bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tree and rate estimation by local evaluation of heterochronous nucleotide data
Authors: Yang Zhu , O'Brien John D. , Zheng Xiaobin , Zhu Huai-Qiu , She Zhen-Su 
Published: November 2006

AbstractMotivation: Heterochronous gene sequence data is important for characterizing the evolutionary processes of fast-evolving organisms such as RNA viruses. A limited set of algorithms exists for estimating the rate of nucleotide substitution and inferring phylogenetic trees from such data. The authors here present a new method, Tree and Rate Estimation by Local Evaluation (TREBLE) that robustly calculates the rate of nucleotide substitution and phylogeny with several orders of magnitude improvement in computational time.Methods: For the basis of its rate estimation TREBLE novelly utilizes a geometric interpretation of the molecular clock assumption to deduce a local estimate of the rate of nucleotide substitution for triplets of dated sequences. Averaging the triplet estimates via a variance weighting yields a global estimate of the rate. From this value, an iterative refinement procedure relying on statistical properties of the triplets then generates a final estimate of the global rate of nucleotide substitution. The estimated global rate is then utilized to find the tree from the pairwise distance matrix via an UPGMA-like algorithm.Results: Simulation studies show that TREBLE estimates the rate of nucleotide substitution with point estimates comparable with the best of available methods. Confidence intervals are comparable with that of BEAST. TREBLE's phylogenetic reconstruction is significantly improved over the other distance matrix method but not as accurate as the Bayesian algorithm. Compared with three other algorithms, TREBLE reduces computational time by a minimum factor of 3000. Relative to the algorithm with the most accurate estimates for the rate of nucleotide substitution (i.e. BEAST), TREBLE is over 10 000 times more computationally efficient.Availability: Contact: jdobrien@ucla.edu
Striped Smith–Waterman speeds database searches six times over other SIMD implementations
Authors: Farrar Michael 
Published: November 2006

AbstractMotivation: The only algorithm guaranteed to find the optimal local alignment is the Smith–Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level.Results: A faster implementation of the Smith–Waterman algorithm is presented. This algorithm achieved 2–8 times performance improvement over other SIMD based Smith–Waterman implementations. On a 2.0 GHz Xeon Core 2 Duo processor, speeds of &gt;3.0 billion cell updates/s were achieved.Availability: Contact: farrar.michael@gmail.com
Resveratrol and curcumin suppress immune response through CD28/CTLA-4 and CD80 co-stimulatory pathway
Authors: Sharma S , Chopra K , Kulkarni S K , Agrewala J N 
Published: November 2006

Summary
The role of resveratrol and curcumin is well documented in cancer, inflammation, diabetes and various other diseases. However, their immunosuppressive action on T cells, B cells and macrophages is not well documented. In the present study, we have ascertained the effect of resveratrol and curcumin on T and B cells and macrophages. The most striking findings were that both resveratrol and curcumin suppressed the activity of T and B cells and macrophages, as evidenced by significant inhibition in proliferation, antibody production and lymphokine secretion. Interestingly, curcumin imparted immunosuppression by mainly down-regulating the expression of CD28 and CD80 and up-regulating CTLA-4. Resveratrol also functioned by decreasing the expression of CD28 and CD80, as well as by augmenting the production of interleukin (IL)-10.
Vegetative phenology constrains the onset of flowering in the perennial herb Lathyrus vernus
Authors: SOLA ANA J. , EHRLÉN JOHAN 
Published: November 2006

