The Estimation of Variance Components in a special Class of Phase-Confounded Designs

This paper considers the estimation of variance components for a special subclass of Phase-confounded designs. It is shown that if the balance existing in the design is utilized relatively simple expressions for the solutions of the normal equations and the relevant sums of squares can be obtained.     

具有亲缘关系矩阵的混合模型的方差组分迭代估计——应用于计算BLUP的方差比值和遗传参数

论述的是来自非均街资料的混合模型中具有亲缘关系矩阵时利用迭代法估计方差组分问题。这篇文章表明计算程序是可行的,只要能够按照混合模型中固定效应的结构矩阵和Henderson方法3的固定效应的假设条件正确地计算二次型约化平方和,就可获得较为精确的方差组分估计值;而且表明方差初始比值k偏高或偏低,不影响迭代求解的最后结果,这是因为在迭代过程中可以通过结构矩阵x'x和x'x的控制而自行调整。这些方差组分不仅可应用于选种种畜用的BLUP计算,还可用来估计遗传参数。     

A New Algorithm for Explicit Determination of Variance Component Estimations in Mixed Models and Mixed Classifications of Balanced ANOVA

This paper deals with the balanced case of the analysis of variance. The use of a classification function leads to an easy determination of all possible sources of variation of any mixed classification. For mixed models a new method is derived, which allows to represent explicit the ANOVA-estimations of the variance components respectively the estimation of the mean sum of squares of the fixed effects for all sources of variation. Thereby the corresponding F-quotients and the approximate confidence intervals of variance components are received in a simple way.     

The Residual Likelihood Ratio Test for the Variance Ratio in a Linear Model with Two Variance Components

Residual maximum likelihood has proved to be a successful approach to the estimation of variance components. In this paper, its counterpart in testing, the residual likelihood ratio test, is applied to testing the ratio of two variance components. The test is compared with the Wald test and the locally most powerful invariant test.     

Intraneuronal amyloid precursor protein (APP) and appearance of extracellular β‐amyloid peptide (aβ) in the brain of aging kokanee salmon

Antibodies to human amyloid precursor protein (APP₆₉₅) and beta‐amyloid peptide (Aβ_1‐42) were used to determine timing of amyloidosis in the brain of kokanee salmon (Oncorhynchus nerka kennerlyi) in one of four reproductive stages: immature (IM), maturing (MA), sexually mature (SM), and spawning (SP), representing a range of aging from somatically mature but sexually immature to spawning and somatic senescence. In IM fish, immunoreactive (ir) intracellular APP occurred in 18 of 23 brain regions. During sexual maturation and aging, the number of neurons expressing APP increased in 11 of these APP‐ir regions. Aβ‐ir was absent in IM fish, present in seven regions in MA fish, moderately abundant in 15 regions in SM fish, and was most abundant in all brain regions of SP fish exhibiting Aβ‐ir. Intracellular APP‐ir was observed in brain regions involved in sensory integration, olfaction, vision, stress responses, reproduction, and coordination. Intra‐ and extracellular Aβ_1‐42 immunoreactivity (Aβ‐ir) was present in all APP‐ir regions except the nucleus lateralis tuberis (hypothalamus) and Purkinje cells (cerebellum). APP‐ir and Aβ deposition increase during aging. APP‐ir is present in IM fish; Aβ‐ir usually appears first in MA or SM fish and increases in SM fish as does APP‐ir. Extracellular Aβ deposition dramatically increases between SM and SP stages (1–2 weeks) in all fish, indicating an extremely rapid and synchronized process. Rapid senescence observed in pacific salmon could make them a useful model to investigate timing of amyloidosis and neurodegeneration during brain aging. © 2002 Wiley Periodicals, Inc. J Neurobiol 53: 11–20, 2002     

Closed-Form Approximations to the REML Estimator of a Variance Ratio (or Heritability) in a Mixed Linear Model

In this article, we estimate heritability or intraclass correlation in a mixed linear model having two sources of variation. In most applications, the commonly used restricted maximum likelihood (REML) estimator can only be obtained via an iterative approach. In some cases, the algorithm used to compute REML estimates may be slow or may even fail to converge. We develop a set of closed-form approximations to the REML estimator, and the performance of these estimators is compared with that of the REML estimator. We provide guidelines regarding how to choose the estimator that best approximates the REML estimator. Examples presented in the article suggest that the closed-form estimators compete with and, in some cases, outperform the REML estimator.     

