Miracle-dz/UniFAR-FTUs huggingface dataset:
Heteroplasmy and atrazine resistance in Chenopodium album and Senecio vulgaris

Abstract Atrazine-resistant weeds are well known, and the resistance is primarily caused by a point mutation in the psbA chloroplast gene encoding the photosystem II D1 protein. Heteroplasmy, the presence of different types of chloroplasts in an individual plant, is also very common. Thus, atrazine-resistant weeds may also partly possess the atrazine-binding sequence and vice versa. The region of the psbA gene containing the mutation was sequenced from atrazine-resistant and atrazine-sensitive Chenopodium album and Senecio vulgaris plants. In atrazine-sensitive C. album plants, the expected AGT triplet was found. The atrazine-resistant plants contained the expected base substitution (AGT to GGT); however, in addition the AGT triplet was found. The atrazine-resistant S. vulgaris plants contained the expected GGT sequence, whereas the atrazine-sensitive plants contained both the AGT and GGT sequences. This clearly indicates that in addition to Gly264 also Ser264 is present in atrazine-resistant plants, and vice versa in atrazine-sensitive plants, indicating heteroplasmy in these weeds.
The role of companies’ codes of ethics in mitigating managers’ escalation behavior in the frame of agency theory

ABSTRACT This study examines the role of codes of ethics used to reduce the tendency for managers to irrationally escalate their investment decision commitments, and compares the effectiveness of such codes of ethics in mitigating the escalation of these commitments. Based on 2 (adverse selection and no adverse selection) x 3 (self-certification of code of ethics with signatures, code reading, and no code of ethics) factorial experimental data, the participants in the adverse selection condition tend to escalate more than those who do not. The code of ethics (self-certification of code of ethics with signatures and code reading) is significantly able to mitigate the manager’s escalation behavior. Furthermore, the code certification with signatures is the most effective method to mitigate the escalation of commitment. This study contributes to the literature on the escalation of commitment by providing empirical evidence of effective de-escalation strategies through the organizational ethics aspect.
The role of extracorporeal membrane oxygenator therapy in the setting of Type A aortic dissection

Patients presenting with type A aortic dissection (TAAD) present with a wide clinical spectrum ranging from hemodynamic stability to multiorgan malperfusion with cardiovascular collapse. Extracorporeal membrane oxygenator (ECMO) therapy is increasingly being utilized as salvage therapy in patients with acute cardiopulmonary failure and for post‐cardiotomy shock. We sought to determine the utility of ECMO implementation post‐TAAD repair.
Magnetic resonance imaging effects of interferon beta-1b in the BENEFIT study: integrated 2-year results.

BACKGROUND In the Betaseron/Betaferon in Newly Emerging Multiple Sclerosis for Initial Treatment (BENEFIT) study, interferon beta-1b delayed conversion to multiple sclerosis in patients with a first clinical event and at least 2 clinically silent brain magnetic resonance imaging (MRI) lesions. OBJECTIVE To examine detailed MRI findings from the first 2 years of this trial. DESIGN Double-blind, placebo-controlled, randomized, parallel-group, multicenter, phase 3 study. SETTING Ninety-eight centers worldwide. PATIENTS A total of 404 individuals with a first demyelinating event suggestive of multiple sclerosis. INTERVENTIONS Patients were randomized to receive interferon beta-1b, 250 microg subcutaneously every other day, or placebo. After 24 months of treatment or on conversion to clinically definite multiple sclerosis, open-label interferon beta-1b treatment was offered. MAIN OUTCOME MEASURES Reported MRI data from patients completing 2 years of follow-up. RESULTS Data were analyzed from 248 patients taking interferon beta-1b and 156 taking placebo. Across 2 years the cumulative number of newly active lesions was lower in patients receiving interferon beta-1b vs placebo (median, 2.0 vs 5.0 [reduction of 60%]; P < .001). This corresponded to lower cumulative numbers of new T2 lesions (median, 1.0 vs 3.0 [reduction of 66%]; P < .001) and new gadolinium-enhancing lesions (median, 0.0 vs 1.0; P < .001) in patients receiving interferon beta-1b vs placebo. From screening to month 24, T2 lesion volume decreased and was more pronounced in patients receiving interferon beta-1b (P = .02). CONCLUSIONS Interferon beta-1b treatment had a robust effect on MRI measures, supporting its value as an early intervention in this patient group. This effect was maintained despite including patients who switched from placebo to interferon beta-1b in the active treatment group. Trial Registration clinicaltrials.gov Identifier: NCT00185211.
Using published bid/ask curves to error dress spot electricity price forecasts

