bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability and photoemission characteristics for GaAs photocathodes in a demountable vacuum system
Authors: Zou Jijun , Chang Benkang , Yang Zhi , Qiao Jianliang , Zeng Yiping
Published: April 2008

The stability and photoemission characteristics for reflection-mode GaAs photocathodes in a demountable vacuum system have been investigated by using spectral response and x-ray photoelectron spectroscopy measurements at room temperature. We find that the shape of the spectral response curve for the cathode changes with time in the vacuum system, but after applying fresh cesium to the degraded cathode, the spectral response can almost be restored. The change and restoration of curve shape are mainly attributed to the evolution of the surface barrier. We illustrate the evolution and analyze the influence of the barrier on the spectral response of the cathode.
Tunable wettability in surface-modified ZnO-based hierarchical nanostructures
Authors: Li Gongping , Chen Tao , Yan Bin , Ma Yun , Zhang Zhou , Yu Ting , Shen Zexiang , Chen Hongyu , Wu Tom
Published: April 2008

Designing geometrical structures and making chemical modifications are two effective routes to tailor wettability. ZnO-based hierarchical nanostructures, in particular, vertically aligned nanoneedles and nanonails were employed as a platform to study the effect of surface morphology. The hydrophobicity and the variation of contact angle in the as-grown samples were attributed to the combined effects of surface roughness and partial water-solid contact. Subsequent chemical modifications with stearic acid led to superhydrophobic ZnO surfaces, while annealing in air resulted into superhydrophilicity. Under the alternations of coating and removal of stearic acid, reversible transitions between superhydrophilicity and hydrophobicity were realized.
Structural and optical properties of nonpolar GaN thin films
Authors: Wu Z. H. , Fischer A. M. , Ponce F. A. , Bastek B. , Christen J. , Wernicke T. , Weyers M. , Kneissl M.
Published: April 2008

A correlation between the structural and optical properties of GaN thin films grown in the [112¯0] direction has been established using transmission electron microscopy and cathodoluminescence spectroscopy. The GaN films were grown on an r-plane sapphire substrate, and epitaxial lateral overgrowth was achieved using SiO2 masks. A comparison between the properties of GaN directly grown on sapphire and GaN laterally grown over the SiO2 mask is presented. The densities and dimensions of the stacking faults vary significantly with a high density of short faults in the window region and a much lower density of longer faults in the wing region. The low-temperature luminescence spectra consist of peaks at 3.465 and 3.41eV, corresponding to emission from donor-bound excitons and basal-plane stacking faults, respectively. A correlation between the structural defects and the light emission characteristics is presented.
Inhibition of neural crest migration underlies craniofacial dysmorphology and Hirschsprung's disease in Bardet–Biedl syndrome
Authors: Tobin Jonathan L. , Di Franco Matt , Eichers Erica , May-Simera Helen , Garcia Monica , Yan Jiong , Quinlan Robyn , Justice Monica J. , Hennekam Raoul C. , Briscoe James , Tada Masazumi , Mayor Roberto , Burns Alan J. , Lupski James R. , Hammond Peter , Beales Philip L.
Published: April 2008

Facial recognition is central to the diagnosis of many syndromes, and craniofacial patterns may reflect common etiologies. In the pleiotropic Bardet–Biedl syndrome (BBS), a primary ciliopathy with intraflagellar transport dysfunction, patients have a characteristic facial “gestalt” that dysmorphologists have found difficult to characterize. Here, we use dense surface modeling (DSM) to reveal that BBS patients and mouse mutants have mid-facial defects involving homologous neural crest-derived structures shared by zebrafish morphants. These defects of the craniofacial (CF) skeleton arise from aberrant cranial neural crest cell (NCC) migration. These effects are not confined to the craniofacial region, but vagal-derived NCCs fail to populate the enteric nervous system, culminating in disordered gut motility. Furthermore, morphants display hallmarks of disrupted Sonic Hedgehog (Shh) signaling from which NCCs take positional cues. We propose a model whereby Bbs proteins modulate NCC migration, contributing to craniofacial morphogenesis and development of the enteric nervous system. These migration defects also explain the association of Hirschsprung's disease (HD) with BBS. Moreover, this is a previously undescribed method of using characterization of facial dysmorphology as a basis for investigating the pathomechanism of CF development in dysmorphic syndromes.
A Miocene to Pleistocene climate and elevation record of the Sierra Nevada (California)
Authors: Mulch A. , Sarna-Wojcicki A. M. , Perkins M. E. , Chamberlain C. P.
Published: April 2008

