Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the coral holobiont through science and scuba

Reef- building corals are a holobiont composed of the coral animal host and its associ- ated eukaryotic and bacterial microbes. Symbiotic dinoflagellates in the genus Symbiodinium, which form the basis of the coral-algal symbiosis and provide the coral host with most of its nutrition, are one of the most familiar members of the coral holobiont. Yet reef- building corals also possess diverse communities of bacteria that play important roles in processes such as nutrient cycling and coral immunity. Understanding the complex relationships between the coral, its algal symbionts, and associated microbes is critical because breakdowns in these relationships result in coral bleach- ing and coral disease outbreaks, both of which are increasing due to global climate change. Here we review recent advances in scuba- based research on the coral holobiont that have expanded our understanding of coral-algal and coral-microbe relationships as well as the role of the coral host in these interactions.
Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling

The Gibbs sampling method has been widely used for sequence analysis after it was successfully applied to the problem of identifying regulatory motif sequences upstream of genes. Since then, numerous variants of the original idea have emerged: however, in all cases the application has been to finding short motifs in collections of short sequences (typically less than 100 nucleotides long). In this paper, we introduce a Gibbs sampling approach for identifying genes in multiple large genomic sequences up to hundreds of kilobases long. This approach leverages the evolutionary relationships between the sequences to improve the gene predictions, without explicitly aligning the sequences. We have applied our method to the analysis of genomic sequence from 14 genomic regions, totaling roughly 1.8 Mb of sequence in each organism. We show that our approach compares favorably with existing ab initio approaches to gene finding, including pairwise comparison based gene prediction methods which make explicit use of alignments. Furthermore, excellent performance can be obtained with as little as four organisms, and the method overcomes a number of difficulties of previous comparison based gene finding approaches: it is robust with respect to genomic rearrangements, can work with draft sequence, and is fast (linear in the number and length of the sequences). It can also be seamlessly integrated with Gibbs sampling motif detection methods.
Identification of a Signal Peptide for Unconventional Secretion*

Homeoproteins are a class of transcription factors defined by the structure of their DNA-binding domain, the homeodomain. In addition to their nuclear cell-autonomous activities, homeoproteins transfer between cells, thanks to two separate steps of secretion and internalization, which both rely on unconventional mechanisms. Internalization is driven by the third helix of the homeodomain (Penetratin) through a non-vesicular and endocytosis-independent mechanism. In contrast, homeoprotein secretion involves vesicular compartments and requires the presence of a sequence of 11 amino acids (Sec sequence) spanning between the second and third helix of the homeodomain. In this study, we report that the SecPen polypeptide, which combines the two identified domains, Penetratin and Sec, bears all of the necessary information to go in and out of cells. We have analyzed key mechanisms and demonstrated that this peptide can efficiently cross a tight junction epithelium.
Levodopa unresponsive symptoms in Parkinson disease

Levodopa has been the mainstay of symptomatic therapy for Parkinson Disease (PD) for 40 years providing benefit to virtually all patients. Levodopa therapy results in improved activities of daily living, enhanced quality of life, and improved mortality. However, the long‐term use of levodopa is associated with the development of motor fluctuations and dyskinesia. In addition, levodopa therapy has further limitations. It has little or no effect on certain motor features (e.g. gait and balance dysfunction) and a non‐motor symptom complex (autonomic dysfunction, pain syndromes, sleep disorders, mood disturbances, dementia). Further, multiple case reports illustrate the potential of levodopa and other dopaminergic agents to cause or reveal a series of impulse control disorders. This review highlights the levodopa unresponsive symptoms in PD. © 2008 Movement Disorder Society
Crowdsourced Software Development in Civic Apps - Motivations of Civic Hackathons Participants

