Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies

A crise taxonomica, em destaque nos ultimos anos, e marcada pela falta de popularidade (desinteresse pela formacao taxonomica) e incentivos financeiros direcionados ao estudo da biodiversidade. Esta situacao somada as questoes envolvidas com a necessidade de se conhecer as inumeras especies ainda desconhecidas tem feito com que novas tecnologias, dentre elas o uso do DNA, tenham surgido como propostas para revitalizacao da taxonomia. Uma parte da comunidade cientifica, entretanto, tem rejeitado o uso dessas ideias inovadoras. O DNA barcoding, principalmente, tem sido alvo de inumeras criticas quanto a sua aplicacao em contraposicao ao uso da morfologia. O presente artigo visa destacar a inconsistencia do debate DNA versus morfologia, pela existencia de uma proposta que corresponde a uniao entre a taxonomia tradicional e o DNA barcoding - a taxonomia integrativa. Os pontos favoraveis e desfavoraveis dessa proposta serao discutidos assim como a sua validade e aplicacao. Com ela, a importância da morfologia e reconhecida e ao mesmo tempo tem-se a revitalizacao da taxonomia tradicional pela aderencia das tecnologias incitadas para transposicao do impedimento taxonomico.
Instructions for use Title Radiosensitization of tumor cells through endoplasmic reticulum stress induced by PEGylated nanogelcontaining gold nanoparticles

Title Radiosensitization of tumor cells through endoplasmic reticulum stress induced by PEGylated nanogel containing gold nanoparticles Author(s) Yasui, Hironobu; Takeuchi, Ryo; Nagane, Masaki; Meike, Shunsuke; Nakamura, Yoshinari; Yamamori, Tohru; Ikenaka, Yoshinori; Kon, Yasuhiro; Murotani, Hiroki; Oishi, Motoi; Nagasaki, Yukio; Inanami, Osamu Citation Cancer Letters, 347(1): 151-158 Issue Date 2014-03 Doc URL http://hdl.handle. net/2115/55287 Type article (author version)
In‐vitro and in‐vivo antibacterial activity evaluation of a polyurethane matrix

Various in‐vitro and in‐vivo methods for evaluation of the duration of antibacterial activity were compared using a controlled‐release polyurethane matrix developed for the prevention of surface bacterial adhesion and growth. Cefadroxil was incorporated into this polyurethane matrix by a solvent casting method before the matrix was coated with polyurethane in tetrahydrofuran solution. The release of cefadroxil from the matrix into distilled water at 37 °C was measured by HPLC. The morphological change of matrices before and after release studies was investigated by scanning electron microscopy (SEM). The duration of antimicrobial activity of the matrix against Escherichia coli and Staphylococcus aureus was evaluated by measuring the diameters of the inhibition zone and the optical density of the broth. The matrices were also implanted subcutaneously in rats and the duration of the antibacterial activity was determined by measuring the inhibition zone. The results showed that duration of antibacterial activity of the polyurethane matrix was successfully determined in‐vitro by these methods, and the results differed from the conventional in‐vitro release study. It was also possible to determine the duration of action of the matrix in‐vivo by implanting the matrix in rats, and then measuring the antibacterial activity of the matrix at predetermined time intervals. While a good correlation was observed between the in‐vitro and in‐vivo methods used in this study to evaluate the duration of the antibacterial activity of the polymeric matrix, the conventional in‐vitro release study did not coincide with these results.
Processed foods : contributions to nutrition 1 , 2

Both fresh and processed foods make up vital parts of the food supply. Processed food contributes to both food security (ensuring that sufficient food is available) and nutrition security (ensuring that food quality meets human nutrient needs). This ASN scientific statement focuses on one aspect of processed foods: their nutritional impacts. Specifically, this scientific statement 1) provides an introduction to how processed foods contribute to the health of populations, 2) analyzes the contribution of processed foods to “nutrients to encourage” and “constituents to limit” in the American diet as recommended by the Dietary Guidelines for Americans, 3) identifies the responsibilities of various stakeholders in improving the American diet, and 4) reviews emerging technologies and the research needed for a better understanding of the role of processed foods in a healthy diet. Analyses of the NHANES 2003–2008 show that processed foods provide both nutrients to encourage and constituents to limit as specified in the 2010 Dietary Guidelines for Americans. Of the nutrients to encourage, processed foods contributed 55% of dietary fiber, 48% of calcium, 43% of potassium, 34% of vitamin D, 64% of iron, 65% of folate, and 46% of vitamin B-12. Of the constituents to limit, processed foods contributed 57% of energy, 52% of saturated fat, 75% of added sugars, and 57% of sodium. Diets are more likely to meet food guidance recommendations if nutrient-dense foods, either processed or not, are selected. Nutrition and food science professionals, the food industry, and other stakeholders can help to improve the diets of Americans by providing a nutritious food supply that is safe, enjoyable, affordable, and sustainable by communicating effectively and accurately with each other and by working together to improve the overall knowledge of consumers. Am J Clin Nutr 2014;99:1525–42.
Comparison between Atmospheric Chemistry Model and Observations Utilizing the RAQMS-CMAQ Linkage, Part II : Impact on PM2.5 Mass Concentrations Simulated

