bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pipelined ADC based design of bandpass ΔΣ‐ADC
Authors: Sarma V. , Sahoo B. 
Published: June 2013

A high‐speed, large dynamic range fS/4 bandpass ΔΣ‐modulator using a first‐order error‐feedback loop is proposed. The internal quantiser is realised using a high‐speed pipelined ADC. Error feedback is achieved by exploiting the implicit latency in a pipelined ADC. The proposed architecture achieves an SNR of 94 dB with an OSR of 32.
Ultra‐low‐power adaptable ASK clock and data recovery circuit for wireless implantable systems
Authors: Yu H. , Li Y. , Jiang L. , Ji Z. 
Published: June 2013

Amplitude shift keying (ASK) and pulse position modulation (PPM) can be used to provide self‐synchronised data and clock for wireless implantable neural recoding systems, and therefore simplifies the circuit architecture. Presented is a novel ultra‐low‐power clock and data recovery (CDR) circuit based on ASK‐PPM. The CDR includes a 1 MHz gain‐boosted front‐end amplifier with an inductive load for ASK demodulation, and a charge‐bump based circuit to extract and recover clock and non‐return‐to‐zero (NRZ) data from the demodulated PPM signal. To increase the input data rate range that is able to be processed by this CDR, the reference voltage required for data recovery is adaptively generated, also from the PPM. The proposed design is fabricated in a standard CMOS 0.25 µm process. It exhibits an input sensitivity of − 13 dBm with 1 MHz input, covers an input data rate range between 19 and 76 kbit/s, and consumes only ∼ 100 µW of power.
Selection of human tissue-specific elementary flux modes using gene expression data
Authors: Rezola Alberto , Pey Jon , de Figueiredo Luis F. , Podhorski Adam , Schuster Stefan , Rubio Angel , Planes Francisco J. 
Published: June 2013

AbstractMotivation: The analysis of high-throughput molecular data in the context of metabolic pathways is essential to uncover their underlying functional structure. Among different metabolic pathway concepts in systems biology, elementary flux modes (EFMs) hold a predominant place, as they naturally capture the complexity and plasticity of cellular metabolism and go beyond predefined metabolic maps. However, their use to interpret high-throughput data has been limited so far, mainly because their computation in genome-scale metabolic networks has been unfeasible. To face this issue, different optimization-based techniques have been recently introduced and their application to human metabolism is promising.Results: In this article, we exploit and generalize the K-shortest EFM algorithm to determine a subset of EFMs in a human genome-scale metabolic network. This subset of EFMs involves a wide number of reported human metabolic pathways, as well as potential novel routes, and constitutes a valuable database where high-throughput data can be mapped and contextualized from a metabolic perspective. To illustrate this, we took expression data of 10 healthy human tissues from a previous study and predicted their characteristic EFMs based on enrichment analysis. We used a multivariate hypergeometric test and showed that it leads to more biologically meaningful results than standard hypergeometric. Finally, a biological discussion on the characteristic EFMs obtained in liver is conducted, finding a high level of agreement when compared with the literature.Contact: fplanes@tecnun.es or arubio@ceit.esSupplementary information: Supplementary data are available at Bioinformatics online.
Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation
Authors: Veal Colin D. , Xu Hang , Reekie Katherine , Free Robert , Hardwick Robert J. , McVey David , Brookes Anthony J. , Hollox Edward J. , Talbot Christopher J. 
Published: June 2013

Abstract
Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design.
Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT.
Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org).
Contact: cjt14@le.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
Inference on periodicity of circadian time series
Authors: Costa Maria J. , Finkenstädt Bärbel , Roche Véronique , Lévi Francis , Gould Peter D. , Foreman Julia , Halliday Karen , Hall Anthony , Rand David A. 
Published: June 2013

