bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting enzymatic function from global binding site descriptors
Authors: Volkamer Andrea , Kuhn Daniel , Rippmann Friedrich , Rarey Matthias 
Published: January 2013

AbstractDue to the rising number of solved protein structures, computer‐based techniques for automatic protein functional annotation and classification into families are of high scientific interest. DoGSiteScorer automatically calculates global descriptors for self‐predicted pockets based on the 3D structure of a protein. Protein function predictors on three levels with increasing granularity are built by use of a support vector machine (SVM), based on descriptors of 26632 pockets from enzymes with known structure and enzyme classification. The SVM models represent a generalization of the available descriptor space for each enzyme class, subclass, and substrate‐specific sub‐subclass. Cross‐validation studies show accuracies of 68.2% for predicting the correct main class and accuracies between 62.8% and 80.9% for the six subclasses. Substrate‐specific recall rates for a kinase subset are 53.8%. Furthermore, application studies show the ability of the method for predicting the function of unknown proteins and gaining valuable information for the function prediction field. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Crystal structure of decaprenylphosphoryl‐β‐ D‐ribose 2'‐epimerase from Mycobacterium smegmatis
Authors: Li Hua , Jogl Gerwald 
Published: January 2013

AbstractDecaprenylphosphoryl‐β‐D‐ribose 2'‐epimerase (DprE1) is an essential enzyme in the biosynthesis of cell wall components and a target for development of anti‐tuberculosis drugs. We determined the crystal structure of a truncated form of DprE1 from Mycobacterium smegmatis in two crystal forms to up to 2.35 Å resolution. The structure extends from residue 75 to the C‐terminus and shares homology with FAD‐dependent oxidoreductases of the vanillyl‐alcohol oxidase family including the DprE1 homologue from M. tuberculosis. The M. smegmatis DprE1 structure reported here provides further insights into the active site geometry of this tuberculosis drug target. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Analysis of a mixed finite‐element pair proposed for an atmospheric dynamical core
Authors: Staniforth Andrew , Melvin Thomas , Cotter Colin 
Published: January 2013

AbstractWe present a numerical dispersion analysis for the P2 − P1DG finite‐element pair applied to the linear shallow‐water equations in one dimension. The aim is to provide insight into the numerical dispersion properties of the RT1 and BDFM1 finite‐element pairs in two dimensions, which have recently been proposed for horizontal discretisations of atmospheric dynamical cores with quasi‐uniform grids. This is achieved via analysis of a one‐dimensional RT1 element. Whilst these finite‐element pairs have been shown to have many desirable properties that extend properties of the C grid to non‐orthogonal quadrilateral and triangular grids, including stationary geostrophic modes on the f plane, and a 2:1 ratio of velocity to pressure degrees of freedom (a necessary condition for the absence of spurious mode branches), it is also important to have appropriately physical numerical wave propagation. In the absence of Coriolis force, we compute the group velocity for P2 − P1DG. We find that, as well as dropping to zero at the grid‐scale, which also occurs for the C‐grid finite‐difference method, the group velocity also drops to zero in a narrow band around kh = π which corresponds to eigenmodes with a wavelength close to two element widths. This is a potential problem because it increases the amount of wavenumber space that needs to be filtered. In this one‐dimensional case, we find that this particular issue can be removed by a small modification of the equations, namely partially lumping the mass matrix, in such a way that the other favourable properties of the scheme are not affected. We discuss various symmetric and asymmetric modifications of the mass matrix, and show that both such modifications preserve energy conservation (having modified the definition of discrete kinetic energy). Finally we illustrate our findings with numerical experiments, and discuss the potential to extend this modification to two‐dimensional schemes.
Glutamine modifies immune responses of mice infected with porcine circovirus type 2
Authors: Ren Wenkai , Li Yinghui , Yu Xinglong , Luo Wei , Liu Gang , Shao Hua , Yin Yulong 
Published: January 2013