Orographic precipitation of Pacific-sourced moisture creates a rain shadow across the central part of the Sierra Nevada (California) that contrasts with the southern part of the range, where seasonal monsoonal precipitation sourced to the south obscures this rain shadow effect. Orographic rainout systematically lowers the hydrogen isotope composition of precipitation (δ
D
ppt
) and therefore δ
D
ppt
reflects a measure of the magnitude of the rain shadow. Hydrogen isotope compositions of volcanic glass (δ
D
glass
) hydrated at the earth's surface provide a unique opportunity to track the elevation and precipitation history of the Sierra Nevada and adjacent Basin and Range Province. Analysis of 67 well dated volcanic glass samples from widespread volcanic ash-fall deposits located from the Pacific coast to the Basin and Range Province demonstrates that between 0.6 and 12.1 Ma the hydrogen isotope compositions of meteoric water displayed a large (>40‰) decrease from the windward to the leeward side of the central Sierra Nevada, consistent with the existence of a rain shadow of modern magnitude over that time. Evidence for a Miocene-to-recent rain shadow of constant magnitude and systematic changes in the longitudinal climate and precipitation patterns strongly suggest that the modern first-order topographic elements of the Sierra Nevada characterized the landscape over at least the last 12 million years.
Tightly coupled brain activity and cerebral ATP metabolic rate
Authors: Du Fei , Zhu Xiao-Hong , Zhang Yi , Friedman Michael , Zhang Nanyin , Uğurbil Kâmil , Chen Wei
Published: April 2008

A majority of ATP in the brain is formed in the mitochondria through oxidative phosphorylation of ADP with the F
1
F
0
-ATP (ATPase) enzyme. This ATP production rate plays central roles in brain bioenergetics, function and neurodegeneration.
In vivo
31
P magnetic resonance spectroscopy combined with magnetization transfer (MT) is the sole approach able to noninvasively determine this ATP metabolic rate via measuring the forward ATPase reaction flux (
F
f,ATPase
). However, previous studies indicate lack of quantitative agreement between
F
f,ATPase
and oxidative metabolic rate in heart and liver. In contrast, recent work has shown that
F
f,ATPase
might reflect oxidative phosphorylation rate in resting human brains. We have conducted an animal study, using rats under varied brain activity levels from light anesthesia to isoelectric state, to examine whether the
in vivo
31
P MT approach is suitable for measuring the oxidative phosphorylation rate and its change associated with varied brain activity. Our results conclude that the measured
F
f,ATPase
reflects the oxidative phosphorylation rate in resting rat brains, that this flux is tightly correlated to the change of energy demand under varied brain activity levels, and that a significant amount of ATP energy is required for “housekeeping” under the isoelectric state. These findings reveal distinguishable characteristics of ATP metabolism between the brain and heart, and they highlight the importance of
in vivo
31
P MT approach to potentially provide a unique and powerful neuroimaging modality for noninvasively studying the cerebral ATP metabolic network and its central role in bioenergetics associated with brain function, activation, and diseases.
The basal-like mammary carcinomas induced by
Brca1
or
Bard1
inactivation implicate the BRCA1/BARD1 heterodimer in tumor suppression
Authors: Shakya Reena , Szabolcs Matthias , McCarthy Ellen , Ospina Elson , Basso Katia , Nandula Subhadra , Murty Vundavalli , Baer Richard , Ludwig Thomas
Published: April 2008

Women with germ-line mutations of the
BRCA1
tumor suppressor gene are highly susceptible to breast and ovarian cancer. The protein product of
BRCA1
is involved in a broad spectrum of biological processes and interacts with many diverse proteins. One of these, BARD1, associates with BRCA1 to form a heterodimeric complex that is enzymatically active as an ubiquitin E3 ligase. Although the BRCA1/BARD1 heterodimer has been implicated in several aspects of BRCA1 function, its role in tumor suppression has not been evaluated. To address this question, we generated mouse strains carrying conditional alleles of either
Bard1
or
Brca1
and used Cre recombination to inactivate these genes in mammary epithelial cells. Significantly, the conditional
Bard1
- and
Brca1
-mutant mice developed breast carcinomas that are indistinguishable from each other (and from those of double conditional
Bard1
/
Brca1
-mutant animals) with respect to their frequency, latency, histopathology, and cytogenetic features. Reminiscent of the basal-like breast carcinomas seen in human BRCA1 mutation carriers, these tumors are “triple negative” for estrogen and progesterone receptor expression and HER2/neu amplification. They also express basal cytokeratins CK5 and CK14, have an elevated frequency of p53 lesions, and display high levels of chromosomal instability. The remarkable similarities between the mammary carcinomas of
Bard1
-,
Brca1
-, and
Bard1
/
Brca1
-mutant mice indicate that the tumor suppressor activities of both genes are mediated through the BRCA1/BARD1 heterodimer.
Sunflower (
Helianthus annuus
L.) as a pre-Columbian domesticate in Mexico
Authors: Lentz David L. , Pohl Mary DeLand , Alvarado José Luis , Tarighat Somayeh , Bye Robert
Published: April 2008

Mexico has long been recognized as one of the world's cradles of domestication with evidence for squash (
Cucurbita pepo
) cultivation appearing as early as 8,000 cal B.C. followed by many other plants, such as maize (
Zea mays
), peppers (
Capsicum annuum
), common beans (
Phaseolus vulgaris
), and cotton (
Gossypium hirsutum
). We present archaeological, linguistic, ethnographic, and ethnohistoric data demonstrating that sunflower (
Helianthus annuus
) had entered the repertoire of Mexican domesticates by
ca.
2600 cal B.C., that its cultivation was widespread in Mexico and extended as far south as El Salvador by the first millennium B.C., that it was well known to the Aztecs, and that it is still in use by traditional Mesoamerican cultures today. The sunflower's association with indigenous solar religion and warfare in Mexico may have led to its suppression after the Spanish Conquest. The discovery of ancient sunflower in Mexico refines our knowledge of domesticated Mesoamerican plants and adds complexity to our understanding of cultural evolution.
Dual-targeted tRNA-dependent amidotransferase ensures both mitochondrial and chloroplastic Gln-tRNA
Gln
synthesis in plants
Authors: Pujol Claire , Bailly Marc , Kern Daniel , Maréchal-Drouard Laurence , Becker Hubert , Duchêne Anne-Marie
Published: April 2008

