bluuebunny/crossref_metadata_2025 huggingface dataset:
Bulk properties of the slow and fast solar wind and interplanetary coronal mass ejections measured by Ulysses: Three polar orbits of observations
Authors: Ebert R. W. , McComas D. J. , Elliott H. A. , Forsyth R. J. , Gosling J. T.
Published: January 2009

We examined plasma and magnetic field observations from all three Ulysses polar orbits of the Sun to study the properties of the slow and fast solar wind and interplanetary coronal mass ejections (ICMEs). We derived equations to characterize the radial and latitudinal variations for these three types of heliospheric plasma and identify distinguishing features in their spatial variations. Most notably, the slow‐wind proton temperature falls less rapidly with distance than does the fast wind, indicating a source of enhanced heating in the low‐speed wind. After removing the radial variations from the measurements, only minor latitudinal gradients were identified. The fast wind has now been shown to be only weakly dependent on solar latitude for two successive solar minima. The spatial variations in the ICME properties do not differ significantly from the slow and fast solar wind, although the variability in their parameters is much larger. We also investigated solar cycle variations in the fast polar coronal hole (PCH) flows by comparing their properties measured over Ulysses' 1st and 3rd orbits. While the latitudinal gradients were similar, slight differences were observed in the radial dependence for the proton density and magnetic field strength. Also, a slight reduction in the proton speed at 1 AU, along with more significant decreases in the proton temperature, density, dynamic pressure, and magnetic field strength, was observed for the 3rd orbit relative to that for the 1st. These results are consistent with recent observations of weaker PCH flows for the current solar minimum.
Parameters of subsurface brines and hydrothermal processes 12–15 months after the 1999 magmatic event at the Main Endeavor Field as inferred from in situ time series measurements of chloride and temperature
Authors: Larson B. I. , Lilley M. D. , Olson E. J.
Published: January 2009

Phase separation at mid‐ocean ridge hydrothermal systems is a widely distributed frequently occurring process. It is highly sensitive to dynamic subsurface pressure and temperature conditions and has a significant impact on chloride concentrations of hydrothermal fluid. Although vapor phases produced by phase separation are observed in a variety of hydrothermal settings, observation of conjugate brines that must be produced concurrently are more rare and the fate of subsurface brines is still not well understood. Here we use an array of in situ chloride sensors deployed at the Main Endeavor Field on the Juan de Fuca Ridge in the wake of a magmatic event to monitor the behavior of hydrothermal vent effluent with high temporal resolution. Our results provide evidence of near‐critical chloride depleted fluids within the crust up to 486 m beneath the seafloor. We estimate that a brine reservoir stored beneath the Main Endeavor Field is constrained to temperatures between 131°C and 326°C for chloride concentrations ranging from 6 to 25 Wt.% NaCl, respectively. Our data suggest that subsurface fluids and circulation pathways vary widely over spatial scales on the order of meters. Under these circumstances, simultaneous measurements of multiple fluid parameters at a high temporal resolution are essential to understanding subsurface hydrothermal processes associated with magmatic events.
Vesiculation in magmas from Stromboli and implications for normal Strombolian activity and paroxysmal explosions in basaltic systems
Authors: Polacci Margherita , Baker Don R. , Mancini Lucia , Favretto Stefano , Hill Reghan J.
Published: January 2009

We performed a series of X‐ray tomographic experiments and lattice Boltzmann permeability simulations on pyroclastic products from explosive activity at Stromboli between December 2004 and May 2006. We reconstructed the 3‐D textures of vesicles to investigate the relationship between the nature of vesiculation in the erupted products and the dynamics of gas transport in the shallow conduit in order to derive implications for the eruptive behavior of basaltic volcanoes. Scoriae from normal Strombolian explosions display remarkably consistent vesicle volume distributions fit by power laws with an exponent of 1 (±0.2). We ascribe the origin of such distributions to the combined effect of coalescence and continuous nucleation events in the steady state, shallow magma system that supplies normal Strombolian activity. Volume distributions and textures of vesicles in pumice clasts from the 5 April 2003 and 15 March 2007 paroxysmal activity are markedly different from those in the scoriae. Besides a power law function with a higher exponent, portions of these distributions can be also fit by an exponential function, suggesting the attempt of the system to reach near‐equilibrium conditions. The investigated pumice clasts also lack the large, connecting vesicles responsible for the development of degassing pathways in the Stromboli magma that erupts the scoriae. This testifies to a decreased degassing efficiency of the magma associated with paroxysmal explosions and potential overpressure buildup at depth. By comparison with degassing experiments on basaltic melts, we derive a time constraint on the order of minutes to hours for the incubation of paroxysms at Stromboli.
Groundwater flow and hydrothermal systems within volcanic edifices: Delineation by electric self‐potential and magnetotellurics
Authors: Aizawa Koki , Ogawa Yasuo , Ishido Tsuneo
Published: January 2009

