bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel therapeutic approach for LPIN1 mutation–associated rhabdomyolysis—The Austrian experience
Authors: Pichler Karin , Scholl‐Buergi Sabine , Birnbacher Robert , Freilinger Michael , Straub Simon , Brunner Jürgen , Zschocke Johannes , Bittner Reginald E. , Karall Daniela 
Published: June 2015

ABSTRACTIntroduction: Lipin 1 gene (LPIN1) mutations lead to cellular energy deficiency and cause up to 50% of the rhabdomyolysis episodes seen in pediatric patients. These episodes are associated with poor prognosis, as treatment options have been limited. We propose a novel therapeutic strategy based on prevention and early treatment of catabolism. Methods: Five patients were diagnosed with LPIN1 mutations. They were instructed to maintain high caloric intake in situations possibly leading to catabolism such as viral infections or excessive physical activity. When an episode of rhabdomyolysis occurred, patients were treated with intravenous high‐concentration glucose at first symptoms. Results: The therapeutic strategies described limited the number of rhabdomyolyis episodes, and the duration of episodes was reduced from 7–10 days, as reported in the literature, to 5 days. Conclusion: In this small series, patients with LPIN1 mutations appear to have benefited from prevention and early treatment of catabolism. Muscle Nerve 52:437–439, 2015
Reference values for jitter recorded by concentric needle electrodes in healthy controls: A multicenter study
Authors: Stålberg Erik , Sanders Donald B. , Ali Sajjad , Cooray Gerald , Leonardis Lea , Löseth Sissel , Machado Flavia , Maldonado Antonio , Martinez‐Aparicio Carmen , Sandberg Arne , Smith Benn , Widenfalk Johan , Aris Kouyoumdjian João 
Published: June 2015

ABSTRACTIntroduction: The aim of this study was to create reference values for jitter measured with concentric needle electrodes. Methods: Operators worldwide contributed recordings from orbicularis oculi (OO), frontalis (FR), and extensor digitorum (ED) muscles in healthy controls. Criteria for acceptable signal quality were agreed upon in advance. Fifteen or 20 recordings of acceptable quality from each muscle were required for voluntary and electrical stimulation recordings, respectively. Results: Recordings from 59 to 92 subjects were obtained for each muscle and activation type. Outlier limits for mean consecutive difference and individual jitter data for voluntary activation were: OO, 31 and 45 µs; FR, 28 and 38 µs; ED, 30 and 43 µs; and for electrical stimulation they were: OO, 27 and 36 µs; FR, 21 and 28 µs; ED, 24 and 35 µs. Conclusion: Reference jitter values from concentric needle electrode recordings were developed from signals of defined quality while seeking to avoid creating supernormal values. Muscle Nerve 53: 351–362, 2016
Sparse solution of nonnegative least squares problems with applications in the construction of probabilistic Boolean networks
Authors: Wen You‐Wei , Wang Man , Cao Zhiying , Cheng Xiaoqing , Ching Wai‐Ki , Vassiliadis Vassilios S. 
Published: June 2015

SummaryIn this paper, we consider finding a sparse solution of nonnegative least squares problems with a linear equality constraint. We propose a projection‐based gradient descent method for solving huge size constrained least squares problems. Traditional Newton‐based methods require solving a linear system. However, when the matrix is huge, it is neither practical to store it nor possible to solve it in a reasonable time. We therefore propose a matrix‐free iterative scheme for solving the minimizer of the captured problem. This iterative scheme can be explained as a projection‐based gradient descent method. In each iteration, a projection operation is performed to ensure the solution is feasible. The projection operation is equivalent to a shrinkage operator, which can guarantee the sparseness of the solution obtained. We show that the objective function is decreasing. We then apply the proposed method to the inverse problem of constructing a probabilistic Boolean network. Numerical examples are then given to illustrate both the efficiency and effectiveness of our proposed method. Copyright © 2015 John Wiley & Sons, Ltd.
Thermodynamics of Self‐Assembly of Dicarboxylate Ions with Binuclear Lanthanide Complexes
Authors: Sørensen Thomas Just , Hill Leila R. , Faulkner Stephen 
Published: June 2015