Summary

The seasonal timing of flower production is a critical event in the life cycle of many plants. A range of abiotic and biotic interactions has been suggested to influence the optimal flowering phenology. More rarely, phenology has been examined from a developmental perspective. Still, the production of a flower or an inflorescence is an integral part of the ontogeny and architecture of a plant.
We investigated to what extent the timing of flowering is coupled to overall ontogeny and architecture in the perennial herb Lathyrus vernus. We asked if the decision to flower is associated with a change in vegetative phenology. We also investigated if onset of flowering depends on the start of shoot growth and leaf unfolding, time to complete shoot growth and leaf unfolding, and plant architecture. Lastly, we investigated whether the resource state of the plant affects vegetative and flowering phenology.
Flowering plants started shoot growth and leaf development significantly earlier than non‐flowering plants. In flowering plants, start of vegetative growth was positively correlated to start of flowering, but there was no positive correlation between development time and start of flowering. Earlier flowering plants produced their first inflorescence at lower positions than late‐flowering plants. Experimental manipulation of resource state affected several components of fitness but did not influence vegetative or flowering phenology.
Our results show that the decision to flower is linked to a change in vegetative phenology in L. vernus, and that differences in the onset of flowering among individuals are correlated to differences in vegetative phenology. A possible interpretation of this pattern is that the evolution of flowering phenology is partly constrained by vegetative development. Alternatively, flowering changes the optimal time of vegetative development. Still, individuals with similar timing of vegetative development may differ considerably in flowering time, suggesting that independent adjustments of vegetative and flowering phenology are possible.
The effects of chewing versus caffeine on alertness, cognitive performance and cardiac autonomic activity during sleep deprivation
Authors: KOHLER MARK , PAVY ALAN , VAN DEN HEUVEL CAMERON 
Published: November 2006

SummaryChewing has been shown to alleviate feelings of sleepiness and improve cognitive performance during the day. This study investigated the effect of chewing on alertness and cognitive performance across one night without sleep as well as the possible mediating role of cardiac autonomic activity. Fourteen adults participated in a randomized, counterbalanced protocol employing a chewing, placebo and caffeine condition. Participants completed tasks assessing psychomotor vigilance, tracking, grammatical reasoning, alertness and sleepiness each hour across the night. All participants received either placebo or caffeine (200 mg), while the chewing condition also chewed on a tasteless and odorless substance for 15 min each hour. Heart rate (HR), root mean square of the successive differences in R‐R intervals on the ECG (RMSSD), and preejection period (PEP) were simultaneously recorded. Alertness and cognitive performance amongst the chewing condition did not differ or were in fact worse when compared with placebo. Similarly, measures of HR and RMSSD remained the same between these two conditions; however, PEP was reduced in the later part of the night in the chewing condition compared with a relative increase for placebo. Caffeine led to improved speed and accuracy on cognitive tasks and increased alertness when compared with chewing. Relative increases in RMSSD and reductions in HR were demonstrated following caffeine; however, no change in PEP was seen. Strong associations between cardiac parasympathetic activity and complex cognitive tasks, as well as between subjective alertness and simpler cognitive tasks, suggest a differential process mediating complex versus simple cognitive performance during sleep deprivation.
Peripheral electrical nerve stimulation and rest‐activity rhythm in Alzheimer's disease
Authors: VAN DIJK KOENE R. A. , LUIJPEN MARIJN W. , VAN SOMEREN EUS J. W. , SERGEANT JOSEPH A. , SCHELTENS PHILIP , SCHERDER ERIK J. A. 
Published: November 2006

SummaryRest‐activity rhythm disruption is a prominent clinical feature of Alzheimer's disease (AD). The origin of the altered rest‐activity rhythm is believed to be degeneration of the suprachiasmatic nucleus (SCN). In accordance with the ‘use it or lose it’ hypothesis of Swaab [Neurobiol Aging1991,12: 317–324] stimulation of the SCN may prevent age‐related loss of neurons and might reactivate nerve cells that are inactive but not lost. Previous studies with relatively small sample sizes have demonstrated positive effects of peripheral electrical nerve stimulation on the rest‐activity rhythm in AD patients. The present randomized, placebo‐controlled, parallel‐group study was meant to replicate prior findings of electrical stimulation in AD in a substantially larger group of AD patients. The experimental group (n = 31) received peripheral electrical nerve stimulation and the placebo group (n = 31) received sham stimulation. Effects of the intervention on the rest‐activity rhythm were assessed by using wrist‐worn actigraphs. Near‐significant findings on the rest‐activity rhythm partially support the hypothesis that neuronal stimulation enhances the rest‐activity rhythm in AD patients. Interestingly,post‐hocanalyses revealed significant treatment effects in a group of patients who were not using acetylcholinesterase inhibitors concomitantly. We conclude that more research is needed before firm general conclusions about the effectiveness of electrical stimulation as a symptomatic treatment in AD can be drawn. In addition, the presentpost‐hocfindings indicate that future studies on non‐pharmacological interventions should take medication use into account.
Prevalence of sleep problems and their association with inattention/hyperactivity among children aged 6–15 in Taiwan
Authors: SUSAN SHUR‐FEN GAU 
Published: November 2006

