bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging heterogeneity of membrane and storage lipids in transgenic Camelina sativa seeds with altered fatty acid profiles
Authors: Horn Patrick J. , Silva Jillian E. , Anderson Danielle , Fuchs Johannes , Borisjuk Ljudmilla , Nazarenus Tara J. , Shulaev Vladimir , Cahoon Edgar B. , Chapman Kent D. 
Published: June 2013

SummaryEngineering compositional changes in oilseeds is typically accomplished by introducing new enzymatic step(s) and/or by blocking or enhancing an existing enzymatic step(s) in a seed‐specific manner. However, in practice, the amounts of lipid species that accumulate in seeds are often different from what one would predict from enzyme expression levels, and these incongruences may be rooted in an incomplete understanding of the regulation of seed lipid metabolism at the cellular/tissue level. Here we show by mass spectrometry imaging approaches that triacylglycerols and their phospholipid precursors are distributed differently within cotyledons and the hypocotyl/radicle axis in embryos of the oilseed crop Camelina sativa, indicating tissue‐specific heterogeneity in triacylglycerol metabolism. Phosphatidylcholines and triacylglycerols enriched in linoleic acid (C18:2) were preferentially localized to the axis tissues, whereas lipid classes enriched in gadoleic acid (C20:1) were preferentially localized to the cotyledons. Manipulation of seed lipid compositions by heterologous over‐expression of an acyl–acyl carrier protein thioesterase, or by suppression of fatty acid desaturases and elongases, resulted in new overall seed storage lipid compositions with altered patterns of distribution of phospholipid and triacylglycerol in transgenic embryos. Our results reveal previously unknown differences in acyl lipid distribution in Camelina embryos, and suggest that this spatial heterogeneity may or may not be able to be changed effectively in transgenic seeds depending upon the targeted enzyme(s)/pathway(s). Further, these studies point to the importance of resolving the location of metabolites in addition to their quantities within plant tissues.
In vivo measurements for high dose rate brachytherapy with optically stimulated luminescent dosimeters
Authors: Sharma Renu , Jursinic Paul A. 
Published: June 2013

Purpose:To show the feasibility of clinical implementation of OSLDs for high dose‐rate (HDR)in vivo dosimetry for gynecological and breast patients. To discuss how the OSLDs were characterized for an Ir‐192 source, taking into account low gamma energy and high dose gradients. To describe differences caused by the dose calculation formalism of treatment planning systems.Methods:OSLD irradiations were made using the GammaMedplus iX Ir‐192 HDR, Varian Medical Systems, Milpitas, CA. BrachyVision versions 8.9 and 10.0, Varian Medical Systems, Milpitas, CA, were used for calculations. Version 8.9 used the TG‐43 algorithm and version 10.0 used the Acuros algorithm. The OSLDs (InLight Nanodots) were characterized for Ir‐192. Various phantoms were created to assess calculated and measured doses and the angular dependence and self‐absorption of the Nanodots. Following successful phantom measurements, patient measurements for gynecological patients and breast cancer patients were made and compared to calculated doses.Results:The OSLD sensitivity to Ir‐192 compared to 6 MV is between 1.10 and 1.25, is unique to each detector, and changes with accumulated dose. The measured doses were compared to those predicted by the treatment planning system and found to be in agreement for the gynecological patients to within measurement uncertainty. The range of differences between the measured and Acuros calculated doses was −10%–14%. For the breast patients, there was a discrepancy of −4.4% to +6.5% between the measured and calculated doses at the skin surface when the Acuros algorithm was used. These differences were within experimental uncertainty due to (random) error in the location of the detector with respect to the treatment catheter.Conclusions:OSLDs can be successfully used for HDRin vivo dosimetry. However, for the measurements to be meaningful one must account for the angular dependence, volume‐averaging, and the greater sensitivity to Ir‐192 gamma rays than to 6 MV x‐rays if 6 MV x‐rays were used for OSLD calibration. The limitations of the treatment planning algorithm must be understood, especially for surface dose measurements. Use of in vivo dosimetry for HDR brachytherapy treatments is feasible and has the potential to detect and prevent gross errors. In vivo HDR brachytherapy should be included as part of the QA for a HDR brachytherapy program.
Maxillofacial prosthesis in a palliative care for terminally ill patient with squamous cell carcinoma
Authors: Haralur Satheesh B , Shah Farhan K 
Published: June 2013

