Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular markers linked to breeding system differences in segregating and natural populations of the cereal aphid Rhopalosiphum padi L.

The aphid Rhopalosiphum padi shows coexistence of sexual and asexual populations, providing an opportunity to study the evolution of breeding system variation in the context of theories on the origin and maintenance of sex. However, assessments of the distribution of sexual and asexual lineages of this aphid are complicated by the difficulties in rapidly characterizing their breeding system. To facilitate this task and to gain insight into the genetic relatedness between sexual and asexual genotypes, molecular markers linked to breeding system differences were recently developed. In this study, we have successfully converted a random amplified polymorphic DNA (RAPD) marker associated with life‐cycle variation in R. padi into a codominant sequence‐characterized amplified region (SCAR). Segregating and natural populations of known breeding systems were examined to evaluate the life cycle–SCAR marker association. Complete linkage was found in segregating populations while the association averaged 94% in field populations. Detailed analysis of allelic distribution and sequence divergence of the SCAR locus among sexual and asexual populations provides further evidence for a unique and apparently ancient loss of sexuality in this aphid. It also suggests that occasional gene flow occurs between populations differing in their breeding system, mediated by males produced by ‘asexual’ lineages. This system provides the possibility for the recurrent emergence of new asexual lineages, ensuring the longer persistence of asexuality, and would have important implications for the assessment of costs and benefits of sex in aphids.
Diversity and the minority nation: a case study of Catalonia’s “National Agreement on Immigration”

This dissertation explores the relationship between immigration, diversity and minority nationalism. Through a study of Catalonia and its relationship with the Spanish state, the dissertation assesses how immigration and the growing social diversity that accompanies it, can challenge, undermine, or reinforce the political claims and objectives of minority nationalists, in particular, their goal of promoting a distinct and self-determining national community. It focuses on an effort by Catalan political and civil society leaders to construct a “national consensus” on immigration, the 2008 National Agreement on Immigration, which provided a 20-year plan for adapting Catalan government services and Catalan society to the pressures and demands of its increasingly diverse population, while at the same time providing mechanisms for the integration of newcomers into the Catalan language and national community. The analysis centres on the text of the National Agreement on Immigration as well as recent Catalan immigration plans and policy documents, in addition to the broader debate surrounding the National Agreement among Catalonia’s major political parties. The dissertation reveals that the National Agreement on Immigration represented both a significant re-framing of Catalan national identity and an attempt to expand the power and autonomy of the Catalan government by the various signatories to the accord. It concludes that the National Agreement represented an important component of a pivotal era in Catalan politics, one that has the potential to radically redefine the region’s relationship with both Spain and Europe, and in which questions surrounding immigration and diversity are increasingly intersecting with broader debates surrounding economic instability and the prospect of Catalan independence.
Sports graduate capabilities and competencies: a comparison of graduate and employer perceptions in six EU countries

Abstract The graduate employment market faces ever-increasing socio-economic and political pressures. Higher Education Institutions and the sport sector in the EU have an important role in contributing to graduate employment. The aims of the study were: (1) to assess general perceptions of employability, and (2) to assess sports graduates’ and employers’ perceptions of specific capabilities and competencies in order to identify possible improvements for sports graduate employability programmes. A cross-sectional survey of sports graduates and employers was administered in six EU countries including the UK, France, Germany, Spain, Greece and the Czech Republic to assess graduate and employer perceptions. A graduate capabilities and competencies framework was devised to assess personal, interpersonal, cognitive, role-specific and generic skills. Responses were elicited from 1132 sports graduates and 327 employers. There was generally a wide difference of opinion between employers and sports graduates in terms of the importance and possession of a number of capabilities and competencies. There is a need for the Higher Education sector and employers to take responsibility in ensuring that work experience, work placement and volunteering opportunities are embedded in curricula and to ensure the fitness of purpose of what and how graduate capabilities and competencies are assessed.
An hpr1 Point Mutation That Impairs Transcription and mRNP Biogenesis without Increasing Recombination

