the ion selectivity. These results suggested the roles of the N and CBS domains in the cytosolic domain and their respective Mg
2+
binding sites. Combined with the current crystal structures, we propose an atomically detailed model of Mg
2+
sensing by MgtE.
Taxonomic and regional uncertainty in species-area relationships and the identification of richness hotspots
Authors: Guilhaumon François , Gimenez Olivier , Gaston Kevin J. , Mouillot David
Published: October 2008

Species-area relationships (SARs) are fundamental to the study of key and high-profile issues in conservation biology and are particularly widely used in establishing the broad patterns of biodiversity that underpin approaches to determining priority areas for biological conservation. Classically, the SAR has been argued in general to conform to a power-law relationship, and this form has been widely assumed in most applications in the field of conservation biology. Here, using nonlinear regressions within an information theoretical model selection framework, we included uncertainty regarding both model selection and parameter estimation in SAR modeling and conducted a global-scale analysis of the form of SARs for vascular plants and major vertebrate groups across 792 terrestrial ecoregions representing almost 97% of Earth's inhabited land. The results revealed a high level of uncertainty in model selection across biomes and taxa, and that the power-law model is clearly the most appropriate in only a minority of cases. Incorporating this uncertainty into a hotspots analysis using multimodel SARs led to the identification of a dramatically different set of global richness hotspots than when the power-law SAR was assumed. Our findings suggest that the results of analyses that assume a power-law model may be at severe odds with real ecological patterns, raising significant concerns for conservation priority-setting schemes and biogeographical studies.
Protein identification and quantification by two-dimensional infrared spectroscopy: Implications for an all-optical proteomic platform
Authors: Fournier Frédéric , Gardner Elizabeth M. , Kedra Darek A. , Donaldson Paul M. , Guo Rui , Butcher Sarah A. , Gould Ian R. , Willison Keith R. , Klug David R.
Published: October 2008

Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Two-dimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to <1 min per protein by using the same technology. Finally, we show that absolute quantification of protein levels is relatively straightforward to achieve and discuss the potential of an all-optical high-throughput proteomic platform based on two-dimensional infrared spectroscopic measurements.
Association of the
Agrobacterium
T-DNA–protein complex with plant nucleosomes
Authors: Lacroix Benoît , Loyter Abraham , Citovsky Vitaly
Published: October 2008

Agrobacterium
represents the only natural example of transkingdom transfer of genetic information, from bacteria to plants. Before the bacterial transferred DNA (T- DNA) can integrate into the plant genome, it should be targeted to and bind the host chromatin. However, the T-DNA association with the host chromatin has not been demonstrated. Here, we study T-DNA binding to plant nucleosomes
in vitro
and show that it is mediated by bacterial and host proteins associated with the T-DNA. The main factor that determines nucleosomal binding of the T-DNA is the cellular VirE2-interacting protein 1 (VIP1), which functions as a molecular link between the T-DNA-associated bacterial virulence protein VirE2 and core histones. The presence of both VIP1 and VirE2 is required for association of the T-DNA with mononucleosomes in which the DNA molecule exists as a tripartite complex DNA–VirE2–VIP1. Furthermore, this nucleosome-associated ternary complex can bind another bacterial virulence factor, VirF, which is an F-box protein known to target both VirE2 and VIP1 for proteasomal degradation and uncoat the T-DNA.
The bacteriophage λ Q antiterminator protein contacts the β-flap domain of RNA polymerase
Authors: Deighan Padraig , Diez Cristina Montero , Leibman Mark , Hochschild Ann , Nickels Bryce E.
Published: October 2008

The multisubunit RNA polymerase (RNAP) in bacteria consists of a catalytically active core enzyme (α
2
ββ′ω) complexed with a σ factor that is required for promoter-specific transcription initiation. During early elongation the stability of interactions between σ and core decreases, in part because of the nascent RNA-mediated destabilization of an interaction between region 4 of σ and the flap domain of the β-subunit (β-flap). The nascent RNA-mediated destabilization of the σ region 4/β-flap interaction is required for the bacteriophage λ Q antiterminator protein (λQ) to engage the RNAP holoenzyme. Here, we provide an explanation for this requirement by showing that λQ establishes direct contact with the β-flap during the engagement process, thus competing with σ
70
region 4 for access to the β-flap. We also show that λQ's affinity for the β-flap is calibrated to ensure that λQ activity is restricted to the λ late promoter P
R′
. Specifically, we find that strengthening the λQ/β-flap interaction allows λQ to bypass the requirement for specific
cis
-acting sequence elements, a λQ-DNA binding site and a RNAP pause-inducing element, that normally ensure λQ is recruited exclusively to transcription complexes associated with P
R′
. Our findings demonstrate that the β-flap can serve as a direct target for regulators of elongation.
A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography
Authors: Lu Mingyang , Ma Jianpeng
Published: October 2008