Aminoacyl-tRNAs are generally formed by direct attachment of an amino acid to tRNAs by aminoacyl-tRNA synthetases, but Gln-tRNA is an exception to this rule. Gln-tRNA
Gln
is formed by this direct pathway in the eukaryotic cytosol and in protists or fungi mitochondria but is formed by an indirect transamidation pathway in most of bacteria, archaea, and chloroplasts. We show here that the formation of Gln-tRNA
Gln
is also achieved by the indirect pathway in plant mitochondria. The mitochondrial-encoded tRNA
Gln
, which is the only tRNA
Gln
present in mitochondria, is first charged with glutamate by a nondiscriminating GluRS, then is converted into Gln-tRNA
Gln
by a tRNA-dependent amidotransferase (AdT). The three subunits GatA, GatB, and GatC are imported into mitochondria and assemble into a functional GatCAB AdT. Moreover, the mitochondrial pathway of Gln-tRNA
Gln
formation is shared with chloroplasts as both the GluRS, and the three AdT subunits are dual-imported into mitochondria and chloroplasts.
Giant saltation on Mars
Authors: Almeida Murilo P. , Parteli Eric J. R. , Andrade José S. , Herrmann Hans J.
Published: April 2008

Saltation
, the motion of sand grains in a sequence of ballistic trajectories close to the ground, is a major factor for surface erosion, dune formation, and triggering of dust storms on Mars. Although this mode of sand transport has been matter of research for decades through both simulations and wind tunnel experiments under Earth and Mars conditions, it has not been possible to provide accurate measurements of particle trajectories in fully developed turbulent flow. Here we calculate the motion of saltating grains by directly solving the turbulent wind field and its interaction with the particles. Our calculations show that the minimal wind velocity required to sustain saltation on Mars may be surprisingly lower than the aerodynamic minimal threshold measurable in wind tunnels. Indeed, Mars grains saltate in 100 times higher and longer trajectories and reach 5-10 times higher velocities than Earth grains do. On the basis of our results, we arrive at general expressions that can be applied to calculate the length and height of saltation trajectories and the flux of grains in saltation under various physical conditions, when the wind velocity is close to the minimal threshold for saltation.
Ghrelin octanoylation mediated by an orphan lipid transferase
Authors: Gutierrez Jesus A. , Solenberg Patricia J. , Perkins Douglas R. , Willency Jill A. , Knierman Michael D. , Jin Zhaoyan , Witcher Derrick R. , Luo Shuang , Onyia Jude E. , Hale John E.
Published: April 2008

The peptide hormone ghrelin is the only known protein modified with an O-linked octanoyl side group, which occurs on its third serine residue. This modification is crucial for ghrelin's physiological effects including regulation of feeding, adiposity, and insulin secretion. Despite the crucial role for octanoylation in the physiology of ghrelin, the lipid transferase that mediates this novel modification has remained unknown. Here we report the identification and characterization of human GOAT, the ghrelin
O
-acyl transferase. GOAT is a conserved orphan membrane-bound
O
-acyl transferase (MBOAT) that specifically octanoylates serine-3 of the ghrelin peptide. Transcripts for both GOAT and ghrelin occur predominantly in stomach and pancreas. GOAT is conserved across vertebrates, and genetic disruption of the GOAT gene in mice leads to complete absence of acylated ghrelin in circulation. The occurrence of ghrelin and GOAT in stomach and pancreas tissues demonstrates the relevance of GOAT in the acylation of ghrelin and further implicates acylated ghrelin in pancreatic function.
Improving fluid intelligence with training on working memory
Authors: Jaeggi Susanne M. , Buschkuehl Martin , Jonides John , Perrig Walter J.
Published: April 2008

Fluid intelligence (
Gf
) refers to the ability to reason and to solve new problems independently of previously acquired knowledge.
Gf
is critical for a wide variety of cognitive tasks, and it is considered one of the most important factors in learning. Moreover,
Gf
is closely related to professional and educational success, especially in complex and demanding environments. Although performance on tests of
Gf
can be improved through direct practice on the tests themselves, there is no evidence that training on any other regimen yields increased
Gf
in adults. Furthermore, there is a long history of research into cognitive training showing that, although performance on trained tasks can increase dramatically, transfer of this learning to other tasks remains poor. Here, we present evidence for transfer from training on a demanding working memory task to measures of
Gf
. This transfer results even though the trained task is entirely different from the intelligence test itself. Furthermore, we demonstrate that the extent of gain in intelligence critically depends on the amount of training: the more training, the more improvement in
Gf
. That is, the training effect is dosage-dependent. Thus, in contrast to many previous studies, we conclude that it is possible to improve
Gf
without practicing the testing tasks themselves, opening a wide range of applications.
Modular patterning of structure and function of the striatum by retinoid receptor signaling
Authors: Liao Wen-Lin , Tsai Hsiu-Chao , Wang Hsiao-Fang , Chang Josephine , Lu Kuan-Ming , Wu Hsiao-Lin , Lee Yi-Chao , Tsai Ting-Fen , Takahashi Hiroshi , Wagner Michael , Ghyselinck Norbert B. , Chambon Pierre , Liu Fu-Chin
Published: April 2008

