bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit
Authors: Vlachakis Dimitrios , Tsagrasoulis Dimosthenis , Megalooikonomou Vasileios , Kossida Sophia 
Published: October 2012

Abstract
Summary: Drugster is a fully interactive pipeline designed to break the command line barrier and introduce a new user-friendly environment to perform drug design, lead and structure optimization experiments through an efficient combination of the PDB2PQR, Ligbuilder, Gromacs and Dock suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process, by providing a seamless interface to all incorporated packages.
Availability: Drugster can be freely downloaded via our dedicated server system at http://www.bioacademy.gr/bioinformatics/drugster/.
Contact: dvlachakis@bioacademy.gr.
MycPermCheck: the Mycobacterium tuberculosis permeability prediction tool for small molecules
Authors: Merget Benjamin , Zilian David , Müller Tobias , Sotriffer Christoph A. 
Published: October 2012

Abstract
Motivation: With &gt;8 million new cases in 2010, particularly documented in developing countries, tuberculosis (TB) is still a highly present pandemic and often terminal. This is also due to the emergence of antibiotic-resistant strains (MDR-TB and XDR-TB) of the primary causative TB agent Mycobacterium tuberculosis (MTB). Efforts to develop new effective drugs against MTB are restrained by the unique and largely impermeable composition of the mycobacterial cell wall.
Results: Based on a database of antimycobacterial substances (CDD TB), 3815 compounds were classified as active and thus permeable. A data mining approach was conducted to gather the physico-chemical similarities of these substances and delimit them from a generic dataset of drug-like molecules. On the basis of the differences in these datasets, a regression model was generated and implemented into the online tool MycPermCheck to predict the permeability probability of small organic compounds.
Discussion: Given the current lack of precise molecular criteria determining mycobacterial permeability, MycPermCheck represents an unprecedented prediction tool intended to support antimycobacterial drug discovery. It follows a novel knowledge-driven approach to estimate the permeability probability of small organic compounds. As such, MycPermCheck can be used intuitively as an additional selection criterion for potential new inhibitors against MTB. Based on the validation results, its performance is expected to be of high practical value for virtual screening purposes.
Availability: The online tool is freely accessible under the URL http://www.mycpermcheck.aksotriffer.pharmazie.uni-wuerzburg.de
Contact: sotriffer@uni-wuerzburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
13CFLUX2—high-performance software suite for 13C-metabolic flux analysis
Authors: Weitzel Michael , Nöh Katharina , Dalman Tolga , Niedenführ Sebastian , Stute Birgit , Wiechert Wolfgang 
Published: October 2012

AbstractSummary: 13C-based metabolic flux analysis (13C-MFA) is the state-of-the-art method to quantitatively determine in vivo metabolic reaction rates in microorganisms. 13CFLUX2 contains all tools for composing flexible computational 13C-MFA workflows to design and evaluate carbon labeling experiments. A specially developed XML language, FluxML, highly efficient data structures and simulation algorithms achieve a maximum of performance and effectiveness. Support of multicore CPUs, as well as compute clusters, enables scalable investigations. 13CFLUX2 outperforms existing tools in terms of universality, flexibility and built-in features. Therewith, 13CFLUX2 paves the way for next-generation high-resolution 13C-MFA applications on the large scale.Availability and implementation: 13CFLUX2 is implemented in C++ (ISO/IEC 14882 standard) with Java and Python add-ons to run under Linux/Unix. A demo version and binaries are available at www.13cflux.net.Contact: info@13cflux.net or k.noeh@fz-juelich.deSupplementary information: Supplementary data are available at Bioinformatics online.
High prevalence of undetected heart failure in long‐term care residents: findings from the Heart Failure in Care Homes (HFinCH) study
Authors: Hancock Helen C. , Close Helen , Mason James M. , Murphy Jerry J. , Fuat Ahmet , Singh Raj , Wood Esther , de Belder Mark , Brennan Gill , Hussain Nehal , Kumar Nitin , Wilson Doug , Hungin A. Pali S. 
Published: October 2012

