Miracle-dz/UniFAR-FTUs huggingface dataset:
Supramolecular structural constraints on Alzheimer's beta-amyloid fibrils from electron microscopy and solid-state nuclear magnetic resonance.

We describe electron microscopy (EM), scanning transmission electron microscopy (STEM), and solid-state nuclear magnetic resonance (NMR) measurements on amyloid fibrils formed by the 42-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1)(-)(42)) and by residues 10-35 of the full-length peptide (Abeta(10)(-)(35)). These measurements place constraints on the supramolecular structure of the amyloid fibrils, especially the type of beta-sheets present in the characteristic amyloid cross-beta structural motif and the assembly of these beta-sheets into a fibril. EM images of negatively stained Abeta(10)(-)(35) fibrils and measurements of fibril mass per length (MPL) by STEM show a strong dependence of fibril morphology and MPL on pH. Abeta(10)(-)(35) fibrils formed at pH 3.7 are single "protofilaments" with MPL equal to twice the value expected for a single cross-beta layer. Abeta(10)(-)(35) fibrils formed at pH 7.4 are apparently pairs of protofilaments or higher order bundles. EM and STEM data for Abeta(1)(-)(42) fibrils indicate that protofilaments with MPL equal to twice the value expected for a single cross-beta layer are also formed by Abeta(1)(-)(42) and that these protofilaments exist singly and in pairs at pH 7.4. Solid-state NMR measurements of intermolecular distances in Abeta(10)(-)(35) fibrils, using multiple-quantum (13)C NMR, (13)C-(13)C dipolar recoupling, and (15)N-(13)C dipolar recoupling techniques, support the in-register parallel beta-sheet organization previously established by Lynn, Meredith, Botto, and co-workers [Benzinger et al. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 13407-13412; Benzinger et al. (2000) Biochemistry 39, 3491-3499] and show that this beta-sheet organization is present at pH 3.7 as well as pH 7.4 despite the differences in fibril morphology and MPL. Solid-state NMR measurements of intermolecular distances in Abeta(1)(-)(42) fibrils, which represent the first NMR data on Abeta(1)(-)(42) fibrils, also indicate an in-register parallel beta-sheet organization. These results, along with previously reported data on Abeta(1)(-)(40) fibrils, suggest that the supramolecular structures of Abeta(10)(-)(35), Abeta(1)(-)(40), and Abeta(1)(-)(42) fibrils are quite similar. A schematic structural model of these fibrils, consistent with known experimental EM, STEM, and solid-state NMR data, is presented.
Classification and quantification of user's emotion on Malay language in social network sites using Latent Semantic Analysis

Social network sites nowadays serve as important medium of communication and dissemination of information to its users. It is crucial to know users' emotion and perception towards information evolved in social network sites. The motivations for creating tools to detect emotion is increasing due to these factors. Various research conducted recently, focusing on the classification of emotion, that is determining the type of emotion based on certain modality rather than quantifying or recognizing the degree of emotions. The classification is said to determine type of emotion perceived and the quantification is to determine degree of the classified emotion. This paper presents the capability of the Latent Semantic Analysis (LSA) in classifying six basic types of emotion and their three levels of quantification. It is a mathematical technique for extracting and comparing the semantic similarity of meaning between words and passages by analyzing textual information. A prototype is developed to test the accuracy of the prediction based on the proposed framework. Results from the prototype produces 58.3% accuracy for classification and 53.8% accuracy for quantification from randomly selected 173 users' comments. Although, the accuracy is literally low on both classification and quantification, a few drawbacks are identified and highlighted in this paper.
STABLE ISOTOPES IN ECOSYSTEM STUDIES

