bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription factor binding predicts histone modifications in human cell lines
Authors: Benveniste Dan , Sonntag Hans-Joachim , Sanguinetti Guido , Sproul Duncan 
Published: September 2014

Significance
The regulation of gene expression is fundamental to biology and is classically predicated on binding of transcription factor proteins to DNA. This view is challenged by large-scale studies correlating gene expression with posttranslational modifications of the histone proteins with which DNA is complexed in cells. Here, we show through a large-scale computational study that histone modifications can be predicted with remarkable accuracy from transcription factor-binding profiles, recapitulating known interactions between transcription factors and chromatin-modifying enzymes. Our results demonstrate that associations between gene expression and histone modifications do not necessarily imply a direct regulatory role for these modifications, but can be explained equally well as an indirect effect of interactions between transcription factors and chromatin-modifying enzymes.
Molecular mechanics of 30S subunit head rotation
Authors: Mohan Srividya , Donohue John Paul , Noller Harry F. 
Published: September 2014

Significance
Ribosomes are the site of protein synthesis in all cells. Ribosomal polypeptide synthesis involves reading the information encoded in the mRNA and adding the correct amino acid via a tRNA. Elongation of the polypeptide chain proceeds through translocation, where the ribosome couples the movement of the mRNA and its associated tRNAs by precisely one codon. Translocation requires large-scale movement of the small-subunit head domain of the ribosome. By comparing 55 ribosome structures, we show that movement universally results from coupled hinging at two separate loci in the small subunit. This mechanism explains the mode of action of the antibiotic spectinomycin and suggests a means by which the ribosome controls translocation.
Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging
Authors: Sapir Amir , Tsur Assaf , Koorman Thijs , Ching Kaitlin , Mishra Prashant , Bardenheier Annabelle , Podolsky Lisa , Bening-Abu-Shach Ulrike , Boxem Mike , Chou Tsui-Fen , Broday Limor , Sternberg Paul W. 
Published: September 2014

Significance
The mevalonate pathway plays a critical role in cholesterol homeostasis and cancer development, two major challenges in modern medicine. Consequently, cholesterol-reducing medications (statins) that target this pathway are the best-selling pharmaceutical drugs in history. Beyond regulation of the enzyme HMG-CoA reductase, little is known about additional posttranslational regulatory nodes in the mevalonate pathway or how this cascade is controlled with age. We have discovered a regulatory circuit that controls HMGS-1, the first enzyme of the mevalonate pathway, during aging. HMGS-1 is regulated by posttranslational ubiquitination and age-dependent sumoylation. Sumoylation is reversed by the spatiotemporally controlled activity of a specific small ubiquitin-like modifier protease. This conserved molecular circuit could serve as a handle for targeting the mevalonate pathway in future therapeutics.
Validity of a trunk‐mounted accelerometer to assess peak accelerations during walking, jogging and running
Authors: Wundersitz Daniel W. T. , Gastin Paul B. , Richter Chris , Robertson Samuel J. , Netto Kevin J. 
Published: September 2014

AbstractThe purpose of this study was to validate peak acceleration data from an accelerometer contained within a wearable tracking device while walking, jogging and running. Thirty‐nine participants walked, jogged and ran on a treadmill while 10 peak accelerations per movement were obtained (n = 390). A single triaxial accelerometer measured resultant acceleration during all movements. To provide a criterion measure of acceleration, a 12‐camera motion analysis (MA) system tracked the position of a retro‐reflective marker affixed to the wearable tracking device. Peak raw acceleration recorded by the accelerometer significantly overestimated peak MA acceleration (P < 0.01). Filtering accelerometer data improved the relationship with the MA system (P < 0.01). However, only the 10 Hz and 8 Hz cut‐off frequencies significantly reduced the errors found. The walk movement demonstrated the highest accuracy, agreement and precision and the lowest relative errors. Linear increases in error were observed for jog compared with walk and for run compared to both other movements. As the magnitude of acceleration increased, the strength of the relationship between the accelerometer and the criterion measure decreased. These results indicate that filtered accelerometer data provide an acceptable means of assessing peak accelerations, in particular for walking and jogging.
Selmer companion curves
Authors: Mazur Barry , Rubin Karl 
Published: September 2014