Accurate forecasts of electricity spot prices are essential to the daily operational and planning decisions made by power producers and distributors. Typically, point forecasts of these quantities suffice, particularly in the Nord Pool market where the large quantity of hydro power leads to price stability. However, when situations become irregular, deviations on the price scale can often be extreme and difficult to pinpoint precisely, which is a result of the highly varying marginal costs of generating facilities at the edges of the load curve. In these situations it is useful to supplant a point forecast of price with a distributional forecast, in particular one whose tails are adaptive to the current production regime. This work outlines a methodology for leveraging published bid/ask information from the Nord Pool market to construct such adaptive predictive distributions. Our methodology is a non-standard application of the concept of error-dressing, which couples a feature driven error distribution in volume space with a non-linear transformation via the published bid/ask curves to obtain highly non-symmetric, adaptive price distributions. Using data from the Nord Pool market, we show that our method outperforms more standard forms of distributional modeling. We further show how such distributions can be used to render `warning systems' that issue reliable probabilities of prices exceeding various important thresholds.
Increased dosage requirements of tobramycin and gentamicin for treating Pseudomonas pneumonia in patients with cystic fibrosis

The pharmacokinetic behavior of tobramycin and gentamicin was evaluated in 27 patients who had cystic fibrosis (CF). A previously studied, age‐matched group of 334 patients who had been treated with gentamicin and who did not have CF served as controls. The CF patients, who ranged in age from 2 to 32 years and who had normal renal function, received 36 treatment courses with either tobramycin (19) or gentamicin (17) to treat Pseudomonas pneumonia. Serum concentrations were determined after a 1.5‐mg/kg dose to compute half‐life (t1/2), elimination rate constant (k), and apparent volume of distribution (V). From these values, doses were calculated to produce steady‐state peak concentrations of 8.0 μg/ml with a dosing interval of every six hours. For tobramycin the mean (± SD) t1/2 was 1.0 (0.4) hours, V was 0.18 (0.06) I/kg, total body clearance (TBC) was 2.19 (0.71) ml/min/kg, and the calculated dose was 8.2 (2.1) mg/kg/day. For gentamicin t1/2 was 1.1 (0.5) hours, V was 0.20 (0.06) I/kg, TBC was 2.28 (0.89) ml/min/kg, and the calculated dose was 8.8 (2.4) mg/kg/day. The pharmacokinetic parameters were not statistically different between the two drugs, but the mean values of t1/2 and TBC of CF patients differed significantly from those of the control group. The calculated doses were larger than the manufacturer's maximum recommended dose of 7.5 mg/kg/day for 63% of tobramycin and 71% of gentamicin treatment courses. A dosing interval change to every four hours would have been appropriate in 28 of the 36 treatment courses (78%). There was wide interpatient and intrapatient variation in pharmacokinetic parameters, and TBC did not correlate with creatinine clearance (CLcr). CF patients require larger doses of aminoglycosides than non‐CF patients, and they must have individualized doses and dosing intervals to obtain desired drug concentrations.
The serotonin transporter polymorphisms and major depression following traumatic brain injury

Objective: The purpose of this study was to examine the role of the serotonin transporter gene polymorphisms on the risk of major depression following traumatic brain injury (TBI). Methods: Seventy-five patients who had sustained a TBI and who met the Diagnostic and Statistical Manual of Mental Disorders (4th ed) (DSM-IV) criteria for mood disorder due to TBI were compared to 99 controls with TBI but no mood disorder. The severity of depression was rated using the Hamilton Depression Rating Scale (HAMD) for the depressed patients. All patients were genotyped for the serotonin transporter gene-linked polymorphic region (5-HTTLPR) with the assay for the rs25531 allelic variant. Results: The distribution of genotype frequencies was not different between the depressed and control groups (χ2= 1.43, df= 2, p= 0.488) and for the depressed patients there was no association between HAMD scores and the polymorphisms (t-test = 1.71, df= 68, p= 0.092). Conclusion: There was no evidence of association between the serotonin transporter gene polymorphisms and depression post-TBI. Future research is indicated into the possible role of other candidate genes as risk factors for depression in this population.
Viral Load and Sequence Analysis Reveal the Symptom Severity, Diversity, and Transmission Clusters of Rhinovirus Infections