The use of stable isotopes to solve biogeochemical problems in ecosystem analysis is increasing rapidly because stable isotope data can contribute both source-sink (tracer) and process information: The elements C, N, S, H, and all have more than one isotope, and isotopic compositions of natural materials can be measured with great precision with a mass spectrometer. Isotopic compositions change in predictable ways as elements cycle through the biosphere. These changes have been exploited by geochemists to understand the global elemental cycles. Ecologists have not until quite recently employed these techniques. The reasons for this are, first, that most ecologists do not have the background in chemistry and geochemistry to be fully aware of the possibilities for exploiting the natural variations in stable isotopic compositions, and second, that stable isotope ratio measurements require equipment not normally available to ecologists. This is unfortunate because some of the more intractable problems in ecology can be profitably addressed using stable isotope measurements. Stable isotopes are ideally suited to increase our understanding of element cycles in ecosystems. This review is written for ecologists who would like to learn more about how stable isotope analyses have been and can be used in ecosystem studies. We begin with an explanation of isotope terminology and fractionation, then summarize isotopic distributions in the C, N, and S biogeochemical cycles, and conclude with five case studies that show how stable isotope measurements can provide crucial information for ecosystem analysis. We restrict this review to studies of natural variations in C, N, and S isotopic abundances, cxcluding from consideration ~5N enrichment studies and hydrogen and oxygen isotope studies. Our focus on C, N, and S derives in part from our
The effects of integration agreements in Western Hemisphere trade, 1970–2014

The paper analyzes the effects of four regional integration agreements (Common Market of the South [MERCOSUR], Andean Community [ANCOM], Central American Common Market [CACM] and North America Free Trade Agreement [NAFTA]) on bilateral trade in 19 countries from the Western Hemisphere for the period 1970–2014. For this purpose we estimate different gravity models to control for trade creation and diversion, export diversification and intra-industry trade using OLS log-linearized gravity model and Poisson pseudo-maximum-likelihood panel data estimators that allow controlling for zero-value trade flows. We find trade creation for ANCOM, MERCOSUR and CACM and trade diversion for NAFTA and MERCOSUR countries. Export diversification negatively affects bilateral trade in all American agreements, while intra-industry trade has contributed to trade expansion in ANCOM and the opposite for NAFTA, MERCOSUR and CACM. Global supply chains may help us explain these results. Finally, we find anticipatory effects on trade several years before the signing of the agreements, but only NAFTA countries seem to be natural trading partners in the region while the rest of Latin American regional agreements have not resulted in a comprehensive, profound and consolidated common market.
Organization of cortico‐cortical associative projections in a rat model of microgyria

Microgyria was experimentally induced by focal freezing lesions of the frontal cortex in newborn rats. Adult microgyric animals received cortical injections of biotinylated dextran amine combined with NMDA, in order to obtain a Golgi-like retrograde labeling of cortico-cortical association neurons. Injections were performed either rostrally or caudally to the microgyric lesion. Results demonstrate that long-range association projections traveling across the zone of the microgyric lesion arise mainly from infragranular layers. In normal animals the same projections originate both from supragranular and infragranular layers. The analysis of single basal dendrites of layer 2/3 in microgyric animals demonstrates a simplified branching pattern, with a number of end points lower than in control animals. Potential implications for microgyria-associated epilepsy are discussed.
Aberrant brain activation and coupling in Depression – Links between Psychopathology and Neurophysiology

1 Zusammenfassung . 4 1. General Introduction . 7 1.1 Topic overview and structure of the present work . 7 1.2 Symptomatology, Epidemiology and Etiology of MDD . 8 1.3 Rumination . 16 1.3.1 The causes and consequences of depressive rumination . 16 1.3.2 Models of depressive rumination . 19 1.4 Treatment Options for Depression and Rumination . 23 1.5 Functional Connectivity . 26 2. Intermediate Summary . 32 3. Background and Rationale for the present projects . 33 3.1 Relations of depression, rumination, structural changes and neuronal activation . 33 3.2 Studies showing increased FC in depression and rumination . 37 3.3 Studies showing attenuated FC in depression and rumination . 38 4. Aims & Linkage of the studies . 41 4.1 Overview over the present studies . 44 4.2 Choice of brain imaging techniques . 45 5. Study 1 – State-dependent altered connectivity in late-life depression: A functional near-infrared spectroscopy study. 46 5.1 Abstract . 47 5.2 Introduction . 48 5.3 Methods and Materials . 51 5.4 Data Analysis . 56
A spiral antenna above a hybrid HIS-EBG reflector