AimsDiagnosis of heart failure in older people in long‐term care is challenging because of co‐morbidities, cognitive deficit, polypharmacy, immobility, and poor access to services. This study aimed to ascertain heart failure prevalence and clinical management in this population.Methods and resultsA total of 405 residents, aged 65–100 years, in 33 UK care facilities were prospectively enrolled between April 2009 and June 2010. The presence of heart failure was determined using European Society of Cardiology guidelines, modified where necessary for immobility. Evaluation of symptoms and signs, functional capacity, and quality of life, portable on‐site echocardiography, and medical record review were completed in 399 cases. The point prevalence of heart failure was 22.8% [n = 91, 95% confidence interval (CI) 18.8–27.2%]; of these, 62.7% (n = 57, 95% CI 59.6–66.5%) had heart failure with preserved ejection fraction and 37.3% had left ventricular systolic dysfunction (n = 34, 95% CI 34.8–40.5%). A total of 76% (n = 61) of previous diagnoses of heart failure were not confirmed, and up to 90% (n = 82) of study cases were new. No symptoms or signs were reliable predictors of heart failure.ConclusionHeart failure was diagnosed in almost a quarter of residents: the prevalence was substantially higher than in other populations. The majority of heart failure cases were undiagnosed, while three‐quarters of previously recorded cases were misdiagnosed. Common symptoms and signs appear to have little clinical utility in this population. Early, accurate differential diagnosis is key to the effective management of heart failure; this may be failing in long‐term care facilities.Trial registrationISRCTN19781227
High prevalence of myocarditis in patients with hypertensive heart disease and cardiac deterioration
Authors: Frustaci Andrea , Francone Marco , Petrosillo Nicola , Chimenti Cristina 
Published: October 2012

AimsStructural abnormalities causing cardiac deterioration in hypertensive heart disease (HHD) are poorly understood. The aim of the study was to evaluate left ventricular (LV) myocardial changes in patients with HHD and cardiac failure.Methods and resultsAmong 1229 patients undergoing an LV or biventricular endomyocardial biopsy because of unexplained LV dysfunction from 2000 to 2010, 45 had HHD. The HHD population had non‐invasive assessment of cardiac wall thickness, diameters, and function; endomyocardial samples were processed for histology, immunohistochemistry, and polymerase chain reaction (PCR) for cardiotropic viruses. Mean LV end‐diastolic diameter was 63.3 ± 5.9 mm, LV ejection fraction 29.7 ± 7.6%, and maximal wall thickness 12.8 ± 0.9 mm. At histology, hypertrophy with degeneration of cardiomyocytes, increased external/lumen ratio of intramural arterioles, and myocardial fibrosis were observed in 17 patients (38%). In the remaining 28 patients (62%), these histological changes were associated with myocarditis. Myocarditis was present in 40.4% of the cohort without HHD. PCR was negative in HHD without inflammation while it was positive in 10 subjects with myocarditis (enterovirus in 3 cases, adenovirus 4, influenza virus 3). Addition of immunosuppression to supportive therapy in the 18 virus‐negative myocarditis subjects was followed at 6 months by significant recovery of LV function in 15 (83%; ejection fraction from 25.3 ±9.3% to 49.5 ±9.8%) while LV function improved to a minor extent (ejection fraction from 25 ± 5.1% to 36 ± 4.4%) in 12 of 27 patients (44%) on supportive treatment alone.ConclusionMyocarditis is a major cause of cardiac deterioration in patients with HHD; its recognition may improve patient treatment and outcome.
Plasma aldosterone levels are elevated in patients with pulmonary arterial hypertension in the absence of left ventricular heart failure: a pilot study
Authors: Maron Bradley A. , Opotowsky Alexander R. , Landzberg Michael J. , Loscalzo Joseph , Waxman Aaron B. , Leopold Jane A. 
Published: October 2012

