bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solar irradiance and primary productivity controlled mercury accumulation in sediments of a remote lake in the Southern Hemisphere during the past 4000 years
Authors: Biester Harald , Pérez‐Rodríguez Marta , Gilfedder Benjamin‐Silas , Martínez Cortizas Antonio , Hermanns Yvonne‐Marie 
Published: August 2017

AbstractMercury (Hg) is a toxic trace element known to highly accumulate in aquatic biota and uptake by algae is the main entry‐point into the aquatic food chain. However, the effect of changes in solar irradiance and climatic conditions on Hg uptake by algae is largely unknown. We analyzed the link between sediment Hg accumulation, cyclic changes in total solar irradiance (TSI), and related changes in lake productivity as well as climate during the past 4.5 thousand years (kyr) in sediments of a small highly productive lake in Southern Patagonia (53°S). The analyses encompass proxies for TSI (based on 10Be), sediment geochemical composition, and lake productivity (FTIR spectra, and hydrogen‐index). The sediment record shows high concentrations of organic matter (median 70%) and strong variations in Hg accumulation rates (14–53 μg m2 yr−1) which correspond to changes in aquatic productivity and TSI. Accumulation of Hg was highest during dryer periods when irradiance and lake productivity was high. During these periods, accumulation was up to fourfold higher compared to those of lower TSI, lower productivity, and wetter climatic conditions. Higher amounts of algae biomass can increase Hg scavenging by organic particles and Hg export to the sediment. To obtain mass balance, we assume that the increase in sediment Hg accumulation rates during periods of lower Hg fluxes from the catchment (drier) caused a decrease in water phase Hg and in rates of Hg evasion from the lake.
Quantitative Analysis of Intravoxel Incoherent Motion (IVIM) Diffusion MRI using Total Variation and Huber Penalty Function
Authors: Kayal Esha Baidya , Kandasamy Devasenathipathy , Khare Kedar , Alampally Jayendra Tiru , Bakhshi Sameer , Sharma Raju , Mehndiratta Amit 
Published: August 2017

PurposeQuantitative analysis in intravoxel incoherent motion (IVIM) imaging commonly uses voxel‐wise estimation of the bi‐exponential model, which might not be reliable for clinical interpretation. Improving model fitting performance and qualitative and quantitative parametric estimation, two novel methodologies are proposed here.MethodsFive IVIM analyses methodologies: (a) Bi‐exponential (BE) model, (b) Segmented BE method with two‐parameter fitting (BEseg‐2), (c) Segmented BE method with one‐parameter fitting (BEseg‐1), (d) BE with adaptive Total Variation penalty function (BE+TV) and (e) BE with adaptive Huber penalty function (BE+HPF) were evaluated. Relative root‐mean‐square error (RRMSE), relative bias (RB) and relative parameters were calculated to estimate the accuracy of methods in simulations. Empirical datasets from 14 patients with bone tumor were analyzed using these methodologies. Coefficient of variation (CV) were estimated for each IVIM parameter in tumor volume to measure the precision of the estimation methods in vivo.ResultsBoth BE+TV and BE+HPF showed consistently lower RRMSE (~10–42%) and lower RB (−4 to 8%) at all noise levels, compared to BE, BEseg‐2 and BEseg‐1 (RRMSE: ~15–120% and RB: −20 to 62%). Estimated for both BE+TV and BE+HPF methods were ~1 (0.96–1.08), whereas BE, BEseg‐2 and BEseg‐1 showed sub‐optimal parameter estimation (0.80–1.62). For clinical data BE+TV and BE+HPF showed 30–50% improved CV in estimating D, D*, and f than BE and improved CV in estimating D* (7–23%) and f (26–30%) than BEseg‐2 and BEseg‐1.ConclusionsBi‐exponential model with penalty function showed quantitatively and qualitatively improved IVIM parameter estimation for both simulated and clinical dataset of bone tumors, thus potentially making this approach suitable for clinical applications in future.
Probabilistic nonconvex constrained optimization with fixed number of function evaluations
Authors: Ghanem Roger , Soize Christian 
Published: August 2017

