Miracle-dz/UniFAR-FTUs huggingface dataset:
phoD Alkaline Phosphatase Gene Diversity in Soil

ABSTRACT Phosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution of phoD genes using whole-genome and metagenome databases. phoD alkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity of phoD, we developed a new set of primers which targets phoD genes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 different phoD operational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalent phoD genes identified in these soils were affiliated with the orders Actinomycetales (13 to 35%), Bacillales (1 to 29%), Gloeobacterales (1 to 18%), Rhizobiales (18 to 27%), and Pseudomonadales (0 to 22%). The primers also amplified phoD genes from additional orders, including Burkholderiales, Caulobacterales, Deinococcales, Planctomycetales, and Xanthomonadales, which represented the major differences in phoD composition between samples, highlighting the singularity of each community. Additionally, the phoD bacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity of phoD in soil and represent a valuable tool for the study of phoD alkaline phosphatase in environmental samples.
Quantitative analysis of pulmonary clearance of exogenous dopamine after cardiopulmonary bypass in humans.

The contribution of the lung to the clearance of exogenous dopamine after cardiopulmonary bypass (CPB) was analyzed quantitatively in humans and compared with the contribution of the lung before CPB. The pulmonary and arterial plasma concentration of dopamine and the pulmonary plasma flow were measured simultaneously during infusion of dopamine. Contribution of the pulmonary circulation was defined as the ratio between clearance through the pulmonary circulation and the total plasma clearance of dopamine. The calculated contribution values after CPB were 12.0, 10.7, 11.4, 16.2, and 16.7% at the doses of 3.0, 4.0, 5.0, 6.0, and 7.0 micrograms.kg-1.min-1, respectively. Those values before CPB were 15.6% and 17.4% at the doses of 1.0 and 2.0 micrograms.kg-1.min-1, respectively. The comparison of the values before and after CPB did not achieve statistical significance. Furthermore, there were no significant correlations between the pulmonary clearance after CPB and mean pulmonary arterial pressure, pulmonary vascular resistance, or CPB time. The results suggest that the pulmonary clearance mechanism for dopamine after CPB is maintained as effectively as that before CPB and is not influenced by pulmonary hypertension or CPB time.
Golden Door Voices: Towards a Critique of the Ellis Island Oral History Project

This article foregrounds the thematic structure of the Ellis Island Oral History Project narratives and the interview strategy adopted by the fieldworkers by focusing on a sample of interviews with emigrants from Great Britain. The analysis makes it possible to reveal the cultural bias informing the work of the Ellis Island researchers – and therefore the whole collection of Ellis Island oral histories – as revealed by their approach to the interview and relationship with the interviewees. The Ellis Island fieldworkers determine most of the elements constituting the fabric of the informants’ narratives as well as many of the “silences” on significant aspects of the migratory experience which characterize the accounts. Furthermore, they display a largely celebratory attitude based essentially on an uncritical acceptance of the American Dream myth. Therefore, though they represent a valuable source for investigating the history of emigration to the United States in the twentieth century, the Ellis Island oral histories fall short of scholars’ expectations.
Stable phase transition control for robot arm motion

A nonlinear-feedback-based algorithm is combined with explicit force control to drive a rigid manipulator from free space to compliant motion. Force control is switched on when the sensors report a contact event. An event-based motion planning method is used. Physically sensible definitions for the stability of a phase transition are given. A nonlinear interaction force model is considered in the analysis. Conditions involving impact velocity are presented for a stable phase transition that allows a finite number of bounces before final contact is eventually established. A sufficient condition for bounceless landing is given. The results are verified by dynamic simulation, which is now in the process of experimental implementation. <<ETX>>
A standard framework for mechatronics

This research aims to highlight the levers that are within the reach of Small and Medium Organizations (SMO) who have the purpose to engage in mechatronics. Subsequently, we consider to gradually build up a framework so as to enable these SMO, presently involved in the general mechanical industry, to evaluate their ability to make mechatronic products, adopt scalable evolution strategies and access the promising mechatronic markets by challenging novel business models, necessary to evolve towards mechatronics.
Ecological and individual level analysis of risk factors for HIV infection in four urban populations in sub-Saharan Africa with different levels of HIV infection

