bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water molecule reorganization in cytochrome
c
oxidase revealed by FTIR spectroscopy
Authors: Maréchal Amandine , Rich Peter R. 
Published: May 2011

Although internal electron transfer and oxygen reduction chemistry in cytochrome
c
oxidase are fairly well understood, the associated groups and pathways that couple these processes to gated proton translocation across the membrane remain unclear. Several possible pathways have been identified from crystallographic structural models; these involve hydrophilic residues in combination with structured waters that might reorganize to form transient proton transfer pathways during the catalytic cycle. To date, however, comparisons of atomic structures of different oxidases in different redox or ligation states have not provided a consistent answer as to which pathways are operative or the details of their dynamic changes during catalysis. In order to provide an experimental means to address this issue, FTIR spectroscopy in the 3,560–3,800 cm
-1
range has been used to detect weakly H-bonded water molecules in bovine cytochrome
c
oxidase that might change during catalysis. Full redox spectra exhibited at least four signals at 3,674(+), 3,638(+), 3,620(−), and 3,607(+) cm
-1
. A more complex set of signals was observed in spectra of photolysis of the ferrous-CO compound, a reaction that mimics the catalytic oxygen binding step, and their D
2
O and H
2
18
O sensitivities confirmed that they arose from water molecule rearrangements. Fitting with Gaussian components indicated the involvement of up to eight waters in the photolysis transition. Similar signals were also observed in photolysis spectra of the ferrous-CO compound of bacterial C
c
O from
Paracoccus denitrificans
. Such water changes are discussed in relation to roles in hydrophilic channels and proton/electron coupling mechanism.
DREME: motif discovery in transcription factor ChIP-seq data
Authors: Bailey Timothy L. 
Published: May 2011

Abstract
Motivation: Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF.
Results: We present DREME, a motif discovery algorithm specifically designed to find the short, core DNA-binding motifs of eukaryotic TFs, and optimized to analyze very large ChIP-seq datasets in minutes. Using DREME, we discover the binding motifs of the the ChIP-ed TF and many cofactors in mouse ES cell (mESC), mouse erythrocyte and human cell line ChIP-seq datasets. For example, in mESC ChIP-seq data for the TF Esrrb, we discover the binding motifs for eight cofactor TFs important in the maintenance of pluripotency. Several other commonly used algorithms find at most two cofactor motifs in this same dataset. DREME can also perform discriminative motif discovery, and we use this feature to provide evidence that Sox2 and Oct4 do not bind in mES cells as an obligate heterodimer. DREME is much faster than many commonly used algorithms, scales linearly in dataset size, finds multiple, non-redundant motifs and reports a reliable measure of statistical significance for each motif found. DREME is available as part of the MEME Suite of motif-based sequence analysis tools (http://meme.nbcr.net).
Contact: t.bailey@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Population status and human impact on the endangered Swayne’s hartebeest (Alcelaphus buselaphus swaynei) in Nechisar Plains, Nechisar National Park, Ethiopia
Authors: Datiko Demeke , Bekele Afework 
Published: May 2011

AbstractThe study on the population status and human impacts on the endemic and endangered Swayne’s hartebeest (Alcelaphus buselaphus swaynei) was carried out in Nechisar Plains, Nechisar National Park, between 2009 and 2010. Direct and total count methods were applied in the population census. Data collected since 1967 were also examined to indicate trends of Swayne’s hartebeest populations and their translocation status. In eight illegal Guji Oromo settlements, a total of 134 household samples were identified for group discussion and interview. A trend on livestock population was carried out. The total count of Swayne’s hartebeest was 12, 11 and 12 during the 1st, 2nd and 3rd counts, respectively. The population has been decreasing and nowadays only 12 individuals remain. Most respondents had a negative attitude towards conservation areas. The increase in livestock population from 1985 to 1996 was 47.8%. It also increased by 49.9% and 56.5% during 2006 and 2010, respectively. There were 12,531 heads of livestock that depended on the grass plains illegally. Overstocking rate of livestock, illegal resource exploitation and loss of wildlife habitat were the major problems encountered. Active measures have to be implemented to control the human impact and safeguard the future of Swayne’s hartebeest.
Thein vivoimmunomodulatory effect of recombinant tumour necrosis factor-alpha in guinea pigs vaccinated withMycobacterium bovisbacille Calmette–Guérin
Authors: Kramp J C , McMurray D N , Formichella C , Jeevan A 
Published: May 2011

