bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimates of biological variation in routinely measured biochemical analytes in clinically healthy dogs
Authors: Ruaux Craig G. , Carney Patrick C. , Suchodolski Jan S. , Steiner Jörg M. 
Published: October 2012

BackgroundThe degree of biological variation in routinely measured concentrations and activities of biochemical analytes has not been well defined in client‐owned pet dogs.ObjectivesThe aim of this study was to define indices of biological variation and, where appropriate, indices of individuality and critical change values for routinely measured serum biochemical analytes in a group of clinically healthy dogs owned and housed privately.MethodsA prospective cohort study was conducted. Serum samples obtained from clinically healthy adult dogs at varying intervals over a 12‐week period were analyzed. For each sample, a panel of 14 analytes was measured. Three levels of outlier analyses were applied (analytical, intra‐individual, and inter‐individual), followed by nested ANOVA to calculate intra‐individual, inter‐individual, and analytical coefficients of variation (CVI, CVG, and CVA, respectively).ResultsSpecimens from 11 dogs were analyzed. Individuality indices ranged from 0.9 for glucose and total triglyceride concentrations to 3.4 for ALT activity. Analytical variation (CVA) was > ½ CVI for 9/14 analytes, failing to meet criteria for acceptable analytical variation when defining critical change values. Where analyzer performance was acceptable, critical change values ranged from 26.4% for glucose concentration to 84.0% for total triglyceride concentration.ConclusionsMany frequently measured analytes included in routine serum biochemical panels have high individuality. Thus, use of standard reference intervals to monitor changes over time in an individual is likely to miss meaningful biological change.
Theileriosis in a reindeer (Rangifer tarandus tarandus) associated with a potentially novel Theileria sp
Authors: Garner Bridget C. , Holman Patricia , Berent Linda M. 
Published: October 2012

AbstractA 5‐year‐old male neutered reindeer (Rangifer tarandus tarandus) from Missouri was presented with a 3‐week history of anorexia, respiratory distress, lethargy, and weight loss. Blood smear review revealed that a small percentage of RBCs contained small (1–2 μm in length) pleomorphic piroplasms (signet ring, rod‐ or pear‐shaped, and elongate forms) with an eccentric magenta nucleus and basophilic cytoplasm. Nested PCR to specifically amplify a portion of the piroplasm small subunit ribosomal RNA (SSU rRNA) gene was performed on DNA extracted from an EDTA specimen of whole blood. Subsequent sequence analyses showed similarity between the reindeer hemoparasite and Theileria spp SSU rRNA gene sequences in the GenBank database, with highest similarity to those of a Theileria sp in a White‐tailed deer from North Texas (AY735132, AY735133). The reindeer and North Texas Theileria sp are genetically distinct from, albeit closely related to, the White‐tailed deer Theileria sp (subsequently referred to as T cervi). To the authors' knowledge, this is the first identification of Theileria of this genotype in a reindeer. Historically, T tarandirangiferis infection was found with associated mortality in reindeer in Russia, but reports predate molecular characterization. Hence, the relationship of T tarandirangiferis with either T cervi or this agent remains unknown. T cervi is not typically pathogenic in White‐tailed deer in the US unless the animal is immune‐compromised by stress or disease; however, mortality from T cervi infection in reindeer has been reported.
Incorporating individual variability into mark–recapture models
Authors: Ford Jessica H. , Bravington Mark V. , Robbins Jooke 
Published: October 2012

Summary

Understanding individual variation is a key challenge in ecology. Inherent individual differences in movement and behaviour pose fundamental problems in the analysis of mark–recapture data as unmodelled individual differences can bias estimates of population size and survival rates. Multi‐state mark–recapture models have been the focus of much recent research but have yet to explicitly incorporate individual variability.

We use a multi‐state mark–recapture model with individual‐level random effects, built in admb‐re, a software tool that automatically provides an accurate analytical approximation of the likelihood which is otherwise intractable. We tested the model using simulation studies and applied the model to data from North Atlantic humpback whales in the Stellwagen Bank National Marine Sanctuary where heterogeneity is apparent in both sighting probability and site preference.

Simulation studies demonstrated accurate estimation of true parameter values with random effects models but bias sometimes resulted from fitting simpler models.

