Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Sequencing of the Bamboo Mitochondrial Genome Using Illumina Technology and Parallel Episodic Evolution of Organelle Genomes in Grasses

Background Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. Methodology/Principal Findings We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Conclusions/Significance Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast genomes in grasses is consistent with lineage effects.
Mixed Finite Element Method for Dirichlet Boundary Control Problem Governed by Elliptic PDEs

In this paper we study the finite element approximation of Dirichlet boundary control problems governed by elliptic PDEs. Based on a mixed variational scheme, we establish a mixed finite element approximation to the underlying optimal control problem. We consider the optimal control problems posed on both polygonal and general smooth domains, and we derive a priori error estimates for optimal control, state, and adjoint state. The optimal and quasi-optimal error estimates are obtained for problems on polygonal and smooth domains, respectively. Numerical experiments are provided to confirm our theoretical results.
Applying software metrics to formal specifications: a cognitive approach

It is generally accepted that failure to reason correctly during the early stages of software development causes developers to make incorrect decisions which can lead to the introduction of faults or anomalies in systems. Most key development decisions are usually made at the early system specification stage of a software project and developers do not receive feedback on their accuracy until near its completion. Software metrics are generally aimed at the coding or testing stages of development, however, when the repercussions of erroneous work have already been incurred. This paper presents a tentative model for predicting those parts of formal specifications which are most likely to admit erroneous inferences, in order that potential sources of human error may be reduced. The empirical data populating the model was generated during a series of cognitive experiments aimed at identifying linguistic properties of the Z notation which are prone to admit non-logical reasoning errors and biases in trained users.
SJUKHUS SOM HÄLSOFRÄMJANDE ARBETSPLATS : MER ÄN BARA FRISKVÅRD?

Under de senaste aren har halso- och sjukvardens intresse for det halsoframjande arbetet okat. Studiens syfte var att kontrastera hur det halsoframjande arbetet gentemot medarbetarna beskrivs mella .
Therapeutic Effects of Oral Zinc Supplementation on Acute Watery Diarrhea with Moderate Dehydration: A Double-Blind Randomized Clinical Trial

Background: To assess the therapeutic effects of oral zinc supplementation on acute watery diarrhea of children with moderate dehydration. Methods: All 9-month to 5-year-old children who were admitted with acute watery diarrhea and moderate dehydration to the Children Ward of Motahari Hospital, Urmia, Iran in 2008 were recruited. After the application of the inclusion and exclusion criteria, the patients were randomly allocated to two groups: one group to receive zinc plus oral rehydration solution (ORS) and the other one to receive ORS plus placebo. All the patients were rehydrated using ORS and then receiving ORS for ongoing loss (10 ml/kg after every defecation). Additionally, the patients in the intervention group received zinc syrup (1 mg/kg/day) divided into two doses. A detailed questionnaire was filled daily for each patient by trained pediatrics residents; it contained required demographic characteristics, nutrition and hydration status, and disease progression. The primary outcome (frequency and consistency of diarrhea) and the secondary outcomes (duration of hospitalization and change in patients’ weight) were compared between the two groups. Results: The mean diarrhea frequency (4.5±2.3 vs. 5.3±2.1; P=0.004) was lower in the group receiving zinc +ORS; however, the average weight was relatively similar between the two groups (10.5±3.1 vs. 10.1±2.3; P=0.14). The qualitative assessment of stool consistency also confirmed earlier improvement in the treatment group in the first three days of hospitalization (P <0.05). The mean duration of hospitalization was significantly lower in the patients receiving zinc supplements (2.5±0.7 vs. 3.3±0.8 days; P=0.001). Conclusion: Our results imply the beneficial effects of therapeutic zinc supplementation on disease duration and severity in patients with acute diarrhea and moderate dehydration in Iran. Trial Registration Number: IRCT201201241580N2
Exenatide alters myocardial glucose transport and uptake depending on insulin resistance and increases myocardial blood flow in patients with type 2 diabetes.