Hackathons are intensive events that typically last from 1 to 3 days, where programmers and sometimes people with interdisciplinary backgrounds (e.g., designers, journalists, activists) collaborate to develop software applications to overcome a challenge proposed by the event organizers. Civic hackathons are a particular type of hackathon that gained momentum in the last years, mainly propelled by city halls and government agencies throughout the world as a way to explore public data repositories. These initiatives became an attempt to crowdsource the development of software applications targeting civic issues. Some articles in academic literature have conflicting arguments about factors that motivate developers to create such apps. Claims are mostly based on anecdotal evidence since research is still scarce in the empirical analysis of civic hackathons. Thus, we decided to do a study to gather data under the perspective of hackathon participants, focusing on what motivation factors make them join such competitions. We conducted a survey research where we intended to provide empirical evidence for a diverse audience (e.g., hackathon organizers, open data specialists) interested in civic hackathons as a form of software crowdsourcing. In this work, we present preliminary results.
Proteomic analysis of Escherichia coli associated with urinary tract infections

Escherichia coli is a major cause of urinary tract infections (UTIs) where the initial infection arises from bacteria originating in the bowel. However, significant differences are observed between the genomes of intestinal and urinary E. coli strains with the latter possessing many adaptations that promote growth in the urinary tract. To define further the adaptation of urinary E. coli isolates, the cellular proteomes of 41 E. coli strains, collected from cases of UTIs or random faecal samples, were compared by 2‐D gel electrophoresis and principal component analysis. The data indicated that individual patients carried relatively homogenous E. coli populations, as defined by their cellular proteomes, but the populations were distinct between patients. For one patient, E. coli, isolated during two recurrent infections 3 months apart, were indistinguishable, indicating that for this patient the infections were possibly caused by the same bacterial population. To understand the basis of the discrimination of the bacteria, selected protein spots were identified by peptide fragment fingerprinting. The identified proteins were involved in a variety of metabolic and structural roles. The data obtained for these E. coli strains provide a basis from which to target key bacterial proteins for further investigation into E. coli pathogenesis.
Short Time Algorithm of Power Waveforms Fundamental Harmonic Estimation With Use of Prony's Methods

This paper presents an example of practical use of Prony ’s method for monitoring of power waveform fundamental harmonic fluctuations, which is required for the analysis of window synchronizations in frequency analyses in power monitoring systems. The example presen ted offers verification of the authors' theoretical considerations published earlier in articles about Prony ’s method and its opportunities for practical use for real life signals. The investigations shown are based on the least squares Prony ’s method, which, in connection with digital filtrations, enables estimations of fundamental frequency at the rate of even tens of times per one fundamental harmonic period.
The efficacy and safety of B‐cell depletion with anti‐CD20 monoclonal antibody in adults with chronic immune thrombocytopenic purpura

Because of its B‐cell depleting effect, rituximab has entered clinical trials in several autoimmune conditions. This study assesses the efficacy and safety of rituximab in 57 adults with chronic immune thrombocytopenic purpura (ITP). All patients had platelet counts <30 × 109/l, all had received two or more previous ITP treatments and 31 had undergone splenectomy. Patients received rituximab 375 mg/m2 weekly for 4 weeks. Thirty‐one patients (54%) responded, achieving a platelet count >50 × 109/l: 18 achieved a complete response (CR: platelet count >150 × 109/l) and 13 a partial response (PR: platelet count 50–150 × 109/l). Twenty‐nine responses occurred within 8 weeks of the first infusion. Sixteen of 18 CR patients (28% overall), including eight who had failed splenectomy, continued in CR after a median of 72·5 weeks; 15 of 16 are >1 year from the first infusion. Only two of 13 maintained a PR. Thirty‐three patients experienced grade 1–2 adverse events and one a grade 3 event, but they all completed treatment. Circulating B cells fell to <0·03 × 109/l. No changes in immunoglobulin levels or infectious complications were seen. In summary, rituximab was well tolerated with no immediate complications and induced a lasting, substantial response in 32% of adults with chronic ITP.
Características epidemiológicas de una población que accedió al Programa de Prevención del Cáncer de Cuello Uterino en Uruguay