In this article, we report a method for coarse-grained normal mode analysis called the minimalist network model. The main features of the method are that it can deliver accurate low-frequency modes on structures without undergoing initial energy minimization and that it also retains the details of molecular interactions. The method does not require any additional adjustable parameters after coarse graining and is computationally very fast. Tests on modeling the experimentally measured anisotropic displacement parameters in biomolecular x-ray crystallography demonstrate that the method can consistently perform better than other commonly used methods including our own one. We expect this method to be effective for applications such as structural refinement and conformational sampling.
Variable stoichiometry of the TatA component of the twin-arginine protein transport system observed by
in vivo
single-molecule imaging
Authors: Leake Mark C. , Greene Nicholas P. , Godun Rachel M. , Granjon Thierry , Buchanan Grant , Chen Shuyun , Berry Richard M. , Palmer Tracy , Berks Ben C.
Published: October 2008

The twin-arginine translocation (Tat) system transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membrane of plant chloroplasts. The essential components of the Tat pathway are the membrane proteins TatA, TatB, and TatC. TatA is thought to form the protein translocating element of the Tat system. Current models for Tat transport make predictions about the oligomeric state of TatA and whether, and how, this state changes during the transport cycle. We determined the oligomeric state of TatA directly at native levels of expression in living cells by photophysical analysis of individual yellow fluorescent protein-labeled TatA complexes. TatA forms complexes exhibiting a broad range of stoichiometries with an average of ≈25 TatA subunits per complex. Fourier analysis of the stoichiometry distribution suggests the complexes are assembled from tetramer units. Modeling the diffusion behavior of the complexes suggests that TatA protomers associate as a ring and not a bundle. Each cell contains ≈15 mobile TatA complexes and a pool of ≈100 TatA molecules in a more disperse state in the membrane. Dissipation of the protonmotive force that drives Tat transport has no affect on TatA complex stoichiometry. TatA complexes do not form in cells lacking TatBC, suggesting that TatBC controls the oligomeric state of TatA. Our data support the TatA polymerization model for the mechanism of Tat transport.
Gene expression changes in the course of normal brain aging are sexually dimorphic
Authors: Berchtold Nicole C. , Cribbs David H. , Coleman Paul D. , Rogers Joseph , Head Elizabeth , Kim Ronald , Beach Tom , Miller Carol , Troncoso Juan , Trojanowski John Q. , Zielke H. Ronald , Cotman Carl W.
Published: October 2008

Gene expression profiles were assessed in the hippocampus, entorhinal cortex, superior-frontal gyrus, and postcentral gyrus across the lifespan of 55 cognitively intact individuals aged 20–99 years. Perspectives on global gene changes that are associated with brain aging emerged, revealing two overarching concepts. First, different regions of the forebrain exhibited substantially different gene profile changes with age. For example, comparing equally powered groups, 5,029 probe sets were significantly altered with age in the superior-frontal gyrus, compared with 1,110 in the entorhinal cortex. Prominent change occurred in the sixth to seventh decades across cortical regions, suggesting that this period is a critical transition point in brain aging, particularly in males. Second, clear gender differences in brain aging were evident, suggesting that the brain undergoes sexually dimorphic changes in gene expression not only in development but also in later life. Globally across all brain regions, males showed more gene change than females. Further, Gene Ontology analysis revealed that different categories of genes were predominantly affected in males vs. females. Notably, the male brain was characterized by global decreased catabolic and anabolic capacity with aging, with down-regulated genes heavily enriched in energy production and protein synthesis/transport categories. Increased immune activation was a prominent feature of aging in both sexes, with proportionally greater activation in the female brain. These data open opportunities to explore age-dependent changes in gene expression that set the balance between neurodegeneration and compensatory mechanisms in the brain and suggest that this balance is set differently in males and females, an intriguing idea.
Photochemistry and electron-transfer mechanism of transition metal oxalato complexes excited in the charge transfer band
Authors: Chen Jie , Zhang Hua , Tomov Ivan V. , Ding Xunliang , Rentzepis Peter M.
Published: October 2008

The photoredox reaction of trisoxalato cobaltate (III) has been studied by means of ultrafast extended x-ray absorption fine structure and optical transient spectroscopy after excitation in the charge-transfer band with 267-nm femtosecond pulses. The Co–O transient bond length changes and the optical spectra and kinetics have been measured and compared with those of ferrioxalate. Data presented here strongly suggest that both of these metal oxalato complexes operate under similar photoredox reaction mechanisms where the primary reaction involves the dissociation of a metal–oxygen bond. These results also indicate that excitation in the charge-transfer band is not a sufficient condition for the intramolecular electron transfer to be the dominant photochemistry reaction mechanism.
A
Drosophila
orphan G protein-coupled receptor BOSS functions as a glucose-responding receptor: Loss of
boss
causes abnormal energy metabolism
Authors: Kohyama-Koganeya Ayako , Kim Yeon-Jeong , Miura Masayuki , Hirabayashi Yoshio
Published: October 2008

