Miracle-dz/UniFAR-FTUs huggingface dataset:
The influence of whole genome duplication and subsequent diversification on environmental robustness and evolutionary innovation in gene regulatory networks

In biological systems, whole genome duplication and subsequent diversification constitute powerful mechanisms for the discovery of new phenotypes and for the protection of these phenotypes against environmental perturbation. Here, we use Random Boolean Networks to investigate the influence of these genetic mechanisms on the relationship between evolutionary innovation and environmental robustness in gene regulatory networks. We find that whole genome duplication is highly deleterious in ancestral environments, but provides fitness advantages in novel environments, which come at the cost of reduced environmental robustness. We then show that the subsequent diversification of duplicated networks, via the loss of regulatory interactions, can partly negotiate this tradeoff, improving evolutionary innovation and environmental robustness. We conclude by discussing the implications, limitations, and future directions of our research.
Relationship between hormone receptor concentration and tumor shrinkage in uterine myoma after treatment with a GnRHa.

BACKGROUND Uterine myomas are benign tumors of the uterus, occurring in up to 25% of women of reproductive age. We examined the possible causes for different degrees of volume reduction in patients with uterine myomas who received gonadotropin-releasing hormone agonist (GnRHa) treatment by investigating the hormone receptors at the end of GnRHa treatment. METHODS This trial was designed as a prospective study of five premenopausal women presenting with symptomatic uterine myoma. All patients were treated with a subcutaneous injection of goserelin depot 3.6 mg every four weeks for 16 weeks. Clinical examinations, hormonal evaluation and ultrasound determinations were performed before, during and after treatment. At the end of the treatment period, all patients underwent myomectomy. The concentrations of the unbound progesterone receptors and estrogen receptors were evaluated. RESULTS The volume of the uterine myoma decreased by 21% to 65%. The percentage of decrease in volume of treated uterine myomas was found to negatively correlate with the concentration of unbound progesterone receptors (r2 = 0.92, p = 0.008). This percentage was not significantly correlated with the concentration of unbound estrogen receptors (r2 = 0.02, p = 0.84). CONCLUSIONS The limited data available suggested that the volume decrease of uterine myomas in GnRHa-treated patients is partly dependent on the concentrations of unbound sex-hormone receptors in the uterine myomas.
Environmental Toxicology and Chemistry in Latin America IMPOSEX REDUCTION AND RESIDUAL BUTYLTIN CONTAMINATION IN SOUTHERN BRAZILIAN HARBORS

The imposex incidence was appraised in South American gastropods, considering the scenario before and after the global ban of tributyltin (TBT). A statistically significant reduction in imposex indexes was observed in Stramonita haemastoma collected in 2006 and 2010 from areas under the influence of four coastal harbors from southern Brazil. This reduction may be because of the effectiveness of the global ban issued by the International Maritime Organization, although the restrictions on TBT-based antifouling paints in Brazil might also have helped. Even so, a residual organotin contamination was still detected in female tissues (levels ranged from 7.6 to 164.9 ng Sn/g for TBT; from <2 to 214.5 ng Sn/g for dibutyltin; from <3.5 to 178.8 ng Sn/g for monobutyltin; and from <1.5 to 53 ng Sn/g for triphenyltin). Thus, although a reduction in imposex and environmental levels of organotins is expected in every ocean worldwide soon after the implementation of national and international restriction regulations, this will depend on the effectiveness of the global TBT ban; the effectiveness of local restrictions on producing, selling, and using TBT-based antifouling paints; and specific characteristics of local sediments, because metabolization rates and sorption/desorption of TBT previously deposited might affect its environmental bioavailability. Therefore, the reduction trend detected in the present study cannot be extrapolated to other Brazilian or South American coastal areas. Environ. Toxicol. Chem. 2012;31:947–954. # 2012 SETAC Keywords—Imposex Reduction Southern Brazil Organotin Temporal trend
Using OWL Contexts and OQE to Improve Web Document Search Precision and Recall

