bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionization effects on the partitioning behavior of food and beverage aroma compounds between aqueous phases and air and organic matrices
Authors: Rayne Sierra , Forest Kaya 
Published: August 2011

AbstractAroma compounds in the Flavornet database were screened for ionizable functional groups such as carboxylic acids, aliphatic and aromatic amines, phenols, alcohols, and thiols. Of the 738 aroma compounds listed in this database, 101 molecules have ionizable moieties with estimated monomeric aqueous pK~a~ values ranging between 1.75 and 10.97. pH dependent effective air/water partitioning coefficients (K~aw,eff~) and n-octanol/water partitioning coefficients (D~ow~) were estimated for all ionizable aroma compounds over the pH range from 0 to 14. The ionizable aroma compounds display a broad range of K~aw,eff~ (1.8 × 10^-23^ to 6.1 atm M^-1^) and log D~ow~ (-6.2 to +7.2 units) values. For many aroma compounds, pH dependent ionization will have a significant effect on the K~aw,eff~ and D~ow~, leading to variations in these physico-chemical properties by up to 11 orders of magnitude over the composite pH range of common foods and beverages. Changes in food and beverage pH affect not only the relative contributions of neutral versus charged forms of ionizable aroma compounds (which directly affects analyte volatility and olfactory reception), but also partitioning between freely dissolved and sorbed forms of the analyte in solution (which indirectly affects analyte volatility).
Permafrost carbon-climate feedbacks accelerate global warming
Authors: Koven Charles D. , Ringeval Bruno , Friedlingstein Pierre , Ciais Philippe , Cadule Patricia , Khvorostyanov Dmitry , Krinner Gerhard , Tarnocai Charles 
Published: August 2011

Permafrost soils contain enormous amounts of organic carbon, which could act as a positive feedback to global climate change due to enhanced respiration rates with warming. We have used a terrestrial ecosystem model that includes permafrost carbon dynamics, inhibition of respiration in frozen soil layers, vertical mixing of soil carbon from surface to permafrost layers, and CH4emissions from flooded areas, and which better matches new circumpolar inventories of soil carbon stocks, to explore the potential for carbon-climate feedbacks at high latitudes. Contrary to model results for the Intergovernmental Panel on Climate Change Fourth Assessment Report (IPCC AR4), when permafrost processes are included, terrestrial ecosystems north of 60°N could shift from being a sink to a source of CO2by the end of the 21st century when forced by a Special Report on Emissions Scenarios (SRES) A2 climate change scenario. Between 1860 and 2100, the model response to combined CO2fertilization and climate change changes from a sink of 68 Pg to a 27 + -7 Pg sink to 4 + -18 Pg source, depending on the processes and parameter values used. The integrated change in carbon due to climate change shifts from near zero, which is within the range of previous model estimates, to a climate-induced loss of carbon by ecosystems in the range of 25 + -3 to 85 + -16 Pg C, depending on processes included in the model, with a best estimate of a 62 + -7 Pg C loss. Methane emissions from high-latitude regions are calculated to increase from 34 Tg CH4/y to 41–70 Tg CH4/y, with increases due to CO2fertilization, permafrost thaw, and warming-induced increased CH4flux densities partially offset by a reduction in wetland extent.
Energetics of Al
13
Keggin cluster compounds
Authors: Armstrong Christopher R. , Casey William H. , Navrotsky Alexandra 
Published: August 2011

The
ϵ
-Al
13
Keggin aluminum hydroxide clusters are essential models in establishing molecular pathways for geochemical reactions. Enthalpies of formation are reported for two salts of aluminum centered ϵ-Keggin clusters, Al
13
selenate, (Na(AlO
4
)Al
12
(OH)
24
(SeO
4
)
4
•12H
2
O) and Al
13
sulfate, (NaAlO
4
Al
12
(OH)
24
(SO
4
)
4
•12H
2
O). The measured enthalpies of solution, ΔH
sol
, at 28 °C in 5 N HCl for the
ε
-Al
13
selenate and sulfate are −924.57 (± 3.83) and −944.30 ( ± 5.66) kJ·mol
-1
, respectively. The enthalpies of formation from the elements, Δ
H

