Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction

In vivo induction of the Escherichia coli lactose operon as a function of inducer concentration generates a sigmoidal curve, indicating a non-linear response. Suggested explanations for this dependence include a 2:1 inducer–repressor stoichiometry of induction, which is the currently accepted view. It is, however, known for decades that, in vitro, operator binding as a function of inducer concentration is not sigmoidal. This discrepancy between in vivo and in vitro data has so far not been resolved. We demonstrate that the in vivo non-linearity of induction is due to cooperative repression of the wild-type lac operon through DNA loop formation. In the absence of DNA loops, in vivo induction curves are hyperbolic. In the light of this result, we re-address the question of functional molecular inducer–repressor stoichiometry in induction of the lac operon

Research in Nepal

Findings from University of Dayton geologist, Umesh Haritashya, after the deadly earthquake in Nepal April 25 will be published in a forthcoming article in Science, the leading journal on original scientific research

Do Mutual Fund Ratings Provide Valuable Information for Retail Investors? Empirical Evidence on Ratings Non-Persistence and the Risk of Mutual Fund Closure

Retail investors use information provided by mutual fund rating agencies to make investment decisions. Using hand-collected data on Morningstar’s mutual fund ratings we examine the rating migration and closure risk of mutual funds from 2005 to 2012. We differentiate between buy-and-hold investment strategies and dynamic investment strategies. To assess the information content of mutual fund ratings for buy-and-hold investment strategies, we determine the rating migration based on the first and the last mutual fund rating during two-, four-, six-, and eight-year horizons. With respect to dynamic investment strategies, we calculate the number of rating changes per fund during these time horizons on a monthly basis. We find that mutual fund rating persistence is low or even inexistent in particular during longer time periods. Only for lower-rated funds the rating appears to indicate higher risk of fund closure. In addition, mutual funds face a large number of up to 38 monthly rating changes in the eight-year window. Overall, due to the extensive rating migration and the high number of monthly rating changes, we conclude that retail investors barely benefit from using mutual fund ratings

Encoding Scores for Electronic Music

A perspective on the specific issues of music encoding dealing with Electronic Music is presented. In many cases the works to be discussed exist in a fixed media format and hence no prescriptive score is necessary to facilitate a ‘valid’ performance. While there are a number of descriptive scores for pieces of Electronic Music, these are to be treated differently, as they are purely aimed at analysis and therefore contain a certain information bias. Data that is more comparable to instrumental scores is contained in rare examples of so-called realization scores. It is argued that these realization scores can be identified as the main subject for encoding of Electronic Music works. For this we will discuss an example from one such score by Karlheinz Stockhausen. For his piece KONTAKTE, Stockhausen released a realization score that unfolds a very detailed documentation of all steps made within the studio production of that work, including the complex patching of studio devices and the specific transformation processes achieved by the use of tape machines. The paper presents an approach to formalize and encode all these steps within the framework of a semantic database. Using technology like the semantic web standard, Linked Data and the corresponding RDF/OWL framework, an Electronic Music production setup and its usage can be encoded, stored, and analyzed

Communicating "cure" to pediatric oncology patients: A mixed-methods study

Abstract Background Uncertainty about cure puts childhood cancer survivors at risk of mental distress. We asked survivors if they had been told they had been cured and investigated associated factors. Procedure We used nationwide registry data and a questionnaire survey for ≥five-year survivors of childhood cancer (n = 301), followed by online focus groups with a purposive sample of Swiss pediatric oncologists (n = 17). Discussions were coded by investigators using thematic analysis. Results Overall, 235 among 301 survivors (78%; 95% confidence interval, 73%?83%) reported having been told they were cured. The proportion was 89% (81%?97%) among lymphoma and 84% (77%?91%) among leukemia survivors, but only 49% (33%?65%) among central nervous system tumor survivors. Pediatric oncologists acknowledged that telling survivors they are cured may reassure them that their cancer lies behind them. However, many refrained from telling all patients. Reasons included the possibility of late effects (cure disrupted by a continued need for follow-up care) or late relapse (uncertainty of biological cure), case-by-case strategies (use of ?cure? according to individual factors), and reluctance (substitution of noncommittal terms for ?cure?; waiting for the patient to raise the topic). Conclusions Not all physicians tell survivors they have been cured; their choices depend on the cancer type and risk of late effects