SummaryThis study investigated the 6‐month prevalence rates of sleep‐related problems and their association with daytime inadvertent napping, inattention, hyperactivity/impulsivity, and oppositional symptoms in children and adolescents. A representative school‐based sample of 2463 first to ninth graders was recruited using a multistage sampling method. The instruments included the Sleep Habits Questionnaire (including dyssomnia, parasomnia, sleep schedules, and sleep‐disordered breathing), the Chinese Health Questionnaire, and the Chinese versions of the Conners’ Parent and Teacher Rating Scales‐Revised: Short forms. The informants were mothers and teachers. The linear and nonlinear mixed models were used for statistical analyses and sex and age were controlled in the model. Results showed that the rates of middle insomnia, disturbed circadian rhythm, mouth breathing, and daytime inadvertent napping increased with age; whereas those of bedwetting, bruxism, sleep terrors decreased with age. Dyssomnia, sleep‐disordered breathing problems, daytime inadvertent napping, and sleep schedules were related to attention‐deficit/hyperactivity disorder (ADHD)‐related symptoms as assessed by mothers’ and teachers’ ratings. Parasomnia was associated with ADHD‐related symptoms as assessed by mothers’ ratings. Our findings suggest an age trend of sleep problems similar to those found in the literature and the association of daytime inadvertent napping, inattention, hyperactivity/impulsivity, and oppositional symptoms with sleep‐related problems.
Changes in dreaming induced by CPAP in severe obstructive sleep apnea syndrome patients
Authors: CARRASCO EVA , SANTAMARIA JOAN , IRANZO ALEX , PINTOR LUIS , PABLO JOAN DE , SOLANAS ANTONIO , KUMRU HATICE , MARTÍNEZ‐RODRÍGUEZ JOSÉ ENRIQUE , BOGET TERESA 
Published: November 2006

SummaryTo study dream content in patients with severe obstructive sleep apnea syndrome (OSAS) and its modification with Continuous Positive Airway Pressure (CPAP) therapy. We assessed twenty consecutive patients with severe OSAS and 17 healthy controls. Polysomnograms were recorded at baseline in patients and controls and during the CPAP titration night, 3 months after effective treatment and 2 years later in patients. Subjects were awakened 5–10 min after the beginning of the first and last rapid eye movement (REM) sleep periods and we measured percentage of dream recall, emotional content of the dream, word count, thematic units, sleep architecture and REM density. Dream recall in REM sleep was similar in patients at baseline and controls (51.5% versus 44.4% respectively; P = .421), decreased to 20% and 24.3% the first and third month CPAP nights, and increased to 39% 2 years later (P = 0.004). Violent/highly anxious dreams were only seen in patients at baseline. Word count was higher in patients than in controls. REM density was highest the first CPAP night. Severe OSAS patients recall dreams in REM sleep as often as controls, but their dreams have an increased emotional tone and are longer. Despite an increase in REM density, dream recall decreased the first months of CPAP and recovered 2 years later. Violent/highly anxious dreams disappeared with treatment. A dream recall decrease with CPAP is associated with normalization of sleep in OSAS patients.
Differential effects of chronic partial sleep deprivation and stress on serotonin‐1A and muscarinic acetylcholine receptor sensitivity
Authors: ROMAN VIKTOR , HAGEWOUD ROELINA , LUITEN PAUL G. M. , MEERLO PETER 
Published: November 2006