Se analiza por primera vez en nuestro pais una muestra de poblacion de 96.858 mujeres que accedieron a un Programa de Prevencion del C ncer de Cuello Uterino con el objetivo de obtener una caracterizacion epidemiologica. En la poblacion estudiada se encontro una prevalencia de resultados con diferente grado de relacion con el c ncer de cuello uterino de 1,20 por ciento. Los factores epidemiologicos que se asociaron con mayor frecuencia a resultados de Papanicolaou vinculados con el c ncer de cuello uterino fueron las enfermedades de transmision sexual HPV (virus del papiloma humano) y HIV (virus de inmunodeficiencia humana), el h bito de fumar y la ausencia de controles preventivos previos. Se plantea la necesidad de aumentar la cobertura preventiva en la poblacion de mujeres carente de recursos. (AU)
Novel Apache Spark based Algorithm to Solve Dirichlet Problem for Poisson Equation in 3D Computational Domain

Parallel computations are essential tool in solving large-scale computationally demanding problems. Due to large diversity and heterogeneity of the currently available parallel processing techniques and paradigms it is usually difficult to find the right solution that will perform well according to every performance metric. As one of the recent developments in parallel computing Apache Spark framework allows to process petabyte-scale data and possesses properties such as fault tolerance, scalability, load balancing and mechanisms of in memory computations across nodes of the cluster. All of these features are attractive for high performance scientific computing. It has been shown that Apache Spark outperforms Hadoop implementation of some machine learning algorithms by orders of magnitude. Since Hadoop platform is not well suited for iterative computing, typical for many computational problems, in this study we investigate performance characteristics of Apache Spark on scientific computing problems, particularly for solving Dirichlet problem for Poisson's equation. An algorithm for solving Dirichlet problem for Poisson's equation is described and analyzed and compared to optimized Hadoop-based implementations. Apache Spark uses new distributed data structure called RDD. Presented algorithm consists of operations on RDD such as mapping, grouping and partitioning. The benefits and drawbacks of the algorithm as well as applicability for stencil type computations are discussed and analyzed.
A 16 b quadrature direct digital frequency synthesizer using interpolative angle rotation algorithm

A quadrature direct digital frequency synthesizer (DDFS) is fabricated in 0.35 /spl mu/m CMOS using a new phase-to-sine conversion algorithm. It achieves a spurious-free dynamic range (SFDR) of 96 dB with small-sized lookup tables and appropriate arithmetic hardware. The prototype DDFS IC generates 16 b cosine and sine outputs with an output frequency tuning resolution of 0.03 Hz. It works at 150 MHz sampling rate, consuming 670 mW.
Conventional drug therapy for inflammatory bowel disease

Abstract Most patients with inflammatory bowel diseases (IBD) are offered conventional medical therapy, because emerging therapies for IBD are regulated by health-care jurisdiction and often limited to academic centres. This review distils current evidence to provide a pragmatic approach to conventional IBD therapy, including aminosalicylates, corticosteroids, thiopurines, methotrexate, calcineurin inhibitors, infliximab and adalimumab. It addresses drug efficacy, safety and salient practice points for optimal and appropriate practice.
Social class inequality in mortality from 1921 to 1972 in England and Wales.

In this paper the data on occupational and social class mortality published decennially for England and Wales are used to examine the trend in the size of class differentials in mortality from 1921 to 1972 for adult men, married women and infants. Using summary measures which take into account changes in the relative sizes of the social classes over time, it was found that absolute inequality in mortality increased among adult men and married women during the 1950s and 1960s and relative inequality increased for all three groups. Two widely recognized potential sources of error, changes in the occupational composition of the social classes over time, and discrepancies between the numerators and denominators of occupation-specific death rates are examined to determine their effect on the trend indicated, and the initial findings are confirmed. Finally, the possible causes and implications of rising inequality coincident with declining overall levels of mortality, relative affluence, and the uniform availab.
Activation-Induced Cytidine Deaminase Expression and Activity in the Absence of Germinal Centers: Insights into Hyper-IgM Syndrome1

