bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma follistatin is elevated in patients with type 2 diabetes: relationship to hyperglycemia, hyperinsulinemia, and systemic low‐grade inflammation
Authors: Hansen J. , Rinnov A. , Krogh‐Madsen R. , Fischer C. P. , Andreasen A. S. , Berg R. M. G. , Møller K. , Pedersen B. K. , Plomgaard P. 
Published: April 2013

AbstractBackgroundPlasma follistatin is elevated in patients with low‐grade inflammation and insulin resistance as observed with polycystic ovary syndrome. In the present study, we evaluated plasma follistatin in patients with type 2 diabetes characterised by low‐grade inflammation and assessed the acute effects of hyperglycemia, hyperinsulinemia and LPS on plasma follistatin.MethodsBaseline plasma follistatin and inflammatory biomarkers were measured in a cross‐sectional study that involved 95 patients with type 2 diabetes and 103 matched controls. To determine the acute effect of hyperglycemia and hyperinsulinemia on follistatin, hyperglycemic and hyperinsulinemic‐euglycemic clamps were performed in five healthy males. Furthermore, 15 patients with type 2 diabetes and 22 healthy controls were challenged with low‐dose LPS to determine the effect on follistatin.ResultsPatients with type 2 diabetes have higher HOMA2‐IR values mean [95% CI] 1.64 [1.40–1.93] versus mean 0.86 [0.75–0.99], p < 0.001 and inflammatory markers compared with controls. Baseline plasma follistatin is elevated in patients with type 2 diabetes compared with controls mean 1564 [1456–1680] versus mean 1328 [1225–1440] ng/L, p = 0.003 and correlates with fasting glucose levels (r = 0.44, p < 0.0001), 2 h glucose (r = 0.48, p < 0.0001), HbA1c (r = 0.41, p < 0.0001), triacylglycerol (r = 0.28, p = 0.008) and total cholesterol (r = 0.33, p = 0.004) in patients but not in controls. No correlation exists between plasma follistatin and inflammatory biomarkers in either of the groups. Neither hyperglycemia, hyperinsulinemia nor LPS increase plasma follistatin.ConclusionsPlasma follistatin is moderately elevated in patients with type 2 diabetes. Our findings suggest that this is not likely caused by hyperglycemia, hyperinsulinemia or systemic low‐grade inflammation. Copyright © 2013 John Wiley & Sons, Ltd.
Testosterone levels and fecundity in the hermaphroditic aquatic snail Lymnaea stagnalis exposed to testosterone and endocrine disruptors
Authors: Giusti Arnaud , Ducrot Virginie , Joaquim-Justo Célia , Lagadic Laurent 
Published: April 2013

Abstract

Endocrine disruptors are known to alter endogenous free and esterified levels of androgenic and estrogenic steroid hormones in aquatic mollusks. The origin of steroids in these animals, however, remains controversial. In the present study, free and esterified testosterone concentrations were measured in the hermaphroditic aquatic gastropod Lymnaea stagnalis exposed to molecules known for their androgenic (testosterone and tributyltin), anti-androgenic (cyproterone-acetate), and estrogenic (chlordecone) properties, by reference to their mode of action in vertebrates. In parallel, snail oviposition and fecundity were followed over a 21-d exposure period. Testosterone exposure resulted in increased esterified testosterone levels, whereas free testosterone concentrations remained stable. In contrast, cyproterone-acetate significantly increased the free form of testosterone with no changes in the esterified form, whereas chlordecone showed a tendency to reduce (though not significantly) esterified testosterone concentrations without changing free testosterone levels. Finally, tributyltin did not alter testosterone homeostasis. The production of egg clutches and eggs was significantly reduced only in the snails exposed to the highest concentrations of chlordecone (19.6 µg/L) and tributyltin (94.2 ng Sn/L). Overall, the present study demonstrates that uptake of testosterone from the exposure medium occurs in L. stagnalis. Moreover, it shows that cyproterone-acetate and, to a lesser extent, chlordecone can alter endogenous testosterone levels in this freshwater snail. However, the relationship between hormonal changes and snail reproduction has not been established. Environ Toxicol Chem 2013;32:1740–1745. © 2013 SETAC
An effects addition model based on bioaccumulation of metals from exposure to mixtures of metals can predict chronic mortality in the aquatic invertebrate hyalella azteca
Authors: Norwood Warren P. , Borgmann Uwe , Dixon D. George 
Published: April 2013