SummaryPrevious studies from our laboratory demonstrated that treatment in vitro with recombinant guinea pig tumour necrosis factor TNF (rgpTNF)-α-enhanced T cell and macrophage functions. Similarly, injection of Mycobacterium tuberculosis-infected guinea pigs with anti-TNF-α altered splenic granuloma organization and caused inflammatory changes and reduced the cell-associated mycobacteria in the tuberculous pluritis model. In this study, rgpTNF-α was injected into bacille Calmette–Guérin (BCG)-vaccinated guinea pigs to modulate immune functions in vivo. Guinea pigs were vaccinated intradermally with BCG, 2 × 103 colony-forming units (CFU) and injected intraperitoneally with either rgpTNF-α (25 µg/animal) or 1% bovine serum albumin (BSA) for a total of 12 injections given every other day. Treatment with rgpTNF-α significantly enhanced the skin test response to purified protein derivative (PPD), reduced the number of CFUs and increased the PPD-induced proliferation in the lymph nodes at 6 weeks after vaccination. The levels of interleukin (IL)-12 mRNA were increased in the lymph node and spleen cells stimulated with PPD. TNF-α treatment induced a decrease in TNF-α, IL-12p40 and IL-10 mRNA levels in peritoneal cells following PPD stimulation while live M. tuberculosis caused an increase in TNF-α mRNA and a decrease in the IL-10 mRNA expression. TNF-α injection also induced an increase in the infiltration of mononuclear cells and in the proportions of CD3+ T cells in the lymph nodes. These results indicate that rgpTNF-α enhances some aspects of T cell immunity and promotes control of mycobacteria in the tissues. Future studies will address the role of TNF-α in BCG-vaccinated guinea pigs following low-dose pulmonary challenge with virulent M. tuberculosis.
Lactobacillus rhamnosus GGandStreptococcus thermophilusinduce suppressor of cytokine signalling 3 (SOCS3) gene expression directly and indirectly via interleukin-10 in human primary macrophages
Authors: Latvala S , Miettinen M , Kekkonen R A , Korpela R , Julkunen I 
Published: May 2011

SummaryIn the present study we have characterized T helper type 2 (Th2) [interleukin (IL)-10]/Th1 (IL-12) cytokine expression balance in human primary macrophages stimulated with multiple non-pathogenic Gram-positive bacteria used in the food industry and as probiotic substances. Bacteria representing Lactobacillus, Bifidobacterium, Lactococcus, Leuconostoc, Propionibacterium and Streptococcus species induced anti-inflammatory IL-10 production, although quantitative differences between the bacteria were observed. S. thermophilus was able to induce IL-12 production, while the production of IL-12 induced by other bacteria remained at a low level. The highest anti-inflammatory potential was seen with bifidobacteria, as evidenced by high IL-10/IL-12 induction ratios. All studied non-pathogenic bacteria were able to stimulate the expression of suppressor of cytokine signalling (SOCS) 3 that controls the expression of proinflammatory cytokine genes. Lactobacillus and Streptococcus species induced SOCS3 mRNA expression directly in the absence of protein synthesis and indirectly via bacteria-induced IL-10 production, as demonstrated by experiments with cycloheximide (CHX) and anti-IL-10 antibodies, respectively. The mitogen-activated protein kinase (MAPK) p38 signalling pathway played a key role in bacteria-induced SOCS3 gene expression. Enhanced IL-10 production and SOCS3 gene expression induced by live non-pathogenic Lactobacillus and Streptococcus is also likely to contribute to their immunoregulatory effects in vivo.
Greenhouse gas fluxes from an Australian subtropical cropland under long‐term contrasting management regimes
Authors: WANG WEIJIN , DALAL RAM C. , REEVES STEVEN H. , BUTTERBACH‐BAHL KLAUS , KIESE RALF 
Published: May 2011