SummaryDisrupted sleep and stress are often linked to each other, and considered as predisposing factors for psychopathologies such as depression. The depressed brain is associated with reduced serotonergic and enhanced cholinergic neurotransmission. In an earlier study, we showed that chronic sleep restriction by forced locomotion caused a gradual decrease in postsynaptic serotonin‐1A receptor sensitivity, whilst chronic forced activity alone, with sufficient sleep time, did not affect receptor sensitivity. The first aim of the present study was to examine whether the sleep loss‐induced change in receptor sensitivity is mediated by adrenal stress hormones. The results show that the serotonin‐1A receptor desensitization is independent of adrenal hormones as it still occurs in adrenalectomized rats. The second aim of the study was to establish the effects of sleep restriction on cholinergic muscarinic receptor sensitivity. While sleep restriction affected muscarinic receptor sensitivity only slightly, forced activity significantly hypersensitized the muscarinic receptors. This hypersensitization is because of the stressful nature of the forced activity protocol as it did not occur in adrenalectomized rats. Taken together, these data confirm that sleep restriction may desensitize the serotonin‐1A receptor system. This is not a generalized effect as sleep restriction did not affect the sensitivity of the muscarinic cholinergic receptor system, but the latter was hypersensitized by stress. Thus, chronic stress and sleep loss may, partly via different pathways, change the brain into a direction as it is seen in mood disorders.
A mutation in Arabidopsis cytochrome b5 reductase identified by high‐throughput screening differentially affects hydroxylation and desaturation
Authors: Kumar Rajesh , Wallis James G. , Skidmore Chris , Browse John 
Published: November 2006

SummaryAs a model for analyzing the production of novel fatty acids in oilseeds, we used the genetic and molecular techniques available for Arabidopsis to characterize modifying mutations affecting the accumulation of hydroxy fatty acids in the seeds of Arabidopsis plants that express a transgene for the castor bean fatty acid hydroxylase, FAH12. We developed a high‐throughput analytical system and used it to identify three complementation classes of mutations with reduced hydroxy fatty acid accumulation from among Arabidopsis M3 seed samples derived from chemical mutagenesis. We identified one of the mutations by positional cloning as a single base pair change in a gene encoding NADH:cytochrome b5 reductase (CBR1, At5g17770). When expressed in yeast, the mutant form of the enzyme was less active and less stable than the wild‐type enzyme. Characterization of homozygous mutant lines with and without the FAH12 transgene (FAH12 cbr1‐1 and cbr1‐1, respectively) indicated that the only detectable consequence of the cbr1‐1 mutation was on desaturase and hydroxylase reactions in the developing seed. The leaf and root fatty compositions, as well as the growth, development and seed production of mutant plants were indistinguishable from wild type. Interestingly, while the cbr1‐1 mutation reduced the accumulation of hydroxy fatty acids in seeds by 85%, the effects on 18:1 and 18:2 desaturation reactions were much less (<25% and <60%, respectively). These results suggest that there is competition in developing seeds among the several reactions that utilize reduced cytochrome b5.
Isolation and characterization of the RAD54 gene from Arabidopsis thaliana
Authors: Osakabe Keishi , Abe Kiyomi , Yoshioka Toji , Osakabe Yuriko , Todoriki Setsuko , Ichikawa Hiroaki , Hohn Barbara , Toki Seiichi 
Published: November 2006