In application to data from the North Atlantic humpback whales, we were able to estimate both annual variation in the local population and three measures of individual‐level variation. Results indicate considerable heterogeneity within this population in both sighting probability and site preference. Ignoring random effects led to bias in estimates of proportion of time within a marine reserve.
A penalized likelihood approach to pooling estimates of covariance components from analyses by parts
Authors: Meyer K. 
Published: October 2012

SummaryEstimates of covariance matrices for numerous traits are commonly obtained by pooling results from a series of analyses of subsets of traits. A penalized maximum‐likelihood approach is proposed to combine estimates from part analyses while constraining the resulting overall matrices to be positive definite. In addition, this provides the scope for ‘improving’ estimates of individual matrices by applying a penalty to the likelihood aimed at borrowing strength from their phenotypic counterpart. A simulation study is presented showing that the new method performs well, yielding unpenalized estimates closer to results from multivariate analyses considering all traits, than various other techniques used. In particular, combining results for all sources of variation simultaneously minimizes deviations in phenotypic estimates if sampling covariances can be approximated. A mild penalty shrinking estimates of individual covariance matrices towards their sum or estimates of canonical eigenvalues towards their mean proved advantageous in most cases. The method proposed is flexible, computationally undemanding and provides combined estimates with good sampling properties and is thus recommended as alternative to current methods for pooling.
Transcriptional suppression of the neuronal PAS domain 4 (Npas4) gene by stress via the binding of agonist‐bound glucocorticoid receptor to its promoter
Authors: Furukawa‐Hibi Yoko , Yun Jaesuk , Nagai Taku , Yamada Kiyofumi 
Published: October 2012

AbstractNeuronal PAS domain 4 (NPAS4), a brain‐specific helix–loop–helix transcription factor, has recently been shown to regulate the development of GABAergic inhibitory neurons. We previously reported that Npas4 mRNA expression levels were reduced in the hippocampus of mice exposed to social isolation or restraint stress, which was accompanied by impairment of memory, emotional behavior, and hippocampal neurogenesis. Therefore, the reduction of NPAS4 expression may play a role in stress‐induced brain dysfunction. In this study, to investigate the transcriptional regulation of Npas4 by stress, we focused on the effect of glucocorticoids (GCs) upon Npas4 transcription. Corticosterone treatment reduced Npas4 expression in the frontal cortex and hippocampus, whereas adrenalectomy caused an increase in expression. GC receptor (GR) antagonist, mifepristone, inhibited the stress‐induced reduction of Npas4 expression. Putative negative glucocorticoid response elements (GREs) were found −2000 to −1000 upstream of the Npas4 transcription initiation site. Npas4 promoter activity was increased by mifepristone or by mutation of the negative GRE sequences. A chromatin immunoprecipitation assay revealed that restraint stress increased the binding of GR to Npas4 promoter region in the hippocampus. These results suggest that transcription of Npas4 is down‐regulated by stress via the binding of agonist‐bound GR to its promoter.
Neuroprotective actions of Glucagon‐like peptide‐1 in differentiated human neuroprogenitor cells
Authors: Velmurugan Kalpana , Bouchard Ron , Mahaffey Gregory , Pugazhenthi Subbiah 
Published: October 2012

AbstractGlucagon‐like peptide‐1 (GLP‐1)‐based therapies are currently available for the treatment of type 2 diabetes, based on their actions on pancreatic β cells. GLP‐1 is also known to exert neuroprotective actions. To determine its mechanism of action, we developed a neuron‐rich cell culture system by differentiating human neuroprogenitor cells in the presence of a combination of neurotrophins and retinoic acid. The neuronal nature of these cells was characterized by neurogenesis pathway‐specific array. GLP‐1 receptor expression was seen mainly in the neuronal population. Culture of neurons in the presence of Aβ oligomers resulted in the induction of apoptosis as shown by the activation of caspase‐3 and caspase‐6. Exendin‐4, a long‐acting analog of GLP‐1, protected the neurons from apoptosis induced by Aβ oligomers. Exendin‐4 stimulated cyclic AMP response element binding protein phosphorylation, a regulatory step in its activation. A transient transfection assay showed induction of a reporter linked to CRE site‐containing human brain‐derived neurotrophic factor promoter IV, by the growth factor through multiple signaling pathways. The anti‐apoptotic action of exendin‐4 was lost following down‐regulation of cAMP response element binding protein. Withdrawal of neurotrophins resulted in the loss of neuronal phenotype of differentiated neuroprogenitor cells, which was prevented by incubation in the presence of exendin‐4. Diabetes is a risk factor in the pathogenesis of Alzheimer's disease. Our findings suggest that GLP‐1‐based therapies can decrease the incidence of Alzheimer's disease among aging diabetic population.
Long‐term exogenous application of melatonin delays drought‐induced leaf senescence in apple
Authors: Wang Ping , Sun Xun , Li Chao , Wei Zhiwei , Liang Dong , Ma Fengwang 
Published: October 2012