In the companion paper (Lee et al., 2012), it was showed that CMAQ simulation using a lateral boundary conditions (LBCs) derived from RAQMS-CMAQ linkage, compared to the CMAQ results with the default CMAQ LBCs, improved ozone simulations in the conterminous US domain. In the present paper, the study is extended to investigate the influence of LBCs on PM2.5 simulation. MM5-SMOKE-CMAQ modeling system was used for meteorological field generation, emissions preparation and air quality simulations, respectively. Realtime Air Quality Modeling System (RAQMS) model assimilated with satellite observations were used to generate the CMAQ-ready LBCs. CMAQ PM2.5 simulations with RAQMS LBCs and predefined LBCs were compared with U.S. EPA Air Quality System (AQS) measurements. Mean PM2.5 lateral boundary conditions taken from RAQMS outputs showed strong variations both in the horizontal grid and vertical layers in the northern and western boundaries and affected the results of CMAQ PM2.5 predictions. CMAQ with RAQMS LBCs could improve CMAQ PM2.5 predictions resulting in the improvement of index of agreement from 0.38 to 0.63.
Choquet Aggregation Using Order Inducing Variables

We discuss the OWA and Choquet integral aggregation operators and point out the central role the ordering operation plays in these operators. We extend the capabilities of the Choquet integral aggregation by allowing the ordering to be induced by some values other then those being aggregated. This allows us to consider an induced Choquet Choquet integral aggregation operator. We look at the properties of this operator. We then look at its applications. Among the applications considered are aggregations guided by linguistic and other ordinal structures. We look at the use of induced aggregation in nearest neighbor methods. We also consider the Choquet aggregation of complex objects such as matrices and vectors.
A new method on finding optimal centers for improving K-means algorithm

The mean center (geometric center) has always been used to represent the cluster center in classical K-means algorithm which may cause error. In this paper, a new method, P-partition Method, is introduced to obtain the center of a cluster, which proved efficient and globally optimal. Then two related clustering algorithms are presented by replacing the mean center of K-means based on the new centers found by P-partition, both of which are verified in experiments to be able to provide a better objective value (averagely about 3% lower than that of K-means) under the same conditions.
Cryopreservation of Boar Semen Impact of the Use of Specific Ejaculate Portions , Concentrated Packaging , and Simplified Freezing Procedures on Sperm Cryosurvival and Potential

Generally, spermatozoa from most boars survive poorly the customary process of cryopreservation. Post-thaw (PT) survivors often show unstable membranes, short life-span, and low fertilising capacity when artificial insemination (AI) is used. This thesis aimed at improving this situation by (i) freezing high sperm numbers in novel packages (MiniFlatPacksTM, MFP) and exploring their degree of PT-survival in vitro and fertility in vivo using deep intrauterine AI (DIU-AI). Moreover, it attempted to find out (ii) why particular portions of the ejaculate better resist cryopreservation and (iii) whether the process could be made attractive for routine use. Spermatozoa from the sperm-rich fraction of the ejaculate (SRF) were densely (2×10 sperm/mL) packed into MFP, frozen and studied post-thaw, alongside controls handled in plastic straws. Cells handled in MFP survived better in vitro than controls. In vivo, single DIU-AIs of these spermatozoa led, despite the very low volume inseminated, to pregnancies, fertilisation rates being higher in MFP than controls, when the interval between DIU-AI and ovulation was -8 to -4 h. Two specific portions of the ejaculate, namely the first 10 mL from the SRF (P1) and (P2) i.e. the rest of the SRF and the post-sperm fraction, were further tested for their resilience to extension, cooling and freezing-thawing in vitro, using a battery of tests for kinematics, membrane integrity/stability and chromatin intactness. Most often, P1spermatozoa best sustained all handling procedures, revealing that capacitation-like sperm destabilisation did not occur during controlled cooling. Such in vitro resilience was not intrinsically sperm-related, but differently influenced by the seminal plasma (SP) of the portions (SP-P1, SP-P2). Pooled SP-P1 (with fewer and different proteins, as well as less bicarbonate, than SP-P2) was able to increase PT motility of cleansed P2-spermatozoa to P1 levels. Using all previous findings, a final study was designed to simplify cryopreservation, by freezing P1 in MFP with a shorter (from 8 to 3.5 h) freezing protocol (SF), excluding primary extension and removal of SP by centrifugation. The P1-SF-processed spermatozoa in MFP survived the process equally as well as SRF controls, but without variation among males or ejaculates, implying that this simpler freezing protocol could be advantageously applied to build genetic banks or commercialise frozen semen primarily for DIU-AI using P1. The P2 could still be used for production of conventional AI doses, allowing the AI enterprise to maintain routine management of commercially relevant stud boars.
Basophil Responsiveness and Clinical Picture of Acetylsalicylic Acid Intolerance