Background Rhinovirus (RV) is one of the main viral etiologic agents of acute respiratory illnesses. Despite the heightened disease burden caused by RV, the viral factors that increase the severity of RV infection, the transmission pattern, and seasonality of RV infections remain unclear. Methods An observational study was conducted among 3935 patients presenting with acute upper respiratory illnesses in the ambulatory settings between 2012 and 2014. Results The VP4/VP2 gene was genotyped from all 976 RV-positive specimens, where the predominance of RV-A (49%) was observed, followed by RV-C (38%) and RV-B (13%). A significant regression in median nasopharyngeal viral load (VL) (P < .001) was observed, from 883 viral copies/µL at 1-2 days after symptom onset to 312 viral copies/µL at 3-4 days and 158 viral copies/µL at 5-7 days, before declining to 35 viral copies/µL at ≥8 days. In comparison with RV-A (median VL, 217 copies/µL) and RV-B (median VL, 275 copies/µL), RV-C-infected subjects produced higher VL (505 copies/µL; P < .001). Importantly, higher RV VL (median, 348 copies/µL) was associated with more severe respiratory symptoms (Total Symptom Severity Score ≥17, P = .017). A total of 83 phylogenetic-based transmission clusters were identified in the population. It was observed that the relative humidity was the strongest environmental predictor of RV seasonality in the tropical climate. Conclusions Our findings underline the role of VL in increasing disease severity attributed to RV-C infection, and unravel the factors that fuel the population transmission dynamics of RV.
[Italian Registry Dialysis and Transplant 2011-2013].

UNLABELLED The Italian Registry of Dialysis and Transplantation (RIDT) has recently resumed the collection of data of patients on RRT in Italy. Data were requested to Regional Registries for the years 2011-2013 and they contributed according to their possibilities. Eighteen Regions or autonomous Provinces provided data with various degrees of completeness and this made possible to bridge the gap between the current and the previous census (referring to 2010). RESULTS Incidencedata were associated to a sample with a coverage of 77% of the national population (46/60 million inhabitants). Patients who started dialysis in these three years were, respectively, 168, 166 and 160 patients pmp. If we project this data to the national population is reasonable to think that 9500-10000 patients per year start the dialytic treatment. PREVALENCE The prevalence of patients on dialysis in Italy range, in the 10 years of RIDT, between 750 and 825 patients pmp. Based on this we can reasonably estimate that in Italy there are 45-49000 dialysis patients. Incidence and prevalence vary widely in different regions. Mortalityon dialysis in Italy during the period 2011-2013 was on average 16.2 per 100 patient-years (95% CI: 16.1-16.7) with regional variation smaller than that observed in incidence and prevalence. CONCLUSIONS In this paper, data analysis are presented in a direct and non comparative manner. However, it provides information on the status of the RRT in Italy and the temporal consistency of the data is a proof of their validity. Registry data were published in the official site of Italian Registry that can be reached through the website of SIN (www.sin-italy.org).
Uma Nota sobre o Impacto da Corrupção no Endividamento dos Estados Brasileiros

Este artigo propoe a estimacao de cinco distintas abordagens utilizadas na literatura internacional recente sobre o endividamento publico de paises, com o objetivo especifico de modelar a Divida Consolidada Liquida (DCL) como razao do Produto Interno Bruto (PIB) dos entes federativos subnacionais brasileiros. A principal inovacao consiste na incorporacao a restricao orcamentaria intertemporal sugerida em Bohn (1998) nao somente de variaveis especificas de controle de natureza economica e fiscal seguindo a vertente de tax smoothing , mas principalmente de uma proxy de corrupcao. A evidencia mais relevante do estudo, obtida a partir da estimacao de um painel balanceado dinâmico, e a mensuracao pela primeira vez na literatura nacional do impacto do aumento de 1% da corrupcao nos estados nas suas relacoes DCL/PIB, o qual e significativo a 1% e oscila entre 0,015% e 0,023%. Evidencia-se de forma robusta que a capacidade de se reduzir o endividamento atraves do combate a corrupcao e maior quando este e aliado a austeridade fiscal do que quando combinado com politicas economicas. Segundo as estimacoes do arcabouco de Benfratello, Del Monte e Pennacchio (2015) para os estados brasileiros, um aumento da corrupcao em 1% anula o efeito que o aumento de 0,54% do PIB real per capita anual poderia exercer sobre a reducao do endividamento dos estados. A relevância do estudo se deve a conjuntura atual, caracterizada pela adocao de politicas economicas inocuas, estados com fragilidade fiscal e corrupcao crescente no pais.
The β‐Globin Gene Cluster Haplotypes in Sickle Cell Anemia Patients from Northeast Brazil: A Clinical and Molecular View