Abstract
Estimation of the period length of time-course data from cyclical biological processes, such as those driven by the circadian pacemaker, is crucial for inferring the properties of the biological clock found in many living organisms. We propose a methodology for period estimation based on spectrum resampling (SR) techniques. Simulation studies show that SR is superior and more robust to non-sinusoidal and noisy cycles than a currently used routine based on Fourier approximations. In addition, a simple fit to the oscillations using linear least squares is available, together with a non-parametric test for detecting changes in period length which allows for period estimates with different variances, as frequently encountered in practice. The proposed methods are motivated by and applied to various data examples from chronobiology.
Germinated Brown Rice Enhances Antioxidant Activities and Immune Functions in Aged Mice
Authors: Wu Fengfeng , Chen Haiying , Yang Na , Duan Xiang , Jin Zhengyu , Xu Xueming 
Published: June 2013

ABSTRACTThe present work was designed to obtain information on the effect of germinated brown rice (GBR) that has undergone different germination times (zero, one, two, three, and four days) on antioxidant activities and immune functions in aged mice. White rice (WR) was also investigated as a comparison. Chemical analysis of rice samples showed that the amounts of most nutritional and bioactive components increased significantly after two days of germination and were much higher in GBR and brown rice (BR) than in WR. Animal feeding experiments showed that dietary GBR and BR performed much better than WR in enhancing antioxidant activities and improving immune function in aged mice, and dietary GBR from three to four days of germination overall exhibited a better effect than GBR from zero to two days of germination.
Psychosocial Dysfunction in Children and Adolescents With Eosinophilic Esophagitis
Authors: Harris Rachel F. , Menard‐Katcher Calies , Atkins Dan , Furuta Glenn T. , Klinnert Mary D. 
Published: June 2013

ABSTRACTObjective:Children with eosinophilic esophagitis (EoE) experience daily challenges related to coping with symptoms and the psychosocial effect of this chronic disease. The aim of this study was to identify features of psychosocial dysfunction experienced by children with EoE who were evaluated in a tertiary care program.Methods:We performed a retrospective review of EoE patients and their families' psychosocial evaluations performed in a tertiary care EoE program. Consecutive evaluations were analyzed to document reports of patients' disease‐related pain/discomfort; feeding/appetite symptoms; sleep, social, and school problems; depression, anxiety; and overall psychological adjustment.Results:Sixty‐four patients received psychosocial evaluation during an 18‐month period and were analyzed. Sixty‐nine percent of children evaluated experienced some form of psychosocial problems, including social difficulties (64%), anxiety (41%), sleep difficulties (33%), depression (28%), and school problems (26%). Adjustment problems were identified in 44% of the sample. Older children experienced more adjustment difficulties than younger children (P = 0.05). Sleep disturbances and feeding problems predominated in the younger children. Anxious behavior and depressive feelings increased with age. Children with gastrostomy tubes (G‐tubes) had more social, school, and psychological adjustment problems than those without.Conclusions:The majority of children with EoE who underwent health and behavior evaluation in a tertiary care program experienced psychosocial adjustment and coping problems. Evaluation and management by mental health professionals would likely benefit a majority of patients with this chronic disease.
Effect of Holder Pasteurization and Frozen Storage on Macronutrients and Energy Content of Breast Milk
Authors: García‐Lara Nadia Raquel , Vieco Diana Escuder , De la Cruz‐Bértolo Javier , Lora‐Pablos David , Velasco Noelia Ureta , Pallás‐Alonso Carmen Rosa 
Published: June 2013