AimsElevated levels of the mineralocorticoid hormone aldosterone are recognized as a modifiable contributor to the pathophysiology of select cardiovascular diseases due to left heart failure. In pulmonary arterial hypertension (PAH), pulmonary vascular remodelling induces right ventricular dysfunction and heart failure in the absence of left ventricular (LV) dysfunction. Hyperaldosteronism has emerged as a promoter of pulmonary vascular disease in experimental animal models of PAH; however, the extent to which hyperaldosteronism is associated with PAH in patients is unknown. Thus, the central aim of the current study is to determine if hyperaldosteronism is an unrecognized component of the PAH clinical syndrome.Methods and resultsPlasma aldosterone levels and invasive cardiopulmonary haemodynamic measurements were obtained for 25 patients referred for evaluation of unexplained dyspnoea or pulmonary hypertension. Compared with controls (n = 5), patients with PAH (n = 18) demonstrated significantly increased plasma aldosterone levels (1200.4 ± 423.9 vs. 5959.1 ± 2817.9 pg/mL, P < 0.02), mean pulmonary artery pressure (21.4 ± 5.0 vs. 45.5 ± 10.4 mmHg, P < 0.002), and pulmonary vascular resistance (PVR) (1.41 ± 0.6 vs. 7.3 ± 3.8 Wood units, P < 0.003) without differences in LV ejection fraction or pulmonary capillary wedge pressure between groups. Among patients not prescribed PAH‐specific pharmacotherapy prior to cardiac catheterization, a subgroup of the cohort with severe pulmonary hypertension, aldosterone levels correlated positively with PVR (r = 0.72, P < 0.02) and transpulmonary gradient (r = 0.69, P < 0.02), but correlated inversely with cardiac output (r = –0.79, P < 0.005).ConclusionsThese data demonstrate a novel cardiopulmonary haemodynamic profile associated with hyperaldosteronism in patients: diminished cardiac output due to pulmonary vascular disease in the absence of LV heart failure.
Collapse of allis shad, Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect?
Authors: Rougier Thibaud , Lambert Patrick , Drouineau Hilaire , Girardin Michel , Castelnaud Gérard , Carry Laurent , Aprahamian Miran , Rivot Etienne , Rochard Eric 
Published: October 2012

AbstractRougier, T., Lambert, P., Drouineau, H., Girardin, M., Castelnaud, G., Carry, L., Aprahamian, M., Rivot, E., and Rochard, E. 2012. Collapse of allis shad, Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect? – ICES Journal of Marine Science, 69: 1802–1811. At the end of the 20th century the allis shad population in the Gironde was the largest in Europe. During the first decade of the 21st century, catches declined dramatically by two orders of magnitude, and a fishery moratorium was implemented in 2008. This deterioration in the status of the stock was confirmed by three independent assessments (abundance of juveniles and of potential and effective spawners). Three hypotheses on the cause of the collapse were examined: (i) an environmental change in freshwater and/or in the estuary; (ii) an increase in marine and/or estuarine mortality; and (iii) the presence of an Allee effect. Changes in flow, temperature, and water quality over the period were inconclusive, but remain a possible causative factor. The instantaneous rate of marine (mean: 0.7 year−1, s.e. 0.1 year−1) and estuarine (mean: 2.6 year−1, s.e. 0.1 year−1) mortalities showed no trend between 1991 and 2003. Nevertheless, the past high estuarine (fishing) mortalities combined with a demographic Allee effect in the reproduction dynamics could explain the population collapse and hamper the stock recovery under the moratorium. This conclusion is, however, tentative as it was not possible to prove the presence of the density-dependent mechanism associated with the demographic Allee effect.
Cod catches taken by the German recreational fishery in the western Baltic Sea, 2005–2010: implications for stock assessment and management
Authors: Strehlow Harry V. , Schultz Norbert , Zimmermann Christopher , Hammer Cornelius 
Published: October 2012