The imaging of hydrothermal systems within volcanoes is critical in evaluating the nature and likelihood of future volcanic activity and hazard assessment. In this study, we present a conceptual model of the hydrothermal system in a volcanic edifice, as deduced from the relationship between electric self‐potential (SP) and high‐resolution resistivity structures. In order to develop a comprehensive model of water flow in volcanoes, we conducted the audiofrequency (10,000–0.3 Hz) magnetotelluric surveys in five large stratovolcanoes (Iwate, Iwaki, Nasu, Nantai, and Nikko‐Shirane) in Japan and found that the obtained 2‐D resistivity profiles have a close relationship to the previously reported SP data: good extensive conductors occur beneath areas without SP anomalies, whereas good localized conductors only occur beneath large spatial wavelength SP anomalies on the volcano side of the SP minimum. Also taking into account the locations of surface geothermal activity, the good conductors roughly correspond to the hydrothermal zone, whose upper limit is sealed by a low‐permeability clay layer. The sealing layer separates an upper groundwater flow from a lower hydrothermal flow in the subsurface and controls the geothermal manifestations and river locations on the surface. We confirmed the feasibility of the proposed model based on numerical simulations of a hydrothermal system. The horizontal extent of the hydrothermal zone is highly heterogeneous even in a volcanic edifice. This heterogeneity can reflect the geological age of flanks that may be related to the occurrence of a previous large sector collapse.
Evidence for Mogi doughnut behavior in seismicity preceding small earthquakes in southern California
Authors: Shearer Peter M. , Lin Guoqing
Published: January 2009

We examine the average space‐time behavior of seismicity preceding M 2–5 earthquakes in southern California from 1981 to 2005 using a high‐resolution catalog and identify regions of enhanced activity in a 1‐day period preceding larger earthquakes at distances comparable to their predicted source radii. The difference in precursory behavior between large and small earthquakes is subtle but statistically significant when averaged over many earthquakes, and it has similarities to the “Mogi doughnut” seismicity pattern observed to occur prior to some M 6 and larger earthquakes. These results indicate that many standard earthquake triggering models do not account for all of the processes involved in earthquake occurrence.
On wind‐wave‐current interactions during the Shoaling Waves Experiment
Authors: Zhang Fei W. , Drennan William M. , Haus Brian K. , Graber Hans C.
Published: January 2009

This paper presents a case study of wind‐wave‐current interaction during the Shoaling Waves Experiment (SHOWEX). Surface current fields off Duck, North Carolina, were measured by a high‐frequency Ocean Surface Current Radar (OSCR). Wind, wind stress, and directional wave data were obtained from several Air Sea Interaction Spar (ASIS) buoys moored in the OSCR scanning domain. At several times during the experiment, significant coastal currents entered the experimental area. High horizontal shears at the current edge resulted in the waves at the peak of wind‐sea spectra (but not those in the higher‐frequency equilibrium range) being shifted away from the mean wind direction. This led to a significant turning of the wind stress vector away from the mean wind direction. The interactions presented here have important applications in radar remote sensing and are discussed in the context of recent radar imaging models of the ocean surface.
Impacts of urban expansion and future green planting on summer precipitation in the Beijing metropolitan area
Authors: Zhang Chao Lin , Chen Fei , Miao Shi Guang , Li Qing Chun , Xia Xiang Ao , Xuan Chun Yi
Published: January 2009

In this study, an analysis of long‐term rainfall data reveals that the rapid urban expansion in Beijing since 1981 is statistically correlated to summer rainfall reduction in the northeast areas of Beijing from 1981 to 2005. This coincides with the period in which the shortage of water in the Beijing area has become a serious factor for sustainable economic development. Meanwhile, an analysis of the aerosol optical depth (AOD) from the Total Ozone Mapping Spectrometer spanning the years from 1980 to 2001 shows that there is no clear secular trend in summer AOD in Beijing. With the particular purpose of further understanding the effects of urban expansion on summer rainfall and the potential measures to mitigate such effects, a mesoscale weather/land‐surface/urban–coupled model along with different urban land‐use change scenarios are used to conduct numerical simulations for two selected heavy summer rainfall events with different, but representative, summer weather patterns in Beijing. Results show that urban expansion can produce less evaporation, higher surface temperatures, larger sensible heat fluxes, and a deeper boundary layer. This leads to less water vapor, more mixing of water vapor in the boundary layer, and hence less (more) convective available potential energy (convective inhibition energy). The combination of these factors induced by expanding urban surfaces is helpful in reducing precipitation for the Beijing area in general and, in particular, for the Miyun reservoir area (the major source for the local water supply). Increasing green vegetation coverage in the Beijing area would produce more rainfall, and model results show that planting grass seems more effective than planting trees. For the same vegetation, the rainfall difference from simulations using two green‐planting layouts (annular and cuneiform) is small.
A 4‐decade record of elevation change of the Amery Ice Shelf, East Antarctica
Authors: King Matt A. , Coleman Richard , Freemantle Anna‐Jane , Fricker Helen Amanda , Hurd Rachael S. , Legrésy Benoit , Padman Laurie , Warner Roland
Published: January 2009