AbstractSelf‐assembly of a range of carboxylic acids (benzoic acid, dinicotinic acid, nicotinic acid, and isophthalic acid) with the europium complex of 5‐nitro‐α,α′‐bis(DO3Ayl)‐m‐xylene (where DO3A is 1,4,7,10‐tetraazacyclododecane‐1,4,7‐triacetic acid) has been explored to establish the thermodynamics of binding in a range of solvent systems and in a range of aqueous buffer solutions. In this system, profound effects are observed as a consequence of competition by the hydroxide ion, which outcompetes even dinicotinate at high pH. In the case of isophthalate, which binds most strongly, and dinicotinate, both enthalpic and entropic contributions to binding have been identified. The europium complex with 5‐nitro‐α,α′‐bis(DO3Ayl)‐m‐xylene is found to have a solution structure significantly different from the related europium complex of 5‐amino‐α,α′‐bis(DO3Ayl)‐m‐xylene. It is found that phosphate binds strongly to the europium complex of the nitro derivate but not to the europium complex of amino derivative. Lactate, citrate, and pyruvate also bind strongly to 5‐nitro‐α,α′‐bis(Eu⋅DO3Ayl)‐m‐xylene, and it is concluded that the solution structure of this binuclear lanthanide complex is significantly different from that of the amino‐substituted complex.
Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect
Authors: Yan Zhiqiang , Wang Jin 
Published: June 2015

ABSTRACTSolvation effect is an important factor for protein–ligand binding in aqueous water. Previous scoring function of protein–ligand interactions rarely incorporates the solvation model into the quantification of protein–ligand interactions, mainly due to the immense computational cost, especially in the structure‐based virtual screening, and nontransferable application of independently optimized atomic solvation parameters. In order to overcome these barriers, we effectively combine knowledge‐based atom–pair potentials and the atomic solvation energy of charge‐independent implicit solvent model in the optimization of binding affinity and specificity. The resulting scoring functions with optimized atomic solvation parameters is named as specificity and affinity with solvation effect (SPA‐SE). The performance of SPA‐SE is evaluated and compared to 20 other scoring functions, as well as SPA. The comparative results show that SPA‐SE outperforms all other scoring functions in binding affinity prediction and “native” pose identification. Our optimization validates that solvation effect is an important regulator to the stability and specificity of protein–ligand binding. The development strategy of SPA‐SE sets an example for other scoring function to account for the solvation effect in biomolecular recognitions. Proteins 2015; 83:1632–1642. © 2015 Wiley Periodicals, Inc.
Alternative Routes to Induce Naïve Pluripotency in Human Embryonic Stem Cells
Authors: Duggal Galbha , Warrier Sharat , Ghimire Sabitri , Broekaert Dorien , Van der Jeught Margot , Lierman Sylvie , Deroo Tom , Peelman Luc , Van Soom Ann , Cornelissen Ria , Menten Björn , Mestdagh Pieter , Vandesompele Jo , Roost Matthias , Slieker Roderick C. , Heijmans Bastiaan T. , Deforce Dieter , De Sutter Petra , De Sousa Lopes Susana Chuva , Heindryckx Björn 
Published: June 2015

Abstract
Human embryonic stem cells (hESCs) closely resemble mouse epiblast stem cells exhibiting primed pluripotency unlike mouse ESCs (mESCs), which acquire a naïve pluripotent state. Efforts have been made to trigger naïve pluripotency in hESCs for subsequent unbiased lineage-specific differentiation, a common conundrum faced by primed pluripotent hESCs due to heterogeneity in gene expression existing within and between hESC lines. This required either ectopic expression of naïve genes such as NANOG and KLF2 or inclusion of multiple pluripotency-associated factors. We report here a novel combination of small molecules and growth factors in culture medium (2i/LIF/basic fibroblast growth factor + Ascorbic Acid + Forskolin) facilitating rapid induction of transgene-free naïve pluripotency in hESCs, as well as in mESCs, which has not been shown earlier. The converted naïve hESCs survived long-term single-cell passaging, maintained a normal karyotype, upregulated naïve pluripotency genes, and exhibited dependence on signaling pathways similar to naïve mESCs. Moreover, they undergo global DNA demethylation and show a distinctive long noncoding RNA profile. We propose that in our medium, the FGF signaling pathway via PI3K/AKT/mTORC induced the conversion of primed hESCs toward naïve pluripotency. Collectively, we demonstrate an alternate route to capture naïve pluripotency in hESCs that is fast, reproducible, supports naïve mESC derivation, and allows efficient differentiation. Stem Cells 2015;33:2686–2698
TRANSLATE
Authors: Goodwin Amanda P. , Jiménez Robert 
Published: June 2015