Abstract

Chronic toxicity tests of mixtures of 9 metals and 1 metalloid (As, Cd, Co, Cr, Cu, Mn, Ni, Pb, Tl, and Zn) at equitoxic concentrations over an increasing concentration range were conducted with the epibenthic, freshwater amphipod Hyalella azteca. The authors conducted 28-d, water-only tests. The bioaccumulation trends changed for 8 of the elements in exposures to mixtures of the metals compared with individual metal exposures. The bioaccumulation of Co and Tl were affected the most. These changes may be due to interactions between all the metals as well as interactions with waterborne ligands. A metal effects addition model (MEAM) is proposed as a more accurate method to assess the impact of mixtures of metals and to predict chronic mortality. The MEAM uses background-corrected body concentration to predict toxicity. This is important because the chemical characteristics of different waters can greatly alter the bioavailability and bioaccumulation of metals, and interactions among metals for binding at the site of action within the organism can affect body concentration. The MEAM accurately predicted toxicity in exposures to mixtures of metals, and predicted results were within a factor of 1.1 of the observed data, using 24-h depurated body concentrations. The traditional concentration addition model overestimated toxicity by a factor of 2.7. Environ Toxicol Chem 2013;32:1672–1681. © 2013 SETAC
Azimuthal anisotropy at Valhall: The Helmholtz equation approach
Authors: Mordret Aurélien , Shapiro Nikolai M. , Singh Satish , Roux Philippe , Montagner Jean‐Paul , Barkved Olav. I. 
Published: April 2013

AbstractWe used 6 h of continuous vertical records from 2320 sensors of the Valhall Life of Fields Seismic network to compute 2,690,040 cross‐correlation functions between the full set of sensor pair combinations. We applied the “Helmholtz tomography” approach combined with the ambient noise correlation method to track the wave front across the network with every station considered as a virtual source. The gradient of the interpolated phase travel time gives us an estimate of the local phase speed and of the direction of wave propagation. By combining the individual measurements for every station, we estimated the distribution of Scholte's wave phase speeds with respect to azimuth. The observed cosine pattern indicates the presence of azimuthal anisotropy. The elliptic shape of the fast anisotropy direction is consistent with results of previous shear wave splitting studies and reflects the strong seafloor subsidence due to the hydrocarbon reservoir depletion at depth and is in good agreement with geomechanical modeling.
Highly time-variable exposure to chemicals—toward an assessment strategy
Authors: Ashauer Roman , Brown Colin D 
Published: April 2013

Abstract
Organisms in the environment experience fluctuating, pulsed, or intermittent exposure to pollutants. Accounting for effects of such exposures is an important challenge for environmental risk assessment, particularly given the simplified design of standard ecotoxicity tests. Dynamic simulation using toxicokinetic-toxicodynamic (TK-TD) models describes the processes that link exposure with effects in an organism and provides a basis for extrapolation to a range of exposure scenarios. In so doing, TK-TD modeling makes the risk assessment more robust and aids use and interpretation of experimental data. Toxicokinetic-toxicodynamic models are well-developed for predicting survival of individual organisms and are increasingly applied to sublethal endpoints. In the latter case particularly, linkage to individual-based models (IBMs) allows extrapolation to population level as well as accounting for differences in effects of toxicant exposure at different stages in the life cycle. Extrapolation between species remains an important constraint because there is currently no systematic understanding of species traits that cause differences in the relevant processes. Toxicokinetic-toxicodynamic models allow interrogation of exposure profiles to determine intrinsic toxicity potential rather than using absolute maximum concentrations or time-weighted averages as surrogates. A decision scheme is proposed to guide selection of risk assessment approaches using dose extrapolation based on Haber's Law, TK-TD models, and/or IBMs depending on the nature of toxic effect and timing in relation to life history. Integr Environ Assess Manag 2013;9:e27–e33. © 2013 SETAC
Draft DG SANCO document: Addressing the new challenges for risk assessment—an industry perspective
Authors: Campbell Peter , Dohmen Peter 
Published: April 2013