The present study was conducted to evaluate the immune-enhancing effects of dietaryl-glutamine supplementation in porcine circovirus type 2 (PCV2)-infected mice, and to examine the clearance effects of glutamine against PCV2 in experimentally infected mice. A total of sixty Kunming female mice were infected with PCV2 at a dose of 100 TCID50(50 % tissue culture infection dose) by intraperitoneal injection after 2 weeks of dietaryl-glutamine supplementation orl-alanine supplementation (as the control (isonitrogenous) group). The measured variables on 3rd, 5th, 7th, 9th and 11th d post-infection (dpi) included: (1) PCV2 virus loaded in the liver, spleen, heart, lung, kidney, ovary and serum was determined by real-time PCR; (2) IL-2, IL-6, IL-10, interferon (IFN)-α, IFN-γ and C-reactive protein levels in serum were measured by ELISA; (3) serum total superoxide dismutase activity was measured spectrophotometrically at 550 nm absorbance. Dietaryl-glutamine supplementation significantly increased serum IL-2 levels on the 3rd (P< 0·01), 5th (P< 0·01), 7th (P< 0·05) and 9th dpi, significantly (P< 0·05) increased serum IL-6 levels on 3rd dpi, significantly (P< 0·05) increased serum IFN-γ levels on the 9th and 11th dpi and significantly decreased (P< 0·01) serum IL-10 levels on the 9th and 11th dpi, compared with those in the control group. Meanwhile, the PCV2 virus genome was detected sporadically throughout the experimental period in both groups. Taken together, the present results suggest that dietaryl-glutamine supplementation enhances immune function in PCV2-infected mice.
Predictors of Discrepancies in Parkinson's Disease Patient and Caregiver Ratings of Apathy, Disinhibition, and Executive Dysfunction before and after Diagnosis
Authors: Schiehser Dawn M. , Liu Lin , Lessig Stephanie L. , Song David D. , Obtera Kristalyn M. , Burke III Mathes M. , Earl Shannon R. , Vincent Filoteo J. 
Published: January 2013

AbstractParkinson's disease (PD) patient and caregiver reports of patient functioning are often used interchangeably in clinical and research settings; however, the consistency of these reports is largely unknown. This study aimed to investigate the consistency and predictors of discrepancy between self- and caregiver reports of patient apathy, disinhibition, and executive dysfunction. Fifty-one pairs of nondemented PD patients and their caregivers completed the Frontal Systems Behavior Scale (FrSBe). Patients were administered a neuropsychological battery, and mood and burden were assessed in a subset of caregivers. Patients and caregivers significantly differed in their ratings of all retrospective prediagnosis behaviors and current levels of disinhibition. Current levodopa equivalent dosages predicted patient-caregiver rating differences in prediagnosis and current apathy and current executive dysfunction, while patient motor function, cognition, and mood failed to predict any disparities in ratings. Caregiver burden and depression were associated with apathy rating discrepancies, while burden was associated with discrepancies in ratings of disinhibition. These results suggest that consistency of patient and caregiver behavioral ratings may vary depending on the behavior assessed; and underscore the importance of considering the reporter when using subjective measures, as discrepancies in behavioral reports may be influenced by specific patient and/or caregiver symptoms or factors. (JINS, 2013, 19, 1–10)
A High-Content, Live-Cell, and Real-Time Approach to the Quantitation of Ligand-Induced β-Arrestin2 and Class A/Class B GPCR Mobilization
Authors: Leonard Anthony P. , Appleton Kathryn M. , Luttrell Louis M. , Peterson Yuri K. 
Published: January 2013

AbstractWe report the development of a method to analyze receptor and β-arrestin2 mobilization between Class A and B GPCRs via time-resolved fluorescent microscopy coupled with semiautomated high-content multiparametric analysis. Using transiently expressed, tagged β2-adrenergic receptor (β2-AR) or parathyroid hormone receptor type 1 (PTH1R), we quantified trafficking of the receptors along with the mobilization and colocalization of coexpressed tagged β-arrestin2. This classification system allows for exclusion of cells with nonoptimal characteristics and calculation of multiple morphological and spatial parameters including receptor endosome formation, β-arrestin mobilization, colocalization, areas, and shape. Stimulated Class A and B receptors demonstrate dramatically different patterns with regard to β-arrestin interactions. The method provides high kinetic resolution measurement of receptor translocation, which allows for the identification of the fleeting β-arrestin interaction found with β2-AR agonist stimulation, in contrast to stronger mobilization and receptor colocalization with agonist stimulation of the PTH1R. Though especially appropriate for receptor kinetic studies, this method is generalizable to any dual fluorescence probe system in which quantification of object formation and movement is desired. These methodologies allow for quantitative, unbiased measurement of microscopy data and are further enhanced by providing real-time kinetics.
Single‐cell versus population‐level reproductive success of bacterial immigrants to pre‐colonized leaf surfaces
Authors: Remus‐Emsermann Mitja N. P. , Kowalchuk George A. , Leveau Johan H. J. 
Published: January 2013