It is the god given right of every human being to appear human. – Ernest L. DaBreo.A 55-year-old man with combined surgical and radiation therapy for buccal mucosa required the prosthetic rehabilitation for full thickness facial cheek defect. Apart from the aesthetics concerns, he had several oral debilities like difficulty in speaking, eating and swallowing. Though the carcinoma is known for high rates of morbidity and mortality, it is an obligation of a prosthodontist to help the patient to have a dignified and normal social life for their remaining lifespan. Palliative dental care's main focus is to re-establish the quality of the remaining life, in addition to the alleviation of physical and psychological suffering of the far-advanced disease patients. This case report summarises the importance of maxillofacial prosthesis in a postoperative malignancy and palliative care.
Sleep-dependent Neurophysiological Processes in Implicit Sequence Learning
Authors: Urbain Charline , Schmitz Rémy , Schmidt Christina , Cleeremans Axel , Van Bogaert Patrick , Maquet Pierre , Peigneux Philippe 
Published: June 2013

Abstract
Behavioral studies have cast doubts about the role that posttraining sleep may play in the consolidation of implicit sequence learning. Here, we used event-related fMRI to test the hypothesis that sleep-dependent functional reorganization would take place in the underlying neural circuits even in the possible absence of obvious behavioral changes. Twenty-four healthy human adults were scanned at Day 1 and then at Day 4 during an implicit probabilistic serial RT task. They either slept normally (RS) or were sleep-deprived (SD) on the first posttraining night. Unknown to them, the sequential structure of the material was based on a probabilistic finite-state grammar, with 15% chance on each trial of replacing the rules-based grammatical (G) stimulus with a nongrammatical (NG) one. Results indicated a gradual differentiation across sessions between RTs (faster RTs for G than NG), together with NG-related BOLD responses reflecting sequence learning. Similar behavioral patterns were observed in RS and SD participants at Day 4, indicating time- but not sleep-dependent consolidation of performance. Notwithstanding, we observed at Day 4 in the RS group a diminished differentiation between G- and NG-related neurophysiological responses in a set of cortical and subcortical areas previously identified as being part of the network involved in implicit sequence learning and its offline processing during sleep, indicating a sleep-dependent processing of both regular and deviant stimuli. Our results suggest the sleep-dependent development of distinct neurophysiological processes subtending consolidation of implicit motor sequence learning, even in the absence of overt behavioral differences.
Why Bilateral Damage Is Worse than Unilateral Damage to the Brain
Authors: Schapiro Anna C. , McClelland James L. , Welbourne Stephen R. , Rogers Timothy T. , Lambon Ralph Matthew A. 
Published: June 2013

Abstract
Human and animal lesion studies have shown that behavior can be catastrophically impaired after bilateral lesions but that unilateral damage often produces little or no effect, even controlling for lesion extent. This pattern is found across many different sensory, motor, and memory domains. Despite these findings, there has been no systematic, computational explanation. We found that the same striking difference between unilateral and bilateral damage emerged in a distributed, recurrent attractor neural network. The difference persists in simple feedforward networks, where it can be understood in explicit quantitative terms. In essence, damage both distorts and reduces the magnitude of relevant activity in each hemisphere. Unilateral damage reduces the relative magnitude of the contribution to performance of the damaged side, allowing the intact side to dominate performance. In contrast, balanced bilateral damage distorts representations on both sides, which contribute equally, resulting in degraded performance. The model's ability to account for relevant patient data suggests that mechanisms similar to those in the model may operate in the brain.
Reapplying the Language Tree Model to the History of Yiddish
Authors: Beider Alexander 
Published: June 2013