Background: Exposure to acetylsalicylic acid (ASA) may exacerbate respiratory or skin diseases or induce anaphylactoid reactions in apparently healthy individuals. We wanted to evaluate specific responsiveness of basophils to ASA in correlation with the clinical picture. Methods: We performed a prospective single-blind study of 59 subjects involved in clinical evaluation and/or ASA provocation testing. Whole blood basophils were stained with anti-CD63/CD123/HLA-DR mAbs after stimulation with 0.25 or 1 mg/ml ASA. Results: We found that 40 subjects were ASA tolerant and 19 were ASA intolerant. Both groups had comparable manifestations of asthma and/or rhinitis (13 in the tolerant and 9 in the intolerant group). Intolerant subjects showed significantly higher basophil responsiveness to ASA in comparison to tolerant subjects, which was concentration-dependent in both groups. The ratio between responses at 1 mg/ml of ASA and at baseline (activation index) was analyzed according to the clinical picture. We demonstrate that the activation index was higher only in the intolerant subjects with anaphylactoid reactions, but not in a subgroup of subjects with asthma/rhinitis. The ROC calculations show that the optimal threshold activation index was more than 2.18. The sensitivity was 80% and the specificity was 83% in the subgroup with anaphylactoid reactions. In the asthma/rhinitis subgroup, the sensitivity was 78% and the specificity was 50%. Conclusions: Our study demonstrates that there is a significantly higher in vitro basophil response to ASA in intolerant as compared to tolerant subjects. ROC analyses suggest that this measurement might only have a diagnostic value in subjects without asthma and/or rhinitis.
An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry

Independent, greedy collection of data events using simple heuristics results in massive over-sampling of the prominent data features in large-scale studies over what should be achievable through “intelligent,” online acquisition of such data. As a result, data generated are more aptly described as a collection of a large number of small experiments rather than a true large-scale experiment. Nevertheless, achieving “intelligent,” online control requires tight interplay between state-of-the-art, data-intensive computing infrastructure developments and analytical algorithms. In this paper, we propose a Software Architecture for Mass spectrometry-based Proteomics coupled with Liquid chromatography Experiments (SAMPLE) to develop an “intelligent” online control and analysis system to significantly enhance the information content from each sensor (in this case, a mass spectrometer). Using online analysis of data events as they are collected and decision theory to optimize the collection of events during an experiment, we aim to maximize the information content generated during an experiment by the use of pre-existing knowledge to optimize the dynamic collection of events.
Basic science for the clinician Role of T-cells in myocardial infarction

Innate immunity has been studied for several decades in the context of ischaemia-reperfusion injury, myocardial remodelling, and healing. In the last years, a number of experimental and clinical studies focused on adaptive immunity in these processes. Meanwhile, there is considerable evidence especially on the role of CD4+ T-cells in myocardial injury and healing, whereas their role in remodelling is less clear. Innate leukocytes are able to recognize a wide array of self and foreign molecular patterns, whereas the activation of adaptive immunity requires the highly specific cooperation of antigen-presenting cells and distinct antigen-specific receptors on lymphocytes. Relevant autoantigens have not yet been definitely identified but experimental evidence indicates that autoantigen recognition is necessary for T-cell activation after myocardial infarction. Non-antigen-specific modes of activation might also play a role especially during acute ischaemia and reperfusion of the myocardium. This review summarizes the current evidence from experimental studies and presents side-by-side recent clinical data on the role of T cells in the pathophysiology of myocardial reperfusion injury and post myocardial infarction healing.
Shaping the College Curriculum: Academic Plans in Context

Major Changes to the Second Edition Chapters have been reorganized for improved understanding of the academic plan model on which the book is based. Greater emphasis is placed on the sociocultural contexts that influence curriculum planning. Includes a new chapter on institutional influences that affect curricular decision-making. Two coordinated chapters on learning and selecting instructional processes provide practical suggestions for instructors. A new chapter on curricular change suggests multiple strategies for promoting curriculum development and revision in varied contexts.
Rayleigh–Taylor instability in cylindrical geometry with compressible fluids