We report on long‐term surface elevation changes of the central Amery Ice Shelf (AIS) by comparing elevation records spanning 4 decades (1968–2007). We use elevation records acquired with the following methods: optical leveling (1968–1969); ERS radar altimetry (1992–2003); GPS (1995–2006); and Ice, Cloud, and land Elevation Satellite (ICESat) laser altimetry (2003–2007). We compute multidecadal elevation trend (dh/dt) values at crossovers between the leveling route and each of the GPS and ICESat tracks as well as shorter‐period dh/dt at ERS‐ERS, GPS‐GPS, and ICESat‐ICESat crossovers. At GPS‐leveling crossovers the mean long‐term dh/dt is −0.003 m a−1, and at ICESat‐leveling crossovers the mean dh/dt is +0.013 m a−1; neither trend is significantly different from zero. The data do, however, exhibit variable trends: near‐zero change between 1991 and mid‐1996, then thickening to ∼2003, followed by thinning ∼2003–2007, with 5 year dh/dt averages exceeding ∼±0.1 m a−1. The changes in dh/dt pattern in mid‐1996 and again in 2003 occur with unexpected speed. The ice shelf exhibits different dh/dt patterns than does the surrounding grounded ice, suggesting that surface mass balance variations or longer‐term variations in firn densification processes are unlikely to be major causes. We conclude that these observed multiyear elevation changes must be due to currently unexplained or presently poorly quantified phenomena involving surface or basal processes and/or ice dynamics. With the multidecadal stability of the AIS established, the short‐term fluctuations that we observe suggests that for other ice shelves, observed strong dh/dt signals over short time periods do not necessarily indicate ice shelf instability.
The Association Between Sleep Duration and General and Abdominal Obesity in Koreans: Data From the Korean National Health and Nutrition Examination Survey, 2001 and 2005
Authors: Park Se Eun , Kim Hee Man , Kim Dae Hyun , Kim Jongoh , Cha Bong Soo , Kim Dae Jung
Published: January 2009

This study aimed to investigate the association between self‐reported sleep duration and general and abdominal obesity in Korean adults. A total of 8,717 adults aged 20–65 years from the Korean National Health and Nutrition Examination Survey (KNHANES) 2001 and 2005 were included. General obesity was defined as BMI ≥25 kg/m2 and abdominal obesity as waist circumference ≥90 cm in men and ≥85 cm in women. To control for sociodemographic and lifestyle factors and comorbidities, multivariable logistic regression was used to calculate the adjusted odds ratios (ORs) and 95% confidence intervals (CIs) of general and abdominal obesity across the following sleep duration categories: ≤5, 6, 7, 8, and ≥9 h/day. Mean sleep duration (±s.d.) was 6.9 ± 1.3 h. Those sleeping ≤5 h/day had the highest BMI and waist circumference compared with those sleeping 7, 8, or ≥9 h/day (P < 0.05 for all comparisons). After controlling for sociodemographic and lifestyle factors, the adjusted ORs (95% CIs) associated with sleeping ≤5 h/day (vs. 7 h/day) were 1.25 (1.06–1.48) for general obesity and 1.24 (1.03–1.48) for abdominal obesity. Further adjustment for hypertension and diabetes mellitus did not significantly affect the associations. These data suggest that short sleep duration is significantly associated with a modest increase in general and abdominal obesity in Korean adults.
Truncal and Abdominal Fat as Determinants of High Triglycerides and Low HDL‐cholesterol in Adolescents
Authors: Tresaco Beatriz , Moreno Luis A. , Ruiz Jonatan R. , Ortega Francisco B. , Bueno Gloria , González‐Gross Marcela , Wärnberg Julia , Gutiérrez Angel , García‐Fuentes Miguel , Marcos Ascensión , Castillo Manuel J. , Bueno Manuel ,   AVENA Study Group
Published: January 2009

We examined whether abdominal and truncal adiposity, assessed with simple anthropometric indices, determines serum triglycerides and high‐density lipoprotein (HDL)–cholesterol levels independently of total adiposity amount in adolescents. A total of 547 Spanish adolescents (284 males and 263 females) aged 13–18.5 years were included in this study. Measures of truncal adiposity included subscapular to triceps ratio, and trunk‐to‐total skinfolds ratio (TTS%). Waist circumference was used as a surrogate of abdominal adiposity, and BMI was used as a measure of total adiposity. The results of the regression models indicated that levels of triglycerides were positively associated with waist circumference and TTS% after controlling for age and Tanner stage in both sexes. Once BMI was entered in the model, these associations remained significant for waist circumference in females. HDL‐cholesterol levels were negatively associated with waist circumference in both sexes, and with subscapular to triceps ratio and TTS% in males, after controlling for age and Tanner stage. Once BMI was entered in the model, these associations remained significant for subscapular to triceps ratio and for TTS% in males. The results of this study suggest that in male adolescents, truncal adiposity is negatively associated with levels of HDL‐cholesterol, whereas in females, abdominal adiposity is positively associated with levels of triglycerides independently of total adiposity. These findings highlight the deleterious effect of both truncal and abdominal fat depots on the lipid profile already from the first decades of life.
Obesity and Menstrual Irregularity: Associations With SHBG, Testosterone, and Insulin
Authors: Wei Shuying , Schmidt Michael D. , Dwyer Terence , Norman Robert J. , Venn Alison J.
Published: January 2009

