Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstructing the Evolutionary History of Transposable Elements

The impact of transposable elements (TEs) on genome structure, plasticity, and evolution is still not well understood. The recent availability of complete genome sequences makes it possible to get new insights on the evolutionary dynamics of TEs from the phylogenetic analysis of their multiple copies in a wide range of species. However, this source of information is not always fully exploited. Here, we show how the history of transposition activity may be qualitatively and quantitatively reconstructed by considering the distribution of transposition events in the phylogenetic tree, along with the tree topology. Using statistical models developed to infer speciation and extinction rates in species phylogenies, we demonstrate that it is possible to estimate the past transposition rate of a TE family, as well as how this rate varies with time. This methodological framework may not only facilitate the interpretation of genomic data, but also serve as a basis to develop new theoretical and statistical models.
Pulsatile stress in middle-aged patients with Type 1 or Type 2 diabetes compared to nondiabetic controls

This is an uncopyedited electronic version of an article accepted for publication in Diabetes Care. The American Diabetes Association, publisher of Diabetes Care, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive publisherauthenticated version will be available in a future issue of Diabetes Care in print and online at http://care.diabetesjournals. org. Diabetes Care Publish Ahead of Print, published online August 6, 2010
Running for Their Lives: A Qualitative Analysis of the Exercise Experience of Female Recreational Runners

This study explores the relationship between self-cognitions and running behavior in a group of female recreational runners. Consistent with theories of self-esteem and exerciser self-schemata, it aims to identify how running can impact on the self, and how self-cognitions can influence motivation and adherence to running. In-depth interviews were conducted with 16 women of varying age, ability, and running experience who had entered a major women’s 10K race. Inductive data analysis revealed that there was a bi-directional relationship between running involvement and self-cognitions. Running provided experiences which led to enhanced self-esteem, notably through perceived improvements to the physical self, but also through increases in mastery/achievement and physical competence. These changes contributed to the value of running for the women, strengthened their exercise self-schema, and increased the likelihood of adherence to running. However, family responsibilities constrained the women in their abili.
Low Gestational Weight Gain Skews Human Sex Ratios towards Females

Background Human males are more vulnerable to adverse conditions than females starting early in gestation and continuing throughout life, and previous studies show that severe food restriction can influence the sex ratios of human births. It remains unclear, however, whether subtle differences in caloric intake during gestation alter survival of fetuses in a sex-specific way. I hypothesized that the ratio of male to female babies born should vary with the amount of weight gained during gestation. I predicted that women who gain low amounts of weight during gestation should produce significantly more females, and that, if gestational weight gain directly influences sex ratios, fetal losses would be more likely to be male when women gain inadequate amounts of weight during pregnancy. Methods I analyzed data collected from over 68 million births over 23 years to test for a relationship between gestational weight gain and natal sex ratios, as well as between gestational weight gain and sex ratios of fetal deaths at five gestational ages. Results Gestational weight gain and the proportion of male births were positively correlated; a lower proportion of males was produced by women who gained less weight and this strong pattern was exhibited in four human races. Further, sex ratios of fetal losses at 6 months of gestation were significantly male-biased when mothers had gained low amounts of weight during pregnancy, suggesting that low caloric intake during early fetal development can stimulate the loss of male fetuses. Conclusion My data indicate that human sex ratios change in response to resource availability via sex-specific fetal loss, and that a pivotal time for influences on male survival is early in fetal development, at 6 months of gestation.
CT Optimization for Diagnosis of Some Acute Abdomen Cases

The acute abdomen is one of the most frequent causes for presentation to the emergency department. Imaging plays an important role for an accurate diagnosis, which in turn diminishes morbidity and mortality. The aim of this study was to demonstrate optimum CT aspects and emphasize on the important features of CT for those patients presenting with an acute abdominal pain at the Emergency Department both in general and in a number of selected conditions (appendicitis, small-bowel obstruction, acute pancreatitis, and diverticulitis). The reported data by this study are based on the author working experience, which forms a continuous protocol adjustment process. The present study provides evidence that CT would result in definite diagnosis of patients with abdominal pain in terms of the detection of some urgent conditions.
An Empirical Study of ADMM for Nonconvex Problems