AbstractThe long‐term effects of conservation management practices on greenhouse gas fluxes from tropical/subtropical croplands remain to be uncertain. Using both manual and automatic sampling chambers, we measured N2O and CH4 fluxes at a long‐term experimental site (1968–present) in Queensland, Australia from 2006 to 2009. Annual net greenhouse gas fluxes (NGGF) were calculated from the 3‐year mean N2O and CH4 fluxes and the long‐term soil organic carbon changes. N2O emissions exhibited clear daily, seasonal and interannual variations, highlighting the importance of whole‐year measurement over multiple years for obtaining temporally representative annual emissions. Averaged over 3 years, annual N2O emissions from the unfertilized and fertilized soils (90 kg N ha−1 yr−1 as urea) amounted to 138 and 902 g N ha−1, respectively. The average annual N2O emissions from the fertilized soil were 388 g N ha−1 lower under no‐till (NT) than under conventional tillage (CT) and 259 g N ha−1 higher under stubble retention (SR) than under stubble burning (SB). Annual N2O emissions from the unfertilized soil were similar between the contrasting tillage and stubble management practices. The average emission factors of fertilizer N were 0.91%, 1.20%, 0.52% and 0.77% for the CT‐SB, CT‐SR, NT‐SB and NT‐SR treatments, respectively. Annual CH4 fluxes from the soil were very small (−200–300 g CH4 ha−1 yr−1) with no significant difference between treatments. The NGGF were 277–350 kg CO2‐e ha−1 yr−1 for the unfertilized treatments and 401–710 kg CO2‐e ha−1 yr−1 for the fertilized treatments. Among the fertilized treatments, N2O emissions accounted for 52–97% of NGGF and NT‐SR resulted in the lowest NGGF (401 kg CO2‐e ha−1 yr−1 or 140 kg CO2‐e t−1 grain). Therefore, NT‐SR with improved N fertilizer management practices was considered the most promising management regime for simultaneously achieving maximal yield and minimal NGGF.
Seasonal hysteresis of net ecosystem exchange in response to temperature change: patterns and causes
Authors: NIU SHULI , LUO YIQI , FEI SHENFENG , MONTAGNANI LEONARDO , BOHRER GIL , JANSSENS IVAN A. , GIELEN BERT , RAMBAL SERGE , MOORS EDDY , MATTEUCCI GIORGIO 
Published: May 2011

AbstractUnderstanding how net ecosystem exchange (NEE) changes with temperature is central to the debate on climate change‐carbon cycle feedbacks, but still remains unclear. Here, we used eddy covariance measurements of NEE from 20 FLUXNET sites (203 site‐years of data) in mid‐ and high‐latitude forests to investigate the temperature response of NEE. Years were divided into two half thermal years (increasing temperature in spring and decreasing temperature in autumn) using the maximum daily mean temperature. We observed a parabolic‐like pattern of NEE in response to temperature change in both the spring and autumn half thermal years. However, at similar temperatures, NEE was considerably depressed during the decreasing temperature season as compared with the increasing temperature season, inducing a counter‐clockwise hysteresis pattern in the NEE–temperature relation at most sites. The magnitude of this hysteresis was attributable mostly (68%) to gross primary production (GPP) differences but little (8%) to ecosystem respiration (ER) differences between the two half thermal years. The main environmental factors contributing to the hysteresis responses of NEE and GPP were daily accumulated radiation. Soil water content (SWC) also contributed to the hysteresis response of GPP but only at some sites. Shorter day length, lower light intensity, lower SWC and reduced photosynthetic capacity may all have contributed to the depressed GPP and net carbon uptake during the decreasing temperature seasons. The resultant hysteresis loop is an important indicator of the existence of limiting factors. As such, the role of radiation, LAI and SWC should be considered when modeling the dynamics of carbon cycling in response to temperature change.
The protective effects of resilience and hope on quality of life of the families coping with the criminal traumatisation of one of its members
Authors: Wu Hui‐Ching 
Published: May 2011