Retinoid signaling plays a crucial role in patterning rhombomeres in the hindbrain and motor neurons in the spinal cord during development. A fundamentally interesting question is whether retinoids can pattern functional organization in the forebrain that generates a high order of cognitive behavior. The striatum contains a compartmental structure of striosome (or “patch”) and intervening matrix. How this highly complex mosaic design is patterned by the genetic programs during development remains elusive. We report a developmental mechanism by which retinoid receptor signaling controls compartmental formation in the striatum. We analyzed RARβ
−/−
mutant mice and found a selective loss of striosomal compartmentalization in the rostral mutant striatum. The loss of RARβ signaling in the mutant mice resulted in reduction of cyclin E2, a cell cycle protein regulating transition from G
1
to S phase, and also reduction of the proneural gene
Mash1
, which led to defective neurogenesis of late-born striosomal cells. Importantly, during striatal neurogenesis, endogenous levels of retinoic acid were spatiotemporally regulated such that transduction of high levels of retinoic acid through RARβ selectively expanded the population of late-born striosomal progenitors, which evolved into a highly elaborate compartment in the rostral striatum. RARβ
−/−
mutant mice, which lacked such enlarged compartment, displayed complex alternations of dopamine agonist-induced stereotypic motor behavior, including exaggeration of head bobbing movement and reduction of rearing activity. RARβ signaling thus plays a crucial role in setting up striatal compartments that may engage in neural circuits of psychomotor control.
LAVH for large uteri by various strategies
Authors: CHANG WEN‐CHUN , HUANG SU‐CHENG , SHEU BOR‐CHING , TORNG PAO‐LING , HSU WEN‐CHIUNG , CHEN SZU‐YU , CHANG DAW‐YUAN
Published: April 2008

Background. To study if there are specific problems in laparoscopically assisted vaginal hysterectomy (LAVH) for a certain weight of bulky uteri and the strategies to overcome such problems. Methods. One hundred and eighty‐one women with myoma or adenomyosis, weighing 350‐1,590 g, underwent LAVH between August 2002 and December 2005. Key surgical strategies were special sites for trocar insertion, uterine artery or adnexal collateral pre‐ligation, laparoscopic and transvaginal volume reduction technique. The basic clinical and operative parameters were recorded for analysis. Results. Based on significant differences in the operative time and estimated blood loss, the patients were divided into medium uteri weighing 350–749 g, n = 138 (76%), and large uteri weighing ≥750 g, n = 43 (24%). There was no significant difference in terms of age, body mass index, preoperative diagnoses, complications and duration of hospital stay among groups. The operative time and estimated blood loss increased with larger uterine size (p<0.001). The operative time (196±53, 115–395 min), estimated blood loss (234±200, 50–1,000 ml) and frequency of excessive bleeding (14%) or transfusion (5%) were significantly greater, but in acceptable ranges, for those with large uteri. Conversion to laparotomy was required in a patient (2%) with a large uterus, and the overall conversion rate was 0.6%. There was no re‐operation or surgical mortality. Conclusion. Using various combinations of special strategies, most experienced gynecologic surgeons can conduct LAVH for most large uteri with minimal rates of complications and conversion to laparotomy.
Italy and the Mediterranean: Relations with the Maghreb countries
Authors: Coralluzzo Valter
Published: April 2008

After outlining the trends of Italian Mediterranean politics, this article examines the relationship between Italy and the Maghreb region. As a result of its central geographic position, acting as a natural bridge between Europe and Africa, Italy is undoubtedly more exposed and vulnerable than other countries to any critical developments in the political and economic situation of this area, so it is understandable that it occupies an increasingly important position in Italian foreign policy. Italy has especially considered it in its national interest to make it a specific, high priority to contribute to stabilising this region through multilateral and bilateral initiatives aimed at reinforcing political dialogue and economic cooperation with the coastal countries on the southern shore of the Mediterranean. The aim has been to create a safety net around Italian maritime borders against the risks posed by an uncontrolled increase in migration (to which Italy is more exposed than other countries), the instability of North African energy resources and Islamist terrorists infiltrating Italian territory. Apart from examining the concerns regarding the Maghreb region that have become crucially important for Italian national interests (security, immigration, development, energy), the article analyses the salient elements of bilateral relations between Italy and the Maghreb countries, particularly Libya.
Relationship between perceptual ratings of nasality and nasometry in children/adolescents with cleft palate and/or velopharyngeal dysfunction
Authors: Sweeney Triona , Sell Debbie
Published: April 2008

Background: Nasometry has supplemented perceptual assessments of nasality, using speech stimuli, which are devoid of nasal consonants. However, such speech stimuli are not representative of conversational speech. A weak relationship has been found in previous studies between perceptual ratings of hypernasality and nasalance scores for passages containing nasal consonants.

Aims: This study aimed to evaluate the relationship between perceptual assessment and acoustic measurements of nasality using controlled speech stimuli.