Abstract
The draft European Commission's Directorate General for Health and Consumer Policy (DG SANCO) document represents the state of the art in environmental risk assessment (ERA) including new trends and combining high level environmental protection and realism. Using the ecosystem services concept, it offers a promising approach to determine which impact may be tolerable, where, and when. Established ERA uses a stepwise approach starting with standardized internationally accepted studies combined with appropriate assessment factors (AFs) and where needed followed by higher tier assessments and respective adjusted AFs. The draft SANCO document follows this approach and presents additional refinements to improve the realism of risk assessment, which is desirable; however, that such additional data becomes a standard requirement without a clear need must be avoided. The idea of additional AFs presented in parts of this article should accordingly first consider risks and benefits in line with this approach and only be requested if data indicates their necessity. In addition, the suggested focus on uncertainty analysis without any obvious according benefits in terms of reduced assessment factors where uncertainty is reduced, is still a challenge. The requirement for science- and/or data-based relevant concerns before requesting more data, and the list of requirements for new innovative approaches that should be met before such approaches can be used in regulatory ecological risk assessments, is well-founded and strongly supported. Modeling has been included in ERA to allow extrapolation of risk assessments without the need of excessive (animal) testing; it will also address uncertainties more quantitatively. However, this should be done in an overall realistic ecological assessment; simply adding up various individual uncertainties and worst-case assumptions must be avoided, as this is counterproductive for the use of this valuable tool. The need for expert judgment should be low at the lower tiers of ERA; however, more complex and less standard ERA will still require significant expertise. Integr Environ Assess Manag 2013;9:e81–e84. © 2013 SETAC
Electrospun PLGA/gelatin fibrous tubes for the application of biodegradable intestinal stent in rat model
Authors: Son So‐Ra , Franco Rose‐Ann , Bae Sang‐Ho , Min Young‐Ki , Lee Byong‐Taek 
Published: April 2013

AbstractA biodegradable fibrous tube was fabricated by electrospinning method using a combination of Poly(lactic‐co‐glycolic acid) (PLGA) and gelatin dissolved in trifluoroethanol (TFE). Different ratios of the two polymers (PLGA/Gelatin: 1/9, 3/7, 5/5) were used for electrospinning to determine the optimum condition appropriate for intestinal stent application. Fiber morphology was visualized and analyzed using a scanning electron microscope (SEM). Characterizations of physical properties were done according to its tensile strength, surface hydrophilicity, swelling ability, and biodegradability. Biocompatibility of the scaffolds was investigated in vitro using IEC‐18 (Rat intestinal epithelial cell). Cell proliferation was quantified using MTT assay and cell adhesion behavior was visualized by SEM and confocal laser scanning microscope. PLGA/Gelatin (5/5) was determined to have adequate material properties and sufficient in vitro biocompatibility. This was then implanted in a male Sprague‐Dawley rat for 14 days to determine in vivo behavior of the sample. Histological examination on the intestinal tissue surrounding the graft showed normal morphology comparable to non‐implanted intestine. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2013.
Changes in Physical Properties of Soils with Land Use Time in the Brazilian Savanna Environment
Authors: Trabaquini Kleber , Formaggio Antônio Roberto , Galvão Lênio Soares 
Published: April 2013

AbstractSoils from central Brazil have been intensively used over the last decades because of the rapid conversion of savannas (Cerrado) into corn/soybean fields. The objective of this work is to study modifications in the physical properties of soils in the Rio Verde watershed, as a function of the land use time for agriculture, determined from classification of Landsat satellite images between 1980 and 2010. Soil samples were collected at surface (0–20 cm) and subsurface (20–40 cm) horizons for the different classes of land use time (<10, 10–20, 20–30, and >30 years). The following physical properties were measured: bulk density (BD), air permeability (Ka), penetration resistance (PR), microporosity (MI), macroporosity (MA), and total porosity (TP). Results showed a strong expansion with time of agriculture that occupied 35·3% (1980), 37·4% (1990), 51·3% (2000), and 60·9% (2010) of the watershed area. When properties were compared with those from the reference areas (preserved soils under native vegetation), significant differences were observed for all the physical attributes of soils for a land use time higher than 20 years. Overall, BD and PR increased with land use time, and the opposite was verified for Ka, MA, and TP. Some physical properties presented values (e.g., 1·54 g cm−3 for BD and 0.06 cm3 cm−3 for MA) close to the critical ones reported to affect crop development, but they were not still impacting on local soybean yield. Copyright © 2013 John Wiley & Sons, Ltd.
Interpreting Oral Pathology at Machu Picchu, Peru
Authors: Turner B. L. 
Published: April 2013

