bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription
Authors: Vilfan Igor D , Tsai Yu-Chih , Clark Tyson A , Wegener Jeffrey , Dai Qing , Yi Chengqi , Pan Tao , Turner Stephen W , Korlach Jonas 
Published: April 2013

Abstract

Background
Zero-mode waveguides (ZMWs) are photonic nanostructures that create highly confined optical observation volumes, thereby allowing single-molecule-resolved biophysical studies at relatively high concentrations of fluorescent molecules. This principle has been successfully applied in single-molecule, real-time (SMRT®) DNA sequencing for the detection of DNA sequences and DNA base modifications. In contrast, RNA sequencing methods cannot provide sequence and RNA base modifications concurrently as they rely on complementary DNA (cDNA) synthesis by reverse transcription followed by sequencing of cDNA. Thus, information on RNA modifications is lost during the process of cDNA synthesis.

Results
Here we describe an application of SMRT technology to follow the activity of reverse transcriptase enzymes synthesizing cDNA on thousands of single RNA templates simultaneously in real time with single nucleotide turnover resolution using arrays of ZMWs. This method thereby obtains information from the RNA template directly. The analysis of the kinetics of the reverse transcriptase can be used to identify RNA base modifications, shown by example for N6-methyladenine (m6A) in oligonucleotides and in a specific mRNA extracted from total cellular mRNA. Furthermore, the real-time reverse transcriptase dynamics informs about RNA secondary structure and its rearrangements, as demonstrated on a ribosomal RNA and an mRNA template.

Conclusions
Our results highlight the feasibility of studying RNA modifications and RNA structural rearrangements in ZMWs in real time. In addition, they suggest that technology can be developed for direct RNA sequencing provided that the reverse transcriptase is optimized to resolve homonucleotide stretches in RNA.
Novel monosaccharide fermentation products in Caldicellulosiruptor saccharolyticus identified using NMR spectroscopy
Authors: Isern Nancy G , Xue Junfeng , Rao Jaya V , Cort John R , Ahring Birgitte K 
Published: April 2013

Abstract

Background

Caldicellulosiruptor saccharolyticus is a thermophilic, Gram-positive, non-spore forming, strictly anaerobic bacterium of interest in potential industrial applications, including the production of biofuels such as hydrogen or ethanol from lignocellulosic biomass through fermentation. High-resolution, solution-state nuclear magnetic resonance (NMR) spectroscopy is a useful method for the identification and quantification of metabolites that result from growth on different substrates. NMR allows facile resolution of isomeric (identical mass) constituents and does not destroy the sample.

Results
Profiles of metabolites produced by the thermophilic cellulose-degrading bacterium Caldicellulosiruptor saccharolyticus DSM 8903 strain following growth on different monosaccharides (D-glucose, D-mannose, L-arabinose, D-arabinose, D-xylose, L-fucose, and D-fucose) as carbon sources revealed several unexpected fermentation products, suggesting novel metabolic capacities and unexplored metabolic pathways in this organism. Both 1H and 13C nuclear magnetic resonance (NMR) spectroscopy were used to determine intracellular and extracellular metabolite profiles. One dimensional 1H NMR spectral analysis was performed by curve fitting against spectral libraries provided in the Chenomx software; 2-D homonuclear and heteronuclear NMR experiments were conducted to further reduce uncertainties due to unassigned, overlapping, or poorly-resolved peaks. In addition to expected metabolites such as acetate, lactate, glycerol, and ethanol, several novel fermentation products were identified: ethylene glycol (from growth on D-arabinose), acetoin and 2,3-butanediol (from growth on D-glucose, L-arabinose, and D-xylose), and hydroxyacetone (from growth on D-mannose, L-arabinose, and D-xylose). Production of ethylene glycol from D-arabinose was particularly notable, with around 10% of the substrate carbon converted into this uncommon fermentation product.