AbstractThis teaching tip shares a research‐based instructional model that uses translation to improve the English reading comprehension of English Learners. Within this instruction, English learners work collaboratively in small groups and use translation to facilitate understandings of their required English language arts curriculum. Students are taught to identify key excerpts and to use selected cognitive strategies to facilitate translation and comprehension. After students create translated texts, they compare and evaluate their translations, and then summarize their newfound understandings. The three main lesson components are described and examples and instructional resources are provided to help educators implement the model within their own teaching. We also provide suggestions of productive teacher moves for teachers who do speak students’ native languages.
The wing and the eye: a parsimonious theory for scaling and growth control?
Authors: Romanova‐Michaelides Maria , Aguilar‐Hidalgo Daniel , Jülicher Frank , Gonzalez‐Gaitan Marcos 
Published: June 2015

How a developing organ grows and patterns to its final shape is an important question in developmental biology. Studies of growth and patterning in the Drosophila wing imaginal disc have identified a key player, the morphogen Decapentaplegic (Dpp). These studies provided insights into our understanding of growth control and scaling: expansion of the Dpp gradient correlated with the growth of the tissue. A recent report on growth of a Drosophila organ other than the wing, the eye imaginal disc, prompts a reconsideration of our models of growth control. Despite striking differences between the two, the Dpp gradient scales with the target tissues of both organs and the growth of both the wing and the eye is controlled by Dpp. The goal of this review is to discuss whether a parsimonious model of scaling and growth control can explain the relationship between the Dpp gradient and growth in these two different developmental systems. WIREs Dev Biol 2015, 4:591–608. doi: 10.1002/wdev.195This article is categorized under:

Establishment of Spatial and Temporal Patterns > Gradients
Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing
Metabolic network modeling of microbial communities
Authors: Biggs Matthew B. , Medlock Gregory L. , Kolling Glynis L. , Papin Jason A. 
Published: June 2015

AbstractGenome‐scale metabolic network reconstructions and constraint‐based analyses are powerful methods that have the potential to make functional predictions about microbial communities. Genome‐scale metabolic networks are used to characterize the metabolic functions of microbial communities via several techniques including species compartmentalization, separating species‐level and community‐level objectives, dynamic analysis, the ‘enzyme‐soup’ approach, multiscale modeling, and others. There are many challenges in the field, including a need for tools that accurately assign high‐level omics signals to individual community members, the need for improved automated network reconstruction methods, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be corresponding advances in the fields of ecology, health science, and microbial community engineering. WIREs Syst Biol Med 2015, 7:317–334. doi: 10.1002/wsbm.1308This article is categorized under:

Analytical and Computational Methods > Computational Methods
Biological Mechanisms > Metabolism
High spatial resolution laser cavity extinction and laser-induced incandescence in low-soot-producing flames
Authors: Tian B. , Gao Y. , Balusamy S. , Hochgreb S. 
Published: June 2015

Abstract
Accurate measurement techniques for in situ determination of soot are necessary to understand and monitor the process of soot particle production. One of these techniques is line-of-sight extinction, which is a fast, low-cost and quantitative method to investigate the soot volume fraction in flames. However, the extinction-based technique suffers from relatively high measurement uncertainty due to low signal-to-noise ratio, as the single-pass attenuation of the laser beam intensity is often insufficient. Multi-pass techniques can increase the sensitivity, but may suffer from low spatial resolution. To overcome this problem, we have developed a high spatial resolution laser cavity extinction technique to measure the soot volume fraction from low-soot-producing flames. A laser beam cavity is realised by placing two partially reflective concave mirrors on either side of the laminar diffusion flame under investigation. This configuration makes the beam convergent inside the cavity, allowing a spatial resolution within 200 μm, whilst increasing the absorption by an order of magnitude. Three different hydrocarbon fuels are tested: methane, propane and ethylene. The measurements of soot distribution across the flame show good agreement with results using laser-induced incandescence (LII) in the range from around 20 ppb to 15 ppm.
Myocardial glucose uptake in patients with the m.3243A > G mutation in mitochondrial DNA
Authors: Lindroos Markus M. , Pärkkä Jussi P. , Taittonen Markku T. , Iozzo Patricia , Kärppä Mikko , Hassinen Ilmo E. , Knuuti Juhani , Nuutila Pirjo , Majamaa Kari 
Published: June 2015