SummaryA methodology is proposed for the efficient solution of probabilistic nonconvex constrained optimization problems with uncertain. Statistical properties of the underlying stochastic generator are characterized from an initial statistical sample of function evaluations. A diffusion manifold over the initial set of data points is first identified and an associated basis computed. The joint probability density function of this initial set is estimated using a kernel density model and an Itô stochastic differential equation (ISDE) constructed with this model as its invariant measure. This ISDE is adapted to fluctuate around the manifold yielding additional joint realizations of the uncertain parameters, design variables, and function values, which are obtained as solutions of the ISDE. The expectations in the objective function and constraints are then accurately evaluated without performing additional function evaluations. The methodology brings together novel ideas from manifold learning and stochastic Hamiltonian dynamics to tackle an outstanding challenge in stochastic optimization. Three examples are presented to highlight different aspects of the proposed methodology.
Finite analytic method for 2D steady fluid flows in heterogeneous porous media with unstructured grids
Authors: Wang Guan‐Wen , Liu Zhi‐Feng , Wang Xiao‐Hong 
Published: August 2017

AbstractThe finite analytic method (FAM) is developed to solve the 2D steady fluid flows in heterogeneous porous media with full tensor permeability on unstructured grids. The proposed FAM is constructed based upon the power‐law analytic nodal solution in the angular domain with arbitrary shape. When approaching the grid node joining the subdomains, 3 different flow patterns may exist: power‐law flow, linear flow, or the stagnant flow. Based on the nodal analytic solution, the triangle‐based FAM is proposed. Numerical examples show that the proposed numerical scheme makes the convergences much quickly than the traditional methods, typically the weighted harmonic mean method under the cell refinement. In practical applications, the grid refinement parameter n = 2 or n = 3 is recommended, and the relative error of the calculated equivalent permeability will below 4% independent of the heterogeneity. In contrast, when using the traditional numerical scheme the refinement ratio for the grid cell needs to increase dramatically to get an accurate result, especially for strong heterogeneous porous medium.
Partial Sleep Deprivation Reduces the Efficacy of Orexin‐A to Stimulate Physical Activity and Energy Expenditure
Authors: DePorter Danielle P. , Coborn Jamie E. , Teske Jennifer A. 
Published: August 2017

ObjectiveSufficient sleep is required for weight maintenance. Sleep deprivation due to noise exposure stimulates weight gain by increasing hyperphagia and reducing energy expenditure (EE). Yet the mechanistic basis underlying the weight gain response is unclear. Orexin‐A promotes arousal and negative energy balance, and orexin terminals project to the ventrolateral preoptic area (VLPO), which is involved in sleep‐to‐wake transitions. To determine whether sleep deprivation reduces orexin function in VLPO and to test the hypothesis that sleep deprivation would attenuate the orexin‐A‐stimulated increase in arousal, physical activity (PA), and EE.MethodsElectroencephalogram, electromyogram, distance traveled, and EE were determined in male Sprague‐Dawley rats following orexin‐A injections into VLPO both before and after acute (12‐h) and chronic (8 h/d, 9 d) sleep deprivation by noise exposure.ResultsOrexin‐A in the VLPO significantly increased arousal, PA, total EE, and PA‐related EE and reduced sleep and respiratory quotient before sleep deprivation. In contrast to after acute sleep deprivation in which orexin‐A failed to stimulate EE during PA only, orexin‐A failed to significantly increase arousal, PA, fat oxidation, total EE, and PA‐related EE after chronic sleep deprivation.ConclusionsSleep deprivation may reduce sensitivity to endogenous stimuli that enhance EE due to PA and thus stimulate weight gain.
Tannins and Their Complex Interaction with Different Organic Nitrogen Compounds and Enzymes: Old Paradigms versus Recent Advances
Authors: Adamczyk Bartosz , Simon Judy , Kitunen Veikko , Adamczyk Sylwia , Smolander Aino 
Published: August 2017