The βS‐globin haplotypes were studied in 78 sickle cell Brazilian patients from Bahia, Northeast Brazil, that has a large population of African origin. Hemoglobin (Hb) profiles were developed by high‐performance liquid chromatography (HPLC), and βS‐globin gene haplotypes were determined by polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) techniques. We identified 44 (55.0%) patients with the CAR/Ben (Central African Republic/Benin) genotype, 16 (20.0%) Ben/Ben, 13 (16.2%) CAR/CAR and seven (8.8%) with other genotypes. Analyses of the phenotypes showed clinical differences related only to Hb F levels and blood transfusion therapy; the presence of − α− 3.7‐thalassemia (thal) demonstrated statistical significance when associated with hematocrit (p = 0.044), MCV (p = 0.0007), MCH (p = 0.012) and spleen sequestration events. The haplotype diversity found in the present study can be justified by information about the origin of the slave traffic period in Bahia during the 19th century. The specific characteristics described among the Bahian sickle cell patients could be confirmed by increasing the number of patients with specific genotypes and further studies of genetic markers.
The neuraminidase of influenza virus

It is the enzyme neuraminidase, projecting form the surface of influenza virus particles, which allows the virus to leave infected cells and spread in the body. Antibodies which inhibit the enzyme limit the infection, but antigenic variation of the neuraminidase renders it ineffective in a vaccine. This article describes the crystal structure of influenza virus neuraminidase, information about the active site which may lead to development of specific and effective inhibitors of the enzyme, and the structure of epitopes (antigenic determinants) on the neuraminidase. The 3‐dimensional structure of the epitopes was obtained by X‐ray diffraction methods using crystals of neuraminidase complexed with monoclonal antibody Fab fragments. Escape mutants, selected by growing virus in the presence of monoclonal antibodies to the neuraminidase, possess single amino acid sequence changes. The crystal structure of two mutants showed that the change in structure was restricted to that particular sidechain, but the change in the epitope was sufficient to abolish antibody binding even though it is known in one case that 21 other amino acids on the neuraminidase are in contact with the antibody.
Gathering Correlated Data in Wireless Sensor Networks Using a Heuristic Algorithm

Abstract We propose a routing scheme for data gathering and aggregation in wireless sensor networks. The scheme aims to optimise an aggregation tree in order to minimise the energy dissipation of data aggregation and transmission. A modified particle swarm optimisation algorithm is developed in the proposed scheme. In addition, the routing scheme uses a generic data aggregation model which accommodates different correlation conditions. The performance of the proposed scheme is evaluated and compared with three other existing data gathering algorithms. Simulation results show that the proposed scheme outperforms existing algorithms in terms of energy consumption and that the scheme can adapt to the change of network connectivity and data correlation conditions.
Kaposi's Sarcoma-Associated Herpesvirus Lytic Switch Protein Stimulates DNA Binding of RBP-Jk/CSL To Activate the Notch Pathway

ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) lytic switch protein, Rta, is a ligand-independent inducer of the Notch signal transduction pathway, and KSHV cannot reactivate from latency in cells null for the Notch target protein RBP-Jk. Here we show that Rta promotes DNA binding of RBP-Jk, a mechanism that is fundamentally different from that established for the RBP-Jk-activating proteins, Notch intracellular domain (NICD) and Epstein-Barr virus EBNA2. Although constitutively active RBP-Jk and NICD do not transactivate KSHV promoters independently, cotransfection of an Rta mutant lacking its transactivation domain robustly restores transcriptional activation. Cooperation requires intact DNA binding sites for Rta and RBP-Jk and trimeric complex formation between the three molecules in vitro. In infected cells, RBP-Jk is virtually undetectable on a series of viral and cellular promoters during KSHV latency but is significantly enriched following Rta expression during viral reactivation. Accordingly, Rta, but not EBNA2 and NICD, reactivates the complete viral lytic cycle.
Outbreaks associated with recreational water in the United States