ABSTRACT THO/TREX, a conserved eukaryotic protein complex, is a key player at the interface between transcription and mRNP metabolism. The lack of a functional THO complex impairs transcription, leads to transcription-dependent hyperrecombination, causes mRNA export defects and fast mRNA decay, and retards replication fork progression in a transcription-dependent manner. To get more insight into the interconnection between mRNP biogenesis and genomic instability, we searched for HPR1 mutations that differentially affect gene expression and recombination. We isolated mutants that were barely affected in gene expression but exhibited a hyperrecombination phenotype. In addition, we isolated a mutant, hpr1-101, with a strong defect in transcription, as observed for lacZ, and a general defect in mRNA export that did not display a relevant hyperrecombination phenotype. In THO single-null mutants, but not in the hpr1 point mutants studied, THO and its subunits were unstable. Interestingly, in contrast to hyperrecombinant null mutants, hpr1-101 did not cause retardation of replication fork progression. Transcription and mRNP biogenesis can therefore be impaired by THO/TREX dysfunction without increasing recombination, suggesting that it is possible to separate the mechanism(s) responsible for mRNA biogenesis defects from the further step of triggering transcription-dependent recombination.
Recurrent Staphylococcus aureus bacteremia

Sequential blood isolates from eight patients with 10 episodes of recurrent Staphylococcus aureus bacteremia were typed by restriction endonuclease analysis of plasmid DNA (REAP DNA fingerprinting) and immunoblotting. There were six early recurrences (within 2 months of stopping antimicrobial therapy) and four late recurrences. All early recurrences isolates were identical to initial isolates. These recurrences were defined as possible relapses. Three of four late recurrence isolates were different from the preceding isolates recovered from four patients. This was considered indicative of new infections. There was complete concordance between REAP DNA fingerprinting and immunoblot typing results. However, four isolates lacked plasmid DNA and could be typed only by immunoblotting. All initial isolates from different patients were different types by immunoblotting and by REAP DNA fingerprinting (except for those lacking plasmid DNA). The bacterial traits detected by these methods appear to be stable in vivo for up to 3 months. Relapsing infections were associated with the presence of intravascular foreign bodies and vancomycin therapy of the preceding episodes.
Imaging the Thoracic Distribution of Normal Breath Sounds

Summary Objective: To assess the feasibility to generate a confident image of normal breath sounds (BS) based on the quantitative analysis of multichannel sensors and imaging them in three known clinical classes, i.e., tracheal, bronchial and vesicular, identifying their spatial distribution with high resolution on the posterior thoracic surface. Methods: Three parametrization techniques, the percentile frequencies, the univariate AR modeling, and the eigenvalues of the covariance matrix were evaluated when applied to BS. These sounds were acquired in twelve healthy subjects by a 5 × 5 sensor array on the posterior thoracic surface plus the sound at the tracheal position, to obtain feature vectors that fed a supervised multilayer neural network. Based on BS classification rate, the spatial distribution of each BS class was obtained by constructing an image using deterministic interpolation. Results: The univariate AR modeling was the best parametrization technique producing a classification performance of 96% during the validation phase and just 4% of not classified feature vectors. Corresponding values for the percentile frequencies were 92% and 7.7%, whereas for the eigenvalues were 91% and 9.0%. Conclusion: This work shows that it is possible to generate confident images associated with the distribution of normal BS classes. Therefore, a detailed image about the spatial distribution of BS in humans might be helpful for detecting lung diseases.
Responding to symptoms suggestive of lung cancer: a qualitative interview study