A synthetic peptide corresponding to a region of the human pericentriolar material 1 (PCM‐1) protein binds β‐amyloid (Aβ1‐42) oligomers

We have recently reported that a ~19‐kDa polypeptide, rPK‐4, is a protein kinase Cs inhibitor that is 89% homologous to the 1171–1323 amino acid region of the 228‐kDa human pericentriolar material‐1 (PCM‐1) protein (Chakravarthy et al. 2012). We have now discovered that rPK‐4 binds oligomeric amyloid‐β peptide (Aβ)_1‐42 with high affinity. Most importantly, a PCM‐1‐selective antibody co‐precipitated Aβ and amyloid β precursor protein (AβPP) from cerebral cortices and hippocampi from AD (Alzheimer's disease) transgenic mice that produce human AβPP and Aβ_1‐42, suggesting that PCM‐1 may interact with amyloid precursor protein/Aβ in vivo. We have identified rPK‐4′s Aβ‐binding domain using a set of overlapping synthetic peptides. We have found with ELISA, dot‐blot, and polyacrylamide gel electrophoresis techniques that a ~ 5 kDa synthetic peptide, amyloid binding peptide (ABP)‐p4‐5 binds Aβ_1‐42 at nM levels. Most importantly, ABP‐p4‐5, like rPK‐4, appears to preferentially bind Aβ_1‐42 oligomers, believed to be the toxic AD‐drivers. As expected from these observations, ABP‐p4‐5 prevented Aβ_1‐42 from killing human SH‐SY5Y neuroblastoma cells via apoptosis. These findings indicate that ABP‐p4‐5 is a possible candidate therapeutic for AD.     

Analysis of asymmetries in the African fruit bats Eidolon helvum and Rousettus egyptiacus (Mammalia: Megachiroptera) from the islands of the Gulf of Guinea. I. Variance and size components of bilateral variation

A set of cranial characters was examined in the fruit bats Rousettus egyptiacus and Eidolon helvum to compare trends and relative importance of major components of bilateral morphometric variation, and their relationship with character size. Using two‐way, sides‐by‐individuals ANOVA , four components of variation were estimated for each bilateral variable: individual variation (I), directional asymmetry (DA), non‐directional asymmetry (NDA) and measurement error (E). Both species exhibit similar major trends of variation in asymmetry across characters, as shown by principal component analysis, using variance components as variables. Degree of interspecific congruence among characters was confirmed by a two‐way ANOVA with species and variance components as fixed factors. Congruence of asymmetry patterns between species suggests that the concept of population asymmetry parameter (PAP) could be extended to higher hierarchies. PAPs above the species level may result from common mechanisms or similar developmental constraints acting on species’ buffering capacities and morphological integration processes.     

Synthesis, structural analysis and anticonvulsant activity of a ternary Cu(II) mononuclear complex containing 1,10-phenanthroline and the leading antiepileptic drug valproic acid

The synthesis and characterization of the binary complex of copper(II) with the antiepileptic drug valproic acid sodium salt (Valp) and the related ternary complex with 1,10-phenanthroline (phen) are reported, as well as the anticonvulsant properties of the latter. The characterization was carried out by means of elemental analyses, infrared (IR), UV–visible (UV–vis) spectrophotometry and Electron Paramagnetic Resonance (EPR). The X-ray crystal structure of the mononuclear complex bis(2-propylpentanoate)(1,10-phenanthroline)copper(II) [Cu(Valp)₂phen] is showed for the first time. It crystallized in C2/c space group with unit cell dimensions of a = 14.939(1) Å, b = 19.280(1) Å, c = 9.726(1) Å, β = 97.27(2)°, V = 2778.8(4) Å ³ and Z = 8. The carboxylates bond in an asymmetric chelating mode and the copper atom adopts a highly distorted octahedral coordination, characterized by the sum of the angles of 365.9° around Cu(II) and its nearest atoms in the CuN₂O₂ + O₂ chromophore instead of the expected 360° for a basal square planar geometry found in most Cu(II) complexes. Molecules assemble three by three through slipped π–π stacking of the aromatic phen with respectively 3.519 and 3.527 Å distances, in a head-to-tail arrangement. Studies of the anticonvulsant properties of this bioligand chelate evidenced its lack of efficacy in preventing MES-induced seizures. Interestingly, complex 4 protected mice against the Minimal Clonic seizures at doses that do not cause Rotorod toxicity, with an ED₅₀ documenting very potent anticonvulsant activity in this model of seizure, a particularly useful pharmacological profile of activity for the treatment of Petit Mal seizures.     