AbstractTo examine the potential roles of melatonin in drought tolerance, we tested the effects of its long‐term exogenous application on ‘Hanfu’ apple (Malus domestica Borkh.). When 100 μm melatonin was added to soils under drought conditions, the resultant oxidative stress was eased and leaf senescence was delayed. This molecule significantly reduced chlorophyll degradation and suppressed the up‐regulation of senescence‐associated gene 12 (SAG12) and pheophorbide a oxygenase (PAO). Such treatment also alleviated the inhibition of photosynthesis brought on by drought stress. We also investigated quenching and the efficiency of Photosystem II (PSII) photochemistry under dark and light conditions and found that melatonin helped to maintain better function of PSII under drought. The addition of melatonin also controlled the burst of hydrogen peroxide, possibly through direct scavenging and by enhancing the activities of antioxidative enzymes and the capacity of the ascorbate–glutathione cycle. Thus, understanding this effect of melatonin on drought tolerance introduces new possibilities to use this compound for agricultural purposes.
Production and Characterization of the Intra‐ and Extracellular Carbohydrates and Polymeric Substances (EPS) of Three Sea‐Ice Diatom Species, and Evidence for a Cryoprotective Role for EPS
Authors: Aslam Shazia N. , Cresswell‐Maynard Tania , Thomas David N. , Underwood Graham J. C. 
Published: October 2012

Diatoms and their associated extracellular polymeric substances (EPS) are major constituents of the microalgal assemblages present within sea ice. Yields and chemical composition of soluble and cell‐associated polysaccharides produced by three sea‐ice diatoms, Synedropsis sp., Fragilariopsis curta, and F. cylindrus, were compared. Colloidal carbohydrates (CC) contained heteropolysaccharides rich in mannose, xylose, galactose, and glucose. Synedropsis sp. CC consisted mainly of carbohydrates <8 kDa size, with relatively soluble EPS, compared to high proportions of less‐soluble EPS produced by both Fragilariopsis spp. F. curta colloidal EPS contained high concentrations of amino sugars (AS). Both Fragilariopsis species had high yields of hot bicarbonate (HB) soluble EPS, rich in xylose, mannose, galactose, and fucose (and AS in F. cylindrus). All species had frustule‐associated EPS rich in glucose–mannose. Nutrient limitation resulted in declines in EPS yields and in glucose content of all EPS fractions. Significant similarities between EPS fractions from cultures and different components of natural EPS from Antarctic sea ice were found. Increased salinity (52) reduced growth, but increased yields of EPS in Fragilariopsis cylindrus. Ice formation was inhibited byF. cylindrus, EPS, and by enhanced EPS content (additional xanthan gum) down to −12°C, with growth rate reduced in the presence of xanthan. Differences in the production and composition of EPS between Synedropsis sp. and Fragilariopsis spp., and the association between EPS, freezing and cell survival, supports the hypothesis that EPS production is a strategy to assist polar ice diatoms to survive the cold and saline conditions present in sea ice.
Oxygen Transport in the Microcirculation and Its Regulation
Authors: Pittman Roland N. 
Published: October 2012