A linear stability analysis of the Rayleigh–Taylor instability (RTI) between two ideal inviscid immiscible compressible fluids in cylindrical geometry is performed. Three-dimensional (3D) cylindrical as well as two-dimensional (2D) axisymmetric and circular unperturbed interfaces are considered and compared to the Cartesian cases with planar interface. Focuses are on the effects of compressibility, geometry, and differences between the convergent (gravity acting inward) and divergent (gravity acting outward) cases on the early instability growth. Compressibility can be characterized by two independent parameters—a static Mach number based on the isothermal sound speed and the ratio of specific heats. For a steady initial unperturbed state, these have opposite influence, stabilization and destabilization, on the instability growth, similar to the Cartesian case [D. Livescu, Phys. Fluids 16, 118 (2004)]. The instability is found to grow faster in the 3D cylindrical than in the Cartesian case in the converge.
AzuR From the SmtB/ArsR Family of Transcriptional Repressors Regulates Metallothionein in Anabaena sp. Strain PCC 7120

Metallothioneins (MTs) are cysteine-rich, metal-sequestering cytosolic proteins that play a key role in maintaining metal homeostasis and detoxification. We had previously characterized NmtA, a MT from the heterocystous, nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 and demonstrated its role in providing protection against cadmium toxicity. In this study, we illustrate the regulation of Anabaena NmtA by AzuR (Alr0831) belonging to the SmtB/ArsR family of transcriptional repressors. There is currently no experimental evidence for any functional role of AzuR. It is observed that azuR is located within the znuABC operon but in the opposite orientation and remotely away from the nmtA locus. Sequence analysis of AzuR revealed a high degree of sequence identity with Synechococcus SmtB and a distinct α5 metal binding site similar to that of SmtB. In order to characterize AzuR, we overexpressed it in Escherichia coli and purified it by chitin affinity chromatography. Far-UV circular dichroism spectroscopy indicated that the recombinant AzuR protein possessed a properly folded structure. Glutaraldehyde cross-linking and size-exclusion chromatography revealed that AzuR exists as a dimer of ∼28 kDa in solution. Analysis of its putative promoter region [100 bp upstream of nmtA open reading frame (ORF)] identified the presence of a 12–2–12 imperfect inverted repeat as the cis-acting element important for repressor binding. Electrophoretic mobility shift assays (EMSAs) showed concentration-dependent binding of recombinant dimeric AzuR with the promoter indicating that NmtA is indeed a regulatory target of AzuR. Binding of AzuR to DNA was disrupted in the presence of metal ions like Zn2+, Cd2+, Cu2+, Co2+, Ni2+, Pb2+, and Mn2+. The metal-dependent dissociation of protein–DNA complexes suggested the negative regulation of metal-inducible nmtA expression by AzuR. Overexpression of azuR in its native strain Anabaena 7120 enhanced the susceptibility to cadmium stress significantly. Overall, we propose a negative regulation of Anabaena MT by an α5 SmtB/ArsR metalloregulator AzuR.
A New Multitracer Approach to Defining the Spiral Arm Width in the Milky Way

We analyze recent observations of the spiral arm width in the Milky Way, as a function of the galactic radius, and we compare this relation with the prediction from the density wave theory. We use the following method: in each spiral arm, we concentrate on the separation (or offset) between the star-forming region (radio masers) near the shock front of a density wave, and the aged star region (diffuse CO gas) near the potential minimum of a density wave; we take this separation between these two tracers as the arm width. New results: we find a typical separation (maser to diffuse CO gas) near 250 ± 50 pc and an increase of this separation with galactic radius of about 25 ± 5 pc per kpc. We note that, as expected, this separation is somewhat smaller than that found earlier between the dust lane and the aged star region. Overall, these results support the basics of a density wave.
Middle East Experience in Palliative Care

Palliative Care (PC) is still a relatively new concept in the Middle East (ME). It was first introduced in Saudi Arabia in 1992 and only recently in countries such as Qatar, Bahrain, and the UAE. Although the majority of Middle-Eastern countries, including Palestine, Iraq, Oman and Lebanon are in the capacity building phase, others such as Saudi and Jordan already have localized provision. In the absence of any of the ME countries approaching integration with the mainstream service providers, Saudi Arabia and Jordan are currently setting examples of achievement in the field. There are still countries with little or no known Palliative Care activity (Yemen and Syria). Political issues, scarcity of resources, and lack of education and awareness seem to be the common factors restricting the progress of this field in most countries. In order to improve the suboptimal PC services in the ME, emphasis should be directed toward providing formal education to professionals and raising awareness of the public. It is also necessary to put all differences aside and develop cross-border collaborations, whether through third party organizations such as the Middle East Cancer Consortium (MECC) or otherwise. This review compiles the available literature on the history and progress of the field of PC in most ME countries, while pointing out the major obstacles encountered by the active parties of each country.