Glucose, one of the most important nutrients for animals, acts as a regulatory signal that controls the secretion of hormones, such as insulin, by endocrine tissues. However, how organisms respond to extracellular glucose and how glucose controls nutrient homeostasis remain unknown. Here, we show that a putative
Drosophila melanogaster
G protein-coupled receptor, previously identified as Bride of sevenless (BOSS), responds to extracellular glucose and regulates sugar and lipid metabolism. We found that BOSS was expressed in the fat body, a nutrient-sensing tissue equivalent to mammalian liver and adipose tissues, and in photoreceptor cells.
Boss
null mutants had small bodies, exhibited abnormal sugar and lipid metabolism (elevated circulating sugar and lipid levels, impaired lipid mobilization to oenocytes), and were sensitive to nutrient deprivation stress. These phenotypes are reminiscent of flies defective in insulin signaling. Consistent with these findings are the observations that
boss
mutants had reduced PI3K activity and phospho-AKT levels, which indicates that BOSS is required for proper insulin signaling. Because human G protein-coupled receptor 5B and the seven-transmembrane domain of BOSS share the same sequence, our results also have important implications for glucose metabolism in humans. Thus, our study provides insight not only into the basic mechanisms of metabolic regulation but also into the pathobiological basis for diabetes and obesity.
A procedure for highly specific, sensitive, and unbiased whole-genome amplification
Authors: Pan Xinghua , Urban Alexander Eckehart , Palejev Dean , Schulz Vincent , Grubert Fabian , Hu Yiping , Snyder Michael , Weissman Sherman M.
Published: October 2008

Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a method using phi29 DNA polymerase and trehalose and optimized control of amplification to create micrograms of specific amplicons without TIPs from down to subfemtograms of DNA. With an input of as little as 0.5–2.5 ng of human gDNA or a few cells, the product could be close to native DNA in locus representation. The amplicons from 5 and 0.5 ng of DNA faithfully demonstrated all previously known heterozygous segmental duplications and deletions (3 Mb to 18 kb) located on chromosome 22 and even a homozygous deletion smaller than 1 kb with high-resolution chromosome-wide comparative genomic hybridization. With 550k Infinium BeadChip SNP typing, the >99.7% accuracy was compared favorably with results on unamplified DNA. Importantly, underrepresentation of chromosome termini that occurred with GenomiPhi v2 was greatly rescued with the present procedure, and the call rate and accuracy of SNP typing were also improved for the amplicons with a 0.5-ng, partially degraded DNA input. In addition, the amplification proceeded logarithmically in terms of total yield before saturation; the intact cells was amplified >50 times more efficiently than an equivalent amount of extracted DNA; and the locus imbalance for amplicons with 0.1 ng or lower input of DNA was variable, whereas for higher input it was largely reproducible. This procedure facilitates genomic analysis with single cells or other traces of DNA, and generates products suitable for analysis by massively parallel sequencing as well as microarray hybridization.
Distinct microRNA expression profiles in acute myeloid leukemia with common translocations
Authors: Li Zejuan , Lu Jun , Sun Miao , Mi Shuangli , Zhang Hao , Luo Roger T. , Chen Ping , Wang Yungui , Yan Ming , Qian Zhijian , Neilly Mary Beth , Jin Jie , Zhang Yanming , Bohlander Stefan K. , Zhang Dong-Er , Larson Richard A. , Le Beau Michelle M. , Thirman Michael J. , Golub Todd R. , Rowley Janet D. , Chen Jianjun
Published: October 2008

MicroRNAs (miRNAs) are postulated to be important regulators in cancers. Here, we report a genome-wide miRNA expression analysis in 52 acute myeloid leukemia (AML) samples with common translocations, including t(8;21)/
AML1(RUNX1)-ETO(RUNX1T1)
, inv(
16
)/
CBFB-MYH11
, t(15;17)/
PML-RARA
, and
MLL
rearrangements. Distinct miRNA expression patterns were observed for t(15;17),
MLL
rearrangements, and core-binding factor (CBF) AMLs including both t(8;21) and inv(
16
) samples. Expression signatures of a minimum of two (i.e., miR-126/126*), three (i.e., miR-224, miR-368, and miR-382), and seven (miR-17–5p and miR-20a, plus the aforementioned five) miRNAs could accurately discriminate CBF, t(15;17), and
MLL
-rearrangement AMLs, respectively, from each other. We further showed that the elevated expression of miR-126/126* in CBF AMLs was associated with promoter demethylation but not with amplification or mutation of the genomic locus. Our gain- and loss-of-function experiments showed that miR-126/126* inhibited apoptosis and increased the viability of AML cells and enhanced the colony-forming ability of mouse normal bone marrow progenitor cells alone and particularly, in cooperation with
AML1-ETO
, likely through targeting Polo-like kinase 2 (
PLK2
), a tumor suppressor. Our results demonstrate that specific alterations in miRNA expression distinguish AMLs with common translocations and imply that the deregulation of specific miRNAs may play a role in the development of leukemia with these associated genetic rearrangements.
The Development of Affect Specificity in Infants' Use of Emotion Cues
Authors: Martin Nicole Gendler , Witherington David C. , Edwards Alison
Published: October 2008