The alternating direction method of multipliers (ADMM) is a common optimization tool for solving constrained and non-differentiable problems. We provide an empirical study of the practical performance of ADMM on several nonconvex applications, including l0 regularized linear regression, l0 regularized image denoising, phase retrieval, and eigenvector computation. Our experiments suggest that ADMM performs well on a broad class of non-convex problems. Moreover, recently proposed adaptive ADMM methods, which automatically tune penalty parameters as the method runs, can improve algorithm efficiency and solution quality compared to ADMM with a non-tuned penalty.
Relationship between Oral Health Behavior and Happiness Index in Elderly People

Copyright © 2016 by Journal of Dental Hygiene Science This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 노인의 구강보건행태와 행복지수와의 관련성 이현옥ᆞ박지영 원광보건대학교 치위생과
Auricular Acupunctures are Effective for the Prevention of Postoperative Agitation in Old Patients

Postoperative cognitive problems and delirium are not uncommon in the elderly. We reported four cases in which auricular acupunctures on the ‘Shenmen’ and ‘Point Zero’ points successfully managed postoperative problematic behaviors of the three patients with dementia and the one patient postoperatively demonstrating an agitated behavior.
Polymorphisms in intron 1 of the EGFR gene in non-small cell lung cancer patients

The epidermal growth factor receptor (EGFR) gene is highly polymorphic and its expression and activity may be affected by various polymorphisms. There have been several studies examining associations between EGFR polymorphisms and clinical outcome of lung cancer therapy; however, the underlying mechanism is largely unknown. The present study investigated EGFR polymorphism status and its correlation with clinicopathological features in Japanese non-small cell lung cancer (NSCLC) patients. We investigated 5 polymorphisms in the EGFR gene (−216G/T, −191C/A, 8227G/A, D994D and R497K) in 274 surgically-treated NSCLC patients. TaqMan single nucleotide polymorphism (SNP) genotyping assays and a PCR-based assay were used to analyze these polymorphisms. In our cohort of patients we did not find any evidence of the −191C/A polymorphism. Our results showed that the patients with the 8227GA or AA type in intron 1 had a significantly better prognosis with the anti-EGFR therapy than the patients with the GG type (p=0.0448) in terms of recurrence of lung cancer. No significant association was observed between 3 other SNPs (−216G/T, D994D and R497K) and clinicopathological features. The EGFR 8227G/A polymorphism in intron 1 may be associated with clinical outcome in NSCLC patients treated with EGFR tyrosine kinase inhibitors.
In vitro isolation and molecular characterization of an Ehrlichia canis strain from São Paulo, Brazil

An Ehrlichia canis isolate was obtained from an naturally infected dog exhibiting clinical signs of ehrlichiosis in São Paulo Municipality, state of São Paulo, Brazil. The isolate was characterized by PCR and DNA sequencing of portions of the ehrlichial genes dsb, 16SrRNA, and p28. Partial dsb and 16S rRNA sequences were identical to three and five other E. canis strains, respectively, from different countries and continents (including North America, Africa, Asia and Europe). Conversely, the p28 partial sequence for this E. canis (São Paulo) differed by 1, 2, and 2 nucleotides from the corresponding sequences of the E. canis strains Jake (from USA), Oklahoma (USA), and VHE (Venezuela), respectively. The results in this study indicate that E. canis is the only recognized Ehrlichia species infecting dogs in Brazil.
Development of a one-run real-time PCR detection system for pathogens associated with bovine respiratory disease complex