AbstractThis study analyzes oral pathological conditions—caries, antemortem tooth loss, and occlusal macrowear—among adults (N = 70) interred at Machu Picchu, Peru. Previous isotopic diet reconstructions at Machu Picchu suggest substantial early‐life variation that may have narrowed somewhat by the last decade of life. This study seeks to further elucidate the intersection of diet, sex, and health at Machu Picchu by analyzing oral pathological conditions with existing carbon and nitrogen isotopic data. Observed caries prevalence is corrected to control for age and tooth loss, and is described for both anterior and posterior teeth; wear data are scored and reported for individual tooth types. Results indicate caries prevalence consistent with carbohydrate‐rich diets and no significant difference between males and females. However, no significant isotopic parameters are associated with caries prevalence in young adult males, while caries prevalence is significantly associated only with enamel carbonate δ13C in older adult males. Dietary protein sources, but not C4 resources, are associated with caries prevalence in young adult females, and to a lesser degree in older adult females. Significant associations between occlusal wear and caries exist among young adult males and young adult females, but involving different tooth types. These findings suggest differential protein consumption at Machu Picchu between males and females, and separate masticatory and physiological processes shaping caries prevalence between the sexes at the site. This study therefore underscores the role that gender roles may have played in diet variation among this population and the need to account for sex in analyzing oral pathology. Copyright © 2013 John Wiley & Sons, Ltd.
Capillary effect on water table fluctuations in unconfined aquifers
Authors: Kong Jun , Shen Cheng‐Ji , Xin Pei , Song Zhiyao , Li Ling , Barry D. A. , Jeng D.‐S. , Stagnitti F. , Lockington D. A. , Parlange J.‐Y. 
Published: April 2013

Key Points
A new governing equation of watertable dynamics was derived.
A new analytical solution for watertable fluctuations was derived.
The effect of finite unsaturated zone thickness was examined.
A fast simulation method for uncertainty quantification of subsurface flow and transport
Authors: Meyer Daniel W. , Tchelepi Hamdi A. , Jenny Patrick 
Published: April 2013

Key Points
new polar Markovian velocity processes (PMVPs) to model macro‐dispersion
generalization of PMVPs for inhomogeneous cases with conductivity measurements
validation of PMVP with Monte Carlo, CPU‐time PMVP = CPU‐time MC / 1000
Circular dichroism calculation for natural products
Authors: Nugroho Alfarius Eko , Morita Hiroshi 
Published: April 2013

AbstractDetermination of the absolute configuration (AC) is often a challenging aspect in the structure elucidation of natural products. When chiral compounds possess appropriate chromophore(s), electronic circular dichroism (ECD) may provide a powerful approach to the determination of their absolute configuration. Recently, ECD calculations by time-dependent density functional theory (TDDFT) have come to be used more commonly. In the present review, we give several examples of recent studies using TDDFT-calculated ECD spectra for the AC determination of natural products.
Vaginal hysterectomy in women with a history of 2 or more cesarean deliveries
Authors: Sheth Shirish S. 
Published: April 2013

AbstractObjectiveTo perform vaginal hysterectomy (VH) safely in women with a history of 2 or more cesarean deliveries (CDs).MethodsA 4‐step method was followed to safeguard the bladder, access the vesicouterine peritoneum (VUP), and perform VH in 312 patients with a history of 2 or more CDs. If access to the VUP did not occur at the end of step 2, step 3 and, if necessary, step 4 were implemented.ResultsHysterectomy was performed vaginally in 311 patients, and the abdominal route was resorted to in 1 patient because of hemorrhage. Only 1 patient incurred bladder trauma, which was promptly repaired.ConclusionIn the absence of contraindications, the 4‐step VH method described and the surgical techniques involved are safe to implement in women with a history of 2 or more CDs who need a hysterectomy.
A comprehensive approach in hospice shared care in Taiwan: Nonelderly patients have more physical, psychosocial and spiritual suffering
Authors: Yang Chiu‐Hsien , Chiu Yu‐Wen , Huang Chia‐Tsuan , Haung Yu‐Wen , Chuang Hung‐Yi 
Published: April 2013

