Miracle-dz/UniFAR-FTUs huggingface dataset:
Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PREMISE OF THE STUDY There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
Metabolic Syndrome and Obesity : Targets and Therapy Insulin detemir for the treatment of obese patients with type 2 diabetes

Correspondence: Priscilla A Hollander Baylor Endocrine Center, Baylor Medical Center, 3600 Gaston Avenue, Suite 656, Dallas, Texas 75246, USA Tel +1 214 820 3459 Fax +1 214 820 3468 Email priscilh@baylorhealth.edu Abstract: The risk for developing type 2 diabetes (T2DM) is greater among obese individuals. Following onset of the disease, patients with T2DM become more likely to be afflicted with diabetic microand macrovascular complications. Decreasing body weight has been shown to lower glycosylated hemoglobin and improve other metabolic parameters in patients with T2DM. Medications used to lower blood glucose may increase body weight in patients with T2DM and this has been repeatedly shown to be the case for conventional, human insulin formulations. Insulin detemir is a neutral, soluble, long-acting insulin analog in which threonine-30 of the insulin B-chain is deleted, and the C-terminal lysine is acetylated with myristic acid, a C14 fatty acid chain. Insulin detemir binds to albumin, a property that enhances its pharmacokinetic/ pharmacodynamic profile. Results from clinical trials have demonstrated that treatment with insulin detemir is associated with less weight gain than either insulin glargine or neutral protamine Hagedorn insulin. There are many potential reasons for the lower weight gain observed among patients treated with insulin detemir, including lower risk for hypoglycemia and therefore decreased defensive eating due to concern about this adverse event, along with other effects that may be related to the albumin binding of this insulin that may account for lower within-patient variability and consistent action. These might include faster transport across the blood–brain barrier, induction of satiety signaling in the brain, and preferential inhibition of hepatic glucose production versus peripheral glucose uptake. Experiments in diabetic rats have also indicated that insulin detemir increases adiponectin levels, which is associated with both weight loss and decreased eating.
CORRIGENDUM of the MJO Transition from Shallow to Deep Convection in Cloudsat-Calipso Data and GISS GCM Simulations

We have identified several errors in the calculations that were performed to create Fig. 3 of Del Genio et al. (2012). These errors affect the composite evolution of precipitation and column water vapor versus lag relative to the Madden-Julian oscillation (MJO) peak presented in that figure. The precipitation and column water vapor data for the April and November 2009 MJO events were composited incorrectly because the date of the MJO peak at a given longitude was assigned to the incorrect longitude band. In addition, the precipitation data for all MJO events were first accumulated daily and the daily accumulations averaged at each lag to create the composite, rather than the averaging of instantaneous values that was used for other composite figures in the paper. One poorly sampled day in the west Pacific therefore biases the composite precipitation in that region at several lags after the MJO peak. Finally, a 4-day running mean was mistakenly applied to the precipitation and column water vapor data rather than the intended 5-day running mean. The results of the corrections are that an anomalous west Pacific precipitation maximum510 days after the MJO peak is removed and the maximum in west Pacific precipitation one pentad before the MJO peak is now more evident; there is now a clear maximum in precipitation for the entire warm pool one pentad before the MJO peak; west Pacific column water vapor now varies more strongly as a function of lag relative to the peak; and precipitation, and to a lesser extent column water vapor, in general vary more smoothly with time. The corrections do not affect any other parts of the paper nor do they change the scientific conclusions we reached. The 4-day running mean error also affects Figs. 1 and 2 therein, with almost imperceptible impacts that do not affect any results or necessitate major changes to the text.
Induction of anti-gp160 cytotoxic T cells cross-reacting with various V3 loop P18 peptides in human immunodeficiency virus type 1 envelope-immunized individuals

Cytotoxic T lymphocytes (CTL) may be important to prevent cell-to-cell transmission of human immunodeficiency virus type 1 (HIV-1), the agent responsible for AIDS. In this study, we investigated the epitope specificity of CTLs induced in individuals immunized against the virus envelope glycoprotein gp160. The determinant of HIV-1 gp160 for the stimulation of CTL is located in a region of high sequence variability among HIV-1 isolates, the so-called V3 loop P18. Using a panel of P18 peptides, we compared the CTL specificities of cells from two individuals immunized with vaccinia virus recombinants expressing the envelope glycoproteins from two different strains of HIV-1, IIIB and SIMI. For this purpose, CTLs specific for the IIIB P18 peptide (RIQRGPGRAFVTIGK) were compared with CTLs for the site from the SIMI isolate (TLHMGPKRAFYATGD). The results indicate that in contrast to CD8+ CTLs induced by the glycoprotein from strain IIIB, CD8+ CTLs induced by strain SIMI strongly cross-reacted with targets presenting P18 peptides as well as envelope proteins from the divergent MN and RF isolates but failed to cross-react with targets that presented the IIIB peptide. These data have implications for the design of an HIV vaccine.
Competition strategies for the decolorization of a textile-reactive dye with the white-rot fungi Trametes versicolor under non-sterile conditions.