Bovine respiratory disease complex (BRDC) is frequently found in cattle worldwide. The etiology of BRDC is complicated by infections with multiple pathogens, making identification of the causal pathogen difficult. Here, we developed a detection system by applying TaqMan real-time PCR (Dembo respiratory-PCR) to screen a broad range of microbes associated with BRDC in a single run. We selected 16 bovine respiratory pathogens (bovine viral diarrhea virus, bovine coronavirus, bovine parainfluenza virus 3, bovine respiratory syncytial virus, influenza D virus, bovine rhinitis A virus, bovine rhinitis B virus, bovine herpesvirus 1, bovine adenovirus 3, bovine adenovirus 7, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, Trueperella pyogenes, Mycoplasma bovis and Ureaplasma diversum) as detection targets and designed novel specific primer-probe sets for nine of them. The assay performance was assessed using standard curves from synthesized DNA. In addition, the sensitivity of the assay was evaluated by spiking solutions extracted from nasal swabs that were negative by Dembo respiratory-PCR for nucleic acids of pathogens or synthesized DNA. All primer-probe sets showed high sensitivity. In this study, a total of 40 nasal swab samples from cattle on six farms were tested by Dembo respiratory-PCR. Dembo respiratory-PCR can be applied as a screening system with wide detection targets.
What Does the Word ‘Globalisation’ Mean to You?: Comparative Perceptions and Evaluations in Australia, New Zealand, the USA and the UK

Political leaders, the media, business people, trade union leaders and academics continually refer to how globalisation is impacting on our lives. Governments may at times argue that globalisation benefits us, and at others attribute to globalisation many of the major problems we currently face. What do ordinary people make of all this? We do not have a systematic account of their understandings, in terms of the primary associations they make with globalisation, and how they orient to it in terms of resistance or support. 302 respondents (groups from the UK, US, Australia and New Zealand) were asked to note the first five things they associate with the word ‘globalisation’. Their most salient associations centre on issues of economy, culture, power and communication. Differences emerge in the contrasting priorities that the groups give these categories and how they evaluate them in positive or negative terms, with the US respondents holding a comparatively more positive outlook.
MicroRNA 22 Regulates Cell Cycle Length in Cerebellar Granular Neuron Precursors

ABSTRACT During cerebellum development, Sonic hedgehog (Shh)-induced proliferation of cerebellar granular neuronal precursors (CGNPs) is potently inhibited by bone morphogenetic proteins (BMPs). We have previously reported the upregulation of TIEG-1 and Mash1, two antimitotic factors that modulate MYCN transcription and N-Myc activity, in response to BMP2. To gain further insight into the BMP antimitotic mechanism, we used microRNA (miRNA) arrays to compare the miRNAs of CGNPs proliferating in response to Shh with those of CGNPs treated with Shh plus BMP2. The array analysis revealed that miRNA 11 (miR-22) levels significantly increased in cells treated with BMP2. Additionally, in P7 mouse cerebellum, miR-22 distribution mostly recapitulated the combination of BMP2 and BMP4 expression patterns. Accordingly, in CGNP cultures, miR-22 overexpression significantly reduced cell proliferation, whereas miR-22 suppression diminished BMP2 antiproliferative activity. In contrast to BMP2, miR-22 did not induce neural differentiation but instead significantly increased cell cycle length. Consistent with the central role played by N-myc on CGNP proliferation, Max was revealed as a direct target of miR-22, and miR-22 expression caused a significant reduction of Max protein levels and N-myc/Max-dependent promoter activity. Therefore, we conclude that, in addition to the previously described mechanisms, miR-22 plays a specific role on downstream BMPs through cerebellum growth.
Offense planning in burglary: A comparison of deliberate and impulsive burglars