Specialised Paediatric PAlliativE CaRe: Assessing family, healthcare professionals and health system outcomes in a multi-site context of various care settings: SPhAERA study protocol

The number of children and adolescents living with life-limiting conditions and potentially in need for specialised paediatric palliative care (SPPC) is rising. Ideally, a specialised multiprofessional team responds to the complex healthcare needs of children and their families. The questions of, how SPPC is beneficial, for whom, and under what circumstances, remain largely unanswered in the current literature. This study's overall target is to evaluate the effectiveness of a SPPC programme in Switzerland with respect to its potential to improve patient-, family-, health professional-, and healthcare-related outcomes.; This comparative effectiveness study applies a quasi-experimental design exploring the effectiveness of SPPC as a complex intervention at one treatment site in comparison with routine care provided in a generalised PPC environment at three comparison sites. As the key goal of palliative care, quality of life - assessed at the level of the patient-, the family- and the healthcare professional - will be the main outcome of this comparative effectiveness research. Other clinical, service, and economic outcomes will include patient symptom severity and distress, parental grief processes, healthcare resource utilisation and costs, direct and indirect health-related expenditure, place of death, and introduction of SPPC. Data will be mainly collected through questionnaire surveys and chart analysis.; The need for SPPC has been demonstrated through numerous epidemiological and observational studies. However, in a healthcare environment focused on curative treatment and struggling with limited resources, the lack of evidence contributes to a lack of acceptance and financing of SPPC which is a major barrier against its sustainability. This study will contribute to current knowledge by reporting individual and child level outcomes at the family level and by collecting detailed contextual information on healthcare provision. We hope that the results of this study can help guiding the expansion and sustainability of SPPC and improve the quality of care for children with life-limiting conditions and their families internationally.; Registered prospectively on ClinicalTrials.gov on January 22, 2020. NCT04236180 PROTOCOL VERSION: Amendment 2, March 01, 2021

Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy

The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non-coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome-wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e.g., mRNA, miRNA, lncRNA) and regulatory genomic regions (e.g., enhancer or TFBS). In a cohort of patients (n = 50) with dilated cardiomyopathy (DCM), 80,635 non-protein-coding elements of the genome are deleted or duplicated by SVs, containing 3,758 long non-coding RNAs and 1,756 protein-coding transcripts. 65.3% of the SV-eQTLs do not harbor a significant SNV-eQTL, and for the regions with both classes of association, we find similar effect sizes. In case of deleted protein-coding exons, we find downregulation of the associated transcripts, duplication events, however, do not show significant changes over all events. In summary, we are first to describe the genomic variability associated with SVs in heart failure due to DCM and dissect their impact on the transcriptome. Overall, SVs explain up to 7.5% of the variation of cardiac gene expression, underlining the importance to study human myocardial gene expression in the context of the individual genome. This has immediate implications for studies on basic mechanisms of cardiac maladaptation, biomarkers, and (gene) therapeutic studies alike

Single-laser 32.5 Tbit/s Nyquist WDM transmission

We demonstrate 32.5 Tbit/s 16QAM Nyquist WDM transmission over a total length of 227 km of SMF-28 without optical dispersion compensation. A number of 325 optical carriers are derived from a single laser and encoded with dual-polarization 16QAM data using sinc-shaped Nyquist pulses. As we use no guard bands, the carriers have a spacing of 12.5 GHz equal to the Nyquist bandwidth of the data. We achieve a high net spectral efficiency of 6.4 bit/s/Hz using a software-defined transmitter which generates the electrical modulator drive signals in real-time.Comment: (c) 2012 Optical Society of America. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modifications of the content of this paper are prohibite

c-MYC expression sensitizes medulloblastoma cells to radio- and chemotherapy and has no impact on response in medulloblastoma patients