Background Late diagnosis of lung cancer can impact on survival rates. Patients delay seeking help for a number of reasons. This study explored symptom appraisal and help-seeking decisions among patients referred to specialist respiratory services with symptoms suggestive of lung cancer. Methods In-depth qualitative interviews with patients as soon as possible after referral, ideally before diagnosis and mainly within 10 weeks, explored factors impacting on their pathways prior to referral. Framework analysis, underpinned by the Model of Pathways to Treatment, was used to explore the data with particular focus on patients’ beliefs and experiences, disease factors and healthcare professional influences. Results 35 patients were interviewed (aged 41–88 years, 15 women, 17 with lung cancer). All described similar presenting symptoms and triggers to seek help. Appraisal of symptoms was influenced by whether they had a lung comorbidity; seriousness of symptoms was interpreted within the context of previous illness experiences. Help-seeking was triggered when: symptoms failed to respond as expected; there was an increased awareness of symptoms of lung cancer; the public nature of a cough meant others were able to endorse help-seeking. Almost half visited the general practitioner (GP) two or more times before referral; during this period they reinterpreted initial symptoms and appraised new symptoms. The meaning given to symptoms changed over time and many became increasingly concerned they may have lung cancer. The GP played a role in ensuring timely further help-seeking but often there was little guidance on how to monitor symptoms or when to reconsult. Conclusions Patients diagnosed with and without lung cancer had similar symptom pathways. Findings provide guidance for lung cancer awareness campaigns on the importance of social networks in endorsing patient help-seeking. The importance of appropriate advice, monitoring and safety-netting procedures by GPs for people presenting with symptoms suggestive of lung cancer is also highlighted.
Knockdown of YAP1 inhibits the proliferation of osteosarcoma cells in vitro and in vivo.

Yes-associated protein 1 (YAP1) is a candidate oncogene that is involved in tumorigenesis and progression of many malignant tumors. Recently, many studies have revealed that YAP1 is highly expressed in human osteosarcoma. To investigate the role of YAP1 in osteosarcoma tumorigenesis, the expression of YAP1 in the osteosarcoma cell lines (MG-63 and HOS) was knocked down by small hairpin RNA (shRNA), and the cell proliferation and colony formation assay showed that knockdown of YAP1 significantly suppressed the cell proliferation and colony formation of osteosarcoma cells. Subsequently, cell cycle distribution was analyzed by flow cytometry, and the results showed an accumulation of YAP1-knockdown cells in the G0/G1 phase, suggesting that YAP1 knockdown results in the arrest of cell cycle progression. Additionally, the knockdown of YAP1 also inhibited the tumorsphere formation in vitro and the growth of xenograft tumors in vivo. Therefore, these data suggest that YAP1 knockdown inhibits the proliferation of osteosarcoma cells. However, the mechanism of action was unclear. Further investigation showed that in the YAP1-knockdown MG-63 and HOS cells, the level of cylinD1 and c-myc expression, target genes of the Wnt signaling pathway and TOP-Flash reporter activity were all significantly decreased, which indicated that the inhibitory effect of YAP1 knockdown on osteosarcoma might be associated with the Wnt signaling pathway. Taken together, our results demonstrated that YAP1 is an important regulator of osteosarcoma tumorigenesis and knockdown of YAP1 would be a novel therapeutic strategy for osteosarcoma.
Low Levels of Human Immunodeficiency Virus Type 1 DNA in High-Risk Seronegative Men

ABSTRACT We detected human immunodeficiency virus type 1 (HIV-1) DNA at very low levels in sequential peripheral blood mononuclear cell samples of five out of six high-risk, seronegative, homosexual men and five out of five individuals 7.8 to 1.6 years prior to seroconversion. These data indicate a high prevalence of low-level HIV-1 DNA in exposed seronegative individuals.
Reliability on ARM Processors Against Soft Errors Through SIHFT Techniques

ARM processors are leaders in embedded systems, delivering high-performance computing, power efficiency, and reduced cost. For this reason, there is a relevant interest for its use in the aerospace industry. However, the use of sub-micron technologies has increased the sensitivity to radiation-induced transient faults. Thus, the mitigation of soft errors has become a major concern. Software-Implemented Hardware Fault Tolerance (SIHFT) techniques are a low-cost way to protect processors against soft errors. On the other hand, they cause high overheads in the execution time and memory, which consequently increase the energy consumption. In this work, we implement a set of software techniques based on different redundancy and checking rules. Furthermore, a low-overhead technique to protect the program execution flow is included. Tests are performed using the ARM Cortex-A9 processor. Simulated fault injection campaigns and radiation test with heavy ions have been performed. Results evaluate the trade-offs among fault detection, execution time, and memory footprint. They show significant improvements of the overheads when compared to previously reported techniques.
Lack of Apoptosis in PanIN-1 and PanIN-2 Lesions Associated with Pancreatic Ductal Adenocarcinoma Is Not Dependent on K-ras Status