Methods & Procedure: A perceptual scale (the Temple Street Scale) describing nasality was devised for this study. Fifty children presenting with nasality were assessed using the Temple Street Scale and nasalance scores were obtained for specified speech samples using the Nasometer (Kay Elemetrics 6200.3). The relationship between the perceptual ratings and the nasometry results was evaluated using correlation analysis, test sensitivity, specificity, and overall efficiency.

Outcomes & Results: Correlation coefficients for perceptual ratings of nasality and nasalance scores ranged from 0.69 to 0.74. The sensitivity of the Nasometer ranged from 0.83 to 0.88; its specificity ranged from 0.78 to 0.95; while its overall efficiency was between 0.82 and 0.92.

Conclusions: The strong relationship between perceptual and acoustic assessments of nasality indicated that the Temple Street Scale and the Nasometer are both valid clinical tools for the evaluation of nasality when a carefully constructed speech sample is used. The need to use the Nasometer as a supplement to perceptual assessment is highlighted.
Grammaticality judgements in adolescents with and without language impairment
Authors: Miller Carol A. , Leonard Laurence B. , Finneran Denise
Published: April 2008

Background: Existing evidence suggests that young children with specific language impairment have unusual difficulty in detecting omissions of obligatory tense‐marking morphemes, but little is known about adolescents' sensitivity to such violations.

Aims: The study investigated whether limitations in receptive morphosyntax (as measured by grammaticality judgements) were present at age 16 years, and, if so, whether participants' profiles showed less sensitivity to omissions of tense and agreement morphemes than to (1) inappropriate uses (intrusions) of these same morphemes, and (2) omissions of morphemes that do not encode tense and agreement. The study also compared adolescents with language impairment and non‐verbal IQ more than 1 standard deviation (SD) below the mean (non‐specific language impairment) to adolescents with specific language impairment.

Methods & Procedures: Adolescents with specific language impairment (n = 48), adolescents with non‐specific language impairment (n = 25), and adolescents with normal language development (n = 108) performed speeded grammaticality judgements of sentences presented over headphones. Half the sentences were ungrammatical. They included omissions of non‐tense morphemes (‐ing and possessive ‐s), omissions of tense morphemes (‐ed and third‐person singular present ‐s), and intrusions of the same tense morphemes. The A′ statistic was used as the dependent variable for comparisons across groups and item types.

Outcomes & Results: Overall, the normal language development group was more sensitive to grammatical violations than the specific language impairment and non‐specific language impairment groups, and there was no significant interaction of group and item type. Post‐hoc analyses showed that the specific language impairment group was less sensitive to violations than the normal language development group on each item type, and the specific language impairment and non‐specific language impairment groups did not differ. Across groups, performance on omission of past tense ‐ed was lowest, and properties of the items that may have contributed to this difference were explored.

Conclusions: The adolescents with language impairment in this study showed evidence of reduced sensitivity to morphological errors, including both tense‐marking and non‐tense‐marking morphemes, but no evidence of any extraordinary difficulty in detecting the omission of tense‐marking morphemes, in contrast to results from other research on younger children with specific language impairment. Participants whose non‐verbal IQ score was too low to meet the criteria for specific language impairment performed similarly to their peers with specific language impairment. Grammatical competence is compromised in these adolescents with specific language impairment and non‐specific language impairment. Neither researchers nor clinicians can assume that adolescents with language impairment have fully mastered grammatical morphology.
Economic aspects of a therapy and support service for people with long‐term stroke and aphasia
Authors: van der Gaag Anna , Brooks Richard
Published: April 2008

Backgound:This paper considers some economic aspects of a therapy and support service for people with stroke and aphasia. This material was part of a broader evaluation of the service, which is reported elsewhere (van derGaaget al.2005, van derGaag and Mowles 2005).

Aims:The purpose of this part of the study was to investigate the feasibility of undertaking economic appraisal in a voluntary sector service providing therapy for people with aphasia and their families.

Methods & Procedures:The costs of delivering therapy and support services were calculated. These costs were compared with the costs of equivalent services in the National Health Service (NHS). The EQ‐5D health‐related quality of life instrument was used to calculate quality‐adjusted life years (QALYs).

Outcomes & Results:The cost of delivering therapy was lower than expected for a customized service of this nature. The study generated cost data for delivering therapy services, allowing some comparisons to be made with equivalent services in NHS settings. QALY data were generated for a sample of 25 clients on one of the programmes.

Conclusions:The economics of speech and language therapy service delivery have received scant attention in the published literature. The paper argues that decision‐making about methods of service delivery can be aided by the explicit consideration of the costs and consequences of different programmes.
Variability of Spanish adolescents’ physical activity patterns by seasonality, day of the week and demographic factors
Authors: Peiró‐Velert Carmen , Devís‐Devís Jose , Beltrán‐Carrillo Vicente J. , Fox Kenneth R.
Published: April 2008