This study examined the emergence of affect specificity in infancy. In this study, infants received verbal and facial signals of 2 different, negatively valenced emotions (fear and sadness) as well as neutral affect via a television monitor to determine if they could make qualitative distinctions among emotions of the same valence. Twenty 12‐ to 14‐month‐olds and 20 16‐ to 18‐month‐olds were examined. Results suggested that younger infants showed no evidence of referential specificity, as they responded similarly to both the target and distracter toys, and showed no evidence of affect specificity, showing no difference in play between affect conditions. Older infants, in contrast, showed evidence both of referential and affect specificity. With respect to affect specificity, 16‐ to 18‐month‐olds touched the target toy less in the fear condition than in the sad condition and showed a larger proportion of negative facial expressions in the sad condition versus the fear condition. These findings suggest a developmental emergence after 15 months of age for affect specificity in relating emotional messages to objects.
Maternal Psychosocial Adversity and the Longitudinal Development of Infant Sleep
Authors: Cronin Alison , Halligan Sarah L. , Murray Lynne
Published: October 2008

Research has identified associations between indicators of social disadvantage and the presence of child sleep problems. We examined the longitudinal development of infant sleep in families experiencing high (n = 58) or low (n = 64) levels of psychosocial adversity, and the contributions of neonatal self‐regulatory capacities and maternal settling strategies to this development. Assessments of infant sleep at 4‐, 7‐, and 12‐weeks postpartum indicated no differences in sleeping difficulties between high‐ and low‐adversity groups. However, more infant sleep difficulties were reported in the high‐ versus low‐adversity groups at 12‐ and 18‐month follow‐ups. Neonatal self‐regulatory capacities were not related to the presence or absence of adversity, or to subsequent infant sleep quality. However, there were group differences in maternal settling strategies that did predict subsequent infant sleep difficulties. The pattern of sleep disturbance observed in association with maternal psychosocial adversity at 18‐months was consistent with risk for broader impairments in child functioning.
The Relation of Cumulative Demographic Risk to Mothers' Responsivity and Control: Examining the Role of Toddler Temperament
Authors: Popp Tierney K. , Spinrad Tracy L. , Smith Cynthia L.
Published: October 2008

The relations of cumulative demographic risk and children's temperament to mothers' parenting behaviors were examined when children were 18 (T1, n = 247) and 30 (T2, n = 216) months of age. Mothers, nonparental caregivers (e.g., child care providers), and observers reported on children's temperament to create a temperament composite, and mothers reported on demographic risk variables. Maternal responsivity and control were observed during 2 mother–child interactions at both time points. Cumulative demographic risk was related to low maternal responsivity concurrently and longitudinally, even after controlling for earlier temperament and responsivity, and demographic risk was positively related to maternal control at T1 and T2. Regulated temperament (i.e., low frustration and high regulation) was linked with high maternal responsivity at T1 and T2 and low maternal control at T2. Moreover, the positive relation between cumulative risk and maternal control at T1 was stronger when children were viewed as less regulated.
How to Build an Intentional Android: Infants' Imitation of a Robot's Goal‐Directed Actions
Authors: Itakura Shoji , Ishida Hiraku , Kanda Takayuki , Shimada Yohko , Ishiguro Hiroshi , Lee Kang
Published: October 2008

This study examined whether young children are able to imitate a robot's goal‐directed actions. Children (24–35 months old) viewed videos showing a robot attempting to manipulate an object (e.g., putting beads inside a cup) but failing to achieve its goal (e.g., beads fell outside the cup). In 1 video, the robot made eye contact with a human before and after it failed the action. In another video, the robot did not make eye contact with the human adult. Only in the former condition did children “imitate” the robot's “intended” but unconsummated actions (e.g., putting beads inside a cup). When the robot did not make eye contact, children performed poorly, at the baseline level. These results suggest that human‐like gaze behaviors, not human‐like morphology, may play an important role in young children's imitation of a nonhuman agent's goal‐directed behaviors.