We say that two elliptic curves

E
1

,

E
2

E_1, E_2

over a number field

K
K

are

n
n

-Selmer companions for a positive integer

n
n

if for every quadratic character

χ
\chi

of

K
K

, there is an isomorphism

Sel
n

⁡
(

E
1
χ

/

K
)
≅

Sel
n

⁡
(

E
2
χ

/

K
)

\operatorname {Sel}_n(E_1^\chi /K) \cong \operatorname {Sel}_n(E_2^\chi /K)

between the

n
n

-Selmer groups of the quadratic twists

E
1
χ

E_1^\chi

,

E
2
χ

E_2^\chi

. We give sufficient conditions for two elliptic curves to be

n
n

-Selmer companions, and give a number of examples of non-isogenous pairs of companions.
Updating conservation priorities over 111 years of species observations
Authors: Milt Austin W. , Palmer Sally R. , Armsworth Paul R. 
Published: September 2014

Summary

Observations of species occurrences are often used to inform spatial prioritizations for the effective use of limited conservation resources. Additional species observations have the potential to change where a conservation group plans to invest. But by how much? How different would conservation priorities be if planners updated current observations with the information they will have next year?

We sought to address these questions using a 111‐year data set that reflects commonly used collection and prioritization practices. We quantify changes in the ranking of Tennessee watersheds brought on by annual additions of species observations made between 1900 and 2010. We ranked watersheds by their complementary contribution to overall species richness. We examine the sensitivity of our results to the number of watersheds prioritized.

We expected the effect of new observations to diminish as the data set grew, and we found this to be the case. Importantly, however, additional observations may continue to significantly change conservation priorities in the future if current data collection trends continue.

We found that, overall, additional observations can greatly affect priorities and that this result is sensitive to the number of watersheds ranked. Thus, the extent of planning activities moderates the effect of including additional data.

Synthesis and applications. Long‐term, opportunistically collected data of species locations are commonly used in conservation planning. We find that when using such data, additional species observations significantly affect subsequent priorities. This effect is most pronounced when data are sparse. As such, data collection should be a focus of very early conservation actions in new areas. Even in well‐studied areas, however, additional observations may continue to change spatial priorities into the future, and so while data collection can decrease in well‐studied areas, it should continue at a lower intensity. Our methods could also be used to determine the balance of data collection and conservation action in a new location.
Effects of 1 year long‐term freezing with different preservatives on milk cholesterol, progesterone and lactoferrin determination
Authors: Altenhofer Christian , Pfaffl Michael , Viturro Enrique 
Published: September 2014

This study was performed to determine the effects of long‐term freezing on milk composition and to evaluate the possible effects on analysis of four preservative substances (Azidiol, Kathon CG, NaOH and Thiomersal) on the determination of milk cholesterol, progesterone and lactoferrin concentration. Collected milk was separated in aliquots, stored at 20 °C in 10mL plastic vials and analysed after 1, 6 and 12 months. It could be shown that the preservatives are not equally appropriate for all analysing methods used in this experiment. Preservatives and storage conditions for milk samples have to be carefully selected during the study design depending on the parameters to be measured.
related: an R package for analysing pairwise relatedness from codominant molecular markers
Authors: Pew Jack , Muir Paul H. , Wang Jinliang , Frasier Timothy R. 
Published: September 2014

AbstractAnalyses of pairwise relatedness represent a key component to addressing many topics in biology. However, such analyses have been limited because most available programs provide a means to estimate relatedness based on only a single estimator, making comparison across estimators difficult. Second, all programs to date have been platform specific, working only on a specific operating system. This has the undesirable outcome of making choice of relatedness estimator limited by operating system preference, rather than being based on scientific rationale. Here, we present a new R package, called related, that can calculate relatedness based on seven estimators, can account for genotyping errors, missing data and inbreeding, and can estimate 95% confidence intervals. Moreover, simulation functions are provided that allow for easy comparison of the performance of different estimators and for analyses of how much resolution to expect from a given data set. Because this package works in R, it is platform independent. Combined, this functionality should allow for more appropriate analyses and interpretation of pairwise relatedness and will also allow for the integration of relatedness data into larger R workflows.
Fine‐tuned regulation of the dissimilatory nitrite reductase gene by oxygen and nitric oxide in Pseudomonas aeruginosa
Authors: Kuroki Miho , Igarashi Yasuo , Ishii Masaharu , Arai Hiroyuki 
Published: September 2014