In this study, we examined the variability of physical activity (and inactivity) patterns in relation to gender, age, type of school, day of the week, and season of the year among a sample of Spanish adolescents aged 12–16 years. Levels of physical activity engagement, “who” was active/inactive, and “when” they were active/inactive were addressed. A Spanish translation and modification of Cale's Four by One‐Day Physical Activity Questionnaire was administered by interviewer to 323 participants to measure estimated energy expenditure. Activity was assessed for two weekdays and two weekend days on two occasions during the autumn and two occasions during the winter. In an effort to better describe adolescents’ active/inactive lifestyles, energy expenditures were translated into physical activity categories (i.e. active, moderately active, inactive, and very inactive). Results revealed that mean adolescent total daily energy expenditure was 41.46 kcal·kg−1·day−1 (s=7.05), which corresponded to the “active” category. Factorial and mixed analyses of variance showed statistically significant differences in energy expenditure by gender, season, day of the week, and type of school (P<0.001). Female adolescents spent less daily energy than their male counterparts and, consequently, they were less active overall, even though they were more moderately active than boys. Participants were more active in winter than in autumn, which was largely due to the accumulation of time engaged in more lifestyle activities than differences in strenuous exercise. Adolescents were also less active on weekdays than during weekends. An interaction effect emerged for day of the week and type of school with adolescents attending public (or state) schools presenting higher daily energy expenditures than those from private schools during weekends (P<0.01). The results suggest that girls may prefer less vigorous forms of activity. They also indicate that adolescents are investing time in physical activity when they have the freedom to participate or not (i.e. weekends), in particular those from public schools. We suggest that differences in gender, seasonality, and weekends versus weekdays, together with the choice of lifestyle activities, should be considered when designing activity promotion strategies among Spanish adolescents.
Polo-like kinase is required for Golgi and bilobe biogenesis in Trypanosoma brucei
Authors: de Graffenried Christopher L. , Ho Helen H. , Warren Graham
Published: April 2008

A bilobed structure marked by TbCentrin2 regulates Golgi duplication in the protozoan parasite Trypanosoma brucei. This structure must itself duplicate during the cell cycle for Golgi inheritance to proceed normally. We show here that duplication of the bilobed structure is dependent on the single polo-like kinase (PLK) homologue in T. brucei (TbPLK). Depletion of TbPLK leads to malformed bilobed structures, which is consistent with an inhibition of duplication and an increase in the number of dispersed Golgi structures with associated endoplasmic reticulum exit sites. These data suggest that the bilobe may act as a scaffold for the controlled assembly of the duplicating Golgi.
Augmin: a protein complex required for centrosome-independent microtubule generation within the spindle
Authors: Goshima Gohta , Mayer Mirjam , Zhang Nan , Stuurman Nico , Vale Ronald D.
Published: April 2008

Since the discovery of γ-tubulin, attention has focused on its involvement as a microtubule nucleator at the centrosome. However, mislocalization of γ-tubulin away from the centrosome does not inhibit mitotic spindle formation in Drosophila melanogaster, suggesting that a critical function for γ-tubulin might reside elsewhere. A previous RNA interference (RNAi) screen identified five genes (Dgt2–6) required for localizing γ-tubulin to spindle microtubules. We show that the Dgt proteins interact, forming a stable complex. We find that spindle microtubule generation is substantially reduced after knockdown of each Dgt protein by RNAi. Thus, the Dgt complex that we name “augmin” functions to increase microtubule number. Reduced spindle microtubule generation after augmin RNAi, particularly in the absence of functional centrosomes, has dramatic consequences on mitotic spindle formation and function, leading to reduced kinetochore fiber formation, chromosome misalignment, and spindle bipolarity defects. We also identify a functional human homologue of Dgt6. Our results suggest that an important mitotic function for γ-tubulin may lie within the spindle, where augmin and γ-tubulin function cooperatively to amplify the number of microtubules.
CENP-E combines a slow, processive motor and a flexible coiled coil to produce an essential motile kinetochore tether
Authors: Kim Yumi , Heuser John E. , Waterman Clare M. , Cleveland Don W.
Published: April 2008

The mitotic kinesin centromere protein E (CENP-E) is an essential kinetochore component that directly contributes to the capture and stabilization of spindle microtubules by kinetochores. Although reduction in CENP-E leads to high rates of whole chromosome missegregation, neither its properties as a microtubule-dependent motor nor how it contributes to the dynamic linkage between kinetochores and microtubules is known. Using single-molecule assays, we demonstrate that CENP-E is a very slow, highly processive motor that maintains microtubule attachment for long periods. Direct visualization of full-length Xenopus laevis CENP-E reveals a highly flexible 230-nm coiled coil separating its kinetochore-binding and motor domains. We also show that full-length CENP-E is a slow plus end–directed motor whose activity is essential for metaphase chromosome alignment. We propose that the highly processive microtubule-dependent motor activity of CENP-E serves to power chromosome congression and provides a flexible, motile tether linking kinetochores to dynamic spindle microtubules.
A role for sex chromosome complement in the female bias in autoimmune disease
Authors: Smith-Bouvier Deborah L. , Divekar Anagha A. , Sasidhar Manda , Du Sienmi , Tiwari-Woodruff Seema K. , King Jennifer K. , Arnold Arthur P. , Singh Ram Raj , Voskuhl Rhonda R.
Published: April 2008