Relationships Between Kendall's Coefficient of Concordance and a Nonparametric Measure of Phenotypic Stability with Implications for the Consistency in Rankings as Affected by Variance Components

For a two-way classification with rows (= genotypes) and columns (= environments) relationships between Kendall's coefficient of concordance W and a nonparametric measure of phenotypic stability S (= variance among the ranks over the environments) are presented. This provides an analogy between Wricke's ecovalence and the sum of squares of genotype-environment interactions on the parametric side and S and Kendall's W on the nonparametric side: S is a genotype's contribution to the discordance (1 — W) in the data set, while Wricke's ecovalence is a genotype's contribution to the genotype-environment interaction sum of squares. Genotype x environment interactions may lead, but must not necessarily lead to non-identical rank orders of the genotypes in different environments (crossover versus noncrossover interactions). When does interaction become rank interaction? The similarity of the rank orders (measured by W) can be approximately expressed by the ratio of the genotypic variance and sum of genotypic variance plus residual variance. For the consistency of rankings this relation leads to an approximate test of significance which is based on variance components. Finally, a numerical example is given using grain yield data of 20 genotypes (varieties) of winter wheat in 10 environments (locations) from German registration trials.     

Critique of the use of fluorescence‐based reporters in Escherichia coli as a screening tool for the identification of peptide inhibitors of Aβ42 aggregation

High‐throughput screens that dispense with the need for expensive synthetic Aβ peptide would be invaluable for identifying novel anti‐aggregants as potential treatments for Alzheimer's disease. A biosynthetic in vivo approach, using a recombinant fluorescent green fluorescent protein (GFP) reporter for the aggregation state of Aβ in Escherichia coli, has been reported by other workers. Here, inducible Aβ–GFP expression in E. coli was coupled to the concurrent constitutive production of a quasi‐random peptide library to screen for anti‐aggregant activity. To attempt to introduce greater robustness, mCherry was also co‐expressed as an internal fluorescence standard to allow ratiometric comparison between samples. However, fluctuations in mCherry expression levels, as well as a low dynamic range of GFP output between positive and negative anti‐aggregant peptides, highlighted limitations with the approach. Despite this, two novel peptides were identified that showed an equivalent in vitro anti‐aggregant activity to that of epigallocatechin‐3‐gallate. Thus, although biosynthetic in vivo strategies show promise as screens for novel activities, unforeseen problems can arise because of the variability inherent in any biological system. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Systemic Central Nervous System (CNS)-targeted Delivery of Neuropeptide Y (NPY) Reduces Neurodegeneration and Increases Neural Precursor Cell Proliferation in a Mouse Model of Alzheimer Disease

Neuropeptide Y (NPY) is one of the most abundant protein transmitters in the central nervous system with roles in a variety of biological functions including: food intake, cardiovascular regulation, cognition, seizure activity, circadian rhythms, and neurogenesis. Reduced NPY and NPY receptor expression is associated with numerous neurodegenerative disorders including Alzheimer disease (AD). To determine whether replacement of NPY could ameliorate some of the neurodegenerative and behavioral pathology associated with AD, we generated a lentiviral vector expressing NPY fused to a brain transport peptide (apoB) for widespread CNS delivery in an APP-transgenic (tg) mouse model of AD. The recombinant NPY-apoB effectively reversed neurodegenerative pathology and behavioral deficits although it had no effect on accumulation of Aβ. The subgranular zone of the hippocampus showed a significant increase in proliferation of neural precursor cells without further differentiation into neurons. The neuroprotective and neurogenic effects of NPY-apoB appeared to involve signaling via ERK and Akt through the NPY R1 and NPY R2 receptors. Thus, widespread CNS-targeted delivery of NPY appears to be effective at reversing the neuronal and glial pathology associated with Aβ accumulation while also increasing NPC proliferation. Overall, increased delivery of NPY to the CNS for AD might be an effective therapy especially if combined with an anti-Aβ therapeutic.     