AbstractMitochondrial mutations impair glucose oxidation and increase glucose uptake in cell cultures and lead to cardiomyopathy in patients. Here we characterize cardiac glucose uptake in 14 patients with the m.3243A > G mutation in mitochondrial DNA. The 14 patients with m.3243A > G and 13 controls were similar in age, physical activity and body mass index. Ten patients had diabetes. Left ventricular glucose uptake per tissue mass (LVGU) was measured with 2‐[18 F]fluoro‐2‐deoxyglucose positron emission tomography during euglycemic hyperinsulinemia. Cardiac morphology and function were assessed with magnetic resonance imaging. We found that the LVGU was 25 % lower in the patients than that in the controls (P = 0.029). LVGU was inversely correlated with mutation heteroplasmy, glycated haemoglobin and fasting lactate in patients. The seven patients with mutation heteroplasmy ≥ 49 % had 44 % lower LVGU than the seven patients with heteroplasmy < 49 %. This difference remained significant after adjustment for concurrent free fatty acid concentration or glycated haemoglobin or glucose uptake in skeletal muscle or all (p < 0.048 [All]). Patients with m.3243A > G had a lower stroke volume and a higher heart rate than the controls, whereas cardiac output and work were similar. Myocardial glucose uptake is not increased but decreased with a threshold effect pattern in patients with the m.3243A > G mutation. The glucose hypometabolism adds to the impaired cardiac energetics and likely contributes to the progression of the mitochondrial cardiomyopathy.
Induced Abortions and Birth Outcomes of Women With a History of Severe Psychosocial Problems in Adolescence
Authors: Lehti V. , Gissler M. , Suvisaari J. , Manninen M. 
Published: June 2015

AbstractObjectiveTo increase knowledge on the reproductive health of women who have been placed in a residential school, a child welfare facility for adolescents with severe psychosocial problems.MethodsAll women (n = 291) who lived in the Finnish residential schools on the last day of the years 1991, 1996, 2001 and 2006 were included in this study and compared with matched general population controls. Register-based information on induced abortions and births was collected until the end of the year 2011.ResultsCompared to controls, women with a residential school history had more induced abortions. A higher proportion of their births took place when they were teenagers or even minors. They were more often single, smoked significantly more during pregnancy and had a higher risk of having a preterm birth or a baby with a low birth weight.ConclusionsThe findings have implications for the planning of preventive and supportive interventions that aim to increase the well-being of women with a residential school history and their offspring.
Median splits, Type II errors, and false–positive consumer psychology: Don't fight the power
Authors: McClelland Gary H. , Lynch, John G. , Irwin Julie R. , Spiller Stephen A. , Fitzsimons Gavan J. 
Published: June 2015

AbstractConsiderable prior statistical work has criticized replacing a continuously measured variable in a general linear model with a dichotomy based on a median split of that variable. Iacobucci, Posovac, Kardes, Schneider, and Popovich (2015‐in this issue) defend the practice of “median splits” using both conceptual arguments and simulations. We dispute their conceptual arguments, and we have identified technical errors in their simulations that dramatically change the conclusions that follow from those simulations. We show that there are no real benefits to median splits, and there are real costs in increases in Type II errors through loss of power and increases in Type I errors through false–positive consumer psychology. We conclude that median splits remain a bad idea.
Bacille Calmette‐Guerin can induce cellular apoptosis of urothelial cancer directly through toll‐like receptor 7 activation
Authors: Yu Dah‐Shyong , Wu Chia‐Lun , Ping Szu‐Yuan , Keng Cheng , Shen Kun‐Hung 
Published: June 2015