This cross‐sectional study aimed to examine the association between different body composition measures, menstrual cycle characteristics, and hormonal factors in a population‐based sample of young women. The study sample included 726 Australian women aged 26–36 years who were not currently taking hormonal contraceptives and were not currently pregnant or breast feeding. Anthropometric measures included BMI, waist circumference (WC), and waist‐hip ratio (WHR). Menstrual cycle characteristics were self‐reported and usual cycles defined as short (≤25 days), normal (26–34 days), or long (≥35 days). Cycles were defined as irregular if there were ≥15 days between the longest and shortest cycle in the past 12 months. Fasting serum levels of sex hormone‐binding globulin (SHBG), testosterone, insulin, and glucose were measured and the free androgen index (FAI) derived. Compared with those of normal weight, obese women had at least a twofold greater odds of having an irregular cycle, whether defined by BMI (odds ratio (OR) = 2.61; 95% CI = 1.28–5.35), WC (OR 2.28; 95% CI = 1.16–4.49), or WHR (OR = 2.27; 95% CI = 1.09–4.72). Body composition measures were significantly positively associated with fasting insulin, testosterone, and FAI, and negatively associated with SHBG (P < 0.01). Fasting insulin, SHBG, and FAI had the strongest influence on the associations between obesity and irregular cycles, with statistically significant ORs of having an irregular cycle being attenuated to near null values following adjustment. In conclusion, both overall and central obesity were significantly associated with having an irregular menstrual cycle. This association was substantially influenced by hormonal factors, particularly insulin and SHBG.
Vitamin D in Overweight/Obese Women and Its Relationship With Dietetic and Anthropometric Variables
Authors: Rodríguez‐Rodríguez Elena , Navia Beatriz , López‐Sobaler Ana M. , Ortega Rosa M.
Published: January 2009

Overweight/obese persons usually have an inadequate vitamin D status, a situation commonly made worse by an inadequate intake of this vitamin. For this reason, the aim of this study was to analyze dietetic and anthropometric differences in a group of young, overweight/obese Spanish women with respect to their vitamin D status. The study subjects were 66 white Spanish women (aged 20–35 years) with a BMI of 24–35 kg/m2. Dietetic, anthropometric, and biochemical data were collected. Women were divided into two groups depending on their serum vitamin D concentrations: LD (women with <90 nmol/l 25(OH)D) and HD (women with ≥90 nmol/l 25(OH)D). The intakes of vitamin D, calcium, and supplements were similar in both groups. The body weight, BMI, and waist circumference of the HD subjects were smaller than those recorded for the LD subjects (68.6 ± 4.2 kg, 26.0 ± 1.3 kg/m2, and 79.4 ± 3.4 cm compared to 76.2 ± 9.8, 28.6 ± 3.2 kg/m2, and 86.2 ± 9.3 cm, respectively; P < 0.05). The hip circumference and the waist/hip ratio were similar in both groups. A BMI of <27.7 kg/m2 (P50) was associated with serum vitamin D concentrations of ≥90 nmol/l (odds ratio = 0.1313; confidence interval: 0.0149–1.1599; P < 0.05). Overweight/obese women are at higher risk of vitamin D deficiency, largely due to excess adiposity rather than inadequate intake.
Long-Term Outcome of the Lidcombe Program for Early Stuttering Intervention
Authors: Miller Barbara , Guitar Barry
Published: January 2009

Purpose

To report long-term outcomes of the first 15 preschool children treated with the Lidcombe Program by speech-language pathologists (SLPs) who were inexperienced with the program and independent of the program developers. Research questions were: Would the treatment have a similar outcome with inexperienced SLPs compared to outcomes when implemented by the developers? Is treatment duration associated with pretreatment measures? Is long-term treatment outcome affected by variables associated with natural recovery?

Method

Fifteen preschool children who completed the Lidcombe Program were assessed prior to treatment and at least 12 months following treatment. Pretreatment data were obtained from archived files; follow-up data were obtained from interviews and recordings completed after the study had been planned.

Results

Measures of stuttering indicated significant changes from pretreatment to follow-up in percentage of syllables stuttered and scores on the Stuttering Severity Instrument, Third Edition. Pretreatment severity was significantly correlated with treatment time. Handedness was the only client characteristic that appeared to be related to long-term treatment outcome.

Conclusions

The treatment produced significant long-term changes in children’s speech, even when administered by SLPs newly trained in the Lidcombe Program. Treatment results appear to be influenced by pretreatment stuttering severity.
Use of Gesture Development in Profiling Children’s Prelinguistic Communication Skills
Authors: Crais Elizabeth R. , Watson Linda R. , Baranek Grace T.
Published: January 2009

Purpose

Comparing children’s skills across and within domains of development has become a standard in providing early intervention services. Profiling a child’s strengths and challenges can help in making decisions regarding eligibility, diagnosis, and intervention. Profiling is particularly important for children who are not yet talking, due to the variability in production skills and the lack of guidelines as to which children are “at risk” for communication deficits versus those who are “late talkers.” One area underutilized in profiling is gesture development, despite the fact that research has indicated that the amount and type of gesture use can help in early identification and is predictive of later language.