This paper discusses antenna characteristics of a two-arm Archimedean spiral antenna above a hybrid HIS-EBG reflector. The hybrid reflector consists of an HIS and an EBG, where the HIS is located over an EBG reflector. The analysis is performed with a spiral antenna backed by a conducting plane (PEC) reflector and an HIS reflector, both with the equal total antenna height. It is shown that the HIS reflector contributes to improve the input impedance and axial ratio. Subsequently, antenna characteristics are analyzed for a spiral antenna above the hybrid HIS-EBG reflector. This revealed that the hybrid HIS-EBG is more effective configuration in improving the input impedance and axial ratio than the HIS configuration.
Purification of flagellar cores of Vibrio cholerae

A procedure is described for the purification of the cores of flagella sheared from Vibrio cholerae. V. cholerae is a monotrichous organism whose flagellar core (FC) is enclosed within a sheath. The purification procedure consists of several cycles of differential centrifugation and cesium chloride density-gradient ultracentrifugation in the presence of a neutral detergent, Triton X-100. Purity of the FC preparations is assessed by electron microscopy, polyacrylamide gel electrophoresis, and chemical analysis. The purified FC preparations are devoid of flagellar sheaths and free from detectable cell wall and cytoplasmic contamination. Antibody prepared in rabbits against purified FC reacts with the flagellum of intact V. cholerae or purified FC as seen by ferritin-labeled antibody studies. Purified FC is composed of a single protein subunit with an estimated molecular weight of 45,000 g/mol and a density of about 1.3 g/cm3.
Microbial co-presence and mutual-exclusion networks in the Bovine rumen microbiome

The recognized significance of rumen microbiome has inspired efforts to examine the composition of rumen microbial communities in a large scale. One of the key research areas is to infer association and dependencies between members of rumen microbial communities through correlation analysis. However, it has been found that due to the compositional nature of data, simply applying correlation-based techniques to the analysis of relative abundance of microbial genes may produce artefactual correlation and loss of information. In an attempt to mitigate the compositional effect on the analysis of rumen microbiome data, this study applied a framework including a compendium of two correlation measures and three dissimilarity metrics that are intrinsically robust to compositionality. Based on the inference of significant positive and negative associations, co-presence and mutual-exclusion networks were constructed. The corresponding modules associated with methane production were identified. The modules are highly enriched with microbial genes associated with methane emissions and encoding enzymes involved in the methane methanogensis pathway. In comparisons to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations.
The Effect of Negative Sampling Strategy on Capturing Semantic Similarity in Document Embeddings

In many machine learning tasks, a model needs to be presented with both correct and incorrect examples during the training. For instance, given a query, a search engine can be trained to predict the relevant (positive) documents from irrelevant (negative) ones. While each query is associated with a handful of relevant documents, the number of irrelevant documents can be vast. This imbalance can bias a document retrieval model while the mere volume of irrelevant documents can result in long training times. In this paper, we show the affect of a tailored negative sampling on the performance of the Deep Structure Semantic Model (DSSM). We show that a naive random sampling method outperforms more sophisticated ways of selecting negative data.
Dynamic pricing of perishable products with random fuzzy demand

This paper considers a dynamic pricing problem for selling a given stock of a perishable product over a finite time horizon. We model the uncertain demand as random fuzzy variable and study the pricing problem in a random fuzzy environment. The retailer's dynamic pricing problem is formulated as three types of random fuzzy programming models-expected revenue maximization model, (α, β)-revenue maximization model and chance maximization model — to meet different goals. Random fuzzy simulations for some functions with random fuzzy parameters are given and embedded into genetic algorithm to design a hybrid intelligent algorithm. Numerical examples are also presented to illustrate the modeling idea and to show the effectiveness of the proposed algorithm.
Proof-of-Principle Phase II MRI Studies in Stroke: Sample Size Estimates From Dichotomous and Continuous Data