Ontologies describe domains and integrate information semantically. This paper examines semantic search, using ontology modules (contexts) and an independent corpus of Web documents, to see how ontology-based query expansion (OQE) might improve information retrieval precision and recall (P&R) compared to traditional keyword-only query; by giving added weight to documents that contain terms relevant to a query context ontology and also by returning relevant Web documents containing none of the original search keywords. To assess search effectiveness, a semantic search tool (SemSeT) has been developed to conduct OQE experiments; by matching OWL file concepts with document text, without resorting to structured semantic query languages or reasoning to automatically refine queries. A vector space model has been used to calculate document relevance scores and the results show that, compared to basic keyword query, OQE can markedly improve P&R.
Thymus and activation‐regulated chemokine in different stages of mycosis fungoides: Tissue and serum levels

Background/Objectives: Thymus and activation‐regulated chemokine (CCL17) is a member of the CC chemokines known to attract T‐helper 2 type memory T cells and to participate in different T‐helper 2 diseases. The aim of this study is to determine both serum and tissue levels of thymus and activation‐regulated chemokine in patients with different stages of mycosis fungoides.
Systematic reviews and economic evaluations conducted for the National Institute for Health and Clinical Excellence in the United Kingdom: A game of two halves?

Background: Decision analytic models, as used in economic evaluations, require data on several clinical parameters. The gold standard approach is to conduct a systematic review of the relevant clinical literature, although reviews of economic evaluations indicate that this is rarely done. Technology appraisals for the National Institute for Health and Clinical Excellence (NICE), which are fully funded, represent the best case scenario for the close integration of economic evaluations and systematic reviews. The objective of this study was to assess the extent to which the systematic review of the clinical literature informs the economic evaluation in NICE technology appraisals. Methods: All NICE technology assessment reports (TARs) published between January 2003 and July 2006 were considered. Data were abstracted on the TAR topics, the primary measure of clinical effectiveness, the approach to pooling in the clinical review, the measure of economic benefit and the use, or non-use, of the systematic review in the economic evaluation. Results: Forty-one TARs were published in the period studied, all of which contained a systematic review. Most of the economic evaluations (85 percent) were cost-utility analyses, reflecting NICE's guidelines for economic evaluation. In seventeen cases, the clinical data were not pooled in the review, owing to heterogeneity in the clinical data or the limited number of studies. In these cases, the economists used alternative approaches for estimating the key effectiveness parameter in the model. The results of the review (when pooled) were always used when the primary clinical effectiveness measure corresponded with the measure of economic benefit (e.g., survival). However, because preference-based quality of life measures are rarely included in clinical trials, the results of the systematic review were never directly used in the cost-utility analyses. Nevertheless, the outputs of the systematic review were used when the data were useful in estimating components of the quality-adjusted life-year (QALY) (e.g., the life-years gained, or the frequencies of health states to which QALYs could be assigned). Problems occurred mainly when the clinical data were not pooled, or when the measure of clinical benefit could not be converted into health states to which QALYs could be assigned. Conclusions: Economic evaluations can benefit from systematic reviews of the clinical literature. However, such reviews are not a panacea for conducting a good economic evaluation. Much of the relevant data for estimating QALYs are not contained in such reviews and the chosen method for summarizing the clinical data may inhibit the assessment of economic benefit. Problems would be reduced if those undertaking the technology assessments discussed the data requirements for the economic model at an early stage.
CS 365 : Image Classification Using Self-taught Learning For Feature Discovery

Image classification is an important task in computer vision which aims at classifying images based on their content. Most techniques for this task require a lot of labeled data to train the model which is scarce and expensive. Self-taught learning[2] tackles this problem by using a generic dataset of unlabeled data to train a generative model and use it for feature discovery. Deep learning techniques have been known to perform well for feature discovery. Convolutional deep belief networks[1] with probabilistic max pooling provide a translational invariant hierarchical generative model supporting both top-down and bottom-up inference that perform well on images. In this work, we employ CDBNs for self-taught learning to learn features from images to classify them.
Finding the Locus of Semantic Satiation: An Electrophysiological Attempt