The Effect of Design Imbalance on the Power of the F‐test of a Variance Component in the One‐Way Random Model

The ANOVA‐based F‐test used for testing the significance of the random effect variance component is a valid test for an unbalanced one‐way random model. However, it does not have an uniform optimum property. For example, this test is not uniformly most powerful invariant (UMPI). In fact, there is no UMPI test in the unbalanced case (see Khuri , Mathew , and Sinha , 1998). The power of the F‐test depends not only on the design used, but also on the true values of the variance components. As Khuri (1996) noted, we can gain a better insight into the effect of data imbalance on the power of the F‐test using a method for modelling the power in terms of the design parameters and the variance components. In this study, generalized linear modelling (GLM) techniques are used for this purpose. It is shown that GLM, in combination with a method of generating designs with a specified degree of imbalance, is an effective way of studying the behavior of the power of the F‐test in a one‐way random model.     

Analysis of the contribution of receptor subdomains to the cooperative binding and internalization of transforming growth factor-beta (TGF-beta) type I and type II receptors

The mechanistic basis underlying the striking cooperativity observed for the assembly of TGF-β family ligand/receptor complexes is not well understood. We report here an investigation in which we used a novel ligand sequestration assay, in combination with immunofluorescent light microscopy and flow cytometry analyses, to examine and quantify cooperative assembly of TGF-β ligand/receptor complexes on the cell surface, as well as ligand/receptor complex internalization. We analyzed the roles played by the ecto/transmembrane (ecto/TM) domains and endodomains of RI and RII TGF-β receptors in these processes by transfecting 293 or HeLa cells with different combinations of receptor mutants. We found that the ecto/TM domains of RII and RI cooperated together to promote the formation of cell surface receptor/ligand complexes. Furthermore, in agreement with the recently determined structure of the TGF-β3/RII ectodomain/RI ectodomain complex [J. Groppe, C.S. Hinck, P. Samavarchi-Tehrani, C. Zubieta, J.P. Schuermann, A.B. Taylor, P.M. Schwarz, J.L. Wrana, A.P. Hinck, Cooperative assembly of TGF-beta superfamily signaling complexes is mediated by two disparate mechanisms and distinct modes of receptor binding, Mol. Cell 29 (2008) 157–168], we observed that the N-terminus of the RII ectodomain was required for full assembly. With respect to endodomains, we found that the RI endodomain enhanced cooperative complex assembly at the cell surface, whereas both the RI and RII endodomains enhanced internalization. Finally, we observed that ligand/receptor internalization, but not complex assembly at the cell surface, was partly raft-dependent. In light of these results, currently proposed mechanisms of cooperative ligand/receptor assembly are discussed.     

Effects of solvent fractions of Allomyrina dichotoma larvae through the inhibition of in vitro BACE1 and β‐amyloid(25–35)‐induced toxicity in rat pheochromocytoma PC12 cells

Amyloid‐β peptide (Aβ) generation initiated by β‐site amyloid precursor protein cleaving enzyme 1 BACE1 is a critical cause of Alzheimer's disease. In the course of our ongoing investigation of natural anti‐dementia resources, the ethyl acetate (EtOAc) fraction exerted strong BACE1‐specific inhibition with the half maximal inhibitory concentration (IC₅₀) value of 9.2 × 10^?5 μg/mL. Furthermore, Aβ(25–35)‐induced cell death was predominantly prevented by the EtOAc fraction of Allomyrina dichotoma larvae through diminishing of cellular oxidative stress and attenuating apoptosis by inhibiting caspase‐3 activity. Taken together, the present study demonstrated that A. dichotoma larvae possess novel neuroprotective properties not only via the selective and specific inhibition of BACE1 activity but also through the alleviation of Aβ(25–35)‐induced toxicity, which may raise the possibility of therapeutic application of A. dichotoma larvae for preventing and/or treating dementia.     