f
,el

, for Al
13
selenate and sulfate are −19,656.35 ( ± 67.30) kJ·mol
-1
, and −20,892.39 ( ± 70.01) kJ·mol
-1
, respectively. In addition, Δ
H

f
,el

for sodium selenate decahydrate was calculated using data from high temperature oxide melt solution calorimetry measurements: −4,006.39 ( ± 11.91) kJ·mol
-1
. The formation of both
ε
-Al
13
Keggin cluster compounds is exothermic from oxide-based components but energetically unfavorable with respect to a gibbsite-based assemblage. To understand the relative affinity of the ϵ-Keggin clusters for selenate and sulfate, the enthalpy associated with two S-Se exchange reactions was calculated. In the solid state, selenium is favored in the Al
13
compound relative to the binary chalcogenate, while in 5 N HCl, sulfur is energetically favored in the cluster compound compared to the aqueous solution. This contribution represents the first thermodynamic study of
ε
-Al
13
cluster compounds and establishes a method for other such molecules, including the substituted versions that have been created for kinetic studies. Underscoring the importance of
ε
-Al
13
clusters in natural and anthropogenic systems, these data provide conclusive thermodynamic evidence that the Al
13
Keggin cluster is a crucial intermediate species in the formation pathway from aqueous aluminum monomers to aluminum hydroxide precipitates.
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
Authors: Kulakovskiy I. V. , Belostotsky A. A. , Kasianov A. S. , Esipova N. G. , Medvedeva Y. A. , Eliseeva I. A. , Makeev V. J. 
Published: August 2011

Abstract
Motivation: Modern experimental methods provide substantial information on protein–DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code.
Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3′-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments.
Contact: ivan.kulakovskiy@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Improved quality control processing of peptide-centric LC-MS proteomics data
Authors: Matzke Melissa M. , Waters Katrina M. , Metz Thomas O. , Jacobs Jon M. , Sims Amy C. , Baric Ralph S. , Pounds Joel G. , Webb-Robertson Bobbie-Jo M. 
Published: August 2011

Abstract
Motivation: In the analysis of differential peptide peak intensities (i.e. abundance measures), LC-MS analyses with poor quality peptide abundance data can bias downstream statistical analyses and hence the biological interpretation for an otherwise high-quality dataset. Although considerable effort has been placed on assuring the quality of the peptide identification with respect to spectral processing, to date quality assessment of the subsequent peptide abundance data matrix has been limited to a subjective visual inspection of run-by-run correlation or individual peptide components. Identifying statistical outliers is a critical step in the processing of proteomics data as many of the downstream statistical analyses [e.g. analysis of variance (ANOVA)] rely upon accurate estimates of sample variance, and their results are influenced by extreme values.
Results: We describe a novel multivariate statistical strategy for the identification of LC-MS runs with extreme peptide abundance distributions. Comparison with current method (run-by-run correlation) demonstrates a significantly better rate of identification of outlier runs by the multivariate strategy. Simulation studies also suggest that this strategy significantly outperforms correlation alone in the identification of statistically extreme liquid chromatography-mass spectrometry (LC-MS) runs.
Availability: https://www.biopilot.org/docs/Software/RMD.php
Contact: bj@pnl.gov
Supplementary information: Supplementary material is available at Bioinformatics online.
Green Light Induces Shade Avoidance Symptoms
Authors: Zhang Tingting , Maruhnich Stefanie A. , Folta Kevin M. 
Published: August 2011

Abstract
Light quality and quantity affect plant adaptation to changing light conditions. Certain wavelengths in the visible and near-visible spectrum are known to have discrete effects on plant growth and development, and the effects of red, far-red, blue, and ultraviolet light have been well described. In this report, an effect of green light on Arabidopsis (Arabidopsis thaliana) rosette architecture is demonstrated using a narrow-bandwidth light-emitting diode-based lighting system. When green light was added to a background of constant red and blue light, plants exhibited elongation of petioles and upward leaf reorientation, symptoms consistent with those observed in a shaded light environment. The same green light-induced phenotypes were also observed in phytochrome (phy) and cryptochrome (cry) mutant backgrounds. To explore the molecular mechanism underlying the green light-induced response, the accumulation of shade-induced transcripts was measured in response to enriched green light environments. Transcripts that have been demonstrated to increase in abundance under far-red-induced shade avoidance conditions either decrease or exhibit no change when green light is added. However, normal far-red light-associated transcript accumulation patterns are observed in cryptochrome mutants grown with supplemental green light, indicating that the green-absorbing form of cryptochrome is the photoreceptor active in limiting the green light induction of shade-associated transcripts. These results indicate that shade symptoms can be induced by the addition of green light and that cryptochrome receptors and an unknown light sensor participate in acclimation to the enriched green environment.
Molecular phylogenetics of the melyrid lineage (Coleoptera: Cleroidea)
Authors: Bocakova M. , Constantin R. , Bocak L. 
Published: August 2011