Method

To guide practicing professionals and researchers in using gesture development to profile children’s communication skills, this article provides an overview of the types of gestures and their development, describes assessment methods and tools to document gesture development, pinpoints behaviors and factors important in identifying children with disabilities, and ends with brief examples of using profiling in assessment and intervention planning.

Conclusions

Gesture use should be an important component in profiling children’s communication skills, and this type of profiling can enhance both the assessment and intervention process.
Evaluation of hatchery-based enhancement of the mud crab, Scylla spp., fisheries in mangroves: comparison of species and release strategies
Authors: Lebata Ma. Junemie Hazel L. , Le Vay Lewis , Walton Mark E. , Biñas Joseph B. , Quinitio Emilia T. , Rodriguez Eduard M. , Primavera Jurgenne H.
Published: January 2009

Ranching, stock enhancement and restocking are management approaches involving the release of wild or hatchery-bred organisms to enhance, conserve or restore fisheries. The present study, conducted from April 2002 to November 2005, evaluated the effectiveness of releasing wild and hatchery-reared (HR) mud crabs in the mangroves of Ibajay, Aklan, Philippines where preliminary studies demonstrated declining fishery yields, abundance and size of crabs. Comparison of survival and growth of wild-released and HR Scylla olivacea and HR Scylla serrata demonstrated the effect of nursery conditioning, size-at-release and species differences. Overall yield and catch per unit effort (CPUE) increased by 46% after stock enhancement trials. Recapture rates of released crabs were highest in wild-released S. olivacea and in crabs measuring 65.0–69.9 mm carapace width (CW) and lowest in non-conditioned HR S. serrata. Growth rates were highest for conditioned HR S. olivacea and lowest for conditioned HR S. serrata (11.7 and 3.7 mm month–1 respectively). Fishing mortality was highest for S. olivacea, whereas natural mortality was greater for S. serrata. Conditioning hatchery-bred animals before release is also important in obtaining higher survival. S. olivacea was the more appropriate of the two species for release in mangrove habitats inundated with low-salinity water. However, there is a need for site-specific studies to evaluate the effectiveness of releases.
An anterior temporal face patch in human cortex, predicted by macaque maps
Authors: Rajimehr Reza , Young Jeremy C. , Tootell Roger B. H.
Published: January 2009

Increasing evidence suggests that primate visual cortex has a specialized architecture for processing discrete object categories such as faces. Human fMRI studies have described a localized region in the fusiform gyrus [the fusiform face area (FFA)] that responds selectively to faces. In contrast, in nonhuman primates, electrophysiological and fMRI studies have instead revealed 2 apparently analogous regions of face representation: the posterior temporal face patch (PTFP) and the anterior temporal face patch (ATFP). An earlier study suggested that human FFA is homologous to the PTFP in macaque. However, in humans, no obvious homologue of the macaque ATFP has been demonstrated. Here, we used fMRI to map face-selective sites in both humans and macaques, based on equivalent stimuli in a quantitative topographic comparison. This fMRI evidence suggests that such a face-selective area exists in human anterior inferotemporal cortex, comprising the apparent homologue of the fMRI-defined ATFP in macaques.
Tbx2b is required for ultraviolet photoreceptor cell specification during zebrafish retinal development
Authors: Alvarez-Delfin Karen , Morris Ann C. , Snelson Corey D. , Gamse Joshua T. , Gupta Tripti , Marlow Florence L. , Mullins Mary C. , Burgess Harold A. , Granato Michael , Fadool James M.
Published: January 2009

The vertebrate rod and cone photoreceptors are highly specialized sensory neurons that transduce light into the chemical and electrical signals of the nervous system. Although the physiological properties of cones and rods are well known, only a handful of genes have been identified that regulate the specification of photoreceptor subtypes. Taking advantage of the mosaic organization of photoreceptors in zebrafish, we report the isolation of a mutation resulting in a unique change in photoreceptor cell fate. Mutation of the
lots-of-rods
(
lor
) locus results in a near one-for-one transformation of UV-cone precursors into rods. The transformed cells exhibit morphological characteristics and a gene-expression pattern typical of rods, but differentiate in a temporal and spatial pattern consistent with UV-cone development. In mutant larvae and adults, the highly ordered photoreceptor mosaic is maintained and degeneration is not observed, suggesting that
lor
functions after the specification of the other photoreceptor subtypes. In genetic chimeras,
lor
functions cell-autonomously in the specification of photoreceptor cell fate. Linkage analysis and genetic-complementation testing indicate that
lor
is an allele of
tbx2b
/
fby
(
from beyond
).
fby
was identified by a pineal complex phenotype, and carries a nonsense mutation in the T-box domain of the tbx2b transcription factor. Homozygous
fby
mutant larvae and
lor
/
fby
transheterozygotes also display the lots-of-rods phenotype. Based upon these data, we propose a previously undescribed function for
tbx2b
in photoreceptor cell precursors, to promote the UV cone fate by repressing the rod differentiation pathway.
Functional coding variation in recombinant inbred mouse lines reveals multiple serotonin transporter-associated phenotypes
Authors: Carneiro Ana M. D. , Airey David C. , Thompson Brent , Zhu Chong-Bin , Lu Lu , Chesler Elissa J. , Erikson Keith M. , Blakely Randy D.
Published: January 2009