SummaryNitrite reductase (NIR) catalyses the reduction of nitrite to nitric oxide (NO) in the denitrification pathway. In Pseudomonas aeruginosa, expression of the gene encoding NIR (nirS) is induced by NO and is under control of the NO‐sensing regulator DNR (dissimilatory nitrate respiration regulator). Because DNR is under control of the oxygen‐sensing regulator ANR (anaerobic regulator of arginine deiminase and nitrate reductase), nirS is expressed only under low oxygen and anaerobic conditions. Both ANR and DNR are FNR (fumarate and nitrate reductase regulator)‐type regulators and recognize the consensus FNR‐binding motif. The motif of the nirS promoter is thought to be recognized only by DNR, and not by ANR. Here, mutant strains expressing either ANR or DNR were constructed and used to analyse the role of ANR and DNR in the activation of nirS expression. Analysis of transcriptional activity by microarray and quantitative reverse transcription polymerase chain reaction revealed that nirS is transcribed under low oxygen conditions in an ANR‐dependent manner, although the expression level was 10‐fold lower than that of the DNR‐dependent expression. An artificial promoter containing the FNR‐binding motif of the nirS promoter was also twofold upregulated by ANR. These results indicate that low‐level expression of NIR in the presence of nitrite may provide NO as a trigger for the full expression of denitrification genes when oxygen is depleted.
Epidemiology, identification and disease management of grape black rot and potentially useful metabolites of black rot pathogens for industrial applications – a review
Authors: Molitor D. , Beyer M. 
Published: September 2014

AbstractPhyllosticta ampelicida (teleomorph: Guignardia bidwellii) is the fungal plant pathogen that causes black rot on grapevine. It is able to infect all green, expanding grape tissues. Black rot poses a threat to both yield and wine quality; a severe attack can virtually cause a complete crop loss. The fungus is native to North America, and was spread to Europe at the end of the 19th century. With the beginning of the 21st century, an increasing importance of the disease was observed in several European winegrowing regions. Successful black rot control strategies combine sanitary measures, cultural techniques, growing cultivars with reduced susceptibility and the use of effective fungicides. Berries are most susceptible to infections between flowering and bunch closure and consequently, fungicide applications against black rot need to focus on this period. In this paper, forecast models and decision support systems that help to achieve satisfactory control with a minimum of fungicide input are presented. Black rot in grapevine was reported to be well controlled in field experiments by a broad range of fungicide classes including quinone outside inhibitors (98 ± 3% efficacy), demethylation inhibitors (98 ± 3% efficacy) and dithiocarbamates (92 ± 7% efficacy). Average efficacies of other fungicide classes tested so far ranged from 32 to 69%; meta data on the efficacy of fungicides in numerous field trials are given. At present, black rot causes major problems primarily if vineyard management and fungicide use were reduced or abandoned. Organically managed vineyards are highly affected. Hence, site and cultivar selection as well as cultural measures are of the highest importance especially in organic viticulture. Recent studies showed that some strains formerly classified as G. bidwellii in fact belong to a distinct species (P. parthenocissi). Black rot pathogens produce some phytotoxic secondary metabolites, such as phenguignardic acid, guignardic acid, alaguignardic acid and the guignardianones A, E and F, which could stimulate the development of new herbicides of natural origin.
Distribution of Galanin and Galanin Receptor 2 in the Pre‐optic Area of the Female Guinea Pig
Authors: Hermanowicz B. , Bogus‐Nowakowska K. , Równiak M. , Żakowski W. , Wasilewska B. , Najdzion J. , Robak A. 
Published: September 2014

SummaryThis study describes the distribution of galanin (Gal) and galanin receptor 2 (GalR2) in the pre‐optic area (POA) of the female guinea pig. Frozen sections were undergone for a routine immunofluorescence labelling. Gal and GalR2 display immunoreactivity in all parts of the pre‐optic area. Gal shows reactivity both in perikarya and fibres, whereas GalR2 was observed only in perikarya. Gal‐ and GalR2‐immunoreactive (‐ir) perikarya were the most numerous in the medial pre‐optic area (MPA) with the highest reactivity in its dorsal part. In the median pre‐optic nucleus (MPN) and periventricular pre‐optic nucleus (PPN), only single Gal‐ and GalR2‐ir neurons were observed. The highest density of Gal‐ir fibres was revealed in the PPN and the lowest in the lateral pre‐optic area (LPA). The results of this study indicate that the distribution pattern of Gal containing neurons overlaps well with the distribution pattern of GalR2‐positive neurons, especially in the MPA. This may suggest GalR2‐dependent activity in this brain region.
The first Australian Baseline Series: Recommendations for patch testing in suspected contact dermatitis
Authors: Toholka Ryan , Wang Yi‐Shi , Tate Bruce , Tam Mei , Cahill Jennifer , Palmer Amanda , Nixon Rosemary 
Published: September 2014