Conclusions
The present research shows that C. saccharolyticus, already of substantial interest due to its capability for biological ethanol and hydrogen production, has further metabolic potential for production of higher molecular weight compounds, such as acetoin and 2,3-butanediol, as well as hydroxyacetone and the uncommon fermentation product ethylene glycol. In addition, application of nuclear magnetic resonance (NMR) spectroscopy facilitates identification of novel metabolites, which is instrumental for production of desirable bioproducts from biomass through microbial fermentation.
Cotrimoxazole plasma levels, dialyzer clearance and total removal by extended dialysis in a patient with acute kidney injury: risk of under-dosing using current dosing recommendations
Authors: Clajus Christian , Kühn-Velten W Nikolaus , Schmidt Julius J , Lorenzen Johan M , Pietsch Daniel , Beutel Gernot , Kielstein Jan T 
Published: April 2013

Abstract

Background
Dosing of antibiotics in critically ill patients is challenging. It becomes even more difficult if renal or hepatic impairment ensue. Modern means of renal replacement therapy are capable of removing antibiotics to a higher rate than decades ago, leaving clinicians with a high degree of uncertainty concerning the dose of antibiotics in this patient population. Cotrimoxazole, a combination of trimethoprim (TMP) and sulfamethoxazole (SMX) is frequently used in the treatment of several infections including Pneumocystis jirovecii pneumonia (PCP).

Case presentation
Here we describe a patient with acute kidney injury in which we investigated the TMP and SMX levels during the course of an ICU stay. Cotrimoxazole was administered every six hours i.v. in a dose of TMP/SMX 15/75 mg/kg/day. Extended dialysis was performed with a high-flux dialyzer. Blood samples, as well as pre- and postdialyzer samples and aliquots of the collected spent dialysate were collected.
Observed peak concentrations (Cmax) were 7.51 mg/l for TMP and 80.80 mg/l for SMX. Decline of blood levels during extended dialysis (TMP 64%; SMX 84%) was mainly due to removal by the dialysis procedure, illustrated by the high dialyzer clearances (median of 4 extended dialysis sessions: TMP 94.0 / SMX 51.0 ml/min), as well as by the absolute amount of both substances in the collected spent dialysate (median of 6 extended dialysis sessions: TMP 556 mg / SMX 130 mg). Within the limitation of a case report our data from 4 consecutive extended dialysis sessions suggest that this procedure substantially removes both TMP and SMX.

Conclusions
Dose reduction, which is usually advocated in patients with acute kidney injury under renal replacement therapy, might lead to significant under-dosing. Pharmacokinetic studies for TMP/SMX dosing in this patient population are necessary to allow adequate dosing.
Non-invasive analytical techniques applied to characterize the components of ancient golden medallions
Authors: Perez-Rodriguez Jose L , Robador María D , Haro María C Jimenez de , Blanes Jose M Martinez , Garofano Isabel , Odriozola Carlos , Duran Adrian 
Published: April 2013

Abstract

Background
The first stable material used to create a gilded surface was gold. False gold was also found in the form of copper-zinc powders or silver covered with resin. There are various ways to make gold leaf adhere to a large surface area. The identification of the materials and processes to make the gilding and the use of non- invasive techniques for gilding study is still an open problem. The gilding of the medallions from the Mudejar palace of Sevilla Alcazar was investigated, and their components were characterised using non-invasive (in situ and laboratory) techniques such as X-ray fluorescence, μ-Raman, infrared spectroscopy, X-ray diffraction and scanning electron microscopy coupled with energy dispersive X-rays. Cross-sections of golden support were also performed and studied by SEM-EDX.

Results
The leaf adhered to the surface was primarily a gold alloy. However, copper, silver and zinc were also found. A layer of lead chromate with some lead sulphate was between the alloy and the support. This yellow pigment (lead chromate) and the layers of bole and white lead were characterised in cross-sections prepared from samples taken from the medallions in which the golden layer was missing. The support was composed of gypsum. Another golden layer applied in oldest time period was also found.