Abstract
The article discusses several definitions of the notion of Yiddish that exist in linguistic studies. The Germanistic approach emphasizes differences between various German and Yiddish dialects. The Judeo-Centric approach, developed during the second half of the 20th century as an alternative method to that used by the Germanistic school, puts the uninterrupted chain of languages spoken by Jews in the center of its linguistic analysis. For the representatives of this school, Yiddish is a fusion language from its inception, the process they generally posit to the period when the first Jewish communities appeared in German-speaking territories. As suggested in this article, for the adequate understanding of the development of Yiddish, several notions used by the two approaches should be combined. Only the Germanistic approach provides appropriate frames for analyzing the genesis of Yiddish according to the Language Tree model. Its (re)application shows the inadequacy of certain basic positions of the Judeo-Centric Approach. Yet, several notions introduced by the proponents of the latter method still represent a major contribution in Yiddish studies. The notion of “fusion” creates an appropriate theoretical tool for studying the development of Yiddish varieties. The consideration of the uninterrupted chain of languages spoken by Jews sheds light on factors that were invisible within the Germanistic approach. The article also suggests a classification of languages spoken by Jews useful for the analysis of their historical development.
Coexistence of Atmospheric Gravity Waves and Boundary Layer Rolls Observed by SAR*
Authors: Li Xiaofeng , Zheng Weizhong , Yang Xiaofeng , Zhang Jun A. , Pichel William G. , Li Ziwei 
Published: June 2013

Abstract
Both atmospheric gravity waves (AGW) and marine atmospheric boundary layer (MABL) rolls are simultaneously observed on an Environmental Satellite (Envisat) advanced synthetic aperture radar (ASAR) image acquired along the China coast on 22 May 2005. The synthetic aperture radar (SAR) image covers about 400 km × 400 km of a coastal area of the Yellow Sea. The sea surface imprints of AGW show the patterns of both a transverse wave along the coastal plain and a diverging wave in the lee of Mount Laoshan (1133-m peak), which indicate that terrain forcing affects the formation of AGW. The AGW have a wavelength of 8–10 km and extend about 100 km offshore. Model simulation shows that these waves have an amplitude over 3 km. Finer-scale (~2 km) brushlike roughness features perpendicular to the coast are also observed, and they are interpreted as MABL rolls. The FFT analysis shows that the roll wavelengths vary spatially. The two-way interactive, triply nested grid (9–3–1 km) Weather Research and Forecasting Model (WRF) simulation reproduces AGW-generated wind perturbations that are in phase at all levels, reaching up to the 700-hPa level for the diverging AGW and the 900-hPa level for the transverse AGW. The WRF simulation also reveals that dynamic instability, rather than thermodynamic instability, is the cause for the MABL roll generation. Differences in atmospheric inflection-point level and instability at different locations are reasons why the roll wavelengths vary spatially.
Mapping Weather-Type Influence on Senegal Precipitation Based on a Spatial–Temporal Statistical Model*
Authors: Rust Henning W. , Vrac Mathieu , Sultan Benjamin , Lengaigne Matthieu 
Published: June 2013

Abstract
Senegal is particularly vulnerable to precipitation variability. To investigate the influence of large-scale circulation on local-scale precipitation, a full spatial–statistical description of precipitation occurrence and amount for Senegal is developed. These regression-type models have been built on the basis of daily records at 137 locations and were developed in two stages: (i) a baseline model describing the expected daily occurrence probability and precipitation amount as spatial fields from monsoon onset to offset, and (ii) the inclusion of weather types defined from the NCEP–NCAR reanalysis 850-hPa winds and 925-hPa relative humidity establishing the link to the synoptic-scale atmospheric circulation. During peak phase, the resulting types appear in two main cycles that can be linked to passing African easterly waves. The models allow the investigation of the spatial response of precipitation occurrence and amount to a discrete set of preferred states of the atmospheric circulation. As such, they can be used for drought risk mapping and the downscaling of climate change projections.
Necessary choices, such as filtering and scaling of the atmospheric data (as well as the number of weather types to be used), have been made on the basis of the precipitation models' performance instead of relying on external criteria. It could be demonstrated that the inclusion of the synoptic-scale weather types lead to skill on the local and daily scale. On the interannual scale, the models for precipitation occurrence and amount capture 26% and 38% of the interannual spatially averaged variability, corresponding to Pearson correlation coefficients of rO = 0.52 and ri = 0.65, respectively.
Changes in Temperature Records and Extremes: Are They Statistically Significant?
Authors: Christiansen Bo 
Published: June 2013