AbstractThe melyrid lineage of beetles form a distinct group of the superfamily Cleroidea with a high level of soft‐bodiedness. Here we present the first molecular phylogenetic analysis of this group. The data matrix included partial sequences of the small and large subunits of rRNA, the mitochondrial large subunit rRNA, and cytochrome oxidase subunit I of 67 melyrid and eight outgroup taxa. The concatenated sequences were analysed using maximum‐parsimony (MP), maximum‐likelihood (ML) and Bayesian analysis (BA) approach. The results strongly supported the monophyly of the melyrid lineage splitting into six major clades: Rhadalidae, Mauroniscidae, Prionoceridae, Melyridae sensu stricto, Dasytidae and Malachiidae. The rhadalids were placed in the most basal position, followed by mauroniscids and prionocerids. Three terminal lineages—the true melyrids, dasytids, and malachiids—are well supported by all analyses, but their mutual relationships remain uncertain as MP analysis proposed alternative topologies to that of the ML and BA trees, with often low node support in the latter two methods. The monophyly of the subfamily Danacaeinae (Dasytidae) with respect to the danacaeine genera of the southern hemisphere (Hylodanacaea, Listrocerus, Amecocerus) was challenged as they were found to be polyphyletic. Similarly, the monophyly of Attalus was rejected by our analyses and shown to be polyphyletic. Based on the preferred phylogenetic hypothesis, the subfamilies Rhadalinae, Dasytinae and Malachiinae are elevated to family rank.© The Willi Hennig Society 2011.
Potato virus X movement in Nicotiana benthamiana: new details revealed by chimeric coat protein variants
Authors: BETTI CAMILLA , LICO CHIARA , MAFFI DARIO , D'ANGELI SIMONE , ALTAMURA MARIA MADDALENA , BENVENUTO EUGENIO , FAORO FRANCO , BASCHIERI SELENE 
Published: August 2011

SUMMARYPotato virus X coat protein is necessary for both cell‐to‐cell and phloem transfer, but it has not been clarified definitively whether it is needed in both movement phases solely as a component of the assembled particles or also of differently structured ribonucleoprotein complexes. To clarify this issue, we studied the infection progression of a mutant carrying an N‐terminal deletion of the coat protein, which was used to construct chimeric virus particles displaying peptides selectively affecting phloem transfer or cell‐to‐cell movement. Nicotiana benthamiana plants inoculated with expression vectors encoding the wild‐type, mutant and chimeric viral genomes were examined by microscopy techniques. These experiments showed that coat protein–peptide fusions promoting cell‐to‐cell transfer only were not competent for virion assembly, whereas long‐distance movement was possible only for coat proteins compatible with virus particle formation. Moreover, the ability of the assembled PVX to enter and persist into developing xylem elements was revealed here for the first time.
The effect of frugivory on postdispersal seed removal and germination in the pantropical forest tree Antiaris toxicaria Leschenault
Authors: Kankam Bright O. , Oduro William 
Published: August 2011

AbstractThe quality of seed treatment by frugivores has an effect on seed removal after dispersal, seed germination and tree recruitment. We provide information on postdispersal seed removal, germination and subsequent recruitment in tropical forest tree species Antiaris toxicaria in Ghana. We tested whether postdispersal seed removal and germination rates were differentially affected by the following seed treatments: seeds that were spat out by monkeys with all fruit pulp removed and spitting seeds with fruit pulp partially removed as observed in some birds and bats. We used seeds of intact ripened fruits as control. Frugivore seed treatment and distance from bole affected seed removal patterns, whereas intact seeds were significantly removed from all seed stations. The germination success was greater for seeds that were spat out by monkeys and poor for seeds with fruit pulp partially removed and intact fruits. More recruits were recorded at the edge of the adult A. toxicaria canopy radius. There was weak relationship (r2 = 0.042) between the number of recruits and distance away from the adult tree. Results suggest that the subsequent recruitment in tropical forest tree species may be enhanced by some frugivore fruit‐handling behaviour where fruit pulp is removed from the seeds without destroying the seeds.
Impact of paediatric human immunodeficiency virus infection on children's and caregivers' daily functioning and well‐being: a qualitative study
Authors: Punpanich W. , Gorbach P. M. , Detels R. 
Published: August 2011