Conclusion
The non-invasive techniques provided useful information about the characterisation of the components of the golden medallions. However, complete characterisation of the medallions required the use of other techniques such as mass spectrometry and scanning electron microscopy- energy dispersive X-ray. This is the first time that lead chromate has been detected in gildings. The external gilding was applied at the beginning of the 19th century using mordant oil (linseed oil).
Fine particulate matter in indoor cultural heritage: a literature review
Authors: Grau-Bové Josep , Strlič Matija 
Published: April 2013

Abstract
Fine particulate matter is, on account of its aerodynamic properties and typical composition (especially diesel particulate matter and carbonaceous particles) the particulate pollutant potentially most harmful to cultural heritage, representing an aesthetic issue and an agent of chemical degradation simultaneously. This paper reviews the current knowledge of the life-cycle of fine particulates, focussing on diesel particulate matter from emission to deposition, including its aesthetic and chemical consequences, and draws attention to some imbalances in the current state of research. The currently available measurements are biased towards coarse dust, and information on the consequences of particle deposition is largely restricted to the outdoor environment. More evidence on the chemical effects of the most common types of fine particulate matter in typical indoor materials is needed to enable risk assessment for indoor collections.
Bone marrow non-mesenchymal mononuclear cells induce functional differentiation of neuroblastoma cells
Authors: Phruksaniyom Chareerut , Dharmasaroja Permphan , Issaragrisil Surapol 
Published: April 2013

Abstract
Less is known about the non-mesenchymal mononuclear cell fraction of human bone marrow on functional adaptation of neuroblastoma cells. Using immunocytochemistry, we showed that bone-marrow mononuclear cell (BMMC)-conditioned medium can induce tyrosine hydroxylase expression in neuroblastoma cells, which is similar to the effect of retinoic acid. Using quantitative RT-PCR, we showed that NGF, CNTF, and BDNF mRNAs were detected in unfractionated BMMC populations from all human donors at different expression levels. Our results suggest that cells of the non-mesenchymal mononuclear cell fraction can induce functional adaptation of neuroblastoma cells, probably via their secreted trophic factors.
Experiences of discrimination among people Using mental health services in England 2008-2011
Authors: Corker Elizabeth , Hamilton Sarah , Henderson Claire , Weeks Craig , Pinfold Vanessa , Rose Diana , Williams Paul , Flach Clare , Gill Valdeep , Lewis-Holmes Elanor , Thornicroft Graham 
Published: April 2013

BackgroundResearch suggests that levels of discrimination against people using mental health services are high; however, reports of these people's experiences are rare.AimsTo determine whether the Time to Change (TTC) programme target of 5% reduction in discrimination has been achieved.MethodSeparate samples of people using mental health services were interviewed annually from 2008 to 2011 using the Discrimination and Stigma Scale to record instances of discrimination.ResultsNinety-one per cent of participants reported one or more experiences of discrimination in 2008 compared with 88% in 2011 (z=-1.9, P=0.05). The median negative discrimination score was 40% in 2008 and 28% in 2011 (Kruskal-Wallis χ2=83.4, P < 0.001).ConclusionsThe proportion of participants experiencing no discrimination increased significantly over the course of TTC but by less than the initial target The overall median discrimination score fell by 11.5%. Data from 2010 and 2011 suggest that these gains may be hard to maintain during economic austerity.
Newspaper coverage of mental illness in England 2008-2011
Authors: Thornicroft Amalia , Goulden Robert , Shefer Guy , Rhydderch Danielle , Rose Diana , Williams Paul , Thornicroft Graham , Henderson Claire 
Published: April 2013

BackgroundBetter newspaper coverage of mental health-related issues is a target for the Time to Change (TTC) anti-stigma programme in England, whose population impact may be influenced by how far concurrent media coverage perpetuates stigma and discrimination.AimsTo compare English newspaper coverage of mental health-related topics each year of the TTC social marketing campaign (2009-2011) with baseline coverage in 2008.MethodContent analysis was performed on articles in 27 local and national newspapers on two randomly chosen days each month.ResultsThere was a significant increase in the proportion of anti-stigmatising articles between 2008 and 2011. There was no concomitant proportional decrease in stigmatising articles, and the contribution of mixed or neutral elements decreased.ConclusionsThese findings provide promising results on improvements in press reporting of mental illness during the TTC programme in 2009-2011, and a basis for guidance to newspaper journalists and editors on reporting mental illness.
Mental health problems in the workplace: Changes in employers' knowledge, attitudes and practices in England 2006-2010
Authors: Henderson Claire , Williams Paul , Little Kirsty , Thornicroft Graham 
Published: April 2013