Introduction K-ras mutations are present in most ductal adenocarcinomas (DACs) of the pancreas and may also be found in ductal precursor lesions and even in normal ductal epithelium. The question is addressed whether mutated K-ras interferes with the regulation of apoptosis or proliferation. Methodology In 50 Whipple resection specimens, tissue adjacent to DACs was histologically screened for ductal lesions that were classified as pancreatic intraepithelial neoplasia (PanIN) according to WHO criteria. PanIN lesions were microdissected and analyzed for K-ras mutations by means of a nested PCR. Apoptosis was identified by the TUNEL method. Proliferation and the expression of p53 and Bcl-2 were immunohistochemically determined. Results On average, 30% of PanIN-1A and B lesions showed mutated K-ras. In PanIN-2 and PanIN-3 lesions, the rate of mutated K-ras increased to 45% and 56%, respectively. Apoptosis was present only in 2 of 26 PanIN-3 lesions. There was a gradual increase in proliferative activity from PanIN-1 to PanIN-3. p53 expression was found in 11% of PanIN-2 and 44% of PanIN-3 lesions. Bcl-2 expression was lacking in PanIN lesions of all grades. In invasive DACs, the apoptotic rate correlated with the degree of tumor differentiation and proliferation, with grade 3 carcinomas showing the highest apoptotic rate. Conclusion In view of the discrepancy between the considerable rate of K-ras mutations in PanIN-1 and PanIN-2 lesions and the lack of apoptosis and Bcl-2 expression, coupled with very low p53 immunoreactivity, it is unlikely that mutated K-ras affects the apoptotic activity in low grade PanINs. Instead, K-ras mutations may have an effect on proliferation in PanIN-1 and PanIN-2.
Does Nutrition Knowledge and Practice of Athletes Translate to Enhanced Athletic Performance? Cross-Sectional Study Amongst Nigerian Undergraduate Athletes

Introduction and Objectives: Nutrition knowledge of an athlete, as well as practice, is expected to influence athlete’s performance. The study assessed the nutrition knowledge and practice as well as athletes’ performance and identified the factors predicting the athletes’ performance. Methodology: A cross-sectional survey, involved 110 purposively selected undergraduate athletes (47 females, 63 males) of University of Ibadan, Nigeria, between July 2013 and December 2013. A semi-structured, self-administered questionnaire assessed the nutrition knowledge and practice. 24-hr diet recall and food frequency questionnaire were done. Anthropometric measurements were taken; body composition was determined by bioelectrical impedance analysis method. Handgrip strength (HGS), as an indirect measure of athlete performance, was assessed with the hand dynamometer. Chi-square and t-test analysis were used for the bivariate analysis. Pearson correlation and simple linear regression were used to determine relationships and predict athletic performance. The level of statistical significance was p<0.05. Results: More than half (58.2%) had good nutrition knowledge (NK), and 62.7% had good nutrition practices (NP). Majority (75.4%) had normal handgrip strength (HGS). More than 70.0% frequently do not consume cereals, roots and tubers, fruits and vegetables, legumes/nuts. About 30.0-40.0% frequently do not consume eggs/milk, meat/fish. Having good NK was significantly associated with good NP (χ2 = 15.520, p=0.000), but not with athlete’s performance (HGS). There is no significant correlation between NK, NP, and HGS. There is a significant positive correlation between HGS and lean muscle mass (LMM) (r=.670, p=0.000), weight (r=.492, p=0.000), height (r=.521, p=0.000) and energy intake (r=.386, p=0.000). There is a significant negative correlation between HGS and percentage body fat (r=-.400, p=0.000). Athletes’ performance was significantly predicted by the resting metabolic rate (β= .454 C.I=0.011 to 0.045, p=0.003), Lean muscle mass (β =.297 C.I=.059 to 0.562, p=0.024) and the weight (β =.228, C.I=1.852 to .489, p=0.047). Conclusion: Having good nutrition knowledge or practice did not directly determine athletic performance. However, there is the need for nutrition education interventions, to improve athlete’s performance by promoting adequate energy intake, lean muscle mass and appropriate weight gain in athletes.
Changing Up the Routine: Intervention-Induced Variability in Motor Learning