ABSTRACTObjectives:The aim of this study was to explore the effect of Holder pasteurization and frozen storage at −20°C after pasteurization on fat, total nitrogen, lactose, and energy content of breast milk. Both procedures are routinely practiced in human milk banks.Methods:A total of 34 samples of frozen breast milk, donated by 28 women, were collected. Once thawed, an aliquot of each sample was analyzed before pasteurization; the remaining milk was pasteurized (Holder method) and split into 8 aliquots. One aliquot was analyzed after pasteurization and the remainder frozen at −20°C and analyzed 30, 60, 90, 120, and 180 days later. For every aliquot, fat, total nitrogen, lactose, and energy content were determined using the device human Milk Analyzer.Results:We observed a significant reduction in fat (3.5%; −0.17 (−0.29; −0.04) g/dL) and energy content (2.8%; −2.03 (−3.60; −0.46) g/dL) after pasteurization. A significant decrease over time was observed for fat, lactose and energy content. No significant changes were observed for nitrogen content. Mean differences between day 0 postpasteurization and day 180 were −0.13 (−0.21; −0.06) g/dL for fat, −0.08 (−0.13; −0.03) g/dL for lactose, and −1.55 (−2.38; −0.71) kcal/dL for energy content. The relative decreases were 2.8%, 1.7%, and 2.2%, respectively. Overall (postpasteurization + frozen storage), a 6.2% and 5% decrease were observed for fat and energy, respectively.Conclusions:Holder pasteurization decreased fat and energy content of human milk. Frozen storage at −20°C of pasteurized milk significantly reduced fat, lactose, and energy content of human milk.
The link between host density and egg production in a parasitoid insect: comparison between agricultural and natural habitats
Authors: Segoli Michal , Rosenheim Jay A. 
Published: June 2013

SummaryTheory predicts that organisms should invest more heavily in overcoming factors that more frequently emerge as the primary constraints to fitness, and especially, those factors that constrain the fitness of the most highly reproductive members of the population.We tested the hypothesis that the fecundity of a pro‐ovigenic parasitoid (where females emerge with their full egg load) should be positively correlated with the mean expectation for oviposition opportunities in the environment. More specifically, we tested whether females from agricultural systems, where hosts are often relatively abundant, emerge with more eggs than those from natural habitats.We studied the pro‐ovigenic parasitoid waspAnagrus daanei, which parasitizes eggs of leafhoppers of the genusErythroneura.Erythroneuraspp. leafhoppers feed onVitisspp. (grapes) and are major pests of commercial vineyards as well as common herbivores of wildVitis californica, which grows in riparian habitats. We sampled leafhoppers and parasitoids from eight vineyards and eight riparian habitats in centralCalifornia.We found that leafhopper density was higher at vineyards than in riparian habitats, whereas leafhopper egg volume and parasitoid body size did not differ among these habitat types. Parasitoids from vineyards had higher egg loads than parasitoids from wild grapes, and fecundity was positively related to host density across field sites. Parasitoid egg volume was larger in natural sites; however, this variation was not significantly correlated with host density across field sites. Within a single population of parasitoids collected from a vineyard, parasitoid egg load was negatively correlated with longevity, suggesting a trade‐off between reproduction and life span.The results may be explained by a rapid evolution of reproductive traits in response to oviposition opportunities; or alternatively, by the occurrence of maternal effects on the fecundity of daughters based on the foraging experience of their mothers.The ability of parasitoid fecundity to track mean host availability is likely to modulate the likelihood that parasitoid fitness will be constrained by a shortage of eggs and strengthen the ability of parasitoids to suppress the population densities of their hosts.
Climatic stress mediates the impacts of herbivory on plant population structure and components of individual fitness
Authors: Louthan Allison M. , Doak Daniel F. , Goheen Jacob R. , Palmer Todd M. , Pringle Robert M. 
Published: June 2013

SummaryPast studies have shown that the strength of top‐down herbivore control on plant physiological performance, abundance and distribution patterns can shift with abiotic stress, but it is still unclear whether herbivores generally exert stronger effects on plants in stressful or in nonstressful environments.One hypothesis suggests that herbivores' effects on plant biomass and fitness should be strongest in stressful areas, because stressed plants are less able to compensate for herbivore damage. Alternatively, herbivores may reduce plant biomass and fitness more substantially in nonstressful areas, either because plant growth rates in the absence of herbivory are higher and/or because herbivores are more abundant and diverse in nonstressful areas.We test these predictions of where herbivores should exert stronger effects by measuring individual performance, population size structure and densities of a common subshrub,Hibiscus meyeri, in a large‐scale herbivore exclosure experiment arrayed across an aridity gradient in East Africa.We find support for both predictions, with herbivores exerting stronger effects on individual‐level performance in arid (stressful) areas, but exerting stronger effects on population size structure and abundance in mesic (nonstressful) areas. We suggest that this discrepancy arises from higher potential growth rates in mesic areas, where alleviation of herbivory leads to substantially more growth and thus large changes in population size structure. Differences in herbivore abundance do not appear to contribute to our results.Synthesis. Our work suggests that understanding the multiple facets of plant response to herbivores (e.g. both individual performance and abundance) may be necessary to predict how plant species' abundance and distribution patterns will shift in response to changing climate and herbivore numbers.
Linking litter decomposition of above‐ and below‐ground organs to plant–soil feedbacks worldwide
Authors: Freschet Grégoire T. , Cornwell William K. , Wardle David A. , Elumeeva Tatyana G. , Liu Wendan , Jackson Benjamin G. , Onipchenko Vladimir G. , Soudzilovskaia Nadejda A. , Tao Jianping , Cornelissen Johannes H.C. 
Published: June 2013