The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT,SLC6A4) figures prominently in the etiology and treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism, and obsessive-compulsive disorder (OCD). Here, we use naturally occurring polymorphisms in recombinant inbred (RI) lines to identify multiple phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by 2 nonsynonymous coding variants [Gly-39 and Lys-152 (GK)]. At these positions, many other mouse lines, including DBA/2J, encode, respectively, Glu-39 and Arg-152 (ER haplotype), amino acids found also in hSERT. Ex vivo synaptosomal 5-HT transport studies revealed reduced uptake associated with the GK variant, a finding confirmed by in vitro heterologous expression studies. Experimental and in silico approaches using RI lines (C57BL/6J × DBA/2J = BXD) identify multiple anatomical, biochemical, and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are several traits associated with alcohol consumption and multiple traits associated with dopamine signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates iron-regulated DA phenotypes. Our studies provide an example of the power of coordinated in vitro, in vivo, and in silico approaches using mouse RI lines to elucidate and quantify the system-level impact of gene variation.
Tetherin-mediated restriction of filovirus budding is antagonized by the Ebola glycoprotein
Authors: Kaletsky Rachel L. , Francica Joseph R. , Agrawal-Gamse Caroline , Bates Paul
Published: January 2009

Mammalian cells employ numerous innate cellular mechanisms to inhibit viral replication and spread. Tetherin, also known as Bst-2 or CD317, is a recently identified, IFN-induced, cellular response factor that blocks release of HIV-1 and other retroviruses from infected cells. The means by which tetherin retains retroviruses on the cell surface, as well as the mechanism used by the HIV-1 accessory protein Vpu to antagonize tetherin function and promote HIV-1 release, are unknown. Here, we document that tetherin functions as a broadly acting antiviral factor by demonstrating that both human and murine tetherin potently inhibit the release of the filovirus, Ebola, from the surface of cells. Expression of the Ebola glycoprotein (GP) antagonized the antiviral effect of human and murine tetherin and facilitated budding of Ebola particles, as did the HIV-1 Vpu protein. Conversely, Ebola GP could substitute for Vpu to promote HIV-1 virion release from tetherin-expressing cells, demonstrating a common cellular target for these divergent viral proteins. Ebola GP efficiently coimmunoprecipitated with tetherin, suggesting that the viral glycoprotein directly interferes with this host antiviral factor. These results demonstrate that tetherin is a cellular antiviral factor that restricts budding of structurally diverse enveloped viruses. Additionally, Ebola has evolved a highly effective strategy to combat this antiviral response elicited in the host during infection.
Mammalian metallopeptidase inhibition at the defense barrier of
Ascaris
parasite
Authors: Sanglas Laura , Aviles Francesc X. , Huber Robert , Gomis-Rüth F. Xavier , Arolas Joan L.
Published: January 2009

Roundworms of the genus
Ascaris
are common parasites of the human gastrointestinal tract. A battery of selective inhibitors protects them from host enzymes and the immune system. Here, a metallocarboxypeptidase (MCP) inhibitor, ACI, was identified in protein extracts from
Ascaris
by intensity-fading MALDI-TOF mass spectrometry. The 67-residue amino acid sequence of ACI showed no significant homology with any known protein. Heterologous overexpression and purification of ACI rendered a functional molecule with nanomolar equilibrium dissociation constants against MCPs, which denoted a preference for digestive and mast cell A/B-type MCPs. Western blotting and immunohistochemistry located ACI in the body wall, intestine, female reproductive tract, and fertilized eggs of
Ascaris
, in accordance with its target specificity. The crystal structure of the complex of ACI with human carboxypeptidase A1, one of its potential targets in vivo, revealed a protein with a fold consisting of two tandem homologous domains, each containing a β-ribbon and two disulfide bonds. These domains are connected by an α-helical segment and a fifth disulfide bond. Binding and inhibition are exerted by the C-terminal tail, which enters the funnel-like active-site cavity of the enzyme and approaches the catalytic zinc ion. The findings reported provide a basis for the biological function of ACI, which may be essential for parasitic survival during infection.
Quantitative peptidomics reveal brain peptide signatures of behavior
Authors: Brockmann Axel , Annangudi Suresh P. , Richmond Timothy A. , Ament Seth A. , Xie Fang , Southey Bruce R. , Rodriguez-Zas Sandra R. , Robinson Gene E. , Sweedler Jonathan V.
Published: January 2009