AbstractBackground  Human immunodeficiency virus (HIV) infection impacts not only upon the physical health of affected children, but also their psychosocial functions, family relationships and economical status. Caregivers are confronted with complex challenges related to the physical, emotional and financial demands of raising these children. The purpose of this study was to enhance our understanding of the impact of HIV disease on both children's and caregivers' well‐being, using a qualitative inquiry approach.Methods  A total of 35 primary caregivers of HIV‐infected children participated in in‐depth interviews. The issues discussed included the major negative impacts on children's daily functioning and well‐being, and the perceived caregiver/parental burden. Participants included parents (40%), grandparents (22.8%), other relatives (e.g. uncles, aunts) (34.3%) and one foster parent (2.8%).Results  Qualitative analysis revealed that the major negative impacts of HIV/AIDS included physical symptoms, school performance and relationship changes. The major negative impacts on caregivers' well‐being included acceptance of the diagnosis, dealing with the financial burden and keeping the diagnosis private.Conclusions  Approaches are needed to address these challenges by enhancing families' coping skills and building supportive networks.
Total and free testosterone concentrations are strongly influenced by age and central obesity in men with type 1 and type 2 diabetes but correlate weakly with symptoms of androgen deficiency and diabetes‐related quality of life
Authors: Biswas Mousumi , Hampton David , Newcombe Robert G. , Rees D. Aled 
Published: August 2011

SummaryObjective  Testosterone levels are commonly lowered in men with diabetes, but it is unclear how these relate to symptoms of hypogonadism and quality of life. We sought to investigate the relationship between testosterone levels, symptoms of androgen deficiency, erectile function and quality of life in men with type 1 and type 2 diabetes.Design and subjects  Cross‐sectional study of 115 men with type 2 diabetes, 93 men with type 1 diabetes and 121 healthy controls.Measurements  Total, bioavailable and free testosterone levels were measured or calculated by Vermuelen’s formula. Quality of life and symptom scores were assessed by the Audit of Diabetes Dependent Quality of Life (ADDQoL), androgen deficiency in the aging male (ADAM) and International Index of Erectile Function (IIEF) questionnaires.Results  Forty‐five and sixty‐one per cent of men with type 2 diabetes had low total and calculated free testosterone (CFT) levels, respectively. Total testosterone (TT) levels were not lowered in men with type 1 diabetes, but 32% had low CFT. After adjustment for age and waist circumference, only CFT in men with type 2 diabetes (−0·037 nm, 95% CI −0·075 to −0·0003, P = 0.048) remained lowered compared with controls. CFT correlated weakly with ADAM (r = −0·26, 95% CI −0.42 to −0·08, P = 0·006), IIEF (r = 0.19, 95% CI 0.01–0.37, P = 0.042) and ADDQoL (r = 0.21, 95% CI 0·03 to 0·38, P = 0·022) scores in men with type 2, but not type 1 diabetes. Age exerted the predominant effect on erectile function in both groups, in a model incorporating age, testosterone level and complications.Conclusions  Testosterone levels are strongly affected by age and central obesity in men with type 1 and type 2 diabetes but correlate weakly with symptoms of androgen deficiency and erectile function. Testosterone levels do not appear to be a major determinant of quality of life in patients with diabetes.
Development of hypothyroidism during long‐term follow‐up of patients with toxic nodular goitre after radioiodine therapy
Authors: Kahraman Deniz , Keller Christian , Schneider Christina , Eschner Wolfgang , Sudbrock Ferdinand , Schmidt Matthias , Schicha Harald , Dietlein Markus , Kobe Carsten 
Published: August 2011