In this article, we review the causes of outbreaks associated with recreational water during 1971 – 2000. A bacterial or protozoan etiology was identified in three-quarters of the outbreaks; 23% of the outbreaks were of undetermined etiology. The most frequently identified agents were Cryptosporidium (15%), Pseudomonas (14%), Shigella (13%), Naegleria (11%), Giardia (6%), and toxigenic E. coli (6%). Outbreaks attributed to Shigella, E. coli O157:H7, and Naegleria were primarily associated with swimming in fresh waters such as lakes, ponds, and rivers. In contrast, outbreaks caused by Cryptosporidium and Giardia were primarily associated with treated water in swimming and wading pools. Important sources of contamination for both treated and untreated recreational waters were the bathers themselves. Contamination from sewage discharges and wild or domestic animals were also important sources for untreated waters. Contributing factors in swimming-pool outbreaks were inadequate attention to maintenance, operation, disinfection, and filtration. Although not all waterborne outbreaks are recognized nor reported, the national surveillance of these outbreaks has helped identify important sources of contamination of recreational waters and the etiologic agents. This information can affect prevention recommendations and research priorities that may lead to improved water quality guidelines.
Development of a High-specificity Enzyme-linked Immunosorbent Assay (ELISA) System for the Quantification and Validation of Intact Rat Osteocalcin

Osteocalcin (OC) exhibits hard tissue-specific expression and binding activity to hydroxyapatite. Therefore, measurement of secreted OC is a very useful index for evaluating osteoblastic differentiation in regenerative bone. In the present study, we established a high-specificity sandwich enzyme-linked immunosorbent assay (ELISA) system for the quantification of intact rat OC, which could be useful for validating tissue-engineered bone samples nondestructively and continuously. The range of detection with the sandwich ELISA system was 0.1–100 ng OC/mL of cell culture media or rat sera. No cross-reactivities were detected with OCs from other species, including human, bovine and mouse OCs, and other mammalian sera, which would contain the corresponding endogenous OCs. The intra- and inter-assay coefficients of variation were ≤4.9% and ≤5.9%, respectively. Recovery tests only showed variation between 89.4% and 103.7%. Using the newly developed direct sandwich ELISA system, we found that the secreted OC levels from rat bone marrow-derived mesenchymal stem cells during osteogenic differentiation with dexamethasone were significantly higher than those from cells undergoing non-osteogenic or adipogenic differentiation. It was established that this ELISA system would be suitable for quantitative assessment of bone formation by cultured cells with or without scaffolds in rat experimental models.
Syndecan-4 signaling at a glance

Summary Syndecan-4, a ubiquitous cell surface proteoglycan, mediates numerous cellular processes through signaling pathways that affect cellular proliferation, migration, mechanotransduction and endocytosis. These effects are achieved through syndecan-4 functioning as both a co-receptor for the fibroblast growth factor receptors (FGFR1–FGFR4) and its ability to independently activate signaling pathways upon ligand binding. As an FGFR co-receptor, syndecan-4 strengthens the duration and intensity of downstream signaling upon ligand binding; this is particularly evident with regard to mitogen-activated protein kinase (MAPK) signaling. In contrast, syndecan-4 also functions as an independent receptor for heparin-binding growth factors, such as fibroblast growth factors (FGFs), vascular endothelial growth factors (VEGFs) and platelet-derived growth factors (PDGFs). These signaling cascades affect canonical signaling components, such as the mammalian target of rapamycin (mTOR), AKT1 and the Rho family of GTPases. In combination with the integrin family of proteins, syndecan-4 is also able to form physical connections between the extracellular matrix (ECM) and cytoskeletal signaling proteins, and it has a key role in regulation of integrin turnover. This unique versatility of the interactions of syndecan-4 is characterized in this Cell Science at a Glance article and illustrated in the accompanying poster.