BackgroundIn 2006 the Shaw Trust charity found high levels of ignorance and poor preparedness to deal with mental health problems among 480 senior employers in the UK. The UK government, non-governmental organisations and Time to Change (TTC) have since provided relevant assistance to employers.AimsTo examine whether there have been improvements in mental health-related knowledge, attitudes and workplace practices among British senior employers between 2006 and 2010.MethodA telephone survey was conducted of senior British employers (n = 480 in 2006 and n = 500 in 2009 and 2010).ResultsAn increased awareness of common mental health problems was detected. Employers continued to believe that job candidates should disclose a mental health problem, but became less likely to view colleagues' attitudes as a barrier to employing someone with such a problem. Formal policies on mental health and the use of workplace accommodations became increasingly common.ConclusionsThese results are consistent with those of the TTC national public attitudes and the Viewpoint survey of service users between 2008 and 2010, which showed improved public attitudes to mental illness and a reduction in experiences of discrimination in employment.
Public knowledge, attitudes and behaviour regarding people with mental illness in England 2009-2012
Authors: Evans-Lacko Sara , Henderson Claire , Thornicroft Graham 
Published: April 2013

BackgroundPublic stigma against people with mental health problems is damaging to individuals with mental illness and is associated with substantial societal burden.AimsTo investigate whether public knowledge, attitudes and behaviour in relation to people with mental health problems have improved among the English population since the inception of the Time To Change programme in 2009.MethodWe analysed longitudinal trends in public knowledge, attitudes and behaviour between 2009 and 2012 among a nationally representative sample of English adults.ResultsThere were improvements in intended behaviour (0.07 standard deviation units, 95% CI 0.01-0.14) and a nonsignificant trend for improvement in attitudes (P=0.08) among the English population. There was, however, no significant improvement in knowledge or reported behaviour.ConclusionsThe findings provide support for effectiveness of the national Time to Change programme against stigma and discrimination in improving attitudes and intended behaviour, but not knowledge, among the public in England.
Anti-stigma training for medical students: The Education Not Discrimination project
Authors: Friedrich Bettina , Evans-Lacko Sara , London Jillian , Rhydderch Danielle , Henderson Claire , Thornicroft Graham 
Published: April 2013

BackgroundEducation Not Discrimination (END) is the component of the Time to Change programme intended to reduce mental health stigma among professionals and professional trainees.AimsTo investigate the impact of the END anti-stigma programme on medical students immediately and after 6 months with regard to knowledge, attitudes, behaviour and empathy.MethodA total of 1452 medical students participated in the study (intervention group n = 1066, control group n = 386).Participants completed questionnaires at baseline, and at immediate and 6-month follow-up. Groups were compared for changes in stigma outcomes.ResultsAll measures improved in both groups, particularly among students with less knowledge and more stigmatising attitudes and intended behaviour at baseline. At immediate follow-up the intervention group demonstrated significantly greater improvements in stigma-related knowledge and reductions in stigma-related attitudes and intended behaviour, relative to the control group. At 6 months' follow-up, however, only one attitude item remained significantly better.ConclusionsAlthough the intervention produced short-term advantage there was little evidence for its persistent effect, suggesting a need for greater integration of ongoing measures to reduce stigma into the medical curriculum.
The effects of behavioral control over stress on GABAergic spontaneous inhibitory postsynaptic currents in prefrontal cortical pyramidal neurons
Authors: Varela Juan A , Wang Jungang , Cooper Donald C 
Published: April 2013