BACKGROUND: To study whether and how c-MYC expression determines response to radio- and chemotherapy in childhood medulloblastoma (MB). METHODS: We used DAOY and UW228 human MB cells engineered to stably express different levels of c-MYC, and tested whether c-MYC expression has an effect on radio- and chemosensitivity using the colorimetric 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) assay, clonogenic survival, apoptosis assays, cell cycle analysis, and western blot assessment. In an effort to validate our results, we analyzed c-MYC mRNA expression in formalin-fixed paraffin-embedded tumor samples from well-documented patients with postoperative residual tumor and compared c-MYC mRNA expression with response to radio- and chemotherapy as examined by neuroradiological imaging. RESULTS: In DAOY - and to a lesser extent in UW228 - cells expressing high levels of c-MYC, the cytotoxicity of cisplatin, and etoposide was significantly higher when compared with DAOY/UW228 cells expressing low levels of c-MYC. Irradiation- and chemotherapy-induced apoptotic cell death was enhanced in DAOY cells expressing high levels of c-MYC. The response of 62 of 66 residual tumors was evaluable and response to postoperative radio- (14 responders (CR, PR) vs. 5 non-responders (SD, PD)) or chemotherapy (23 CR/PR vs. 20 SD/PD) was assessed. c-MYC mRNA expression was similar in primary MB samples of responders and non-responders (Mann-Whitney U test, p = 0.50, ratio 0.49, 95% CI 0.008-30.0 and p = 0.67, ratio 1.8, 95% CI 0.14-23.5, respectively). CONCLUSIONS: c-MYC sensitizes MB cells to some anti-cancer treatments in vitro. As we failed to show evidence for such an effect on postoperative residual tumors when analyzed by imaging, additional investigations in xenografts and larger MB cohorts may help to define the exact function of c-MYC in modulating response to treatment

Use of Mutagenesis, Genetic Mapping and Next Generation Transcriptomics to Investigate Insecticide Resistance Mechanisms

Insecticide resistance is a worldwide problem with major impact on agriculture and human health. Understanding the underlying molecular mechanisms is crucial for the management of the phenomenon; however, this information often comes late with respect to the implementation of efficient counter-measures, particularly in the case of metabolism-based resistance mechanisms. We employed a genome-wide insertional mutagenesis screen to Drosophila melanogaster, using a Minos-based construct, and retrieved a line (MiT[w−]3R2) resistant to the neonicotinoid insecticide Imidacloprid. Biochemical and bioassay data indicated that resistance was due to increased P450 detoxification. Deep sequencing transcriptomic analysis revealed substantial over- and under-representation of 357 transcripts in the resistant line, including statistically significant changes in mixed function oxidases, peptidases and cuticular proteins. Three P450 genes (Cyp4p2, Cyp6a2 and Cyp6g1) located on the 2R chromosome, are highly up-regulated in mutant flies compared to susceptible Drosophila. One of them (Cyp6g1) has been already described as a major factor for Imidacloprid resistance, which validated the approach. Elevated expression of the Cyp4p2 was not previously documented in Drosophila lines resistant to neonicotinoids. In silico analysis using the Drosophila reference genome failed to detect transcription binding factors or microRNAs associated with the over-expressed Cyp genes. The resistant line did not contain a Minos insertion in its chromosomes, suggesting a hit-and-run event, i.e. an insertion of the transposable element, followed by an excision which caused the mutation. Genetic mapping placed the resistance locus to the right arm of the second chromosome, within a ∼1 Mb region, where the highly up-regulated Cyp6g1 gene is located. The nature of the unknown mutation that causes resistance is discussed on the basis of these results