In silico and in vitro studies to elucidate the role of Cu2+ and galanthamine as the limiting step in the amyloid beta (1–42) fibrillation process

The formation of fibrils and oligomers of amyloid beta (Aβ) with 42 amino acid residues (Aβ_1–42) is the most important pathophysiological event associated with Alzheimer''s disease (AD). The formation of Aβ fibrils and oligomers requires a conformational change from an α-helix to a β-sheet conformation, which is encouraged by the formation of a salt bridge between Asp 23 or Glu 22 and Lys 28. Recently, Cu²⁺ and various drugs used for AD treatment, such as galanthamine (Reminyl®), have been reported to inhibit the formation of Aβ fibrils. However, the mechanism of this inhibition remains unclear. Therefore, the aim of this work was to explore how Cu²⁺ and galanthamine prevent the formation of Aβ_1–42 fibrils using molecular dynamics (MD) simulations (20 ns) and in vitro studies using fluorescence and circular dichroism (CD) spectroscopies. The MD simulations revealed that Aβ_1–42 acquires a characteristic U-shape before the α-helix to β-sheet conformational change. The formation of a salt bridge between Asp 23 and Lys 28 was also observed beginning at 5 ns. However, the MD simulations of Aβ₁₋₄₂ in the presence of Cu²⁺ or galanthamine demonstrated that both ligands prevent the formation of the salt bridge by either binding to Glu 22 and Asp 23 (Cu²⁺) or to Lys 28 (galanthamine), which prevents Aβ₁₋₄₂ from adopting the U-characteristic conformation that allows the amino acids to transition to a β-sheet conformation. The docking results revealed that the conformation obtained by the MD simulation of a monomer from the 1Z0Q structure can form similar interactions to those obtained from the 2BGE structure in the oligomers. The in vitro studies demonstrated that Aβ remains in an unfolded conformation when Cu²⁺ and galanthamine are used. Then, ligands that bind Asp 23 or Glu 22 and Lys 28 could therefore be used to prevent β turn formation and, consequently, the formation of Aβ fibrils.     

Validation of a high-performance liquid chromatographic-mass spectrometric method for the measurement of 5-chloro-2′,3′-dideoxy-3′-fluorouridine (935U83) in human plasma

An isocratic reversed-phase LC-MS method for measuring concentrations of 5-chloro-2′,3′-dideoxy-3′-fluorouridine (935U83; I) directly and its 5′-glucuronide metabolite (5-chloro-2′,3′-dideoxy-5′-O-β- -glucopyranuronosyl-3′-fluorouridine) indirectly in human plasma was developed, validated, and applied to a Phase I clinical study. The pyrimidine nucleoside, I, was extracted from human plasma by using anionic solid-phase extraction. The concentration of the glucuronide conjugate was determined from the difference between the molar concentration of I in a sample hydrolyzed with β-glucuronidase and the nonhydrolyzed sample. Recovery of I from human plasma averaged 90%. The bias of the assay for I ranged from −5.5 to 7.1% during the validation and from −6.0 to 1.4% during application of the assay to the Phase I single-dose escalation study. The intra- and inter-day precision was less than 8% for I and its glucuronide conjugate. The lower and upper limits of quantitation for a 50-μl sample were 4 ng/ml and 3000 ng/ml, respectively. No significant endogenous interferences were noted in human plasma obtained from drug-free volunteers nor from predose samples of HIV-infected patients.     

Aβ1–42 triggers the generation of a retrograde signaling complex from sentinel mRNAs in axons

Neurons frequently encounter neurodegenerative signals first in their periphery. For example, exposure of axons to oligomeric Aβ_1‐42 is sufficient to induce changes in the neuronal cell body that ultimately lead to degeneration. Currently, it is unclear how the information about the neurodegenerative insult is transmitted to the soma. Here, we find that the translation of pre‐localized but normally silenced sentinel mRNAs in axons is induced within minutes of Aβ_1–42 addition in a Ca²⁺‐dependent manner. This immediate protein synthesis following Aβ_1–42 exposure generates a retrograde signaling complex including vimentin. Inhibition of the immediate protein synthesis, knock‐down of axonal vimentin synthesis, or inhibition of dynein‐dependent transport to the soma prevented the normal cell body response to Aβ_1–42. These results establish that CNS axons react to neurodegenerative insults via the local translation of sentinel mRNAs encoding components of a retrograde signaling complex that transmit the information about the event to the neuronal soma.