Background and Purpose— Since the failure of a number of phase III trials of neuroprotection in ischemic stroke, the need for smaller phase II studies with MRI surrogates has emerged. There is, however, little information available about sample size requirements for such phase II trials and rarely enough patients in single studies to make robust estimates. We have formed an international collaborative group to assemble larger datasets and from these have generated sample size tables for MRI-based infarct expansion as the outcome measure. Methods— Twelve centers from Australia, Europe, and North America contributed data from patients with hemispheric ischemic stroke. Infarct expansion was defined from initial diffusion-weighted images and later fluid-attenuated inversion recover or T2 images. Sample size estimates were calculated from data on infarct expansion ratios treated as dichotomous or continuous variables. A nonparametric approach was used because the distribution of infarct expansion was resistant to all forms of transformation. Results— As an example, a 20% absolute reduction in infarct expansion ratio (≤1), 80% power, and &agr;=0.05 requires 99 patients in each arm. To achieve an equivalent effect size with a continuous approach requires 61 patients. Conclusions— These tables will be useful in planning phase II trials of therapy with the use of MRI outcome measures. For positive studies, biologically plausible surrogates such as these may provide a rationale for proceeding to phase III trials.
Activation of enhancer sequences in type II human T-cell leukemia virus and bovine leukemia virus long terminal repeats by virus-associated trans-acting regulatory factors

The ability of the sequences present in the long terminal repeats (LTRs) of human T-cell leukemia viruses type I and II (HTLV-I and HTLV-II) and of bovine leukemia virus to function as enhancer elements was investigated. Recombinant plasmids that contained the HTLV-I, HTLV-II, and bovine leukemia virus LTRs at a distance from a simian virus 40 promoter element located 5' to the bacterial gene encoding chloramphenicol acetyltransferase (EC 2.3.1.28) were constructed. We report that all three LTR sequences contain enhancer elements capable of increasing the level of gene expression directed from a distal heterologous promoter. The enhancer present in the HTLV-I LTR was active in uninfected cells of lymphoid and nonlymphoid origin. In contrast, the enhancer activity of the HTLV-II and bovine leukemia virus LTR sequences was evident only in virus-infected cells. This activity is likely due to virus-associated trans-acting transcriptional factors previously shown to be present in HTLV- and bovine leukemia virus-infected cells. The implication of these observations for virus replication and transforming activity are discussed.
Revealing and solving the TCP instability problem in 802.11 based multi-hop mobile ad hoc networks

We report the so-called "TCP instability problem" in 802.11-based wireless mobile multi-hop networks. Our results show that the throughput performance of multi-hop TCP traffic in such a network may suffer from severe oscillation. By illustrating the multi-layer traces, we show that this problem is rooted in the MAC layer. Furthermore, a resolution is proposed to eliminate this problem.
A Portfolio Approach to the Property-Liability Insurance Industry

This paper contains an analysis of a portfolio model which simultaneously optimizes the investment and insurance portfolios of the property-liability insurance industry. The mathematical formulation is an extension of earlier approaches in that it permits the direct development of the envelope efficiency frontier for all levels of insurance leverage. Using data on nineteen insurance lines and two types of assets for the period 1956-1971, efficient portfolios for both unconstrained and also constrained solutions are obtained. In each case, some insurance lines tend to be consistently excluded from the optimal portfolios because of their risk-return characteristics. The implications of this effect on the availability of insurance and rate-making are discussed. Finally, in contrast to accepted practice and theory it is found that the investment policy of the firm need not necessarily become more conservative as the insurance portfolio becomes more risky. In analyzing the structure and performance of the property-liability insurance industry many approaches and measures have been used, each with its own merits. For example, Hensley [6] undertook a study of the competitive aspects of the insurance industry as well as other aspects of its structure and more recently these issues have been studied by Joskow
A supertree analysis and literature review of the genus Drosophila and closely related genera (Diptera, Drosophilidae)