AbstractObjectiveCells require energy to carry out their functions and they typically use oxidative phosphorylation to generate the needed ATP. Thus, cells have a continuous need for oxygen, which they receive by diffusion from the blood through the interstitial fluid. The circulatory system pumps oxygen‐rich blood through a network of increasingly minute vessels, the microcirculation. The structure of the microcirculation is such that all cells have at least one nearby capillary for diffusive exchange of oxygen and red blood cells release the oxygen bound to hemoglobin as they traverse capillaries.MethodsThis review focuses first on the historical development of techniques to measure oxygen at various sites in the microcirculation, including the blood, interstitium, and cells.ResultsNext, approaches are described as to how these techniques have been employed to make discoveries about different aspects of oxygen transport. Finally, ways in which oxygen might participate in the regulation of blood flow toward matching oxygen supply to oxygen demand is discussed.ConclusionsOverall, the transport of oxygen to the cells of the body is one of the most critical functions of the cardiovascular system and it is in the microcirculation where the final local determinants of oxygen supply, oxygen demand, and their regulation are decided.
Nuclear factor‐κB and p38 mitogen‐activated protein kinase signaling pathways are critically involved in Porphyromonas gingivalis lipopolysaccharide induction of lipopolysaccharide‐binding protein expression  in human oral keratinocytes
Authors: Ding P.‐H. , Wang C.‐Y. , Darveau R.P. , Jin L.J. 
Published: October 2012

SummaryLipopolysaccharide (LPS) ‐binding protein (LBP) plays a crucial role in innate host response to bacterial challenge. Porphyromonas gingivalis is a keystone pathogen in periodontal disease and the shift of P. gingivalis LPS lipid A structure from penta‐acylated (LPS1690) to tetra‐acylated (LPS1435/1449) isoform may significantly contribute to periodontal pathogenesis. We recently demonstrated that LBP is expressed in human gingiva and contributes to periodontal homeostasis. Furthermore, different isoforms of P. gingivalis LPS differently modulate the immuno‐inflammatory response, and P. gingivalis LPS1690 induces LBP expression in human oral keratinocytes (HOKs). This study further examined the signaling mechanisms of P. gingivalis LPS1690‐induced and Escherichia coli LPS‐induced LBP expression in HOKs. Both P. gingivalis LPS1690 and E. coli LPS were potent inducers of LBP expression in HOKs. The former activated phosphorylation of IκBα, p65, p38 mitogen‐activated protein kinase (MAPK) and stress‐activated protein kinase/c‐Jun N‐terminal kinase (SAPK/JNK), whereas the latter phosphorylated IκBα, p38 MAPK and SAPK/JNK. A nuclear translocation of NF‐κB transcription factor was confirmed upon stimulation by both forms of LPS. Further blocking assay showed that P. gingivalis LPS1690 induction of LBP was through NF‐κB and p38 MPAK pathways, whereas E. coli LPS‐induced LBP expression was mediated by NF‐κB, p38 MPAK and JNK pathways. This study demonstrates that NF‐κB and p38 MAPK signaling pathways are involved in P. gingivalis LPS1690 induction of LBP expression in HOKs. The current findings could enhance the understanding of the molecular mechanisms of innate defense in maintenance of periodontal homeostasis.
Genetic variation at KIT locus may predispose to melanoma
Authors: Bourillon Agnes , Hu Hui‐Han , Hetet Gilles , Lacapere Jean‐Jacques , André Jocelyne , Descamps Vincent , Basset‐Seguin Nicole , Ogbah Zighereda , Puig Susana , Saiag Philippe , Bagot Martine , Bensussan Armand , Grandchamp Bernard , Dumaz Nicolas , Soufir Nadem 
Published: October 2012

SummaryAs loss of KIT frequently occurs in melanoma progression, we hypothesized that KIT is implicated in predisposition to melanoma (MM). Thus, we sequenced the KIT coding region in 112 familial MM cases and 143 matched controls and genotyped tag single‐nucleotide polymorphisms (SNPs) in two cohorts of melanoma patients and matched controls. Five rare KIT substitutions, all predicted possibly or probably deleterious, were identified in five patients, but none in controls [RR = 2.26 (1.26–2.26)]. Expressed in melanocyte lines, three substitutions inhibited KIT signaling. Comparison with exomes database (7020 alleles) confirmed a significant excess of rare deleterious KIT substitutions in patients. Additionally, a common SNP, rs2237028, was associated with MM risk, and 6 KIT variants were associated with nevus count. Our data strongly suggest that rare KIT substitutions predispose to melanoma and that common variants at KIT locus may also impact nevus count and melanoma risk.
Gray Hausdorff distance measure for medical image comparison in dermatology: Evaluation of treatment effectiveness by image similarity
Authors: Spyridonos Panagiota , Gaitanis Georgios , Bassukas Ioannis D. , Tzaphlidou Margaret 
Published: October 2012