Aim.  This paper investigated the possible predictive and mediating determinates of quality of life in this often forgotten population, focusing specifically on the role of sociodemographics, mental impairments, coping mechanisms, resilience and hope on subjective quality of life.Background.  The family members of survivors of man‐made trauma are sometimes severely traumatised themselves and may suffer from post‐traumatic stress disorder, depression and poor quality of life. Most studies focus on the victims and ignore the effect of the incidents on the victim’s family members.Method.  Data were collected between October 2007–March 2008, a self‐report questionnaire incorporating seven scales was administrated to 175 family members of victims of man‐made trauma. One‐way anova was performed to compare the variance in the reported quality of life. The structural equation models of path analysis was used to evaluate the main effects and interactions and interrelations among variables.Results.  Of the psychosocial factors, having a personal previous traumatic experience was found to significantly affect post‐traumatic stress disorder, depression and physical health. Post‐traumatic stress disorder and depression were found to directly and indirectly affect quality of life. Coping mechanism, resilience and a hope state mediated the effect of post‐traumatic stress disorder and depression making the three significant predictors of subjective quality of life.Conclusion.  Based on these findings and the scores of the different scales, clinicians may be able to design treatment plans that encourage the poorly adapting family members of victims of trauma, especially those with symptoms of post‐traumatic stress disorder or depression, to accept changes as a part of life, nurture a positive view of the self, make connections for better social support and maintain or re‐create a hopeful outlook towards life goals.Relevance to clinical practice.  Knowledge of the psychosocial factors associated with resistance to severe trauma can also help in the prevention and treatment of individuals at high risk for developing post‐traumatic stress disorder or depression.
Knowledge of using acetaminophen syrup and comprehension of written medication instruction among caregivers with febrile children
Authors: Chang Mei‐Chuan , Chen Yueh‐Chih , Chang Shu‐Chuan , Smith Graeme D 
Published: May 2011

Aim.  This article aims to explore caregivers’ knowledge of acetaminophen and comprehension of written medication instructions about acetaminophen syrup when administered to febrile children.Background.  Fever is one of the most common problems about which primary caregivers seek medical advice for their children. Administration of acetaminophen is the most common form of treatment for febrile children. Medication safety is of the upmost importance for medication administration in this patient group.Design.  A cross‐sectional study design was used.Methods.  The study included 102 caregivers with febrile children under six years old. A self‐designed questionnaire was used to solicit participants’ responses concerning: (1) approaches to fever management prior to hospital admission; and (2) knowledge and comprehension of antipyretic medication administration. Caregivers were asked to answer specific questions about the instructions provided with the medication.Results.  Antipyretic by oral (66%) and antipyretic suppository (60%) were the most commonly used forms of fever management in febrile children. After reading the written medication instructions, one‐third of the participants had more than one misunderstanding of the instructions for medication with timing, time interval of administration and/or medication dosage. Almost two‐thirds of the participants misunderstood the side effects of acetaminophen. Participants with a poorer academic background were associated with poorer comprehension of the provided instructions.Conclusion.  Administration of antipyretic medication is the most common approach taken to reduce children’s temperature. A significant percentage of primary caregivers appear to lack a thorough understanding of the instructions provided with antipyrexial medication.Relevance to clinical practice.  Written medication instruction is a major source of information for primary caregivers. Clinical nurses have a potentially important role to play to provide caregivers with legible and understandable medication instructions and to ensure that caregivers fully comprehend this information.
Intentions and statins prescribing: can the Theory of Planned Behaviour explain physician behaviour in following guideline recommendations?
Authors: Rashidian Arash , Russell Ian 
Published: May 2011

AbstractObjectives  Few studies have assessed the utility of the Theory of Planned Behaviour (TPB) in explaining physicians' behaviour. This study uses the TPB for explaining physicians' implementation of guidelines' prescribing recommendations.Methods  We developed the questionnaire via conducting qualitative interviews and pilot study. A random sample of 155 general practitioners (GPs) in England participated in the study. Prescribing and practice data were collected from routine sources. We analysed the data using regression methods.Results  TPB explained 48% of variation in reported intentions to follow guidelines' prescribing recommendations. Attitude and perceived controls, but not subjective norms, were predictors of variation in intentions. TPB belief variables significantly explained variation in effective and efficient prescribing indicators (14% and 12% respectively). Normative, control and behavioural beliefs contributed to the models. Only for efficient prescribing, the TPB items retained their significance in presence of demographic variables. We found no significant relationship between intention and prescribing.Conclusions  TPB helped understanding of GPs prescribing behaviour and their intentions to implement a clinical guideline. Beliefs (e.g. normative beliefs) were better predictors of behaviour than the composite scores for their corresponding higher‐level construct (e.g. indirect subjective norm). TPB models should be tested alongside randomized trials to test the assumption of causality that change in beliefs ultimately results in change in behaviour.
Corrosion patterns of seep‐carbonates from the eastern Mediterranean Sea
Authors: Himmler Tobias , Brinkmann Florian , Bohrmann Gerhard , Peckmann Jörn 
Published: May 2011