Abstract
Strehlow, H. V., Schultz, N., Zimmermann, C., and Hammer, C. 2012. Cod catches taken by the German recreational fishery in the western Baltic Sea, 2005–2010: implications for stock assessment and management. – ICES Journal of Marine Science, 69: 1769–1780. Next to the commercial fishery, the recreational fishery plays an important role in the removal of biomass from fish stocks. In this study, we present estimates of German recreational cod (Gadus morhua) catches in the western Baltic Sea between 2005 and 2010. Fishing effort was estimated using a stratified mail survey and annual sales of fishing licences. Catch per unit effort was estimated by stratified random sampling of access points and interviews about completed trips. Length distributions of cod catches were acquired by sampling recreational cod catches from charter boats and data from community fishing events. Estimates of the total cod biomass removed by the recreational fishery fluctuated between 2159 t in 2009 and 4127 t in 2005. Annual recreational fishery cod harvests accounted for a significant share of the total landings, with a yearly variation from 34 to 70% of the German commercial cod landings from the western Baltic Sea. The majority of recreational fishery cod catches were taken from private boats and charter vessels. Because of the amount and specifically the variability of the recreational catches, they are important for the assessment and management of the resource and, therefore, need to be surveyed annually.
Relationships between North Atlantic salmon, plankton, and hydroclimatic change in the Northeast Atlantic
Authors: Beaugrand Grégory , Reid Philip C. 
Published: October 2012

Abstract
Beaugrand, G. and Reid, P. C. 2012. Relationships between North Atlantic salmon, plankton, and hydroclimatic change in the Northeast Atlantic – ICES Journal of Marine Science, 69: 1549–1562. The abundance of wild salmon (Salmo salar) in the North Atlantic has declined markedly since the late 1980s as a result of increased marine mortality that coincided with a marked rise in sea temperature in oceanic foraging areas. There is substantial evidence to show that temperature governs the growth, survival, and maturation of salmon during their marine migrations through either direct or indirect effects. In an earlier study (2003), long-term changes in three trophic levels (salmon, zooplankton, and phytoplankton) were shown to be correlated significantly with sea surface temperature (SST) and northern hemisphere temperature (NHT). A sequence of trophic changes ending with a stepwise decline in the total nominal catch of North Atlantic salmon (regime shift in ∼1986/1987) was superimposed on a trend to a warmer dynamic regime. Here, the earlier study is updated with catch and abundance data to 2010, confirming earlier results and detecting a new abrupt shift in ∼1996/1997. Although correlations between changes in salmon, plankton, and temperature are reinforced, the significance of the correlations is reduced because the temporal autocorrelation of time-series substantially increased due to a monotonic trend in the time-series, probably related to global warming. This effect may complicate future detection of effects of climate change on natural systems.
Atlantic cod (Gadus morhua) feed during spawning off Newfoundland and Labrador
Authors: Krumsick Kyle J. , Rose George A. 
Published: October 2012

Abstract
Krumsick, K. J., and Rose, G. A. 2012. Atlantic cod (Gadus morhua) feed during spawning off Newfoundland and Labrador. – ICES Journal of Marine Science, 69: 1701–1709. We test a current assumption that Atlantic cod (Gadus morhua) off Newfoundland and Labrador, Canada, do not feed during the protracted spawning season (March–September). Stomach contents were analysed from 10 473 cod from four Northwest Atlantic Fisheries Organization regions (2J, 3K, 3L, and 3Ps) over 9 years from which gonads were also analysed to determine sex and maturity status. Adult cod in spawning condition did feed in all regions, usually at rates equivalent to or even greater than non-spawning fish and juveniles. Both sexes fed during spawning, though females consumed lesser amounts. Regional differences were evident. The total fullness index was greater in the northern (2J) than the southern (3Ps) region, with no consistent differences between spawners and non-spawners. The most southerly region (3Ps) exhibited the greatest prey diversity, the northern region (2J) the least. Shrimp was the major diet item in the northern regions. Capelin, zooplankton, crab, and other fish increased in importance to the south. Differences in prey items between non-spawning and spawning individuals of both sexes were possibly related to spawning behaviour. Models using consumption rates should not assume that cod do not feed during the protracted spawning season in these waters.
Indicators of fishing pressure and seafloor integrity
Authors: Piet G. J. , Hintzen N. T. 
Published: October 2012