AbstractImmunotherapy using bacille Calmette‐Guerin (BCG) instillation is the mainstay treatment modality for superficial urothelial cancer (UC) through toll‐like receptor (TLR) activation of cognitive immune response. We investigated the roles of TLR7 in the activation of apoptosis in UC cells after BCG treatment. The in vitro cytotoxicity effect of BCG on UC cells was measured by a modified 3‐(4,5‐dimethylthiazo‐2‐yl)‐2,5‐diphenyl tetrazolium assay. Expressions of TLR7 mRNA and protein in native UC cells prior to and after BCG treatment were analyzed using real‐time quantitative polymerase chain reaction and western blot methods. Phagocytotic processes after BCG treatment in UC cells were observed microscopically using a specific immunostain, subsequent cellular apoptosis‐related signals induced by TLR7 were analyzed by western blot. Low‐grade UC cells, TSGH8301, showed significant cellular death (4.23‐fold higher than the high‐grade UC cells T24 and J82) when treated with BCG and the BCG cytotoxicity was displayed in a dose–time‐dependent manner. TSGH8301 cells had the highest content of TLR7 mRNA, 7.2‐ and 4.5‐fold higher than that of T24 and J82 cells, respectively. TLR7 protein expression was also significantly increased in TSGH8301 cells. Phagocytosis‐related markers, including beclin 1, ATG2, and LC3, were increased when TSGH8301 cells were treated by BCG. Interleukin‐1 receptor‐associated kinases 2 and 4 were also increased markedly in TSGH8301 cells. On the contrary, cellular apoptosis of TSGH8301 cells decreased by 34% when TLR7 activation was suppressed by the TLR antagonist IRS661 after BCG treatment. Our findings suggest that well differentiated TCC cells have higher expression of TLR7 and BCG can drive cellular death of TCC cells directly via TLR7 activation and related apoptotic pathway.
Non-axisymmetric flows in a differential-disk rotating system
Authors: Vo Tony , Montabone Luca , Read Peter L. , Sheard Gregory J. 
Published: June 2015

The non-axisymmetric structure of an unstable Stewartson shear layer generated via a differential rotation between flush disks and a cylindrical enclosure is investigated numerically using both three-dimensional direct numerical simulation and a quasi-two-dimensional model. Previous literature has only considered the depth-independent quasi-two-dimensional model due to its low computational cost. The three-dimensional model implemented here highlights the supercritical instability responsible for the polygonal deformation of the shear layer in the linear and nonlinear growth regimes and reveals that linear stability analysis is capable of accurately determining the preferred azimuthal wavenumber for flow conditions near the onset of instability. This agreement is lost for sufficiently forced flows where nonlinear effects encourage the coalescence of vortices towards lower-wavenumber structures. Time-dependent flows are found for large Reynolds numbers defined based on the Stewartson layer thickness and azimuthal velocity differential. However, this temporal behaviour is not solely characterized by Reynolds number but is rather a function of both the Rossby and Ekman numbers. At high Ekman and Rossby numbers, unsteady flow emerges through a small-scale azimuthal destabilization of the axial jets within the Stewartson layers; at low Ekman numbers, unsteady flow emerges through a modulation in the strength of one of the axial vortices rolled up by non-axisymmetric instability of the Stewartson layer.
“Civilizing” the Colonial Subject: The Co-Evolution of State and Slavery in South Carolina, 1670–1739
Authors: Grant Daragh 
Published: June 2015

AbstractSouth Carolina was a staggeringly weak polity from its founding in 1670 until the 1730s. Nevertheless, in that time, and while facing significant opposition from powerful indigenous neighbors, the colony constructed a robust plantation system that boasted the highest slave-to-freeman ratio in mainland North America. Taking this fact as a point of departure, I examine the early management of unfree labor in South Carolina as an exemplary moment of settler-colonial state formation. Departing from the treatment of state formation as a process of centralizing “legitimate violence,” I investigate how the colonial state, and in particular the Commons House of Assembly, asserted an exclusive claim to authority by monopolizing the question of legitimacy itself. In managing unfree laborers, the colonial state extended its authority over supposedly private relations between master and slave and increasingly recast slavery in racial terms. This recasting of racial slavery rested, I argue, on a distinction, pervasive throughout English North America, which divided the world into spheres of savagery and civility. Beneath the racial reordering of colonial life, the institution of slavery was rooted in the same ideological distinction by which the colonial state's claims to authority were justified, with the putative “savagery” of the slave or of the Indian being counterpoised to the supposed civility of English settlers. This article contributes to the literatures on Atlantic slavery and American colonial history, and invites comparison with accounts of state formation and settler colonialism beyond Anglo-America.