Objective: To identify factors that could explain differences in rate of spread of HIV between different regions in sub-Saharan Africa. Design: Cross-sectional study. Methods: The study took place in two cities with a relatively low HIV prevalence (Cotonou, Benin and Yaoundé, Cameroon), and two cities with a high HIV prevalence (Kisumu, Kenya and Ndola, Zambia). In each of these cities, a representative sample was taken of about 1000 men and 1000 women aged 15-49 years. Consenting men and women were interviewed about their socio-demographic background and sexual behaviour; and were tested for HIV, herpes simplex virus type 2 (HSV-2), syphilis, Chlamydia trachomatis and Neisseria gonorrhoea infection, and (women only) Trichomonas vaginalis. Analysis of risk factors for HIV infection was carried out for each city and each sex separately. Adjusted odds ratios (aOR) were obtained by multivariate logistic regression. Results: The prevalence of HIV infection in sexually active men was 3.9% in Cotonou, 4.4% in Yaoundé, 21.1% in Kisumu, and 25.4% in Ndola. For women, the corresponding figures were 4.0, 8.4, 31.6 and 35.1%. High-risk sexual behaviour was not more common in the high HIV prevalence cities than in the low HIV prevalence cities, but HSV-2 infection and lack of circumcision were consistently more prevalent in the high HIV prevalence cities than in the low HIV prevalence cities. In multivariate analysis, the association between HIV infection and sexual behavioural factors was variable across the four cities. Syphilis was associated with HIV infection in Ndola in men [aOR = 2.7, 95% confidence interval (CI) = 1.5-4.9] and in women (aOR = 1.7, 95% CI = 1.1-2.6). HSV-2 infection was strongly associated with HIV infection in all four cities and in both sexes (aOR ranging between 4.4 and 8.0). Circumcision had a strong protective effect against the acquisition of HIV by men in Kisumu (aOR = 0.25, 95% CI = 0.12-0.52). In Ndola, no association was found between circumcision and HIV infection but sample sizes were too small to fully adjust for confounding. Conclusion: The strong association between HIV and HSV-2 and male circumcision, and the distribution of the risk factors, led us to conclude that differences in efficiency of HIV transmission as mediated by biological factors outweigh differences in sexual behaviour in explaining the variation in rate of spread of HIV between the four cities.
Date Palm (Phoenix dactylifera): Protection and Remedy Food

Phoenix dactylifera belongs to the Arecaceae family; its leaves, barks, pits, fruits and pollens have antioxidant, anticancer, hepatoprotective, neuroprotective, nephroprotective, gastrointestinal protective, antidiabetic, antihyperlipidemic, fertility improvement and antimicrobial potentials. The broad pharmacological effects of P. dactylifera may be attributed to the powerful and beneficial ingredients including phenolics, flavonoids, carotenoids, vitamins, minerals, amino acids, fatty acids and organic acids. This review was conducted to explain the pharmacological preventive and curative potentials of P. dactylifera by searching PubMed and Google scholar databases through January, 2016 and selecting unique studies under each pharmacological potential of P. dactylifera.
Análisis Crítico sobre el Efecto de los Medios en el Aprendizaje (Critical Analysis of the Effect of Media on Learning)

Resumen. En el presente analisis se exponen las bases del clasico debate entre Richard Clark y Robert Kozma, autores reconocidos en el campo de Tecnologia Instruccional y la Educacion a Distancia por la relevancia de sus aportaciones; a partir del argumento inicial presentado por Richard Clark en 1983 contenido en su articulo denominado Reconsidering research on learning from media; donde describe evidencias suficientes que apoyan su opinion respecto a que los medios instruccionales no ejercen influencia alguna en el nivel de aprovechamiento de los estudiantes durante el proceso de ensenanzaaprendizaje. Palabras claves. Tecnologia instruccional, educacion a distancia, medios, aprendizaje, ensenanza.
The interactive FogScreen

The FogScreen is an immaterial projection screen that consists of air and a little humidity, and enables high-quality projected images in thin air. Objects and images appear to float in mid-air, and touching or walking through them enhances the impression, as the screen feels just like air. One nice feature is the possibility to project different images on each side without having them interfere with each other.
Implementing child-focused family nursing into routine adult psychiatric practice: hindering factors evaluated by nurses.

AIMS AND OBJECTIVES The aim of this study is to describe nurses' evaluations of factors that are hindering implementation of child-focused family nursing (CF-FN) into adult psychiatric practice. In addition, it explains the nurses' evaluations of the hindering factors related to the hospital organizational structure, the individual nurse, nursing and family. BACKGROUND There is an increasing amount of families with dependent children in adult psychiatry. Although these families have long-term benefits from preventive family interventions, implementation of CF-FN is not routine mental health practice. DESIGN AND METHODS Data were collected via a questionnaire-survey completed by Registered Psychiatric Nurses (n = 223) and practical Mental Health Nurses (n = 88) from 45 adult psychiatric units in five Finnish university hospitals. The response rate was 51%. RESULTS Family-related factors, such as families' fears and lack of time, were considered as 'most hindering' to CF-FN. Nurses who used a family-centred approach and had further family education considered most of the factors as 'less hindering' in comparison to other nurses. CONCLUSION To meet the needs of the families in mental health services, it is essential to develop nursing intervention methods such as CF-FN. There is a need for further education and use of family-centred care to develop this preventive approach. RELEVANCE TO CLINICAL PRACTICE The results of this study could be considered when developing mental health services and family interventions for families with parental mental illness.
Intracerebroventricular Passive Immunization. I. The Effect of Intracerebroventricular Administration of an Antiserum to Tumor Necrosis Factor-α on the Plasma Adrenocorticotropin Response to Lipopolysaccharide in Rats.