AbstractWhile symptomatic differences exist between younger and older advanced cancer patients, few studies have examined the differences in their care with respect to age. Our goals were to examine the influences of age differences on physical, psychosocial and spiritual distress among advanced cancer patients. Advanced cancer patients who resided in Kaohsiung Medical University Hospital during 2007–2008 were recruited. Data were collected through professional consultants. The influences of age variations on physical, psychosocial and spiritual distress in nonelderly (<60 years old) and elderly (≧60 years old) patients were analyzed. A total of 1013 advanced cancer patients were included in the analyses with 467 nonelderly patients and 546 elderly patients. Nonelderly patients were identified to have a higher baseline pain level (4.0 vs. 2.8, p < 0.001), breakthrough pain (19.3% vs. 9.9%, p < 0.01), insomnia (6.4% vs. 2.7%, p = 0.006), emotional distress (69.0% vs. 60.6%, p = 0.013), and unwillingness to pass away because of concern for loved ones (18.8% vs. 11.9%, p = 0.003) with significant difference. Elderly ones were concerned about unfulfilled wishes (29.7% vs. 18.4%, p < 0.001) in spiritual concerns. After adjustments in regression models, nonelderly age (<60 years old) still revealed significant positive or negative impact on all categories of distress. Patients aged under 60 years have more physical, psychosocial and spiritual suffering. This study suggested that professional practitioners should provide intensive care for vulnerable terminally ill cancer patients.
tmVar: a text mining approach for extracting sequence variants in biomedical literature
Authors: Wei Chih-Hsuan , Harris Bethany R. , Kao Hung-Yu , Lu Zhiyong 
Published: April 2013

Abstract
Motivation: Text-mining mutation information from the literature becomes a critical part of the bioinformatics approach for the analysis and interpretation of sequence variations in complex diseases in the post-genomic era. It has also been used for assisting the creation of disease-related mutation databases. Most of existing approaches are rule-based and focus on limited types of sequence variations, such as protein point mutations. Thus, extending their extraction scope requires significant manual efforts in examining new instances and developing corresponding rules. As such, new automatic approaches are greatly needed for extracting different kinds of mutations with high accuracy.
Results: Here, we report tmVar, a text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants described at protein, DNA and RNA levels according to a standard nomenclature developed by the Human Genome Variation Society. By doing so, we cover several important types of mutations that were not considered in past studies. Using a novel CRF label model and feature set, our method achieves higher performance than a state-of-the-art method on both our corpus (91.4 versus 78.1% in F-measure) and their own gold standard (93.9 versus 89.4% in F-measure). These results suggest that tmVar is a high-performance method for mutation extraction from biomedical literature.
Availability: tmVar software and its corpus of 500 manually curated abstracts are available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/pub/tmVar.
Contact: zhiyong.lu@nih.gov
LibSBMLSim: a reference implementation of fully functional SBML simulator
Authors: Takizawa Hiromu , Nakamura Kazushige , Tabira Akito , Chikahara Yoichi , Matsui Tatsuhiro , Hiroi Noriko , Funahashi Akira 
Published: April 2013

Abstract
Motivation: The Systems Biology Markup Language (SBML) is currently supported by &gt;230 software tools, among which 160 support numerical integration of ordinary differential equation (ODE) models. Although SBML is a widely accepted standard within this field, there is still no language-neutral library that supports all features of SBML for simulating ODE models. Therefore, a demand exists for a simple portable implementation of a numerical integrator that supports SBML to enhance the development of a computational platform for systems biology.
Results: We implemented a library called libSBMLSim, which supports all the features of SBML and confirmed that the library passes all tests in the SBML test suite including those for SBML Events, AlgebraicRules, ‘fast’ attribute on Reactions and Delay. LibSBMLSim is implemented in the C programming language and does not depend on any third-party library except libSBML, which is a library to handle SBML documents. For the numerical integrator, both explicit and implicit methods are written from scratch to support all the functionality of SBML features in a straightforward implementation. We succeeded in implementing libSBMLSim as a platform-independent library that can run on most common operating systems (Windows, MacOSX and Linux) and also provides several language bindings (Java, C#, Python and Ruby).
Availability: The source code of libSBMLSim is available from http://fun.bio.keio.ac.jp/software/libsbmlsim/. LibSBMLSim is distributed under the terms of LGPL.
Contact: funa@bio.keio.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.