Abstract
Piet, G. J., and Hintzen, N. T. 2012. Indicators of fishing pressure and seafloor integrity. – ICES Journal of Marine Science, 69: 1850–1858. This study calculates a suite of indicators reflecting the spatial extent of fishing and its impact on the seafloor and discusses the usefulness of these indicators to inform future management and the issues to consider. It explores several methods to calculate the indicators and shows that they can be informative to report on both fishing pressure and the status of the seafloor. However, although observed overall trends were robust against the specific method of calculation, the absolute values vary greatly with the calculation method. As both aspects are important from a policy perspective, agreement on the methodology to calculate the indicators is required. This study based on the Dutch Exclusive Economic Zone (EEZ) shows that it is possible to calculate indicators required to inform decision-makers on the pressure of fishing as well as the status of the seafloor pending a decision on the following issues: (i) choice of an appropriate grid cell resolution, (ii) use of interpolated VMS tracks instead of VMS position registrations, (iii) choice of an “intensity threshold” dependent on the benthic community recovery capacity, and (iv) the level of confidence required when assessing if an area is not impacted.
Effects of Varying CDS Levels and Drying and Cooling Temperatures on Flowability Properties of DDGS
Authors: Bhadra Rumela , Muthukumarappan Kasiviswanathan , Rosentrater Kurt A. 
Published: October 2012

ABSTRACTDemand for alternative fuels and the need to reduce dependence on fossil fuels have triggered the growth of corn‐based ethanol production, which is expected to rise in future years. Transportation of the coproduct distillers dried grains with solubles (DDGS) from this industry occurs under various environmental conditions. Transporting DDGS is often problematic, because caking between the particles can lead to flow problems. In this study, we have prepared DDGS by combining condensed distillers solubles (CDS) with distillers wet grains and then drying. We investigated the effects of CDS level (10, 15, and 20%, wb), drying temperature (100, 200, and 300°C), and cooling temperature (–12, 25, and 35°C) on the flowability of the resulting DDGS. Statistical analyses of the resulting data found significant differences among the cooling temperature levels for angle of repose, total flow and flood indices, dispersibility, water activity, and protein dispersibility index. Additionally, significant interaction effects between CDS, drying temperature, and cooling temperature levels for angle of repose, total flow and flood indices, dispersibility, and protein dispersibility index were observed. Response surface regression on selected dimensionless flowability parameters was also applied. However, multivariate PLS regression yielded better results (R2 > 0.8) than response surface plots. Understanding the effects of drying and cooling temperatures as well as CDS levels can be used to help improve the industrial processing of DDGS and improve storage and transportation.
Amount and Size Distribution of Monomeric and Polymeric Proteins in the Grain of Organically Produced Wheat
Authors: Hussain Abrar , Larsson Hans , Kuktaite Ramune , Prieto‐Linde Maria Luisa , Johansson Eva 
Published: October 2012

ABSTRACTIn the present study, we evaluated 444 organically grown wheat genotypes for the amount and size distribution of polymeric proteins by size‐exclusion HPLC. The investigated genotypes were divided into six genotype groups—selection, spelt, old cultivar, primitive, landrace, and cultivar—and these were grown in four different locations, namely, Alnarp, Bohuslän, Gotland, and Uppsala in Sweden. The results showed that the percentage of unextractable polymeric proteins in total polymeric proteins (%UPP) and percentage of large unextractable polymeric proteins in total polymeric proteins were higher in the cultivar group as compared with the rest of the investigated genotype groups. The amounts of total extractable polymeric proteins (TOTE) and total unextractable polymeric proteins were low in cultivars and selections, respectively. Spring wheat grain was found to have a significantly higher amount of all protein fractions as compared with winter wheat. The genotype Kenya was found to belong to both groups of the 20 genotypes with the highest TOTE and %UPP. Thus, the genotype Kenya might be of relevance for consumption and future breeding to improve the breadmaking quality of organically produced wheat.