&NA; Variability is often introduced by an external agent (e.g., an instructor) during practice with the purpose of enhancing motor learning. Using a task analysis approach, we provide a framework to examine the effects of intervention-induced variability. We propose that variability may have markedly different consequences on learning depending on the task level at which it is introduced.
Protein kinase D1 is essential for Ras-induced senescence and tumor suppression by regulating senescence-associated inflammation

Significance Oncogene-induced senescence (OIS) is an initial barrier for cancer development. Reactive oxygen species (ROS) play critical roles in oncogenic Ras OIS. Senescent cells develop a senescence-associated secretory phenotype (SASP), which has important role in tumor suppression and tissue repair. However, the mechanisms underlying the SASP regulation are not clear. In this paper, we show that ROS-protein kinase Cδ (PKCδ)-protein kinase D1 (PKD1) axis is essential for SASP induction and maintenance via modulation of NF-κB activity. Considering the pivotal role of both SASP and ROS in systemic aging and age-related diseases, the link between ROS-PKCδ-PKD1 pathway and SASP regulation elucidated here may provide a new target to intervene in age-related inflammation and diseases. Oncogene-induced senescence (OIS) is an initial barrier to tumor development. Reactive oxygen species (ROS) is critical for oncogenic Ras OIS, but the downstream effectors to mediate ROS signaling are still relatively elusive. Senescent cells develop a senescence-associated secretory phenotype (SASP). However, the mechanisms underlying the regulation of the SASP are largely unknown. Here, we identify protein kinase D1 (PKD1) as a downstream effector of ROS signaling to mediate Ras OIS and SASP. PKD1 is activated by oncogenic Ras expression and PKD1 promotes Ras OIS by mediating inflammatory cytokines interleukin-6 (IL-6) and interleukin-8 (IL-8) via modulation of NF-κB activity. We demonstrate that ROS-protein kinase Cδ (PKCδ)-PKD1 axis is essential for the establishment and maintenance of IL-6/IL8 induction. In addition, ablation of PKD1 causes the bypass of Ras OIS, and promotes cell transformation and tumorigenesis. Together, these findings uncover a previously unidentified role of ROS-PKCδ-PKD1 pathway in Ras OIS and SASP regulation.
Translational embryology: Using embryonic principles to generate pancreatic endocrine cells from embryonic stem cells

Diseases that affect endodermally derived organs such as the lungs, liver, and pancreas include cystic fibrosis, chronic hepatitis, and diabetes, respectively. Despite the prevalence of these diseases, cures remain elusive. While several promising transplantation‐based therapies exist for some diseases such as Type 1 diabetes, they are currently limited by the availability of donor‐derived tissues. Embryonic stem cells are a promising and renewable source of tissue for transplantation; however, directing their differentiation into specific, adult cell lineages remains a significant challenge. In this review, we will focus on one endodermally derived organ, the pancreas, and discuss how studies of embryonic pancreas development have been used as the basis for the directed, step‐wise differentiation of mouse and human embryonic stem cells into pancreatic endocrine cells that are capable of rescuing Type 1 diabetes in animal models. Developmental Dynamics 236:3218–3227, 2007. © 2007 Wiley‐Liss, Inc.
Family Economics in Developing Countries

This dissertation covers two topics within the research area of family economics: violence against women in the form of female genital cutting and gender differences in fertility choices. In Part I of my dissertation, I analyze the harmful tradition of female genital cutting (FGC) from an economic perspective. It is estimated that 80 to 130 million women are circumcised/mutilated worldwide, with 3 million girls at risk of undergoing this procedure every year. Chapter 2 starts with a cross-country analysis and connects FGC rates with women's status in different countries. Chapter 3 places its emphasis on within-country variation and the interaction of FGC with marriage and education. In both chapters, the analysis and discussion of policies to reduce FGC play an important role. Part II focuses on fertility outcomes, in particular on differences in completed fertility by gender and the role of polygyny for potential fertility gaps in developing countries.