Terra Nova, 23, 206–212, 2011AbstractPorous seep‐carbonates are exposed at mud volcanoes in the eastern Mediterranean Sea. The 13C‐depleted aragonitic carbonates formed as a consequence of the anaerobic oxidation of methane in a shallow sub‐surface environment. Besides the macroscopically visible cavernous fabric, extensive carbonate corrosion was revealed by detailed analysis. After erosion of the background sediments, the carbonates became exposed to oxygenated bottom waters that are periodically influenced by the release of methane and upward diffusion of hydrogen sulphide. We suggest that carbonate corrosion resulted from acidity locally produced by aerobic oxidation of methane and hydrogen sulphide in the otherwise, with respect to aragonite, oversaturated bottom waters. Although it remains to be tested whether the mechanisms of carbonate dissolution suggested herein are valid, this study reveals that a better estimate of the significance of corrosion is required to assess the amount of methane‐derived carbon that is permanently fixed in seep‐carbonates.
Lithospheric characterization of the Central Pyrenees based on new magnetotelluric data
Authors: Campanyà Joan , Ledo Juanjo , Queralt Pilar , Marcuello Alex , Liesa Montserrat , Muñoz Josep A. 
Published: May 2011

Terra Nova, 23, 213–219, 2011AbstractThe Pyrenees resulted from the continent–continent collision between the Iberian and European plates during the Alpine orogeny. Although the subduction of the Iberian lower crust is currently accepted, the physical processes that occur at the boundary between the plates are still a topic of open discussion today, as illustrated by the debate about the presence or absence of partial melting in the Iberian Subducted Lower Crust. Long Period Magnetotelluric data acquired for the first time in the Central Pyrenees constrain the low electrical resistivity structure in the Iberian Subducted Lower Crust better than previous studies, plotting their upper limit 9 km deeper. This new upper limit reinforces the hypothesis of partial melting. Additionally, Long Period Magnetotelluric data constrain the lithosphere–asthenosphere boundary at 90 and 130 km deep below the Iberian and European plates, respectively, and are compatible with electrical resistivity values between 10 and 18 ohm·m for the asthenosphere.
Do Indonesian community pharmacy workers respond to antibiotics requests appropriately?
Authors: Puspitasari H. P. , Faturrohmah A. , Hermansyah A. 
Published: May 2011

SummaryObjective  To quantify antibiotics sales without a prescription and to explore provision of patient assessment and medicine information related to antibiotics requested with or without a prescription in Surabaya community pharmacies.Methods  Scenarios of specific product requests (ciprofloxacin tablets and tetracycline capsules) and a request of amoxicillin dry syrups based on a new prescription were presented by simulated patients to 105 purposively selected pharmacies. Data were recorded by simulated patients after their purchase of each product. They documented the questions asked in patient assessment, the content of information given, recommendations provided and pharmacy workers’ characteristics.Results  Antibiotics requested without a prescription were sold in 80 (91%) pharmacies. Information related to ciprofloxacin tablets and tetracycline capsules was only provided when requested by the simulated patient in 69% and 68% of pharmacies for the two scenarios, respectively. Very few pharmacies assessed patients. Medicine information on indication, dosing, duration and direction for use was provided more frequently in all cases. Medicine information was more likely to be given when a new prescription of amoxicillin dry syrups being presented. Overall, the majority of sampled pharmacies responded antibiotics requests inappropriately.Conclusion  Inappropriate responses to antibiotic requests with or without a prescription remain an issue in Indonesia with pharmacy workers often failing to adequately assess patients. The illegality of delivering antibiotics without a prescription is of a considerable concern. Therefore, strategies to control antibiotics dispensing in community pharmacies should be seriously considered.