Summary

Conceptual frameworks relating plant traits to ecosystem processes such as organic matter dynamics are progressively moving from a leaf‐centred to a whole‐plant perspective. Through the use of meta‐analysis and global literature data, we quantified the relative roles of litters from above‐ and below‐ground plant organs in ecosystem labile organic matter dynamics.

We found that decomposition rates of leaves, fine roots and fine stems were coordinated across species worldwide although less strongly within ecosystems. We also show that fine roots and stems had lower decomposition rates relative to leaves, with large differences between woody and herbaceous species. Further, we estimated that on average below‐ground litter represents approximately 33 and 48% of annual litter inputs in grasslands and forests, respectively.

These results suggest a major role for below‐ground litter as a driver of ecosystem organic matter dynamics. We also suggest that, given that fine stem and fine root litters decompose approximately 1.5 and 2.8 times slower, respectively, than leaf litter derived from the same species, cycling of labile organic matter is likely to be much slower than predicted by data from leaf litter decomposition only.

Synthesis. Our results provide evidence that within ecosystems, the relative inputs of above‐ versus below‐ground litter strongly control the overall quality of the litter entering the decomposition system. This in turn determines soil labile organic matter dynamics and associated nutrient release in the ecosystem, which potentially feeds back to the mineral nutrition of plants and therefore plant trait values and plant community composition.
Rare species advantage? Richness of damage types due to natural enemies increases with species abundance in a wet tropical forest
Authors: Bachelot Bénédicte , Kobe Richard K. 
Published: June 2013

Summary

The Janzen–Connell hypothesis (JC) is one potential mechanism to explain the maintenance of high alpha diversity of tree species in tropical forests, operating through differential pressure by natural enemies.

We proposed that this differing pressure could arise from the richness of damage types due to natural enemies (RDNE). Following a community compensatory trend (CCT), we hypothesized greater RDNE on common species than on rare species.

We evaluated this novel interpretation of the JC by assessing damage patterns on leaves, as a proxy for natural enemy species in 44 tree species. We first evaluated which abiotic and biotic factors affect RDNE. Then, we tested whether increasing RDNE leads to an increasing amount of foliar damage.

We found that RDNE

Was affected by biotic environments: RDNE increased with mean seedling species abundance. RDNE was higher on species occurring near more closely related neighbours.
Was not impacted by abiotic factors. Yet, seedlings of shade‐tolerant species hosted a higher RDNE than seedlings of shade‐intolerant species.
Was positively correlated with amount of foliar damage at the species level.

Finally, we tested whether RDNE increased seedling mortality risk. We found that

Foliar damage, species abundance and RDNE2 increased mortality risk.
Richness of damage types due to natural enemies linearly decreased mortality risk more strongly than RDNE2 increased it.
Seedling age decreased mortality risk.