The present study examined the effect of massed repetition of an initial category name upon the subsequent semantic categorization of a target word by means of an electrophysiological measure of semantic processing: the N400. Results showed the classic N400 effect, whereby evoked potentials were more negative for targets that were not members of the repeated category than for member targets. Moreover, repetition of the category name led to an increased and sustained positivity. The N400 effect was not modified, however, by repetition. Hence, insomuch as the N400 reflects meaning integration processes, these results do not support the hypothesis that massed repetition exerts its influence at the level of meaning integration.
Meat consumption in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohorts: results from 24-hour dietary recalls

Abstract Objective: To evaluate meat intake patterns in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohorts. Design and setting: 24-Hour dietary recalls were assessed within the framework of a prospective cohort study in 27 centres across 10 European countries by means of standardised computer-assisted interviews. Subjects: In total, 22 924 women and 13 031 men aged 35–74 years. Results: Mean total meat intake was lowest in the ‘health-conscious’ cohort in the UK (15 and 21 g day−1 in women and men, respectively) and highest in the north of Spain, especially in San Sebastian (124 and 234 g day−1, respectively). In the southern Spanish centres and in Naples (Italy), meat consumption was distinctly lower than in the north of these countries. Central and northern European centres/countries showed rather similar meat consumption patterns, except for the British and French cohorts. Differences in the intake of meat sub-groups (e.g. red meat, processed meat) across EPIC were even higher than found for total meat intake. With a few exceptions, the Mediterranean EPIC centres revealed a higher proportion of beef/veal and poultry and less pork or processed meat than observed in central or northern European centres. The highest sausage consumption was observed for the German EPIC participants, followed by the Norwegians, Swedish, Danish and Dutch. Conclusions: The results demonstrate distinct differences in meat consumption patterns between EPIC centres across Europe. This is an important prerequisite for obtaining further insight into the relationship between meat intake and the development of chronic diseases.
Zidovudine Pharmacokinetics During Pregnancy

As the indications for zidovudine (ZDV) treatment in human immunodeficiency virus-infected individuals expand, we anticipate an increased use of this drug during pregnancy. We report pharmacokinetics data from a patient studied both in the third trimester and intrapartum. ZDV peak-plasma levels and serum half-lives were comparable to nonpregnant adults. High concentrations of ZDV and its glucuronide metabolite were found in umbilical cord blood and in amniotic fluid.
Line segregation.

Six experiments investigated the preattentive segregation of line-like patterns composed of discrete elements in a background of distractors. The results indicate that other factors in addition to spatial density influence line segregation. Edge alignment, edge length and principal axis orientation also affect line segregation. Differences in the outputs of Gabor filters fail to account for the perceived segregation of the lines. Possible models of line segregation based on element grouping, feature density and search are briefly discussed.
Two murine coronavirus genes suffice for viral RNA synthesis

We identified two mouse hepatitis virus (MHV) genes that suffice for MHV RNA synthesis by using an MHV-JHM-derived defective interfering (DI) RNA, DIssA. DIssA is a naturally occurring self-replicating DI RNA with nearly intact genes 1 and 7. DIssA interferes with most MHV-JHM-specific RNA synthesis, except for synthesis of mRNA 7, which encodes N protein; mRNA 7 synthesis is not inhibited by DIssA. Coinfection of MHV-JHM containing DIssA DI particles and an MHV-A59 RNA- temperature-sensitive mutant followed by subsequent passage of virus at the permissive temperature resulted in elimination of most of the MHV-JHM helper virus. Analysis of intracellular RNAs at the nonpermissive temperature demonstrated efficient synthesis of DIssA and mRNA 7 but not of the helper virus mRNAs. Oligonucleotide fingerprinting analysis demonstrated that the structure of mRNA 7 was MHV-JHM specific and therefore must have been synthesized from the DIssA template RNA. Sequence analysis revealed that DIssA lacks a slightly heterogeneous sequence, which is found in wild-type MHV from the 3' one-third of gene 2-1 to the 3' end of gene 6. Northern (RNA) blot analysis of intracellular RNA species and virus-specific protein analysis confirmed the sequence data. Replication and transcription of another MHV DI RNA were supported in DIssA-replicating cells. Because the products of genes 2 and 2-1 are not essential for MHV replication, we concluded that expression of gene 1 proteins and N protein was sufficient for MHV RNA replication and transcription.
Inhibition of neutrophil apoptosis after severe trauma is NFkappabeta dependent.