The honey bee genome predicts ≈100 peptides from 36 prohormones, but the functions of many of these peptides are unknown. We used differential isotope labeling combined with mass spectrometric analysis to quantify ≈50% of known bee brain peptides in the context of foraging, with 8 showing robust and dynamic regulation. Some showed differences in brain abundance as a function of experience; specifically, nectar and pollen collection led to quick changes in abundance. These changes were related to the act of food collection, not ingestion, because foragers bring food back to the hive for storage rather than eating it themselves. Other peptide differences in brain abundance were seen in bees that either flew to a nectar feeder or a pollen feeder, but did not yet collect any food. These differences likely reflect well-known predispositions of some bees to collect either nectar or pollen, but not both. Tachykinin, PBAN, and sNPF were among the peptides with the strongest changes in association with nectar and pollen foraging. These peptides are known to be involved in regulating food intake in solitary insects, suggesting an evolutionary connection between that behavior and social foraging. These results demonstrate that it is now possible to use quantitative peptidomics to help determine which brain peptides are bioactive and to elucidate their function in the regulation of behavior.
Advance Bandwidth Scheduling Algorithms in Dedicated Networks
Authors: Lin Yunyue , Wu Qishi , Rao Nageswara S. V. , Zhu Mengxia
Published: January 2009

An increasing number of high performance research network testbeds and production networks have the capability of provisioning dedicated channels for high speed data transfer in support of large scale scientific applications. Each dedicated channel in these networks typically consists of one or more physical links that are shared by multiple applications in both time and bandwidth through in advance reservation. The design of efficient bandwidth scheduling algorithms is critical to maximizing the utilization of dedicated network resources and meeting diverse end-to-end transport performance requirements.

The topology of a dedicated network is represented by a graph, where each link maintains a list of residual bandwidths specified as segmented constant functions of time. Given a graph with an aggregated time-bandwidth table combining the reservation information on all links, designated source, and destination vertices, and a specified data size, we formulate and investigate five bandwidth scheduling problems to minimize the data transfer end time under different path and bandwidth constraints: (i) variable path with variable bandwidth (VPVB), which computes the widest (highest bandwidth) path in each time slot; (ii) fixed path with variable bandwidth (FPVB), which computes a fixed path with varying bandwidths across different time slots; (iii) variable path with fixed bandwidth (VPFB), which computes one path in each time slot with the same bandwidth; (iv) fixed path with fixed bandwidth (FPFB), which computes a fixed path with a constant bandwidth; and (v) multiple fixed paths with fixed bandwidths (MFPFB), which computes multiple concurrent fixed paths with constant bandwidths. Among these problems, VPVB represents the most flexible scenario where the network resources are fully utilized and the minimal transfer end time is achieved, while FPFB imposes the most stringent transport conditions by fixing both path and bandwidth. We design an optimal algorithm for each of these scheduling problems. VPVB is solved using an extension of the classical Dijkstra's algorithm, and FPVB is solved using Maximum Permutation Algorithm, which tries all possible permutations of throughputs at different time slots to obtain the minimal transfer end time. The algorithm for VPFB, FPFB, and MFPFB are based on Adjacent Time Slots Search, which finds the minimum transfer end time by examining the possibility of data transfer in any number of contiguous time slots. All these algorithms are of polynomial or pseudo polynomial time complexity with respect to the network size and the total number of time slots in a bandwidth reservation table.
A Rate Control Scheme of the Even Low Bit-Rate Video Encoder
Authors: Zhou Bing , Su Shi-Mei , Zhang Xingjin , Li Xiaoqiang
Published: January 2009

Rate control plays an important role in transmitting low-delay and high-quality images over the channel of very low bandwidth. The rate control algorithm in MPEG-4 or H.26X only defined the rate control model of P-frame, and did not introduce the rate control model of I-frame as it supposed that only the first frame is an I-frame, the others are all P-frames. However, in practical applications, a certain number of I-frames have to be inserted to meet the demand for fault-tolerant transmission and information retrieval. Oriented toward the application demand of remote surveillance system based on PSTN, a rate control strategy is proposed for encoding video at even low bit-rate in this paper. The strategy includes a rate-control algorithm for I-frame and introduces a quadratic rate distortion model, which solves the problem of the rate control used at very low bit-rate preferably. The rate distortion model of I-frame is designed referring to that of P-frame. It mainly involves three processes: initial quantization parameter calculation, objective bit number allocation, and objective quantization parameter calculation.

TM5 of MPEG-2 proposed the target bit-number allocation model of I, P, and B frame, but the algorithm for the model is a bit complex. Based on the quadratic rate distortion model, a novel algorithm for the target bit-number allocation is presented in this paper.

In order to keep the stability of image quality, VM8 limits the change range of the new quantization parameter from −0.25 to 0.25 times of the previous frame. As a result, if the previous frame's quantization parameter is small but the current frame's quantization parameter is calculated to be large, the current frame's quantization parameter should have been corrected with a small value, which will cause excessive coding bits, and worsen the transmission delay. In this paper, we present a correction algorithm for the computation of P-frame's quantization parameter.