CONTEXT Glucagon-like peptide-1 (GLP-1) and GLP-1 receptor agonists provide beneficial cardiovascular effects by protecting against ischemia and reperfusion injury. Type 2 diabetes mellitus patients have reduced glycolysis in the heart. OBJECTIVE We hypothesized that cardioprotection by GLP-1 is achieved through increased glucose availability and utilization and aimed to assess the effect of exenatide, a synthetic GLP-1 receptor agonist, on myocardial glucose uptake (MGU), myocardial glucose transport, and myocardial blood flow (MBF). DESIGN AND METHODS We conducted a randomized, double-blinded, placebo-controlled crossover study in eight male, insulin-naive, type 2 diabetes mellitus patients without coronary artery disease. Positron emission tomography was used to determine the effect of exenatide on MGU and MBF during a pituitary-pancreatic hyperglycemic clamp with (18)F-fluorodeoxyglucose and (13)N-ammonia as tracers. RESULTS Overall, exenatide did not alter MGU. However, regression analysis revealed that exenatide altered initial clearance of glucose over the membrane of cardiomyocytes and MGU, depending on the level of insulin resistance (P = 0.017 and 0.010, respectively). Exenatide increased MBF from 0.73 ± 0.094 to 0.85 ± 0.091 ml/g · min (P = 0.0056). Except for an increase in C-peptide levels, no differences in circulating hormones or metabolites were found. CONCLUSIONS The action of exenatide as an activator or inhibitor of the glucose transport and glucose uptake in cardiomyocytes is dependent on baseline activity of glucose transport and insulin resistance. Exenatide increases MBF without changing MGU.
Clustering Longitudinal Clinical Marker Trajectories from Electronic Health Data: Applications to Phenotyping and Endotype Discovery

Diseases such as autism, cardiovascular disease, and the autoimmune disorders are difficult to treat because of the remarkable degree of variation among affected individuals. Subtyping research seeks to refine the definition of such complex, multi-organ diseases by identifying homogeneous patient subgroups. In this paper, we propose the Probabilistic Subtyping Model (PSM) to identify subgroups based on clustering individual clinical severity markers. This task is challenging due to the presence of nuisance variability — variations in measurements that are not due to disease subtype — which, if not accounted for, generate biased estimates for the group-level trajectories. Measurement sparsity and irregular sampling patterns pose additional challenges in clustering such data. PSM uses a hierarchical model to account for these different sources of variability. Our experiments demonstrate that by accounting for nuisance variability, PSM is able to more accurately model the marker data. We also discuss novel subtypes discovered using PSM and the resulting clinical hypotheses that are now the subject of follow up clinical experiments.
Optimization of electrophoretic separations of thirteen phenolic compounds using single peak responses and an interactive computer technique

An interactive computer method is proposed for the electrophoretic separation of 13 phenolic compounds from extra-virgin olive oil using single peak response values. A central composite design was executed for optimization of the sodium tetraborate concentration, pH and applied voltage. Statistical models were determined for eight resolution responses and thirteen effective mobilities. Six of the resolution models had highly significant ANOVA lack of fit values, limiting their accuracies for use in Derringer´s desirability function search for optimal separation conditions. None of the 13 effective mobility models suffered from significant lack of fit. Since it is not possible to define effective mobility target values for the desirability function, an interactive computer program developed in our laboratories was applied to the single peak models. Mouse or cursor movements were executed to define experimental conditions in model simulations of the electropherogram. These simulations resulted in superior peak separations, especially for the apigenin and luteolin peaks, in 35 min, compared with those obtained in close to 50 min with the resolution models. Verification experiments performed 2 and 3 years later confirmed the robustness of the models.
COMMON PHASES OF COMPUTER FORENSICS INVESTIGATION MODELS

The increasing criminal activities using digital information as the means or targets warrant for a structured manner in dealing with them. Since 1984 when a formalized process been introduced, a great number of new and improved computer forensic investigation processes have been developed. In this paper, we reviewed a few selected investigation processes that have been produced throughout the years and then identified the commonly shared processes. Hopefully, with the identification of the commonly shard process, it would make it easier for the new users to understand the processes and also to serve as the basic underlying concept for the development of a new set of processes. Based on the commonly shared processes, we proposed a generic computer forensics investigation model, known as GCFIM.
MicroRNAs: Not “Fine-Tuners” but Key Regulators of Neuronal Development and Function

MicroRNAs (miRNAs) are a class of short non-coding RNAs that operate as prominent post-transcriptional regulators of eukaryotic gene expression. miRNAs are abundantly expressed in the brain of most animals and exert diverse roles. The anatomical and functional complexity of the brain requires the precise coordination of multilayered gene regulatory networks. The flexibility, speed, and reversibility of miRNA function provide precise temporal and spatial gene regulatory capabilities that are crucial for the correct functioning of the brain. Studies have shown that the underlying molecular mechanisms controlled by miRNAs in the nervous systems of invertebrate and vertebrate models are remarkably conserved in humans. We endeavor to provide insight into the roles of miRNAs in the nervous systems of these model organisms and discuss how such information may be used to inform regarding diseases of the human brain.
Predicting Corporate Financial Distress: A Time-Series CUSUM Methodology