AbstractBackground and ObjectivesPatch testing is a standard diagnostic tool used in the identification of causative allergens in allergic contact dermatitis. Ongoing surveillance of rates of allergen positivity is vitally important to detect trends and allow comparisons between countries. The objective of this study was to propose the first evidence‐based Australian baseline series, based on retrospective review of our patch test data. We aimed to identify the most important and most relevant allergens in our population.MethodsWe conducted a 10‐year (2001–2010) retrospective review of data from the contact dermatitis clinic and the occupational dermatitis clinic from our institution.ResultsWe patch tested 5281 patients in all. The top 20 allergens with the highest number of relevant positive patch test reactions were: fragrance mix 1: nickel, potassium dichromate, Myroxylon pereirae, formaldehyde, p‐phenylenediamine (PPD), thiuram mix, colophony (rosin), dermatophagoides mix, ammonium persulfate, quaternium‐15, cobalt chloride, methylchloroisothiazolinone or methylisothiazolinone, diazolidinylurea, epoxy resin, 1,3‐dimethylol‐5,5‐dimethyl hydantoin, Compositae mix, toluenesulfonamide formaldehyde resin, basic red 46 and imidazolidinyl urea.ConclusionWe have elucidated the most frequent and relevant contact allergens in our patient population and used this information to construct the first Australian baseline series.
Chromium chloride increases insulin‐stimulated glucose uptake in the perfused rat hindlimb
Authors: Doerner P. G. , Liao Y.‐H. , Ding Z. , Wang W. , Ivy J. L. , Bernard J. R. 
Published: September 2014

AbstractAimTo determine the effect of chromium chloride (CrCl3) on healthy skeletal muscle glucose uptake in the absence and presence of submaximal insulin using the rat hindlimb perfusion technique.MethodsSprague–Dawley rats were randomly assigned to an experimental group: basal (Bas), chromium chloride (Cr), submaximal insulin (sIns) or chromium chloride plus submaximal insulin (Cr‐sIns).ResultsInsulin significantly increased [H3]‐2 deoxyglucose (2‐DG) uptake in the gastrocnemius muscles. Additionally, Cr‐sIns displayed greater rates of 2‐DG uptake than sIns (Cr‐sIns 6.86 ± 0.74 μmol g h−1 vs. sIns 4.83 ± 0.42 μmol g h−1). There was no difference between Cr and Bas treatment groups. It has been speculated that chromium works to increase glucose uptake by increasing insulin signalling. We found that Akt and AS160 phosphorylation was increased in the sINS treatment group, while chromium treatment had no additional effect on Akt or AS160 phosphorylation in the absence or presence of insulin. Cr‐sIns significantly increased plasma membrane GLUT4 concentration above that of sIns (Cr‐sIns 72.22 ± 12.7%, sIns 53.4 ± 6.1%), but in the absence of insulin, chromium had no effect.ConclusionExposure of healthy skeletal muscle to chromium may increase skeletal muscle insulin‐stimulated GLUT4 translocation and glucose uptake. However, these effects do not appear to result from enhanced insulin signalling proximal to AS160.
Dorsolateral prefrontal hemodynamic responses during a verbal fluency task in hypomanic bipolar disorder
Authors: Nishimura Yukika , Takahashi Katsuyoshi , Ohtani Toshiyuki , Ikeda‐Sugita Reina , Kasai Kiyoto , Okazaki Yuji 
Published: September 2014