SummaryWe assessed how preemptive inoculation of plant leaves with bacteria affected the establishment of secondary colonizers. We quantified the latter in two ways: (i) at the population level, i.e. as counts of colony‐forming units and (ii) at the level of single cells by tracking the reproductive success of individual bacteria. Both analyses showed that the ability of secondary immigrants to establish on the leaf was negatively correlated with the level of pre‐population by primary colonizers. This effect was best described by an inverse dose–response curve with an apparent half‐point inhibition efficacy of approximately 106 cells of primary colonizers per gram leaf. This efficacy was the same whether calculated from population‐ or average single‐cell data. However, single‐cell data revealed that even under conditions of heavy pre‐population with primary colonizers, a small fraction of secondary immigrants still produced offspring, although the corresponding population measurement showed no increase in total population size. This observation has direct relevance for biocontrol strategies that are based on the principle of preemptive exclusion of foliar bacterial pathogens: even at seemingly saturating levels of primary inoculum, some secondary colonizers may still be able to reproduce and possibly reach a quorum to trigger behaviours that enhance survival or virulence.
How do dentists and their teams incorporate evidence about preventive care? An empirical study
Authors: Sbaraini Alexandra , Carter Stacy Marie , Evans Robin Wendell , Blinkhorn Anthony 
Published: January 2013

AbstractObjectivesTo identify how dentists and their teams adopt evidence‐based preventive care.MethodsA qualitative study using grounded theory methodology was conducted. We interviewed 23 participants working in eight dental practices about their experience and work processes, while adopting evidence‐based preventive care. During the study, Charmaz's grounded theory methodology was employed to examine the social process of adopting preventive dental care in dental practices. Charmaz's iteration of the constant comparative method was used during the data analysis. This involved coding of interview transcripts, detailed memo‐writing and drawing diagrams. The transcripts were analyzed as soon as possible after each round of interviews in each dental practice. Coding was conducted primarily by AS, supported by team meetings and discussions when researchers compared their interpretations.ResultsParticipants engaged in a slow process of adapting evidence‐based protocols and guidelines to the existing logistics of the practices. This process was influenced by practical, philosophical, and historical aspects of dental care, and a range of barriers and facilitators. In particular, dentists spoke spontaneously about two deeply held ‘rules’ underpinning continued restorative treatment, which acted as barriers to provide preventive care: (i) dentists believed that some patients were too ‘unreliable’ to benefit from prevention; and (ii) dentists believed that patients thought that only tangible restorative treatment offered ‘value for money’. During the adaptation process, some dentists and teams transitioned from their initial state – selling restorative care – through an intermediary stage – learning by doing and educating patients about the importance of preventive care – and finally to a stage where they were offering patients more than just restorative care. Resources were needed for the adaptation process to occur, including: the ability to maintain the financial viability of the practice, appropriate technology, time, and supportive dental team relationships.ConclusionsThe findings from this study show that with considerable effort, motivation and coordination, it is possible for dental practices to work against the dental ‘mainstream’ and implement prevention as their clinical norm. This study has shown that dental practice is not purely scientific, but it includes cultural, social, and economic resources that interfere with the provision of preventive care.
Safety, tolerability, pharmacokinetics and pharmacodynamics following 4 weeks' treatment with empagliflozin once daily in patients with type 2 diabetes
Authors: Heise T. , Seewaldt‐Becker E. , Macha S. , Hantel S. , Pinnetti S. , Seman L. , Woerle H. J. 
Published: January 2013