Somatic hypermutation normally occurs as a consequence of the expression of activation-induced cytidine deaminase (AID) by Ag-activated, mature B cells during T cell-dependent germinal center responses. Nonetheless, despite their inability to express CD154 and initiate GC responses, patients with type 1 hyper-IgM syndrome (HIGM1) support populations of IgM+IgD+CD27+ B cells that express mutated Ig genes. The origin of these mutated B cells is unknown; the IgM+IgD+CD27+ cells do not express AID and appear to acquire mutations independent of stringent selection by Ag. Here, we demonstrate that immature/transitional 1 B cells from the bone marrow of CD154-deficient mice express AID and acquire Ig mutations that lack the hallmarks of antigenic selection via BCR signaling. Comparable levels of AID expression was found in developmentally immature B cells recovered from murine fetal liver and from human immature/transitional 1 B cells recovered from umbilical cord blood. AID expression in human fetal liver was also robust, approaching that of human tonsil tissue and the human germinal center B cell line, Ramos. These observations led us to conclude that AID expression in developing human B cells is the origin of the mutated IgM+IgD+CD27+ B cells present in HIGM1 patients, and we propose that both mice and humans share a latent, AID-dependent pathway for the preimmune diversification of B lymphocytes that is more prominent in chicken, sheep, and rabbits.
Acculturation and Dietary Intakes by Gender Among Mongolians in South Korea: Nutrition Education Implication for Multicultural Families

We explored the relationship between acculturation and dietary intake by gender for 500 Mongolians residing in South Korea. The high acculturation (HA) group females consumed more fish and shellfish, vegetables, beans, and rice, and less meats, flours, and oil than the low acculturation (LA) group did. However, there was no statistical difference in food group intake between HA and LA group males. HA group females showed higher intake of carbohydrates, fiber, sodium, potassium, calcium, vitamin A, and folate compared with LA group females. However, only folate and vitamin B2 intake was statistically different between HA and LA group males. Acculturation and gender interactions were found for the consumption of meats, flours, fish and shellfish, beans, and vegetables. The findings from this study have implications for developing customized nutrition intervention programs by gender for immigrants.
Les pays d’Europe centrale et orientale dans la division du travail en Europe

Cet article analyse les echanges entre l’Union europeenne et les dix pays candidats, sous plusieurs angles: evolution des specialisations, effets de la segmentation internationale des processus productifs, nature des echanges et positionnement des Peco sur l’echelle de qualite. Il montre que les PECO dans leur ensemble restent globalement specialises dans les industries intensives en main d’œuvre et en ressources naturelles, mais qu’il y a une differenciation croissante entre les pays d’Europe centrale et les autres.
Should any genetic defect affecting α‐granules in platelets be classified as gray platelet syndrome?

There is much current interest in the role of the platelet storage pool of α‐granule proteins both in hemostasis and non‐hemostatic events. As well as in the arrest of bleeding, the secreted proteins participate in wound healing, inflammation, and innate immunity while in pathology they may be actors in arterial thrombosis and atherosclerosis as well as cancer and metastasis. For a long time, gray platelet syndrome (GPS) has been regarded as the classic inherited platelet disorder caused by an absence of α‐granules and their contents. While NBEAL2 is the major source of mutations in GPS, other gene variants may give rise to significant α‐granule deficiencies in platelets. These include GATA1, VPS33B, or VIPAS39 in the arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome and now GFI1B. Nevertheless, many phenotypic differences are associated with mutations in these genes. This critical review was aimed to assess genotype/phenotype variability in disorders of platelet α‐granule biogenesis and to urge caution in grouping all genetic defects of α‐granules as GPS. Am. J. Hematol. 91:714–718, 2016. © 2016 Wiley Periodicals, Inc.
NO-induced reversible switching of the electronic interaction between a porphyrin-coordinated cobalt ion and a silver surface.