ObjectivesNeuroimaging studies have suggested prefrontal dysfunction in response to cognitive activation in bipolar disorder (BD). However, its characteristics in manic states have not been well understood. Thus, we compared prefrontal hemodynamic responses during a cognitive task between hypomanic and depressive states in BD. We then longitudinally compared hypomanic and subsequent euthymic states.MethodsThe prefrontal function of 27 patients with BD (11 hypomanic and 16 depressed) and 12 age‐ and gender‐matched healthy controls (HCs) was evaluated using near‐infrared spectroscopy (NIRS) during a verbal fluency task (VFT). Hypomanic symptoms were assessed using the Young Mania Rating Scale. Among the 11 hypomanic patients, eight participated in the second NIRS measurement after their hypomanic symptoms resolved.ResultsVFT performance did not differ among hypomanic, depressed, and HC groups. Both BD groups exhibited significantly lower activation during the VFT than HCs in the broader bilateral prefrontal cortex. Hemodynamic changes in the left dorsolateral prefrontal cortex (DLPFC) in the hypomanic patients with BD were significantly larger than those in the depressed patients. In addition, hypomanic symptom severity was positively correlated with activation in the left DLPFC and frontopolar cortex in patients with BD. Follow‐up measurement of the hypomanic patients revealed that prefrontal activation was decreased after hypomanic symptoms resolved.ConclusionsCombining cross‐sectional and longitudinal assessments, the present results suggest that prefrontal hemodynamic responses associated with cognitive activation differ between hypomanic and depressive states in BD. NIRS measurement could be a useful tool for objectively evaluating state‐dependent characteristics of prefrontal hemodynamics in BD.
Approaches to academic growth assessment
Authors: Anderman Eric M. , Gimbert Belinda , O'Connell Ann A. , Riegel Lisa 
Published: September 2014

BackgroundThere is much interest in assessing growth in student learning. Assessments of growth have important implications and affect many policy decisions at many levels.AimsIn the present article, we review some of the different approaches to measuring growth and examine the implications of their usage.SampleSamples used in research on growth models typically include students enrolled in public schools that primarily serve kindergarten through the 12th grade.MethodDefinitions of growth and gain are reviewed, and five types of growth models are examined: (1) Student Gain Score Model, (2) The Covariate Adjustment Model, (3) The Student Percentile Gain Model – referred to as single‐wave value‐added models, (4) Univariate Value‐Added Response Models, and (5) Multivariate Value‐Added Response Models.ResultsModelling approaches are vastly different, whereas Student Gain Models are mathematically and conceptually simple, Multivariate Models are highly complex.ConclusionEducators assessing growth must make critical decisions about measurement. The type of instrument that is selected and the type of analytic techniques selected are of great importance. Growth must be considered from technical, pedagogical, and policy perspectives.
Factors associated with the timing and onset of cannabis use and cannabis use disorder: Results from the 2007 Australian National Survey of Mental Health and Well‐Being
Authors: Butterworth Peter , Slade Tim , Degenhardt Louisa 
Published: September 2014

AbstractIntroduction and AimsTo investigate the predictors of both initiation of cannabis use and transition to cannabis use disorder (CUD) in a nationally representative sample using discrete‐time survival analyses.Design and MethodsData from a nationally representative sample of 6935 Australian adults. Retrospective data on age of first cannabis use and onset of CUD were used to construct pseudo‐longitudinal datasets and survival models used to evaluate factors associated with age of first use and time from first use to onset of CUD.ResultsThe oldest cohort (born 1942–1951) had lower cannabis use than younger cohorts, with first use also occurring at an older age. Multivariable discrete‐time survival models showed other substance use, tobacco and alcohol use at very young ages, and mental disorders were associated with increased risk of cannabis use. There were 7.5% of those <65 years old at interview who had a lifetime CUD; mean time from first use to the onset of CUD was 3.3 years, with 90% of cases within eight years. Younger age of initiation and other substance use were strong predictors of the transition from use to CUD. Women with depression were more likely to develop a CUD; social phobia and panic disorder were also associated with transition from cannabis use to CUD.Discussion and ConclusionsPatterns of cannabis use differ across birth cohorts. There are multiple factors associated with use and transition to CUD, with other substance use a strong predictor. Mental disorders also predict initiation and progression to CUD. [Butterworth P, Slade T, Degenhardt L. Factors associated with the timing and onset of cannabis use and cannabis use disorder: Results from the 2007 Australian National Survey of Mental Health and Well‐Being. Drug Alcohol Rev 2014;33:555‐563]