AMBER NICOLE SANDERS. Offense planning in burglary: A comparison of deliberate and impulsive burglars. (Under the direction of Dr. JOE KUHNS) While certain burglars are more opportunistic than others who may engage in more planning, comparison between the two distinct patterns of offense planning has not been explored. As different types of offenders may have unique offending patterns, such research yields importance for crime prevention. The present study captures the decision making process of over 400 incarcerated male and female burglars in three states. We explore motivations, target selection strategies, factors that deter, techniques and tools used during burglary, and responses to prevention measures for two groups of burglars, who vary in their levels of deliberation and planning. Overall, burglars are motivated by a need for cash, select targets based on visual cues surrounding the target, may have intricate techniques for committing a burglary and are typically deterred by prevention measures. More specifically, we find that deliberate burglars are more likely to be younger, male, less motivated by drugs, more proactive and thoughtful when selecting a target and more likely to use burglary tools while offending. These findings imply that situational crime prevention actions and measures may be more effective for impulsive burglars, but that deliberate burglars still consider such measures when selecting a target and carrying out their burglary. We also find that motivations differ for deliberate and impulsive burglars. This suggests that treatment services rendered to burglars may need to vary based on unique motivation.
A Discussion On The Self - Concept Among Final Year Engineering Students In A University College

Generally educators, parents and government leaders agree that we need to develop individuals with healthy or high self - concept characterized by tolerance and respect for others. Individuals who accept responsibility for their actions, have integrity, take pride in their accomplishments are self - motivated. The objective of this study is to develop students with high self - esteem who are well balanced in reality and have an equal sense of worth and competence. These individuals must portray qualities agreed upon by educators, parents and government leaders as essential to effectively function in this era. This research is a quantitative study of the perceptions students. The findings of the study are discussed and recommendations are given based on the five different approaches to build self- concept in students. This paper also examines the positive and negative impacts of peer interactions, assignment marks, lecturer comments and gain in knowledge and skills on academic self concept.
Physical activity, well-being and the basic psychological needs in cardiac rehabilitation graduates: A path analysis

Both physical activity and well-being have been shown to be related to cardiovascular disease; however, the relationship between these variables is not well understood in this population. According to Ryan, Huta and Deci's (2008) empirical model, eudaimonic living (as a motive) fosters well-being through the satisfaction of the basic psychological needs. The purpose of this study was to first test the empirical model proposed by Ryan, Huta & Deci (2008) in cardiac rehabilitation graduates and second to examine if physical activity is best served as a predictor or an outcome of the model. Participants (N=52, Mage = 62.9 [SD =14.85]; 79% male) wore an Actigraph GT3X accelerometer for 9 days to objectively assess moderate-to-vigorous physical activity. Participants completed questionnaires on eudaimonic and hedonic motives, eudaimonic and hedonic well-being, and the basic psychological needs of autonomy, relatedness and competence. Separate path analyses in MPlus were conducted to examine (a) the empirical eudaimonic model and physical activity as a (b) predictor and (c) outcome of the model. The empirical eudaimonic model was supported as both motives strongly predicted the basic psychological needs (β>.64) and the basic psychological needs were strongly related with eudaimonic well-being (β=.63). A small to moderate relationship was found with physical activity as a predictor of eudaimonic motives (β=.26) and as an outcome of eudaimonic well-being (β=.23). The empirical eudaimonic model appears to hold in a cardiac sample but the role of physical activity remains unclear. A longitudinal study testing alternative models would provide additional insight for future physical activity and well-being interventions. Acknowledgments: CS was supported by the Social Sciences and Humanities Research Council of Canada (SSHRC). This research was funded by the Fonds de recherche du Quebec - Sante (FRQS).
Specific binding of host cellular proteins to multiple sites within the 3' end of mouse hepatitis virus genomic RNA