Most autoimmune diseases are more common in women than in men. This may be caused by differences in sex hormones, sex chromosomes, or both. In this study, we determined if there was a contribution of sex chromosomes to sex differences in susceptibility to two immunologically distinct disease models, experimental autoimmune encephalomyelitis (EAE) and pristane-induced lupus. Transgenic SJL mice were created to permit a comparison between XX and XY within a common gonadal type. Mice of the XX sex chromosome complement, as compared with XY, demonstrated greater susceptibility to both EAE and lupus. This is the first evidence that the XX sex chromosome complement, as compared with XY, confers greater susceptibility to autoimmune disease.
Validation of the load-resilient ion cyclotron resonance frequency antenna concept on Tore Supra plasmas
Authors: Vulliez K. , Argouarch A. , Bosia G. , Berger-By G. , Bremond S. , Colas L. , Lombard G. , Mendes A. , Millon L. , Mollard P. , Volpe D. , Beaumont B. , Bécoulet A. , Clairet F. , Ekedahl A. , Elkhaldi M. , Gunn J. , Hoang G.T.
Published: April 2008

In the framework of the ion cyclotron resonance frequency heating development at CEA Cadarache, a prototype antenna based on the load-resilient electrical layout foreseen for ITER has been built. This prototype was recently tested in Tore Supra. The ITER-like electrical scheme has been validated during fast perturbations at the edge plasma. Clear load resilience properties are reported. The main conclusions and consequences learned from the development of the ITER antenna are discussed.
MAMOT: hidden Markov modeling tool
Authors: Schütz Frédéric , Delorenzi Mauro
Published: April 2008

Summary: Hidden Markov models (HMMs) are probabilistic models that are well adapted to many tasks in bioinformatics, for example, for predicting the occurrence of specific motifs in biological sequences. MAMOT is a command-line program for Unix-like operating systems, including MacOS X, that we developed to allow scientists to apply HMMs more easily in their research.

One can define the architecture and initial parameters of the model in a text file and then use MAMOT for parameter optimization on example data, decoding (like predicting motif occurrence in sequences) and the production of stochastic sequences generated according to the probabilistic model. Two examples for which models are provided are coiled-coil domains in protein sequences and protein binding sites in DNA. A wealth of useful features include the use of pseudocounts, state tying and fixing of selected parameters in learning, and the inclusion of prior probabilities in decoding.

Availability: MAMOT is implemented in C++, and is distributed under the GNU General Public Licence (GPL). The software, documentation, and example model files can be found at http://bcf.isb-sib.ch/mamot

Contact:  Mauro.Delorenzi@isb-sib.ch
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
Authors: Strimmer Korbinian
Published: April 2008

Summary: False discovery rate (FDR) methodologies are essential in the study of high-dimensional genomic and proteomic data. The R package ‘fdrtool’ facilitates such analyses by offering a comprehensive set of procedures for FDR estimation. Its distinctive features include: (i) many different types of test statistics are allowed as input data, such as P-values, z-scores, correlations and t-scores; (ii) simultaneously, both local FDR and tail area-based FDR values are estimated for all test statistics and (iii) empirical null models are fit where possible, thereby taking account of potential over- or underdispersion of the theoretical null. In addition, ‘fdrtool’ provides readily interpretable graphical output, and can be applied to very large scale (in the order of millions of hypotheses) multiple testing problems. Consequently, ‘fdrtool’ implements a flexible FDR estimation scheme that is unified across different test statistics and variants of FDR.

Availability: The program is freely available from the Comprehensive R Archive Network (http://cran.r-project.org/) under the terms of the GNU General Public License (version 3 or later).

Contact:  strimmer@uni-leipzig.de
Acoustic seabed classification: current practice and future directions
Authors: Anderson John T. , Van Holliday D. , Kloser Rudy , Reid Dave G. , Simard Yvan
Published: April 2008

Anderson, J. T., Holliday, D. V., Kloser, R., Reid, D. G., and Simard, Y. 2008. Acoustic seabed classification: current practice and future directions. – ICES Journal of Marine Science, 65: 1004–1011. Acoustic remote sensing of the seabed using single-beam echosounders, multibeam echosounders, and sidescan sonars combined and individually are providing technological solutions to marine-habitat mapping initiatives. We believe the science of acoustic seabed classification (ASC) is at its nascence. A comprehensive review of ASC science was undertaken by an international group of scientists under the auspices of ICES. The review was prompted by the growing need to classify and map marine ecosystems across a range of spatial scales in support of ecosystem-based science for ocean management. A review of the theory of sound-scattering from seabeds emphasizes the variety of theoretical models currently in use and the ongoing evolution of our understanding. Acoustic-signal conditioning and data quality assurance before classification using objective, repeatable procedures are important technical considerations where standardization of methods is only just beginning. The issue of temporal and spatial scales is reviewed, with emphasis on matching observational scales to those of the natural world. It is emphasized throughout that the seabed is not static but changes over multiple time-scales as a consequence of natural physical and biological processes. A summary of existing commercial ASC systems provides an introduction to existing capabilities. Verification (ground-truthing) methods are reviewed, emphasizing the difficulties of matching observational scales with acoustic-backscatter data. Survey designs for ASC explore methods that extend beyond traditional oceanographic and fisheries survey techniques. Finally, future directions for acoustic seabed classification science were identified in the key areas requiring immediate attention by the international scientific community.
Effects of stochastic parametrization on conceptual climate models
Authors: Wilks Daniel S
Published: April 2008