The present study tested the hypothesis that the cytokine tumor necrosis factor-α (TNF-α) is an important central nervous system mediator of the rat hypothalamo-pituitary-adrenal (HPA) axis response to the iv administration of lipopolysaccharide (LPS; 5 μg/kg). LPS produced a rapid (within 30 min) rise in plasma TNF-α levels, which preceded elevations in plasma ACTH (commencing at 45 min). Despite a lack of detectable TNF-α biological activity in the brain 30 min to 2 h after LPS administration, intracerebroventricular (icv) pretreatment (−20 h) with 5 μl anti-TNF-α antiserum significantly delayed the onset of the plasma ACTH response to LPS, suggesting that TNF-α acts within the brain. However, we also noted that the icv infusion of anti-TNF-α 20 h earlier produced experimentally significant concentrations of the same anti-TNF-α antibodies in systemic blood. This suggested the possibility that the effect of this antiserum was due to its leakage to the periphery. Indeed, 5 μl anti-TNF-α administered iv at.
Enhanced dendritic cell antigen presentation in RNA-based immunotherapy.

BACKGROUND Dendritic cells pulsed with mRNA provide a unique approach to tumor immunotherapy. We hypothesized that increased mRNA transfection efficiency and dendritic cell maturation would improve antigen processing and presentation as well as T-cell costimulation, resulting in enhanced induction of antimelanoma immune responses. METHODS Immature monocyte-derived dendritic cells were transfected with mRNA by passive pulsing, lipofection, or electroporation. Dendritic cells were either left untreated or matured using the double-stranded RNA poly(I:C). T-Cell cultures were generated by stimulation of naïve T-cells with each set of dendritic cells. Specific antigen presentation and specific effector T-cell generation were analyzed by an IFN-gamma release Elispot assay. RESULTS Greatest intracellular green fluorescent protein was observed by flow cytometry following dendritic cell electroporation with green fluorescent protein mRNA. DC presentation of Mart-1/Melan A peptide, as measured by Elispot assay using a specific T-cell clone, was greatest following transfection with Mart-1/Melan A mRNA by electroporation. Maturation of dendritic cells further improved antigen presentation regardless of transfection technique. Specific Mart-1/Melan A effector T cells were produced after culture of naïve T cells with dendritic cells that were electroporated with Mart-1/Melan A mRNA and then matured, but not for dendritic cells that remained immature. CONCLUSIONS Efficient mRNA transfection by electroporation as well as dendritic cell maturation results in increased levels of Mart-1/Melan A antigen presentation and enhanced production of antigen-specific effector T cells. This combination of strategies may be used to enhance immune responses to RNA-based dendritic cell vaccines.
Chronic Constipation: An Evidence-Based Review

Background: Chronic constipation is a common condition seen in family practice among the elderly and women. There is no consensus regarding its exact definition, and it may be interpreted differently by physicians and patients. Physicians prescribe various treatments, and patients often adopt different over-the-counter remedies. Chronic constipation is either caused by slow colonic transit or pelvic floor dysfunction, and treatment differs accordingly. Methods: To update our knowledge of chronic constipation and its etiology and best-evidence treatment, information was synthesized from articles published in PubMed, EMBASE, and Cochrane Database of Systematic Reviews. Levels of evidence and recommendations were made according to the Strength of Recommendation taxonomy. Results: The standard advice of increasing dietary fibers, fluids, and exercise for relieving chronic constipation will only benefit patients with true deficiency. Biofeedback works best for constipation caused by pelvic floor dysfunction. Pharmacological agents increase bulk or water content in the bowel lumen or aim to stimulate bowel movements. Novel classes of compounds have emerged for treating chronic constipation, with promising clinical trial data. Finally, the link between senna abuse and colon cancer remains unsupported. Conclusions: Chronic constipation should be managed according to its etiology and guided by the best evidence-based treatment.
Second-and higher-order perturbations of a spherical spacetime