AbstractTannins, an abundant group of plant secondary compounds, raise interest in different fields of science, owing to their unique chemical characteristics. In chemical ecology, tannins play a crucial role in plant defense against pathogens, herbivores, and changing environmental conditions. In the food industry and in medicine, tannins are important because of their proven positive effect on human health and disease treatment. Such wide interests fueled studies on tannin chemistry, especially on their flagship ability to precipitate proteins. In this Review, we expand the basic knowledge on tannin chemistry to the newest insights from the field. We focus especially on tannin reactions with different non‐protein organic N compounds, as well as the complex interactions of tannins with enzymes, resulting in either an increase or decrease in enzyme activity.
A 3D tri‐culture system reveals that activin receptor‐like kinase 5 and connective tissue growth factor drive human glomerulosclerosis
Authors: Waters John P , Richards Yvonne C , Skepper Jeremy N , Southwood Mark , Upton Paul D , Morrell Nicholas W , Pober Jordan S , Bradley John R 
Published: August 2017

AbstractGlomerular scarring, known as glomerulosclerosis, occurs in many chronic kidney diseases and involves interaction between glomerular endothelial cells (GECs), podocytes, and mesangial cells (MCs), leading to signals that promote extracellular matrix deposition and endothelial cell dysfunction and loss. We describe a 3D tri‐culture system to model human glomerulosclerosis. In 3D monoculture, each cell type alters its phenotype in response to TGFβ, which has been implicated as an important mediator of glomerulosclerosis. GECs form a lumenized vascular network, which regresses in response to TGFβ. MCs respond to TGFβ by forming glomerulosclerotic‐like nodules with matrix deposition. TGFβ treatment of podocytes does not alter cell morphology but increases connective tissue growth factor (CTGF) expression. BMP7 prevents TGFβ‐induced GEC network regression, whereas TGFβ‐induced MC nodule formation is prevented by SMAD3 siRNA knockdown or ALK5 inhibitors but not BMP7, and increased phospho‐SMAD3 was observed in human glomerulosclerosis. In 3D tri‐culture, GECs, podocytes, and MCs form a vascular network in which GECs and podocytes interact intimately within a matrix containing MCs. TGFβ treatment induces formation of nodules, but combined inhibition of ALK5 and CTGF is required to prevent TGFβ‐induced nodule formation in tri‐cellular cultures. Identification of therapeutic targets for glomerulosclerosis depends on the 3D culture of all three glomerular cells. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Risk of preeclampsia after gestational exposure to selective serotonin reuptake inhibitors and other antidepressants: A study from The Norwegian Mother and Child Cohort Study
Authors: Lupattelli Angela , Wood Mollie , Lapane Kate , Spigset Olav , Nordeng Hedvig 
Published: August 2017

AbstractPurposeTo describe the risk of early‐ and late‐onset preeclampsia across pregnancies exposed to antidepressants and to evaluate the impact of timing and length of gestational exposure to antidepressants, particularly selective serotonin reuptake inhibitors (SSRIs), on preeclampsia.MethodsThe Norwegian Mother and Child Cohort, a prospective population‐based study, and the Medical Birth Registry of Norway provided information on antidepressant exposure, depression, and anxiety symptoms in pregnancy, preeclampsia diagnoses, and important covariates. Within a pregnancy cohort of depressed women, we compared the risk of late‐onset preeclampsia between SSRI‐exposed and nonmedicated pregnancies using marginal structural models (weighted) and modified Poisson regression models.ResultsOf the 5887 pregnancies included, 11.1% were exposed at any time before week 34 to SSRIs, 1.3% to serotonin‐norepinephrine reuptake inhibitors, 0.4% to tricyclic antidepressants, and 0.5% to other antidepressants. The risks of early‐ and late‐onset preeclampsia by exposure status in pregnancy were 0.3% and 3.6% (nonmedicated), 0.4% and 3.7% (SSRIs), 1.5% and 4.1% (serotonin‐norepinephrine reuptake inhibitors), and 7.1% and 10.0% (tricyclic antidepressants). Compared with nonmedicated pregnancies, SSRI‐exposed in mid and late gestation had adjusted relative risks for late‐onset mild preeclampsia of 0.76 (95% confidence interval, 0.38‐1.53) and 1.56 (0.71‐3.44) (weighted models), respectively. There was no association between SSRI exposure in pregnancy and severe late‐onset preeclampsia.ConclusionsWe have provided evidence that SSRI use in early and midpregnancy does not substantially increase the risk of late‐onset preeclampsia.
Characterization of opioid use in sickle cell disease
Authors: Han Jin , Zhou Jifang , Saraf Santosh L. , Gordeuk Victor R. , Calip Gregory S. 
Published: August 2017