SummaryHomologous recombination (HR) is an essential process in maintaining genome integrity and variability. In eukaryotes, the Rad52 epistasis group proteins are involved in meiotic recombination and/or HR repair. One member of this group, Rad54, belongs to the SWI2/SNF2 family of DNA‐stimulated ATPases. Recent studies indicate that Rad54 has important functions in HR, both as a chromatin remodelling factor and as a mediator of the Rad51 nucleoprotein filament. Despite the importance of Rad54 in HR, no study of Rad54 from plants has yet been performed. Here, we cloned the full‐length AtRAD54 cDNA sequence; an open reading frame of 910 amino acids encodes a protein with a predicted molecular mass of 101.9 kDa. Western blotting analysis showed that the AtRad54 protein was indeed expressed as a protein of approximately 110 kDa in Arabidopsis. The predicted protein sequence of AtRAD54 contains seven helicase domains, which are conserved in all other Rad54s. Yeast two‐hybrid analysis revealed an interaction between Arabidopsis Rad51 and Rad54. AtRAD54 transcripts were found in all tissues examined, with the highest levels of expression in flower buds. Expression of AtRAD54 was induced by γ‐irradiation. A T‐DNA insertion mutant of AtRAD54 devoid of full‐length AtRAD54 expression was viable and fertile; however, it showed increased sensitivity to γ‐irradiation and the cross‐linking reagent cisplatin. In addition, the efficiency of somatic HR in the mutant plants was reduced relative to that in wild‐type plants. Our findings point to an important role for Rad54 in HR repair in higher plants.
PDX1 is essential for vitamin B6 biosynthesis, development and stress tolerance in Arabidopsis
Authors: Titiz Olca , Tambasco‐Studart Marina , Warzych Ewelina , Apel Klaus , Amrhein Nikolaus , Laloi Christophe , Fitzpatrick Teresa B. 
Published: November 2006

SummaryVitamin B6 is an essential coenzyme for numerous metabolic enzymes and is a potent antioxidant. In plants, very little is known about its contribution to viability, growth and development. The de novo pathway of vitamin B6 biosynthesis has only been described recently and involves the protein PDX1 (pyridoxal phosphate synthase protein). Arabidopsis thaliana has three homologs of PDX1, two of which, PDX1.1 and PDX1.3, have been demonstrated as functional in vitamin B6 biosynthesis in vitro and by yeast complementation. In this study, we show that the spatial and temporal expression patterns of PDX1.1 and PDX1.3, investigated at the transcript and protein level, largely overlap, but PDX1.3 is more abundant than PDX1.1. Development of single pdx1.1 and pdx1.3 mutants is partially affected, whereas disruption of both genes causes embryo lethality at the globular stage. Detailed examination of the single mutants, in addition to those that only have a single functional copy of either gene, indicates that although these genes are partially redundant in vitamin B6 synthesis, PDX1.3 is more requisite than PDX1.1. Developmental distinctions correlate with the vitamin B6 content. Furthermore, we provide evidence that in addition to being essential for plant growth and development, vitamin B6 also plays a role in stress tolerance and photoprotection of plants.
ROX1, a gene induced by rolB, is involved in procambial cell proliferation and xylem differentiation in tobacco stamen
Authors: Cecchetti Valentina , Altamura Maria Maddalena , Serino Giovanna , Pomponi Mirella , Falasca Giuseppina , Costantino Paolo , Cardarelli Maura 
Published: November 2006

SummaryThe Agrobacterium rhizogenes oncogene rolB mimics the effects of auxin in that it increases the sensitivity of transformed cells to this hormone. Here we isolated a tobacco gene, ROX1, acting downstream of rolB. We show that plants with reduced levels of ROX1 mRNA, due to the expression of a 35S‐driven ROX1‐antisense construct, have flowers with stamens and pistils longer than normal because of an increased number of cells. Localized expression of rolB in anthers results in overexpression of ROX1 and reduced growth of stamens, due to a reduced number of cells. In addition, the longer stamens of antisense plants show a delayed xylem differentiation in the lateral bundles, primarily of the junction region between anther and filament, while the shorter stamens of ROX1‐overexpressing plants show a precocious differentiation of xylem cells in the same tissues. Expression of ROX1 in stamens peaks at early stages of stamen growth, and ROX1 mRNA is localized mostly in anther procambial cells. The sequence of ROX1 shares a conserved element with a number of plant genes, including TED3, which is involved in xylem differentiation. These results point to a role of ROX1 in the balance between proliferation of procambial cells and xylem differentiation during stamen development.