The results of experiments show that the proposed scheme reduces the delay of encoder buffering greatly, and improves the quality of reconstructed images clearly at the same time. In terms of the system's transmission delay, our scheme uses reasonable algorithms for computing the quantization parameters of I-frame and P-frame, and adjusting the GOP length dynamically. The transmission delays are significantly decreased and the buffer overflows are avoided. In terms of the reconstructed image quality, the test sequence's PSNRs with our scheme are higher than VM8's at all the bit rates, and the coded bit-number of our scheme is less than VM8's at the same bit rate. In terms of the deviation of output bit-streams, the average deviation of our algorithm is much less than VM8's. The less the deviation of the output bit-stream is, the more appropriate it is to be transmitted at the given bandwidth, and the less the transmission delay is.
An Efficient Software-Managed Cache Based on Cell Broadband Engine Architecture
Authors: Guofu Feng , Xiaoshe Dong , Xuhao Wang , Ying Chu , Xingjun Zhang
Published: January 2009

While the CBEA (Cell Broadband Engine Architecture) offers substantial computational power, its explicit multilevel memory hierarchy poses significant challenges to traditional programming, especially in performance and programmability. Software-managed cache is a technique that attempts to address such issues. But there still remain some limitations in current software-managed cache technologies. First, a complex managing logic of the full implementation of the software-managed cache which is not suitable for SPU designed as a vector computational unit influences computation significantly. Second, the external managing code of the software-managed cache causes the amount of computing code explosion. Besides increasing the computing burden of the accelerator, the external code occupies precious room of local storage which is shared by computing code and data. Finally, its inconvenient user interface presents significant obstacles for it to be widely applied. Based on the locality of memory access, this paper proposes an efficient software-managed cache named ECellS cache. In the paper, several customized library interfaces were designed respectively to simplify the cache implementation and reduce cache code size. On the other hand, the code segment of the application which accesses data residing in main memory frequently is defined as a cache section. Several of these types of cache sections could be combined into a “cache bind” and be managed in parallel by using SIMD technology. By this type of coarse-grain managing method and additional simplifying the construction of software cache, ECellS cache reduces both the burden of SPU to manage the cache buffer and the size of the cache managing code. Finally, based on local address remapping technology, a more convenient programming interface which is similar to OpenMP directive is presented to facilitate programming. By this technology, requesting for data residing in the main memory will be automatically mapped to cache buffer in local storage of SPE, and there needs to be no extra modifying for the computing source code inside the cache section except for inserting the directive outside of it. Experimental results of this paper based on the Cell processor demonstrate that our proposed software-managed cache improves performance by 15-35% over the CBE SDK software-managed cache in most test cases. With ECellS cache it could be more convenient for the user to develop and port applications based on CBE architecture.
Using Affine Transformation to Obtain Approximate Offset Surface
Authors: Zhao Hongxing , Ye Zhenglin , Meng Yaqin , Wang Man
Published: January 2009

For an arbitrary function C1 surface, we can use segment affine transformation to obtain a surface as its approximate offset surface. Each segment of the approximate offset surface and the corresponding segment of the original surface are proved to be of the same function type. After affine transformation, the geometric invariance of the original surface is proved to be retained in the approximate offset surface. The numerical example demonstrated the efficiency of our method.
Ant-Based Delay-Sensitive Query Processing for Wireless Sensor Networks
Authors: Yu Jianping , Lin Yaping , Hu Yupeng
Published: January 2009

The technologies of wireless sensor networks (WSNs) have been developed rapidly in the most recent years. As WSNs are characterized by data-centric storage and routing under most circumstances, any application involved requires data management and processing technologies, especially the query processing mechanisms. The WSNs are often deployed in diverse application specific contexts, which can be treated as distributed databases. The event-involved responses can be obtained by issuing queries to this kind of database. Certain of the applications with real-time requirement have tight constraints on query delay. However, the existing query algorithms are not satisfied with them. The problem we focus on can be simply described as: once an event has happened, how to optimize the replication energy cost due to storing the event data from the event source to multiple positions and how to optimize the searching energy cost and query delay due to finding one replica of the event and copying the event data on demand if subsequent queries for the event are performed.

Ant algorithms adopt a group of intelligent agents called ants to carry out local search, using the historical information obtained to guide the ongoing search and having characteristics of collective intelligence, it can find better routing paths without knowing the global information of the network. Aiming at the real-time applications, an ant-based delay-sensitive query processing algorithm (ADSQP) taking advantage of ant colony optimization with the characteristics of self-organization and positive feedback is proposed, in which the priority-based multiple-ring storage scheme and the ant-based distributed search mechanism are adopted to improve the integrated performance of the energy-efficiency, delay, and query success rate.

To reduce the replication cost of ADSQP, the cluster-based aggregation approach and the ring-based storage method according to the importance level of the events are proposed, in which the aggregated events with higher priority will be stored in the nodes on the farther ring to the aggregation nodes. To reduce the search cost and the query delay of ADSQP, the ant-based search mechanism for the queried events and the second replication approach for the found events are also proposed.

The simulation results demonstrated that not only the performance of energy-efficiency and query success rate can be improved but also significant smaller query delay can be achieved by the ADSQP when comparing with other query processing algorithms. Moreover, the new algorithm is flexible and demands merely local information to find queried events efficiently and determine the number and allocation of replicas adaptively.