AbstractPurposeOpioid analgesics are commonly used to treat vaso‐occlusive pain episodes in sickle cell disease (SCD), but comprehensive evidence characterizing opioid use in this patient population is limited. Our objective was to characterize opioid use patterns among SCD patients using a large nationwide database.MethodsA large, US medical claims database was utilized to identify a cohort of 3882 SCD patients, and characteristics of opioid use were analyzed. Clinical variables including age, gender, medication use, health care utilization, and medical history were evaluated for correlations with opioid use.ResultsForty percent of patients took opioid medications during a 12‐month span, and the prevalence of any opioid use was highest for 20 to 29‐year‐old patients (58%). The median daily opioid dose was 1.85 mg (interquartile range: 0.62–10.68 mg) oral morphine equivalents (OME). While most opioid users took between 0 and 5 mg OME daily, 3% of pediatric patients and 23% of adult patients used more than 30‐mg OME daily. High‐dose opioid use was associated with older age, hydroxyurea therapy, nonsteroidal anti‐inflammatory drug (NSAID) use, and frequent inpatient hospitalizations. In multivariable‐adjusted analyses, patients with vaso‐occlusive complications such as pain crisis (OR = 3.8, 95% CI 2.7–5.3) and avascular necrosis (AVN) (OR = 3.7, 95% CI 2.7–5.1) were associated with high‐dose opioid use.ConclusionsOur study showed that only 40% SCD patients were on opioid analgesics during a 12‐month span. However, a non‐trivial number of patients used a much higher dose of opioids despite a relatively low average daily opioid dose among SCD patients, particularly with vaso‐occlusive complications.
The airway microbiota in early cystic fibrosis lung disease
Authors: Frayman Katherine B. , Armstrong David S. , Grimwood Keith , Ranganathan Sarath C. 
Published: August 2017

AbstractInfection plays a critical role in the pathogenesis of cystic fibrosis (CF) lung disease. Over the past two decades, the application of molecular and extended culture‐based techniques to microbial analysis has changed our understanding of the lungs in both health and disease. CF lung disease is a polymicrobial disorder, with obligate and facultative anaerobes recovered alongside traditional pathogens in varying proportions, with some differences observed to correlate with disease stage. While healthy lungs are not sterile, differences between the lower airway microbiota of individuals with CF and disease‐controls are already apparent in childhood. Understanding the evolution of the CF airway microbiota, and its relationship with clinical treatments and outcome at each disease stage, will improve our understanding of the pathogenesis of CF lung disease and potentially inform clinical management. This review summarizes current knowledge of the early development of the respiratory microbiota in healthy children and then discusses what is known about the airway microbiota in individuals with CF, including how it evolves over time and where future research priorities lie.
New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
Authors: Kinjo Akira R. , Bekker Gert‐Jan , Wako Hiroshi , Endo Shigeru , Tsuchiya Yuko , Sato Hiromu , Nishi Hafumi , Kinoshita Kengo , Suzuki Hirofumi , Kawabata Takeshi , Yokochi Masashi , Iwata Takeshi , Kobayashi Naohiro , Fujiwara Toshimichi , Kurisu Genji , Nakamura Haruki 
Published: August 2017

AbstractThe Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode‐Elastic server for normal mode analysis, a virtual reality system for the eF‐site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.
Homology modeling in a dynamical world
Authors: Monzon Alexander Miguel , Zea Diego Javier , Marino‐Buslje Cristina , Parisi Gustavo 
Published: August 2017

AbstractA key concept in template‐based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well‐established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved using a priori information coming from the structure‐function relationship. We show that protein families with low conformational diversity show a well‐correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair TBM results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.
Functional response and multiple predator effects of two generalist predators preying on Tuta absoluta eggs
Authors: Michaelides Georgios , Sfenthourakis Spyros , Pitsillou Maria , Seraphides Nicos 
Published: August 2017