ABSTRACTAimTo investigate the safety, tolerability, pharmacokinetics and pharmacodynamics of empagliflozin in patients with type 2 diabetes following oral administration of 10, 25 or 100 mg doses once daily over 28 days.MethodsA total of 78 patients were assigned to empagliflozin 10 mg (n = 16), 25 mg (n = 16) or 100 mg (n = 30) or placebo (n = 16) for 28 days. Assessments included adverse events (AEs) and pharmacokinetic and pharmacodynamic endpoints.ResultsEmpagliflozin exposure increased dose‐proportionally over the dose range 10–100 mg and showed linear pharmacokinetics with respect to time. Urinary glucose excretion (UGE) increased from baseline to day 1 by 74, 90 and 81 g with empagliflozin 10, 25 and 100 mg, respectively. The increases in UGE were maintained over 28 days with multiple dosing. Virtually no change in UGE was observed in the placebo group. Significant reductions from baseline in mean daily plasma glucose and fasting plasma glucose were observed with empagliflozin compared with placebo. The incidence of AEs was similar in the empagliflozin and placebo groups (50.0, 56.3 and 66.7% with empagliflozin rising doses and 62.5% with placebo). The most frequently reported AEs were pollakiuria (10.3%), nasopharyngitis (9.0%), constipation (9.0%) and headache (7.7%).ConclusionsOral administration of empagliflozin at doses of 10, 25 or 100 mg once daily over 28 days resulted in significant increases in UGE and reductions in blood glucose compared with placebo, and were well tolerated in patients with type 2 diabetes.
Explaining recreational angling catch rates of Eurasian perch, Perca fluviatilis: the role of natural and fishing‐related environmental factors
Authors: Heermann L. , Emmrich M. , Heynen M. , Dorow M. , König U. , Borcherding J. , Arlinghaus R. 
Published: January 2013

AbstractAngling catch records are frequently used to reveal fish population developments. It is therefore important to understand the determinants of angling catches. This study focused on angler‐related, biotic and abiotic factors influencing catchability of Eurasian perch, Perca fluviatilis L. A multi‐lake (21 lakes) study based on angling diaries collected in Mecklenburg‐Vorpommern, Germany (2006/2007), found that angler‐related factors such as fishing experience, species preference and bait/lure type had a large impact on perch catch rates. Additionally, environmental conditions (nutritional status and water transparency) affected either the size or the number of perch caught by anglers. Catch rates varied seasonally, which was confirmed by an experimental fishery on a gravel pit (2008). This portion of the study showed that altered food availabilities in the course of the year caused food limitation in perch, which in turn facilitated high catch rates and female‐biased exploitation in autumn. It is concluded that both angler‐related and abiotic factors interact affecting perch catch rates and size of perch captured in recreational angling.
Language Policy in Practice: Re‐bordering the Nation
Authors: Baba Marietta L. , Dahl‐Jørgensen Carla 
Published: January 2013

AbstractWe present findings from an anthropological field study on the role of language and language policy in migration from Poland to Norway, and the larger implications for emerging language and immigration policy in Europe. Initial fieldwork in Norway found that Polish workers without knowledge of the Norwegian language struggled to secure employment in the formal economy. The 2008 financial crisis intensified competition in the labour market and underscored fluency in Norwegian as a means of discriminating among workers. Comparative case studies of language schools revealed that these organizations are active participants in channeling Polish migrants' movements into a segmented labour market, often in ways that involve cooperation between private companies and the State. We frame the Norwegian case within the larger context of Europe and the trend there toward favoring integration over multiculturalism. The emergence of restrictive language policies in Europe may be interpreted as a legally and culturally acceptable means for discouraging access to rights associated with permanent residency or citizenship by work migrants fromCEEcountries, while at the same time permitting them access to the labour market for temporary work. The long‐term consequences of such policies for European society are uncertain.
Major cluster of chilblain cases in a cold dry Western Australian winter
Authors: Larkins Nicholas , Murray Kevin J 
Published: January 2013