In the 17 years since the last familywide taxonomic analysis of the Drosophilidae, many studies dealing with a limited number of species or groups have been published. Most of these studies were based on molecular data, but morphological and chromosomal data also continue to be accumulated. Here, we review more than 120 recent studies and use many of those in a supertree analysis to construct a new phylogenetic hypothesis for the genus Drosophila and related genera. Our knowledge about the phylogeny of the genus D rosophila and related genera has greatly improved over the past two decades, and many clades are now firmly supported by many independent studies. The genus Drosophila is paraphyletic and comprises four major clades interspersed with at least five other genera, warranting a revision of the genus. Despite this progress, many relationships remain unresolved. Much phylogenetic work on this important family remains to be done.
Preparation and properties of polylactic acid-based composite fluorescent membrane based on layer-by-layer assembly

In this paper, a kind of multi-functional polylactic acid-based membrane with adjustable aggregate thickness and properties was prepared. When the number of assembled layers was 20 bilayers, the mean thickness of every bilayer was found to be 10.75±0.25 nm, and the tensile strength was increased by 20% compared with the polylactic acid (PLA) films. The assembled layered double hydroxides (LDHs) could serve as a type of promising organic-inorganic luminescent material, and endow PLA with photoluminescent properties. Besides, the photoluminescence of the composite films was discovered to be highly tunable by simply adjusting the structural constituents of LDHs, and the fluorescence intensity was uniformly enhanced as the number of assembled layers increases, which was not eliminated by the isolation due to cellulose nanocrystals (CNCs). Moreover, the composite films exhibited excellent fluorescence stability in comparison with the literature. After being repeatedly bleached 1000 times by confocal laser scanning fluorescence microscope, the fluorescence intensity of the PLA/(CNCs/Mg-Al-Eu LDHs) 10 film remained 96%. It could be concluded that the immobilization of CNCs and LDHs realized the microscopic controllability of the optical functional molecular spacing. With satisfactory fluorescence, the resulting PLA-based membranes exhibited considerable application potential in optoelectronic devices and anti-counterfeiting packaging.
A novel approach to detect Atrial Fibrillation efficiently and accurately from 48 hours of ECG data

An algorithm for automatic detection of Atrial Fibrillation (AF) using R peak to R peak (RR) interval from electrocardiograph (ECG) signals has been developed and evaluated. The algorithm consists of a preprocessing which is based on Pan-Tompkins method to extract reliable QRS complex thus RR interval, followed by a 3 steps approach to detect AF using RR interval in ECG. The first step computes the Root Mean Square of the Successive Differences of the RR intervals extracted from a 48 hours ECG recording to identify the presence of arrhythmia. The second step defines the precise starting and stopping time of an arrhythmia episode through applying autocorrelation on the squared ECG signal within an arrhythmia window detected by the first step. The last step discerns AF from other type of arrhythmias through computing the Shannon Entropy (ShE) for the entire range of arrhythmia episode defined in step 2. The evaluation of the proposed algorithm was carried out utilizing normal sinus rhythm, AF and the arrhythmia ECGs provided in MIT-BIH database. The result demonstrates a 100% reliability in the detection of AF with accuracy of 99.5% in the identification of the start and stop time of an AF episode. In addition, the relationship between ShE threshold value of AF and duration of AF episode is studied with a formula proposed based on the results. The total processing time for the 48 hours ECG data is approximately 8 minutes, demonstrating the high efficiency of this algorithm.
Harmonic reduction via optimal power flow and the frequency coupling matrix

In this paper we propose a new optimal power flow scheme that takes into account the harmonics generated by power electronics interfaced distributed generation (DG). The objective is to minimize the cost of generation under constraints on the total harmonic distortion (THD) of voltage. The frequency coupling matrix (FCM) is used to model the harmonic current injected by a converter. Network current and voltage are modeled for each harmonic frequency. Constraints limiting the maximum voltage THD are introduced to the three-phase optimal power flow (OPF) problem. We construct a semidefinite relaxation, which can be solved using commercially available software packages. We give numerical results for the harmonic-constrained optimal power flow for two test systems.