The Gerlach and Sengupta (GS) formalism of coordinate-invariant, first-order, spherical and nonspherical perturbations around an arbitrary spherical spacetime is generalized to higher orders, focusing on second-order perturbation theory. The GS harmonics are generalized to an arbitrary number of indices on the unit sphere and a formula is given for their products. The formalism is optimized for its implementation in a computer-algebra system, something that becomes essential in practice given the size and complexity of the equations. All evolution equations for the second-order perturbations, as well as the conservation equations for the energy-momentum tensor at this perturbation order, are given in covariant form, in Regge-Wheeler gauge.
Polarized Uterine Epithelial Cells Preferentially Present Antigen at the Basolateral Surface: Role of Stromal Cells in Regulating Class II-Mediated Epithelial Cell Antigen Presentation1

To study Ag presentation in the female reproductive tract, DO11.10 TCR transgenic mice specific for the class II MHC-restricted OVA323–339 peptide and nontransgenic BALB/c mice were used. We report here that freshly isolated uterine epithelial cells, uterine stromal, and vaginal APCs present OVA and OVA323–339peptide to naive- and memory T cells, which is reduced when cells are incubated with Abs to CD80 and 86. To determine whether polarized primary epithelial cells present Ags, uterine epithelial cells were cultured on cell inserts in either the upright or inverted position. After reaching confluence, as indicated by high transepithelial resistance (>2000 ohms/well), Ag presentation by epithelial cells incubated with memory T cells and OVA323–339 peptide placed on the basolateral surface (inverted) was 2- to 3-fold greater than that seen with epithelial cells in contact with T cells and peptide on the apical surface (upright). In contrast, whereas freshly isolated epithelial cells process OVA, polarized epithelial cells did not. When epithelial cells grown upright on inserts were incubated with T cells and OVA323–339 peptide, coculture with either hepatocyte growth factor or conditioned stromal medium increased epithelial cell Ag presentation (∼90% higher than controls). These studies indicate that uterine stromal cells produce a soluble factor(s) in addition to a hepatocyte growth factor, which regulates epithelial cell Ag presentation. Overall, these results demonstrate that polarized epithelial cells are able to present Ags and suggest that uterine stromal cells communicate with epithelial cells via a soluble factor(s) to regulate Ag presentation in the uterus.
Asymmetric Adjustment of Realized Volatility

Using the multiple threshold autoregressive and moving average (TARMA) model we analyze the nonlinearities in the dynamics of realized volatilities of daily stock returns of 30 companies in the Dow Jones index. We find that the realized volatility processes can be characterized by the high, moderate, and low regimes and that the persistence, variance and ARMA error term change with each regime. Also, we find that spiked jumps in realized volatilities are better captured by the TARMA model than by ARMA or fractional ARMA models. Forecasts by the TARMA model tend to outperform those by the ARMA and fractional ARMA models.
Commentary: Cognitive and emotional empathy in transdiagnostic research - reflections on Klapwijk et al. (2016).

Evidence across multiple disorders indicates that empathy is a transdiagnostic dimension of psychopathology. Klapwijk et al.'s (2016) functional MRI study examines whether autism spectrum disorder (ASD) and conduct disorder (CD) can be distinguished by the constructs of 'cognitive' and 'emotional' empathy - with the former focusing on accurate emotion perception and the latter on shared affective experience. This commentary examines the implications of the cognitive/emotional empathy distinction, and how it fits with existing accounts of perceptual differences in ASD. Cognitive empathy overlaps substantially with the constructs of emotion perception and Theory of Mind - both well studied among individuals with ASD, but generally viewed as fairly distinct from empathy. CD, on the other hand, is typically not associated with frank perceptual deficits. Although the brain imaging data from this study do not provide strong support for the constructs of cognitive and emotional empathy, the general approach used in this study is precisely the kind needed to test the validity and utility of transdiagnostic mechanisms of psychopathology.
Isolation and Proteomic Characterization of the Arabidopsis Golgi Defines Functional and Novel Components Involved in Plant Cell Wall Biosynthesis1[W][OA]

The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized.
Lack of lamins A and C in mammalian hemopoietic cell lines devoid of intermediate filament proteins.

Using immunofluorescence microscopy and immunoblot analysis, we have examined the composition of the nuclear lamina in several murine and human cell lines. Whereas it was shown that intermediate filament-positive Ehrlich ascites tumor and HeLa-S3 cells contain the three major mammalian lamin subspecies, only lamin B could be detected in several myeloid- and lymphoid-derived cell lines representative of distinct stages in hemopoietic differentiation but all devoid of cytoplasmic intermediate filament proteins. These included the murine plasmacytoma cell types MPC-11 and MOPC-31C, murine myeloma cells X63-Ag8.6. 5.3 and human promyelocytic leukemia cells HL-60. Our results provide the first evidence that mammalian somatic cells capable of normal proliferation may lack both cytoplasmic intermediate filament proteins and a normal complement of nuclear lamins.