BACKGROUND Systemic inflammation may inhibit neutrophil (PMN) apoptosis and promote multiple organ dysfunction syndrome. We hypothesize that severe trauma causes dysregulation of PMN apoptosis. METHODS Neutrophils were isolated from trauma patients (24-72 hours after injury; n = 16) and controls (healthy volunteers) and incubated for 18 hours. In separate experiments, control cells were treated +/- the nuclear factor kappa beta (NFkappabeta) inhibitor pyrrolidinithiocarbamate then incubated with 25% patient or control plasma. Apoptosis was quantified by enzyme-linked immunosorbent assay for histone-associated DNA and annexin V fluorescence-activated cell sorter. NFkappabeta activation was determined by Western blot for phosphorylated I kappabeta. RESULTS Apoptosis was inhibited in trauma patient PMN. Neutrophil apoptosis correlated with multiple organ dysfunction syndrome score, Acute Physiology and Chronic Health Evaluation II, and platelet count. Patient plasma inhibited apoptosis and induced phosphorylation of I kappabeta in control cells. Inhibition of PMN apoptosis by patient plasma was blocked by pretreatment with pyrrolidinithiocarbamate. CONCLUSION NFkappabeta-dependent inhibition of neutrophil apoptosis occurs after trauma. Early inhibition of PMN apoptosis is dependent on the magnitude of injury.
In Situ High-Volume Modified Continuous Closed and/or Open Lavage for Infected Necrotizing Pancreatitis

Objectives: To evaluate the clinical significance of high-volume modified continuous closed and/or open lavage for the treatment of infected necrotizing pancreatitis. Methods: From August 1997 to December 2006, 53 patients with infected necrotizing pancreatitis who underwent in situ high-volume (>20 L/d) continuous closed lavage using a single-lumen rubber catheter and/or open lavage were retrospectively studied in our hospital, and the advantages of this new technique were analyzed. Results: Modified continuous closed lavage was the initial treatment for all patients; in 6 patients with secondary retroperitoneal sepsis or abscess, continuous open lavage was performed. Impaired tube patency and lavage fluid retention did not occur in any of these patients. The overall mortality was 17.0% (9/53). Twelve patients underwent early surgery, and 5 (41.7%) died; 41 patients underwent delayed surgery, and 4 (9.8%) died. Significant local complications occurred in 14 patients (26.4%); the incidence of bleeding, abscess, and fistula was 13.2% (7/53), 9.4% (5/53), and 9.4% (5/53), respectively. Conclusions: Our technique of in situ high-volume modified continuous closed and/or open lavage has produced a better control of infected necrotizing pancreatitis.
Impact of connection type on the efficiency of wireless power transfer systems

Analysing a wireless power transfer system is necessary to understand its performance and how different parameters can affect it. The associated analysis can be used as a reference to choose the suitable parameters given the constraints in any required design. This paper presents: a theoretical analysis of four topologies of wireless power transfer systems; determines the efficiency and gives the associated experimental measurements. Magnetic resonance coupling theory is used in conjunction with basic circuit analysis in this study. The topologies studied are series-series SS, series-parallel SP, parallel-series PS and parallel-parallel PP connections. Each topology has a different performance for the same combination. This gives a variety from which to choose suitable designs for specific systems with different loads, where the impact of the load on the efficiency also needs to be considered.
Modelling Methodology for Engineering of Complex Sociotechnical Systems

Different Systems Engineering techniques and approaches are applied to design and develop complex sociotechnical systems for complex problems. In a complex sociotechnical system cognitive and social humans use information technology to make sense of a situation in support of decisions. The complex dynamic system elements, their interaction and, the complex environment make sociotechnical systems difficult to develop. A modelling and assessment methodology in support of the Systems Engineering process is required to understand the sociotechnical system's behaviour and underlying structure. It must capture the dynamic interaction as well as the effect of humans performing work in a complex environment. Cognitive Work Analysis and System Dynamics are two complementary approaches that can be applied in support of each other within this context.
Root formation.