Abstract
The author investigates whether the increasing numbers of warm records and warm extremes in the extratropical Northern Hemisphere over the last decade are statistically significant. For the extremes, the focus is on summer mean temperatures; for warm records it is on daily and monthly means. Statistical significance is a highly nontrivial problem because the atmosphere is both spatially and temporally strongly autocorrelated. Therefore, a method is applied to produce an ensemble of surrogate fields that are statistically similar to the observed temperature field except that the surrogates are stationary. The significance is then estimated by comparing the number of records or extremes in the observations to similar numbers in the surrogates.
The number of warm records and the number of extreme summers are found to have the same general temporal development, with a slow decrease from the late 1940s to a minimum in the 1970s followed by an increase to the present high values. However, there is a strong difference in the statistical significance of the different quantities. With very strong statistical significance, the recent large number of warm daily records and the number of extremely warm summers cannot be explained as chance occurrences. Both of these quantities show numbers of recent consecutive years with values above the 95% level that are much larger than any similar numbers found in the ensemble of 1000 surrogates. No significant change in the number of monthly warm records is found. The statistical significance weakens when considering the individual seasons or smaller regions like Europe.
Variability of the Heat and Salt Budget in the Subtropical Southeastern Pacific Mixed Layer between 2004 and 2010: Spice Injection Mechanism
Authors: Kolodziejczyk Nicolas , Gaillard Fabienne 
Published: June 2013

Abstract
The mixed layer heat and salt budget in the southeastern subtropical Pacific are estimated using 7 years (2004–10) of Argo-profiling float data, surface fluxes, precipitation, surface velocity data, and wind observations and reanalysis. In this region, the mixed layer heat budget is characterized by a strong annual cycle mainly modulated by the shortwave radiation annual cycle. During the austral fall and winter, the shortwave radiation input minimum is overwhelmed by the heat loss mainly because of the latent heat flux. The mixed layer salt budget also presents a strong annual cycle with a minimum of salt content during the late austral winter. In contrast with the heat budget, the salt budget is mainly driven by the unresolved terms computed as the residual of the budget. Among these missing terms, the most likely candidate is the vertical turbulent mixing as a result of convection caused by the heat surface buoyancy loss and the destabilizing vertical gradient of salinity at the base of the mixed layer. This downward flux of salt at the base of the mixed layer could explain the annual spiciness injection and interannual spiciness variability in the permanent thermocline in the southeastern Pacific.
Processes Controlling the Structure and Longevity of Two Quasi-Linear Convective Systems Crossing the Southern New England Coast
Authors: Lombardo Kelly , Colle Brian A. 
Published: June 2013

Abstract
This paper explores the structural evolution and physical processes that explain the modification of two quasi-linear convective systems (QLCSs) that encountered the densely populated New York City–Atlantic coastal region. One QLCS on 31 May 2002 traversed the Atlantic coastal boundary with little change in its intensity, producing widespread severe wind damage across New York City and Long Island. During this event, warm air advection at 925 hPa helped destabilize the layer above this level over the coastal zone, while the marine boundary layer deepened below this level. The 0–3-km line-perpendicular vertical wind shear was relatively strong, which supported ascent along the leading edge of the diabatically generated cold pool. The surface-based convective system became slightly elevated as it moved over the marine waters. In contrast, the 23 July 2002 QLCS decayed upon encountering the Atlantic coastline, despite its coincidence with a surface cold front. The most unstable CAPE values during this decaying event were 400–800 J kg−1 greater than the sustaining 31 May event, though the 0–3-km vertical wind shear was approximately half. Weaker shear likely contributed to limited ascent along the leading edge of the surface based cold pool, and ultimately the demise of the convective line. Sensitivity tests highlight the importance of the relationship between the cold pool and vertical shear during these two events, and illustrate the limited role of the marine layer in modifying the evolution of these two convective systems.
Genetic variation and relationships of seven sturgeon species and ten interspecific hybrids
Authors: Zhang Xiaomin , Wu Wenhua , Li Linmiao , Ma Xufa , Chen Jinping 
Published: June 2013