Synthesis. The richness of damage types due to natural enemies increased with abundance of the host species, suggesting an important role of enemy diversity in the maintenance of tree diversity. Supporting a novel interpretation of the Janzen–Connell hypothesis, we found a greater mortality risk with increasing RDNE2, but not with increasing RDNE. There was a stronger negative linear effect of RDNE on mortality risk. Rare species with low RDNE as well as species with very high RDNE suffered greater mortality than species hosting intermediate RDNE, reinforcing the complexity of the effect of multiple enemies on prey.
Does Auditor Industry Specialization Improve Audit Quality?
Authors: MINUTTI‐MEZA MIGUEL 
Published: June 2013

ABSTRACTThis study examines whether auditor industry specialization, measured using the auditor's within‐industry market share, improves audit quality and results in a fee premium. After matching clients of specialist and nonspecialist auditors on a number of dimensions, as well as only on industry and size, there is no evidence of differences in commonly used audit‐quality proxies between these two groups of auditors. Moreover, there is no consistent evidence of a specialist fee premium. The matched sample results are confirmed by including client fixed effects in the main models, examining a sample of clients that switched auditors, and using an alternative proxy that aims to capture the auditor's industry knowledge. The combined evidence in this study suggests that the auditor's within‐industry market share is not a reliable indicator of audit quality. Nevertheless, these findings do not imply that industry knowledge is not important for auditors, but that the methodology used in extant archival studies to examine this issue does not fully parse out the effects of auditor industry specialization from client characteristics.
Wnt/β‐catenin signaling and adipogenic genes are associated with intramuscular fat content in the longissimus dorsi muscle of Korean cattle
Authors: Jeong J. Y. , Kim J. S. , Nguyen T. H. , Lee H. ‐J. , Baik M. 
Published: June 2013

SummaryIntramuscular fat (IMF) is an important trait that influences beef quality. In two studies, we examined the possible involvement of the Wnt/β‐catenin signaling pathway in IMF deposition in Korean cattle. In study 1, using a group of bulls and steers, we found that castration, a non‐genetic factor, decreased (P < 0.01) the expression of both the WNT10B and CTNNB1 genes, whereas it increased the expression of the Wnt antagonist secreted frizzled‐related proteins 4 (SFRP4, P < 0.001) and the adipogenic CCAAT/enhancer binding protein (C/EPB), alpha (CEBPA, P < 0.001) and peroxisome proliferator‐activated receptor gamma (PPARG, P < 0.05) genes in longissimus dorsi muscle (LM) tissue. The WNT10B and CTNNB1 mRNA levels showed strong (P < 0.001) negative correlations (r = −0.68 and r = −0.73 respectively) with the IMF content, whereas the SFRP4, CEBPA and PPARG mRNA levels showed strong (P < 0.01) positive correlations (r = 0.70, 0.70 and 0.64 respectively) with the IMF content. Large variation still exists in the IMF content of steers, implying that genetic factors affect IMF deposition. Using a different group of steers, a correlation analysis in study 2 also showed that the expression of the WNT10B and CTNNB1 genes, and SFRP4 and adipogenic genes was negatively and positively associated with the IMF content respectively. Our findings suggest that downregulation of the Wnt/β‐catenin signaling pathway genes, but upregulation of Wnt antagonist SFRP4 and adipogenic gene expression following castration, contributes to increased IMF deposition in the LM. Our results demonstrate that both non‐genetic factors (castration) and genetic variation within the steer group affect the gene expression pattern of the Wnt/β‐catenin signaling pathway.
Equine developmental orthopaedic diseases – a genome‐wide association study of first phalanx plantar osteochondral fragments inStandardbred trotters
Authors: Lykkjen S. , Dolvik N. I. , McCue M. E. , Rendahl A. K. , Mickelson J. R. , Røed K. H. 
Published: June 2013

SummaryPalmar/plantar osteochondral fragments (POF) in fetlock joints commonly affect and influence the athletic performance of horses. In this study, we used the EquineSNP50 BeadChip®to perform a genome‐wide association study of metatarsophalangealPOFin 176 Norwegian Standardbred trotter yearlings. Putative quantitative trait loci (QTL) for medial and/or lateralPOF, and medialPOFonly were identified onECA1, 2, 7, 9 and 31, whereas for lateralPOF, only onECA7, 11, 27 and X. The moderate number ofQTLevidences a complex inheritance and suggests various genes controllingPOFdevelopment in medial and lateral locations.