This paper provides an overview of recent studies that have enhanced our understanding of the biological mechanisms that operate during root development. For the most part, these studies have been performed on rodents. As significant species differences have been shown to exist, this data cannot necessarily be extrapolated to the human model. The events associated with root odontoblast differentiation are reviewed in comparison to similar events in coronal odontoblast differentiation. Morphological as well as phenotypic differences are outlined and the inductive role of the epithelial root sheath is discussed. Both acellular and cellular cementum formation are reviewed highlighting morphological and phenotypic differences. The potential influence of the epithelial root sheath in the formation of both tissues is compared and contrasted. Finally, a discussion of the fate of the epithelial root sheath is presented with emphasis placed upon the possible roles of apoptosis and epithelium-mesenchymal transition.
Manic Depressive Illness in Adolescence and Childhood: Review and Case Report

The literature on this topic from its inception by Kraepelin is reviewed. While Kraepelin and the French school always recognized juvenile mania, the Anglo-American school has no such unanimity of opinion. Less than 100 cases are described in the world literature. In Canada affective psychoses are rarely diagnosed under age 10 and of all affective psychoses admitted to institutions less than 5% are under age 20. The differences between child and adult mania are outlined. It is proposed that manic-depressive illness occurs in children but is not diagnosed more often because of its dissimilar presentation to the adult form and doubts about its existence in childhood. The case history of a 14 year old boy who presented in a hypomanic state is described. There was a strong family history of affective disorder. Both his parents and his half-sister were already on lithium for manic-depressive illness.
Circular Structure for High Mechanical Bending Stability of a-IGZO TFTs

We employ a circular (Corbino) thin-film transistor (TFT) structure, in which the outer-ring is the drain and the inner-ring is the source, to improve the stability of amorphous–indium–gallium–zinc–oxide TFTs under tensile bending strain. We attribute the stability improvement to a more uniform electric field distribution across the circular channel, as it is isolated from local electric field crowding at sharp corners or channel edges. In addition, the effect of strain-induced increase in channel charge concentration is small in Corbino TFTs, owing to the larger outer-ring electrode, which depletes more electrons than the drain of rectangular TFTs. Furthermore, the circular shape results in bending direction independence, which is very important in multi-TFT circuits, where TFT orientation varies with position.
Cross-Cultural Validation of the Scale of Oral Health-Related Outcomes for 5-Year-Old-Children with a Low-Income Sample from the Dominican Republic

Aims and Objectives: To conduct a thorough psychometric assessment and validation of a Spanish-adapted version of the Scale of Oral Health-Related Outcomes for 5-Year-Old-Children (SOHO-5). Materials and Methods: The sample consisted of 69 children aged 6 and 7 years attending a public school from a low-income community in the Dominican Republic. Outcomes consisted of SOHO-5 test scores and caries lesion severity scores, with the latter measured according to the International Caries Detection and Assessment System criteria. The IBM SPSS Statistics 20 and Mplus 7.4 programs were used for the statistical analyses. Results: A confirmatory factor analysis revealed an excellent fit for the theoretical one-factor structure of the SOHO-5, with all the items having high loadings on this latent factor. In addition, the SOHO-5 was able to significantly explain a large amount of variance (37%) in caries lesion severity (P < 0.001), while its scale scores had good internal consistency reliability (Cronbach's alpha [α] = 0.85, 95% confidence interval [CI] 0.79–0.90). Further, the SOHO-5 could identify children with moderate and extensive caries lesions (area under the receiver operating characteristic curve = 0.82, 95% CI 0.70–0.94, P < 0.001). Conclusions: The current findings highlight the good psychometric properties and criterion-related validity of the Spanish-adapted SOHO-5 for young children who come from impoverished backgrounds.