Conceptual climate models are very simple mathematical representations of climate processes, which are especially useful because their workings can be readily understood. The usual procedure of representing effects of unresolved processes in such models using functions of the prognostic variables (parametrizations) that include no randomness generally results in these models exhibiting substantially less variability than do the phenomena they are intended to simulate. A viable yet still simple alternative is to replace the conventional deterministic parametrizations with stochastic parametrizations, which can be justified theoretically through the central limit theorem. The result is that the model equations are stochastic differential equations. In addition to greatly increasing the magnitude of variability exhibited by these models, and their qualitative fidelity to the corresponding real climate system, representation of unresolved influences by random processes can allow these models to exhibit surprisingly rich new behaviours of which their deterministic counterparts are incapable.
An applied mathematics perspective on stochastic modelling for climate
Authors: Majda Andrew J , Franzke Christian , Khouider Boualem
Published: April 2008

Systematic strategies from applied mathematics for stochastic modelling in climate are reviewed here. One of the topics discussed is the stochastic modelling of mid-latitude low-frequency variability through a few teleconnection patterns, including the central role and physical mechanisms responsible for multiplicative noise. A new low-dimensional stochastic model is developed here, which mimics key features of atmospheric general circulation models, to test the fidelity of stochastic mode reduction procedures. The second topic discussed here is the systematic design of stochastic lattice models to capture irregular and highly intermittent features that are not resolved by a deterministic parametrization. A recent applied mathematics design principle for stochastic column modelling with intermittency is illustrated in an idealized setting for deep tropical convection; the practical effect of this stochastic model in both slowing down convectively coupled waves and increasing their fluctuations is presented here.
Impact of a quasi-stochastic cellular automaton backscatter scheme on the systematic error and seasonal prediction skill of a global climate model
Authors: Berner J , Doblas-Reyes F.J , Palmer T.N , Shutts G , Weisheimer A
Published: April 2008

The impact of a nonlinear dynamic cellular automaton (CA) model, as a representation of the partially stochastic aspects of unresolved scales in global climate models, is studied in the European Centre for Medium Range Weather Forecasts coupled ocean–atmosphere model. Two separate aspects are discussed: impact on the systematic error of the model, and impact on the skill of seasonal forecasts. Significant reductions of systematic error are found both in the tropics and in the extratropics. Such reductions can be understood in terms of the inherently nonlinear nature of climate, in particular how energy injected by the CA at the near-grid scale can backscatter nonlinearly to larger scales. In addition, significant improvements in the probabilistic skill of seasonal forecasts are found in terms of a number of different variables such as temperature, precipitation and sea-level pressure. Such increases in skill can be understood both in terms of the reduction of systematic error as mentioned above, and in terms of the impact on ensemble spread of the CA's representation of inherent model uncertainty.
Stochastic parametrization of multiscale processes using a dual-grid approach
Authors: Shutts Glenn , Allen Thomas , Berner Judith
Published: April 2008

Some speculative proposals are made for extending current stochastic sub-gridscale parametrization methods using the techniques adopted from the field of computer graphics and flow visualization. The idea is to emulate sub-filter-scale physical process organization and time evolution on a fine grid and couple the implied coarse-grained tendencies with a forecast model. A two-way interaction is envisaged so that fine-grid physics (e.g. deep convective clouds) responds to forecast model fields. The fine-grid model may be as simple as a two-dimensional cellular automaton or as computationally demanding as a cloud-resolving model similar to the coupling strategy envisaged in ‘super-parametrization’. Computer codes used in computer games and visualization software illustrate the potential for cheap but realistic simulation where emphasis is placed on algorithmic stability and visual realism rather than pointwise accuracy in a predictive sense. In an ensemble prediction context, a computationally cheap technique would be essential and some possibilities are outlined. An idealized proof-of-concept simulation is described, which highlights technical problems such as the nature of the coupling.
Stochastic models of the meridional overturning circulation: time scales and patterns of variability
Authors: Monahan Adam H , Alexander Julie , Weaver Andrew J
Published: April 2008

The global meridional overturning circulation (MOC) varies over a wide range of space and time scales in response to fluctuating ‘weather’ perturbations that may be modelled as stochastic forcing. This study reviews model studies of the effects of climate noise on decadal to centennial MOC variability, on transitions between the MOC regimes and on the dynamics of Dansgaard–Oeschger events characteristic of glacial periods.
Comparison of stochastic parametrization approaches in a single-column model
Authors: Ball Michael A , Plant Robert S
Published: April 2008

We discuss and test the potential usefulness of single-column models (SCMs) for the testing of stochastic physics schemes that have been proposed for use in general circulation models (GCMs). We argue that although single-column tests cannot be definitive in exposing the full behaviour of a stochastic method in the full GCM, and although there are differences between SCM testing of deterministic and stochastic methods, SCM testing remains a useful tool. It is necessary to consider an ensemble of SCM runs produced by the stochastic method. These can be usefully compared with deterministic ensembles describing initial condition uncertainty and also with combinations of these (with structural model changes) into poor man's ensembles. The proposed methodology is demonstrated using an SCM experiment recently developed by the GCSS (GEWEX Cloud System Study) community, simulating transitions between active and suppressed periods of tropical convection.