The initial step in mouse hepatitis virus (MHV) RNA replication is the synthesis of negative-strand RNA from a positive-strand genomic RNA template. Our approach to begin studying MHV RNA replication is to identify the cis-acting signals for RNA synthesis and the proteins which recognize these signals at the 3' end of genomic RNA of MHV. To determine whether host cellular and/or viral proteins interact with the 3' end of the coronavirus genome, an RNase T1 protection/gel mobility shift electrophoresis assay was used to examine cytoplasmic extracts from mock- and MHV-JHM-infected 17Cl-1 murine cells for the ability to form complexes with defined regions of the genomic RNA. We demonstrated the specific binding of host cell proteins to multiple sites within the 3' end of MHV-JHM genomic RNA. By using a set of RNA probes with deletions at either the 5' or 3' end or both ends, two distinct binding sites were located. The first protein-binding element was mapped in the 3'-most 42 nucleotides of the genomic RNA [3' (+42) RNA], and the second element was mapped within an 86-nucleotide sequence encompassing nucleotides 171 to 85 from the 3' end of the genome (171-85 RNA). A single potential stem-loop structure is predicted for the 3' (+)42 RNA, and two stem-loop structures are predicted for the 171-85 RNA. Proteins interacting with these two elements were identified by UV-induced covalent cross-linking to labeled RNAs followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The RNA-protein complex formed with the 3'-most 42 nucleotides contains approximately five host polypeptides, a highly labeled protein of 120 kDa and four minor species with sizes of 103, 81, 70, and 55 kDa. The second protein-binding element, contained within a probe representing nucleotides 487 to 85 from the 3' end of the genome, also appears to bind five host polypeptides, 142, 120, 100, 55, and 33 kDa in size, with the 120-kDa protein being the most abundant. The RNA-protein complexes observed with MHV-infected cells in both RNase protection/gel mobility shift and UV cross-linking assays were identical to those observed with uninfected cells. The possible involvement of the interaction of host proteins with the viral genome during MHV replication is discussed.
Validez y confiabilidad de una escala de cuidado profesional en español

La Escala de Cuidado Profesional es derivada de la Caring Professional Scale (CPS) de la Dra. Swanson y permite la medicion del cuidado en un ambiente ambulatorio y hospitalario. Objetivo: Determinar la validez y confiabilidad de la Escala de Cuidado Profesional version en espanol, ano 2011, en la atencion ofrecida a las mujeres gestantes en una localidad de la ciudad de Bogota, Colombia. Metodologia: Estudio metodologico en el que se aplicaron pruebas para la Validez Facial con una muestra heterogenea de 471 mujeres con un nivel academico bajo. La Validez de Contenido fue realizada por un panel de 11 enfermeras expertas, quienes juzgaron la importancia de los items; y la Validez de Constructo y Confiabilidad, con una muestra de 150 mujeres gestantes que acudian al control prenatal. Resultados: La comprensibilidad bruta supero el 94%. Revelo una Validez de Contenido con un Indice de Validez de Contenido Global de 0,893. Mostro un Alfa de Cronbach de 0,907. El constructo reconocio en su estructura teorica dos factores: Sanador compasivo y Sanador competente. Conclusion: La escala es altamente comprensible, con gran validez de contenido de acuerdo al criterio de expertos y con un alto nivel de confiabilidad; ademas, mide el constructo de cuidado profesional.
CQS: A Conflict-free Query Scheduling Approach in Wireless Sensor Networks

Conflict-free real-time query scheduling is one of the difficult tasks in Wireless Sensor Networks (WSNs). To accommodate this claim, we propose a Conflict-free Query Scheduling Approach (CQS) in WSNs. CQS works with three new schedulers, a Non-preemptive Conflict-free Query Scheduler(NCQS), Pre-emptive Conflict-free Query Scheduler (PCQS), and Advanced Conflict-free Query Scheduler (ACQS). Our simulation results indicate that NCQS results in high real-time performance but response time is high for high priority queries due to priority inversion. Whereas, PCQS supports preemption which can reduce the priority inversion. ACQS combines the advantages of both NCQS and PCQS and enhances the adequacy admitting affair that is the end-to-end deadlines of queries. The simulation results also indicate better performance of our approach as compared to the existing approaches. The simulation results are validated through NS-2.