AbstractBACKROUNDInteractions among invertebrate predators could affect a pest suppression. The hemipteran species Macrolophus pygmaeus (Rambur) and Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae) are natural enemies of several pests in agroecosystems and coexist in tomato crops in Mediterranean countries. By using the multiplicative risk model (MRM) and the substitutive model, the multiple predator effects (MPEs) on prey suppression were calculated when two individuals of the predators foraged at the same densities on South American tomato pinworm, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), eggs.RESULTSEgg consumption increased with increasing egg density and the two predators exhibited a type III functional response. Predation rates were strongly affected by prey density. Using the MRM, we found risk reduction at intraspecific treatments at high prey density. Applying the substitutive model, we detect risk enhancement at interspecific treatments at high egg density.CONCLUSIONSAt low prey densities, most of the interactions were independent, whereas at high densities most interactions were not independent and resulted in prey risk reduction, indicating antagonism between the individuals involved. We also showed that N. tenuis is a more competitive predator species for T. absoluta eggs than M. pygmaeus; however, combination of the two predator species will lead to better pest suppression at high T. absoluta population densities. © 2017 Society of Chemical Industry
How to identify promising metal scavengers? d‐penicillamine with copper as a study case
Authors: Martínez Ana , Vargas Rubicelia , Galano Annia 
Published: August 2017

AbstractTherapeutic chelating agents are used to prevent the effects of the metal accumulation. These are molecules that form complexes with transition metals and they are referred here as metal scavengers. The main idea of this investigation is to recognize the most relevant chemical features to identify potential metal scavengers. d‐penicillamine with copper (DPEN‐Cu) is used for this purpose. The first requirement that must be fulfilled by a good metal scavenger is the exergonicity of the chelating reaction. In the DPEN‐Cu case the most likely complexation pathway was found to have ΔG equal to −24.3 kcal/mol. It is desirable that the chelating molecule could also be a free radical scavenger. d‐penicillamine is a good free radical scavenger following the hydrogen atom transfer reaction. An additional advantage is that the DPEN‐Cu may act as •OH‐inactivating ligand. It is proposed that chelating agents fulfilling these requirements may be a promising candidate to be used in metal chelation therapies as metal scavengers.
Proteome characterization of human pancreatic cyst fluid from intraductal papillary mucinous neoplasm by liquid chromatography/tandem mass spectrometry
Authors: Park Joonho , Han Dohyun , Do Misol , Woo Jongmin , Wang Joseph I. , Han Youngmin , Kwon Wooil , Kim Sun‐Whe , Jang Jin‐Young , Kim Youngsoo 
Published: August 2017

RationaleIn recent years, the molecular components of pancreatic cyst fluid have been used for diagnosis and prognosis. Because the protein markers that are currently used in clinical tests are unreliable, proteomic studies to find new protein markers are being conducted. However, such researches have been limited due to the complexity of pancreatic cyst fluid and the immaturity of proteomic techniques.MethodsTo overcome these limitations and provide a pancreatic cyst proteome dataset, we examined cyst fluid proteome with tandem mass spectrometry. The proteomic analysis was performed using a Orbitrap‐based mass spectrometer (Q‐Exactive) coupled with a 50‐cm‐long nano‐liquid chromatography column. Protein mutations were identified using mutation sequence database search.ResultsA total of 5850 protein groups were identified from microliters of cyst fluid. Among those, 3934 protein groups were reported for the first time in pancreatic cyst fluid. Although high‐abundance proteins were not depleted in the experiment, our dataset detected almost all pancreatic tumor markers such as mucin family members, S100 proteins, and CEA‐related proteins. In addition, 590 protein mutation marker candidates were discovered.ConclusionsWe provide a comprehensive cyst proteome dataset that includes cystic cellular proteins and mutated proteins. Our findings would serve as a rich resource for further IPMN studies and clinical applications. The MS data have been deposited in the ProteomeXchange with identifier PXD005671 (http://proteomecentral.proteomexchange.org/dataset/PXD005671).