AbstractIntroductionIn clinical dermatology, the stabilization of the overall skin condition can be in many cases the earliest qualitative measure of the effectiveness of the therapeutic intervention. Subjective image comparisons, that offer empirical ‘qualitative’ judgments of degrees of image similarities, are traditionally employed by the involved physicians.ObjectivesTo quantify, by means of an image similarity metric, the degree of stabilization of an expanding skin disease, and to identify the situation of ‘no further change’ of the skin condition of the patient, providing thus the physician with an early, objective measure of the efficacy of the used therapy.MethodsFor treatment assessment, a variant of gray Hausdorff distance metric was employed to compare images of lesional skin segments of a patient, taken at different time points during a therapeutic course. Prior to image comparison, an effective preprocessing scheme was adapted to constrain wide pose and light variations. The proposed similarity algorithm was tested on raw clinical image data sets of patients diagnosed with toxic epidermal necrolysis, a life‐threatening condition with rapid evolution. Fine tuning of algorithm's parameters was optimized using Precision‐Recall curves.ResultsProposed image comparison method resulted in a high‐degree of image similarity (about 96%) between pictures taken at second and fifth day of hospitalization. Current similarity results substantiate a significant agreement between the computer‐treatment assessment, by means of image comparison, and the corresponding clinical experts’ review of skin condition.ConclusionObjective evidence of ‘no further change’ situation may provide (a) intuitive clinical decision support to dermatologists in assessing aggressive skin conditions, where the timely evaluation of treatment response is of vital importance and (b) a versatile end‐point measure for corresponding therapeutic clinical trials.
Apical myosin XI anticipates F‐actin during polarized growth of Physcomitrella patens cells
Authors: Furt Fabienne , Liu Yen‐Chun , Bibeau Jeffrey P. , Tüzel Erkan , Vidali Luis 
Published: October 2012

SummaryTip growth is essential for land colonization by bryophytes, plant sexual reproduction and water and nutrient uptake. Because this specialized form of polarized cell growth requires both a dynamic actin cytoskeleton and active secretion, it has been proposed that the F‐actin‐associated motor myosin XI is essential for this process. Nevertheless, a spatial and temporal relationship between myosin XI and F‐actin during tip growth is not known in any plant cell. Here, we use the highly polarized cells of the moss Physcomitrella patens to show that myosin XI and F‐actin localize, in vivo, at the same apical domain and that both signals fluctuate. Surprisingly, phase analysis shows that increase in myosin XI anticipates that of F‐actin; in contrast, myosin XI levels at the tip fluctuate in identical phase with a vesicle marker. Pharmacological analysis using a low concentration of the actin polymerization inhibitor latrunculin B showed that the F‐actin at the tip can be significantly diminished while myosin XI remains elevated in this region, suggesting that a mechanism exists to cluster myosin XI‐associated structures at the cell's apex. In addition, this approach uncovered a mechanism for actin polymerization‐dependent motility in the moss cytoplasm, where myosin XI‐associated structures seem to anticipate and organize the actin polymerization machinery. From our results, we inferred a model where the interaction between myosin XI‐associated vesicular structures and F‐actin polymerization‐driven motility function at the cell's apex to maintain polarized cell growth. We hypothesize this is a general mechanism for the participation of myosin XI and F‐actin in tip growing cells.
Sequential Quadratic Programming for Robust Optimization With Interval Uncertainty
Authors: Zhou Jianhua , Cheng Shuo , Li Mian 
Published: October 2012

Abstract
Uncertainty plays a critical role in engineering design as even a small amount of uncertainty could make an optimal design solution infeasible. The goal of robust optimization is to find a solution that is both optimal and insensitive to uncertainty that may exist in parameters and design variables. In this paper, a novel approach, sequential quadratic programming for robust optimization (SQP-RO), is proposed to solve single-objective continuous nonlinear optimization problems with interval uncertainty in parameters and design variables. This new SQP-RO is developed based on a classic SQP procedure with additional calculations for constraints on objective robustness, feasibility robustness, or both. The obtained solution is locally optimal and robust. Eight numerical and engineering examples with different levels of complexity are utilized to demonstrate the applicability and efficiency of the proposed SQP-RO with the comparison to its deterministic SQP counterpart and RO approaches using genetic algorithms. The objective and/or feasibility robustness are verified via Monte Carlo simulations.