Traumatic events may lead to anxiety, depression and post-traumatic stress disorder (PTSD). However, the majority of individuals exposed to trauma do not develop these disorders. The stressor controllability paradigm has been widely used as a model for understanding the neurobiology underlying factors that confer vulnerability and resilience to the outcome of traumatic events. In this paradigm rats receive a series of tail shocks: one group of rats have control over the termination of the shock by means of turning a wheel (escapable shock, ES), while the other “yoked” group of rats receive physically identical shocks but have no control over shock termination (inescapable shock, IS). In subsequent behavioral tests that model components of anxiety and depression, IS rats without control show increased signs of behavioral depression, while ES rats that have control over the shock behave as naïve home caged (HC) rats. We have previously reported that individual deep layer pyramidal neurons from the ventral medial prefrontal cortex (vmPFC) exhibit changes in their intrinsic excitability following ES. To examine if there is a corresponding reduction in synaptic inhibition, we tested IS, ES and HC deep layer pyramidal neurons under identical conditions. Collecting such electrophysiological data from pyramidal neurons after exposure to stress is a technical challenge, yet very useful for conductance-based neural simulations and computational modeling. Here we present a data set of spontaneous inhibitory postsynaptic currents (sIPSCs) gathered from whole-cell patch-clamp recordings of individual prefrontal cortical deep layer neurons from adult rats (60-70 days old) after exposure to ES, IS or HC. In order to analyze the data, we provide our script used for the detection of synaptic events written for the scientific/engineering program Igor Pro that allows users to define their own event detection parameters.
The Evolution of Compact Binary Star Systems
Authors: Postnov Konstantin A. , Yungelson Lev R. 
Published: April 2013

AbstractWe review the formation and evolution of compact binary stars consisting of white dwarfs (WDs), neutron stars (NSs), and black holes (BHs). Binary NSs and BHs are thought to be the primary astrophysical sources of gravitational waves (GWs) within the frequency band of ground-based detectors, while compact binaries of WDs are important sources of GWs at lower frequencies to be covered by space interferometers (LISA). Major uncertainties in the current understanding of properties of NSs and BHs most relevant to the GW studies are discussed, including the treatment of the natal kicks which compact stellar remnants acquire during the core collapse of massive stars and the common envelope phase of binary evolution. We discuss the coalescence rates of binary NSs and BHs and prospects for their detections, the formation and evolution of binary WDs and their observational manifestations. Special attention is given to AM CVn-stars — compact binaries in which the Roche lobe is filled by another WD or a low-mass partially degenerate helium-star, as these stars are thought to be the best LISA verification binary GW sources.
Modified Newtonian Dynamics (MOND): Observational Phenomenology and Relativistic Extensions
Authors: Famaey Benoît , McGaugh Stacy S. 
Published: April 2013

AbstractA wealth of astronomical data indicate the presence of mass discrepancies in the Universe. The motions observed in a variety of classes of extragalactic systems exceed what can be explained by the mass visible in stars and gas. Either (i) there is a vast amount of unseen mass in some novel form — dark matter — or (ii) the data indicate a breakdown of our understanding of dynamics on the relevant scales, or (iii) both. Here, we first review a few outstanding challenges for the dark matter interpretation of mass discrepancies in galaxies, purely based on observations and independently of any alternative theoretical framework. We then show that many of these puzzling observations are predicted by one single relation — Milgrom’s law — involving an acceleration constant a0 (or a characteristic surface density Σ† = a0/G) on the order of the square-root of the cosmological constant in natural units. This relation can at present most easily be interpreted as the effect of a single universal force law resulting from a modification of Newtonian dynamics (MOND) on galactic scales. We exhaustively review the current observational successes and problems of this alternative paradigm at all astrophysical scales, and summarize the various theoretical attempts (TeVeS, GEA, BIMOND, and others) made to effectively embed this modification of Newtonian dynamics within a relativistic theory of gravity.
Dynamical Boson Stars
Authors: Liebling Steven L. , Palenzuela Carlos 
Published: April 2013

AbstractThe idea of stable, localized bundles of energy has strong appeal as a model for particles. In the 1950s, John Wheeler envisioned such bundles as smooth configurations of electromagnetic energy that he called geons, but none were found. Instead, particle-like solutions were found in the late 1960s with the addition of a scalar field, and these were given the name boson stars. Since then, boson stars find use in a wide variety of models as sources of dark matter, as black hole mimickers, in simple models of binary systems, and as a tool in finding black holes in higher dimensions with only a single Killing vector. We discuss important varieties of boson stars, their dynamic properties, and some of their uses, concentrating on recent efforts.