SummaryObjective  To investigate the cure rate and incidence of hypothyroidism of radioiodine treatment with a calculated dose regimen and an intended thyroid dose of 150 Gy in patients with toxic nodular goitre during long‐term follow‐up.Patients  A total of 265 consecutive patients with toxic nodular goitre were treated between March 2003 and August 2004 at our institute and followed up for a maximum of 8 years. Preliminary radioiodine testing with volumetric measurement of the thyroid by ultrasound as well as individual thyroidal radioiodine uptake and half‐life measurements were performed before radioiodine therapy. The estimated radiation dose to the thyroid was 150 Gy.Measurements  Follow‐up controls with respect to success of therapy and development of hypothyroidism were performed 3 months, 1 and up to 8 years after radioiodine treatment. The relation of the achieved thyroid dose to the success rate of treatment and to the incidence of hypothyroidism was analysed.Results  The cure rates were 85% at 3 months, 98% at 1 year and 98% at the end of follow‐up. Above an achieved thyroid dose of more than 120 Gy, there was no significant association between the dose achieved in the thyroid and the cure rate on follow‐up. The incidences of hypothyroidism at 3 months, at 1 year and at the end of follow‐up were 32%, 55% and 73%, respectively.Conclusions  Radioiodine treatment with a calculated dose regimen is a highly effective treatment option in patients with toxic goitre with an overall success rate of 98%. However, radioiodine treatment with an intended thyroid dose of 150 Gy leads to a high incidence of hypothyroidism on long‐term follow‐up. This finding supports the suggestion that in future intended thyroid doses could be lowered in patients treated with a calculated dose regimen for toxic nodular goitre.
Glucose fluctuations in subjects with normal glucose tolerance, impaired glucose regulation and newly diagnosed type 2 diabetes mellitus
Authors: Wang Chun , Lv Lifang , Yang Yanzhi , Chen Dawei , Liu Guanjian , Chen Lihong , Song Yuanxia , He Liping , Li Xiujun , Tian Haoming , Jia Weiping , Ran Xingwu 
Published: August 2011

SummaryObjective  Glycemic variability is poorly studied in the nondiabetic individuals and newly diagnosed patients with type 2 diabetes. The aim of the study is to investigate the characteristics of glucose fluctuations in subjects with normal glucose tolerance (NGT), impaired glucose regulation (IGR) and newly diagnosed, drug‐naïve type 2 diabetes mellitus (DM‐2).Design and patients  This is a cross‐sectional study of three groups including 53 subjects with IGR, 56 DM‐2 patients and 53 NGT individuals. Monitoring by a continuous glucose monitoring system (CGMS® System Gold™) was performed for three consecutive days.Measurements  Mean blood glucose (MBG), standard deviation of MBG (SDBG), largest amplitude of glycemic excursions (LAGE) and mean amplitude of glycemic excursions (MAGE) were calculated to estimate intraday blood glucose variability. Interday variability of glucose was evaluated by absolute means of daily differences (MODD). Postprandial glucose excursion (PPGE) was calculated to assess the influence of meals on glucose fluctuation.Results  Twenty‐two percentage of NGT and 33·9% of IGR individuals experienced blood glucose ≥11·1 mmol/l; 49·1% of NGT, 50·9% of IGR and 30·8% of DM‐2 participants had hypoglycemic episodes (CGM values <3·9 mmol/l). The IGR and DM‐2 groups had greater SDBG (P = 0·010 and P < 0·001), LAGE (P = 0·014 and P < 0·001) and MAGE (P = 0·044 and P < 0·001) compared with the NGT group. Significantly greater MODD and PPGEs were found in the DM‐2 groups than in the IGR and NGT groups (P < 0·001). The DM‐2 patients had higher 72‐MBG and glucose levels overnight than the NGT and IGR subjects (P < 0·001). In the patients with diabetes, MAGE was positively associated with MODD (r = 0·558, P < 0·001) and PPGEs (r = 0·738–0·843, P < 0·001).Conclusions  Glucose variability is present to an increasing degree from NGT to IGR and IGR to DM‐2. Compared with the NGT individuals, the IGR and DM‐2 subjects show more predominant intraday glucose fluctuations. The DM‐2 patients demonstrate increased PPGEs, higher glucose levels overnight and greater interday fluctuations.