AbstractBackgroundSturgeon cultivation is important for both industry and aquaculture in China. To date, more than 17 species or strains have been farmed for fillets and caviar production. Crossbreeding among different sturgeon species is frequent and the F2 hybrids are fertile. However, large-scale farming can have negative impacts on wild populations i.e. escape of exotic sturgeons and must be taken into consideration. Escape of exotic sturgeons can cause severe ecological problems, including threatening native sturgeon species once the exotic varieties become established or hybridize with native individuals. However, little is known about their genetic resources and variation.MethodsGenetic diversity and introgression of seven sturgeon species were analyzed using mitochondrial DNAcytochrome oxidase subunit I(COI) and nine microsatellite markers. This study included 189 individuals from seven sturgeon species and 277 individuals from ten lineages of F2 hybrid strains.ResultsMtDNACOIsequences (632 bp long) were generated from 91 individuals across the 17 sturgeon strains and produced 23 different haplotypes. Haplotype diversity was high (h = 0.915 ± 0.015) and nucleotide diversity was low (π = 0.03680 ± 0.00153) in the seven sturgeon species and ten interspecific hybrids. Phylogenetic analyses resulted in almost identical tree topologies, and different haplotype structures were mainly related with sturgeons of different female parents. Analysis of molecular variance revealed that 81.73% of the genetic variance was due to matrilineal differences, while 9.40% resulted from strain variation. Pairwise Fst values obtained with POLYSAT software, were high among strains and ranged from 0.031 to 0.164. Admixture analysis assigned seven distinct groups and ten genotypes of admixed clusters composed of hybrid strains using STRUCTURE when assuming K = 7.ConclusionsThe interspecific mtDNA gene tree corresponded to the expected taxonomic divisions. These relationships were also supported by the results from the microsatellite analysis and contributed to unambiguously identify seven sturgeon species and ten F2 hybrid strains from sturgeon farms in China. Moreover, we found that introgressive hybridization is pervasive, exists in both purebred and hybrid sturgeons, and may reflect widespread mismanagement in sturgeon breeding in China.
Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding
Authors: He Ximiao , Chatterjee Raghunath , John Sam , Bravo Hector , Sathyanarayana B K , Biddie Simon C , FitzGerald Peter C , Stamatoyannopoulos John A , Hager Gordon L , Vinson Charles 
Published: June 2013

Abstract

Background
Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS.

Results
We used a logistic regression to evaluate how well the propensity for nucleosome binding and co-occurrence of a secondary motif identify which canonical motifs are bound in vivo. We used ChIP-seq data for three transcription factors binding to their canonical motifs: c-Jun binding the AP-1 motif (TGAC/GTCA), GR (glucocorticoid receptor) binding the GR motif (G-ACA---T/CGT-C), and Hoxa2 (homeobox a2) binding the Pbx (Pre-B-cell leukemia homeobox) motif (TGATTGAT). For all canonical TFBS in the mouse genome, we calculated intrinsic nucleosome occupancy scores (INOS) for its surrounding 150-bps DNA and examined the relationship with in vivo TF binding. In mouse mammary 3134 cells, c-Jun and GR proteins preferentially bound regions calculated to be well-bound by nucleosomes in vitro with the canonical AP-1 and GR motifs themselves contributing to the high INOS. Functional GR motifs are enriched for AP-1 motifs if they are within a nucleosome-sized 150-bps region. GR and Hoxa2 also bind motifs with low INOS, perhaps indicating a different mechanism of action.

Conclusion
Our analysis quantified the contribution of INOS and co-occurring sequence to the identification of functional canonical motifs in the genome. This analysis revealed an inherent competition between some TFs and nucleosomes for binding canonical TFBS. GR and c-Jun cooperate if they are within 150-bps. Binding of Hoxa2 and a fraction of GR to motifs with low INOS values suggesting they are not in competition with nucleosomes and may function using different mechanisms.