The electronic interaction between a porphyrin-coordinated Co ion and a silver surface was switched by an axial nitric oxide (NO) ligand on the Co ion. This process is reversible and was monitored with X-ray and UV-photoelectron spectroscopy (XPS and UPS). The Co−Ag interaction leads to an electron transfer from the Ag surface to the Co ion and to a new electronic state close to the Fermi level. Both effects vanish if an axial NO ligand coordinates to the Co ion, indicating that the Co−Ag interaction is suppressed. As a possible explanation, we discuss a competition, similar to the trans effect, between the two axial ligands on the Co ion: the NO molecule and the Ag surface. These findings have important implications for sensor technology and for catalysis on supported metalloporphyrins, in which the catalytic activity of the metal center is controlled by the interaction with the underlying surface.
Spectrum allocation and medium access in cognitive radio wireless networks

This paper1 focuses on spectrum allocation and medium access in future cognitive radio wireless networks, e.g. IEEE 802.22 networks. For a given network topology, the proposed spectrum allocation method first generates an interference graph (or conflict graph) based on the network topology, traffic flows and interference constraints. Then a graph coloring algorithm is applied to the interference graph and the chromatic number of the graph is obtained. This number is the minimum number of distinct spectrum slices required. Further, spectrum allocation is done based on the max-min fair share algorithm or proportional fair algorithm according to the spectrum demands for different spectrum blocks. For medium access among secondary users, we then describe and implement a MAC protocol for 802.22-type cognitive radio networks. Simulation results are presented to demonstrate its effectiveness.
Statistics of Resistance Drift Due to Structural Relaxation in Phase-Change Memory Arrays

The phase-change memory (PCM), based on the reversible phase transition in a chalcogenide material, is among the most attractive memory concepts for next-generation nonvolatile memories. Due to the metastable nature of the amorphous state, the memory can exhibit a time variation of resistance after programming as a result of two main mechanisms: 1) structural relaxation (SR), which is an atomic rearrangement to minimize the defect density, and 2) crystallization of the amorphous chalcogenide. SR has been mostly studied at the single-cell level, whereas a statistical analysis and modeling is necessary for device reliability estimation and prediction. This work studies the statistical behavior of SR in PCM devices, through experimental and modeling approaches. Statistical SR data from PCM arrays are shown, and a Monte Carlo model for SR statistics is proposed, based on previous physical modeling of the SR process. This model allows for long-term, physics-based, and array-level reliability extrapolations in large PCM arrays.
Increased Phosphorylation of Ser-Gln Sites on SUPPRESSOR OF GAMMA RESPONSE1 Strengthens the DNA Damage Response in Arabidopsis thaliana

The number of phosphorylated sites on transcription factor SOG1 affects the strength of various DNA damage responses including DNA repair, replication arrest, cell death, and cell differentiation. The Arabidopsis thaliana transcription factor SUPPRESSOR OF GAMMA RESPONSE1 (SOG1) regulates hundreds of genes in response to DNA damage, and this results in the activation of cell cycle arrest, DNA repair, endoreduplication, and programmed cell death. However, it is not clear how this single transcription factor regulates each of these pathways. We previously reported that phosphorylation of five Ser-Gln (SQ) motifs in the C-terminal region of SOG1 are required to activate downstream pathways. In this study, we introduced Ser-to-Ala (AQ) substitutions in these five SQ motifs to progressively eliminate them and then we examined the effects on DNA damage responses. We found that all SQs are required for the full activation of SOG1 and that the expression level of most downstream genes changed incrementally depending on the number of phosphorylated SQ sites. Genes involved in DNA repair and cell cycle progression underwent stepwise activation and inhibition respectively as the number of phosphorylated SQ sites increased. Also, inhibition of DNA synthesis, programmed cell death, and cell differentiation were incrementally induced as the number of phosphorylated SQ sites increased. These results show that the extent of SQ phosphorylation in SOG1 regulates gene expression levels and determines the strength of DNA damage responses.