The ability to predict corporate financial distress can be strengthened using models that account for serial correlation in the data, incorporate information from more than one period and include stationary explanatory variables. This paper develops a stationary financial distress model for AMEX and NYSE manufacturing and retailing firms based on the statistical methodology of time-series Cumulative Sums (CUSUM). The model has the ability to distinguish between changes in the financial variables of a firm that are the result of serial correlation and changes that are the result of permanent shifts in the mean structure of the variables due to financial distress. Tests performed show that the model is robust over time and outperforms similar models based on the popular statistical methods of Linear Discriminant Analysis and Logit.
Improving Discrimination of Savanna Tree Species Through a Multiple-Endmember Spectral Angle Mapper Approach: Canopy-Level Analysis

Differences in within-species phenology and structure are controlled by genetic variation, as well as topography, edaphic properties, and climatic variables across the landscape, and present important challenges to species differentiation with remote sensing. The objectives of this paper are as follows: 1) to evaluate the classification performance of a multiple-endmember spectral angle mapper (SAM) classification approach in discriminating ten common African savanna tree species and 2) to compare the results with the traditional SAM classifier based on a single endmember per species. The canopy spectral reflectance of the tree species ( Acacia nigrescens, Combretum apiculatum , Combretum imberbe, Dichrostachys cinerea, Euclea natalensis, Gymnosporia buxifolia, Lonchocarpus capassa, Pterocarpus rotundifolius, Sclerocarya birrea, and Terminalia sericea) was extracted from airborne hyperspectral imagery that was acquired using the Carnegie Airborne Observatory system over Kruger National Park, South Africa, in May 2008. This study highlights three important phenomena: 1) Intraspecies spectral variability affected the discrimination of savanna tree species with the SAM classifier; 2) the effect of intraspecies spectral variability was minimized by adopting the multiple-endmember approach, e.g., the multiple-endmember approach produced a higher overall accuracy (mean of 54.5% for 20 bootstrapped replicates) when compared to the traditional SAM (mean overall accuracy = 20.5%); and 3) targeted band selection improved the classification of savanna tree species (the mean overall percent accuracy is 57% for 20 bootstrapped replicates). Higher overall classification accuracies were observed for evergreen trees than for deciduous trees.
Ano1, a Ca2+‐activated Cl− channel, coordinates contractility in mouse intestine by Ca2+ transient coordination between interstitial cells of Cajal

Ano1, a Ca2+‐activated Cl− channel, is expressed in interstitial cells of Cajal (ICC) throughout the gut. We report here that it is required to maintain coordinated Ca2+ transients within myenteric ICC of mouse small intestine. Ca2+ transients in Ano1 WT mice were rhythmic and coordinated whereas uncoordinated Ca2+ transients were seen in knockout mice. Ca2+ transients were un‐coordinated following pharmacological block of Ano1 in WT mice using niflumic acid, 5‐nitro‐2‐(3‐phenylpropylamino) benzoic acid and 4,4′‐diisothiocyanato‐2,2′‐stilbenedisulfonic acid disodium salt. Transient knockdown of Ano1 in organotypic cultures with short hairpin RNA to Ano1 in WT tissues also caused loss of coordinated Ca2+ transients. Contractility of Ano1 knockout mouse intestinal segments in organ bath experiments was significantly decreased, less coordinated and non‐rhythmic. Spatiotemporal maps from knockout mouse small intestine also showed loss of phasic contractile activity. This study provides important information on the basic mechanisms driving coordinated contractile activity in the gastrointestinal tract.
Transparence de l'information : les stratégies de communication financière des grandes sociétés françaises cotées

Cette these traite des strategies de communication financiere des grandes societes francaises cotees. L'objectif est de mettre en evidence, a partir d'une revue de litterature theorique et empirique, et de tester les principaux determinants du niveau de transparence de l'information financiere produite par ces firmes. Ce niveau est mesure a partir de la construction d'un indice de transparence/opacite de la communication financiere applique au rapport annuel des firmes formant le sbf 120. Cet indice de transparence permet d'attribuer un score a chaque firme de l'echantillon, a partir duquel deux groupes d'entreprises opaques et transparentes sont constitues. Les resultats des tests de difference de moyenne entre ces deux groupes montrent que les entreprises transparentes detiennent une information a communiquer moins favorable et presentent une meilleure liquidite ainsi qu'un risque concurrentiel moins fort que les firmes opaques. Les regressions logistiques effectuees permettent de conclure que la probabilite qu'une firme produise une information transparente est d'autant plus forte que l'information qu'elle detient est defavorable, le marche de son titre liquide et l'intensite du conflit d'agence entre les dirigeants et les bailleurs de fonds elevee.
The politics of the new centre