AimPrimary chilblains are an idiopathic cold‐induced vasculopathy affecting the soft tissues of the hands and feet. Secondary chilblains occur in different forms of vasculitis and chronic autoimmune connective tissue disorders. Idiopathic chilblains are rarely reported in children and may generate significant anxiety to doctors and patients. We describe a cluster of idiopathic chilblains encountered over the winter of 2010 in Perth, Western Australia.MethodsThis is a retrospective review of patients identified from a prospectively compiled database of all new cases seen in our department. Data on history, examination, investigations, prescribed treatments and outcomes were collected.ResultsThirty‐two patients with isolated idiopathic chilblains were included, including 20 females and 12 males with a median age at onset of 13.5 years. Lesions were papular with signs of peripheral vasoconstriction causing acrocyanosis, and uncomfortable due to pain and/or pruritis in most. Thickening of the small joints was common where lesions involved these areas. Ulceration of lesions also occurred in some. One patient required hospitalisation for secondary bacterial infection. Most received some form of treatment including non‐steroidal anti‐inflammatory drugs, prednisolone or nifedipine. Most patients improved spontaneously with warmer weather or responded to cold protection advice. All had resolved completely by late spring (November).ConclusionOur cluster of chilblains was associated with an unusually cold winter in Perth 2010. It is the largest series reported in the literature, suggesting that chilblains may be more common than previously thought. Chilblains are almost always benign in nature and patients are systemically well and usually need no further investigation and only symptomatic treatment. Prompt recognition can avoid excessive investigation and anxiety, allowing appropriate simple advice and treatment.
Astrocytic Ca2+ signals are required for the functional integrity of tripartite synapses
Authors: Tanaka Mika , Shih Pei-Yu , Gomi Hiroshi , Yoshida Takamasa , Nakai Junichi , Ando Reiko , Furuichi Teiichi , Mikoshiba Katsuhiko , Semyanov Alexey , Itohara Shigeyoshi 
Published: January 2013

Abstract

Background
Neuronal activity alters calcium ion (Ca2+) dynamics in astrocytes, but the physiologic relevance of these changes is controversial. To examine this issue further, we generated an inducible transgenic mouse model in which the expression of an inositol 1,4,5-trisphosphate absorbent, “IP3 sponge”, attenuates astrocytic Ca2+ signaling.

Results
Attenuated Ca2+ activity correlated with reduced astrocytic coverage of asymmetric synapses in the hippocampal CA1 region in these animals. The decreased astrocytic ‘protection’ of the synapses facilitated glutamate ‘spillover’, which was reflected by prolonged glutamate transporter currents in stratum radiatum astrocytes and enhanced N-methyl-D-aspartate receptor currents in CA1 pyramidal neurons in response to burst stimulation. These mice also exhibited behavioral impairments in spatial reference memory and remote contextual fear memory, in which hippocampal circuits are involved.

Conclusions
Our findings suggest that IP3-mediated astrocytic Ca2+ signaling correlates with the formation of functional tripartite synapses in the hippocampus.
Characterization of Patients with Difficult-to-Treat Acute Pain Following Total Knee Arthroplasty Using Multi-Modal Analgesia
Authors: Azim Syed A. , Sangster Rebecca , Curcio Christine , Coleman Dominick , Shah Usman , Zhang Shaonan , Reinsel Ruth A. , Glass Peter S.A. , Nicholson James , Benveniste Helene 
Published: January 2013

Objective:
To determine the efficacy of post-operative pain control over the first 24 hours in patients undergoing unilateral total knee arthroplasty (TKA) using a multi-modal analgesia protocol including femoral nerve catheters (FNC).

Materials and Methods:
119 patients who underwent unilateral TKA between 2009 and 2010 under regional anesthesia with FNC were studied. Electronic charts were reviewed for numerical rating scale (NRS) pain scores at baseline, from the time the patients entered the post-operative care unit and every 4 hours thereafter until FNC was discontinued at 24 hours post-surgery. Opioid usage was also recorded during the same time period.

Results:
Analysis of average NRS pain scores from all patients demonstrated that 69% had NRS pain scores ≤ 5 (‘low pain’ (LP) group) and 31% had NRS pain scores ≥ 6 (‘high pain’ (HP) group). Time analysis showed that HP patients' high pain scores persisted for 24 hours post-surgery and they were characterized by being younger when compared to the LP patients.The majority of HP patients were female. Further analysis demonstrated that the average body mass index (BMI) of the female HP
patients was significantly greater than females with LP.

Conclusions:
In spite of a diverse multi-modal analgesia protocol designed for TKA surgery, 31% of our patients had ‘difficult-to-treat’ pain (NRS pain scores ≥ 6) for 24hours postsurgery. Our analysis implicates age, pre-operative pain scores, female gender and obesity as potential risk factors for
experiencing insufficient pain control with the currently evaluated multimodal pain protocol post-TKA surgery.