Preface: Anthony Giddens. Introduction: Mark Leonard. Foreword to the Original German edition. 1. Breaking the Mould. 2. The Maxims of a Proactive State. 3. The Future of the Parties. 4. The Beginnings of a New Corporatism. 5. What Can We Learn From Others? 6. New Paths to Growth and Full Employment. 7. Policies for a Proactive Society. Postscript: Gerhard Schroder. Appendix: The Third Way, Die Neue Mitte: Tony Blair and Gerhard Schroder. Index.
Building Optimal Radio-Frequency Signal Maps

A popular way for using radio-frequency (RF) signals (e.g. WiFi) to position people or device indoors is by matching received radio signal strength (RSS) to fingerprints that are spatial signatures of such measures. Traditionally such signal maps are built by manual collection of repeated measurements at predefined locations following a spatial sampling scheme. Recently, such labor intensive processes are being replaced by robot-based automation or crowd-sourced simultaneous localization and mapping (SLAM). These new approaches produce time-stamped trajectories along with time-stamped RSS as the human or robot moves freely about the building. However, they require an additional procedure to segment the continuous RF samples into fingerprint cells to produce a robust signal map. In this paper, we explore several strategies for building optimal signal maps from RSS collected along robotic or pedestrian trajectories. We compare two clustering algorithms with a baseline strategy that divides the trajectories into a hierarchy of fixed-size grids. We study the trade-off between the spatial extent of the fingerprint cells and the differentiability of the RSS distribution in each cell, as well as their impact on localization accuracy and on fingerprint storage. We experimented with traces collected by an autonomous robot exploring a large multi-floor office building.
Updating the CTD Story: From Tail to Epic

Eukaryotic RNA polymerase II (RNAPII) not only synthesizes mRNA but also coordinates transcription-related processes via its unique C-terminal repeat domain (CTD). The CTD is an RNAPII-specific protein segment consisting of repeating heptads with the consensus sequence Y1S2P3T4S5P6S7 that has been shown to be extensively post-transcriptionally modified in a coordinated, but complicated, manner. Recent discoveries of new modifications, kinases, and binding proteins have challenged previously established paradigms. In this paper, we examine results and implications of recent studies related to modifications of the CTD and the respective enzymes; we also survey characterizations of new CTD-binding proteins and their associated processes and new information regarding known CTD-binding proteins. Finally, we bring into focus new results that identify two additional CTD-associated processes: nucleocytoplasmic transport of mRNA and DNA damage and repair.
Redescription of Elaeophora Schneideri Wehr and Dikmans, 1935 (Nematoda: Filarioidea).

Elaeophora schneideri Wehr and Dikmans, 1935, is redescribed on the basis of specimens obtained from Odocoileus hemionus, Odocoileus virginianus, Ovis aries, and Cervls canadensis. Recently Adcock, Hibler, Abdelbaki, and Davis (1965) reported that Elaeophora schneideri Wehr and Dikmans, 1935, caused blindness in North American elk (Cervus canadensis). This nematode is a common parasite of mule deer (Odocoileus hemionus) and domestic sheep (Ovis aries) in the mountainous regions of the western and southwestern United States, but has not been previously reported from elk. Specimens obtained from elk thus far are somewhat smaller than those found in sheep and deer, otherwise they are morphologically identical; moreover, except for the size of the specimens from elk, those from all three hosts are morphologically identical to the type specimens used by Wehr and Dikmans (1935). However an examination of the type specimens, and the specimens collected in the present study, has revealed several discrepancies in the original description. MATERIALS AND METHODS Redescription of E. schneideri is based on specimens obtained from deer, sheep, and elk. Some of those from mule deer were collected in Colorado by the late Dr. Lee Seghetti. The remainder were collected by one of us (C. P. H.) from mule deer and white-tailed deer (Odocoiletus virginianus) in Arizona, and mule deer in New Mexico. Specimens from sheep were collected in Colorado by Jensen and Seghetti (1955), and by one of us (C. P. H.) from sheep originating in the same general area. Specimens from elk were collected by the authors from animals in Arizona, Colorado, New Mexico, and Wyoming. Measurements of adults are based on five males and five females from each host, and are given in microns unless otherwise indicated, the average listed first, the range in parentheses. Illustrations Received for publication 13 May 1968. * This investigation was supported by research grant 5-R01-NB06199-02 from the NIH, Institute of Neurological Diseases and Blindness, and by the Arizona Came and Fish Commission. are based on specimens from the mule deer. Drawings were made with the aid of a camera lucida. Microfilariae were obtained by macerating skin in physiological salt solution. They were fixed in 70% alcohol, cleared in glycerin, and studied with the aid of a phase contrast microscope. Measurements are based on 25 specimens from the skin of mule deer. Redescription of Elaeophora schneideri Wehr and Dikmans, 1935 (Table I, Figs. 1-13)