A variety of white-rot fungi can oxidize textile dyes under sterile conditions; however, an important consideration for their use in treating wastewater containing textile dyes is whether similar degrees of treatment can be achieved under non-sterile conditions. Four strategies were investigated for their potential in optimizing the use of the fungus Trametes versicolor in non-sterile culture for treating wastewater containing the diazo textile dye C.I. Reactive Black 5 (RB5). Three strategies with suspended culture were designed to increase the decolorization activity in suspended culture from a given amount of T. versicolor inoculum based on its tolerance of low pH (pH reduction in medium), production of extracellular enzymes (use of suspended enzymes alone), and its ability to produce enzymes independent of growth (nitrogen limitation in medium). The results showed that reduction of the medium pH to 3 did not suppress bacterial growth, while enzyme production by T. versicolor ceased. The use of the extracellular enzymes alone would allow the decoupling of the process of fungal growth from wastewater treatment; however, the enzyme activity of an enzyme suspension decreased rapidly under non-sterile conditions. The strategy of limiting nitrogen in the medium to suppress bacterial growth has potential together with the fourth strategy, the cultivation of fungi on organic solids to produce inocula for a decolorization process under non-sterile conditions. A high degree of decolorization of RB5 under non-sterile conditions was achieved with T. versicolor grown on grains as sole substrate. The rate of decolorization was dependent on the amount of fungal inoculum used.
Estudio de los sedimentos recientes de la Plataforma Continental y Bahia de Cadiz

El presente trabajo aborda el estudio de los sedimentos recientes no consolidados de la plataforma continental y bahia de cadiz, en la zona comprendida entre la desembocadura del guadalquivir y el cabo de trafalgar. Se aborda el estudio granulometrico y mineralogico de dichos sedimentos, diferenciandose las diferentes fracciones (total, pesados y arcillas) y realizandose a continuacion la determinacion de las diferentes asociaciones mineralogicas en base al calculo estadistico mediante analisis factorial. Se ha determinado y cuantificado asimismo, la presencia en los sedimentos de metales pesados, materia organica, carbonatos, nitrogeno, fosforo y pigmentos, obteniendo asi, diferentes mapas de distribucion de los distintos parametros presentes en el area estudiada. A partir de los resultados experimentales obtenidos, se elabora un modelo sedimentologico general sobre la evolucion y origen de los sedimentos recientes del area, en los que el cuarzo aparece como mineral prioritario, estableciendose los posibles origenes y areas fuente del mismo. Se establece la naturaleza general del sedimento de este area y se definen los diferentes sectores caracterizados por la granulometria presente. En relacion con el estudio de los minerales pesados, son establecidas las provincias petrograficas, asi como las asociaciones entre estos, de donde es posible establecer la existencia de una constancia en los aportes sedimentarios a la zona, asi como la dinamica de estos, constante desde la orogenia alpina hasta la actualidad y en la que se diferencian basicamente dos zonas de diferente tasa de sedimentacion. Estos datos, unidos a los geofisicos, indican un modelo de dinamica sedimentaria progradante, desde la desembocadura del rio guadalquivir hacia el se, diferenciandose en el, dos zonas; una al s del paralelo de cadiz, con arenas cuarciferas de grano medio a fino, depositadas en un momento en que el nivel del mar estaba por debajo del ac
Thermal and Structure Analysis Based on Exfoliation of Clay in Thermosensitive Polymer by in-situ Polymerization

Poly(N-vinylcaprolactam) (PNVCL) offers superior characteristics as a thermoresponsive polymer for various potential applications. An attractive procedure, namely in-situ polymerization, was used to prepare NVCL/clay nanocomposite in different clay ratios. Organo-modified clay as C20 and B30 were employed in a range between 1–5% based on weight. Thermogravimetric analysis (TGA) and Fourier transform infrared spectroscopy (FTIR) were used to study thermal decomposition and to assess bond conversion during polymerization of the nanocomposite. This research was conducted to study PNVCL characteristics with the addition of clay as a nanocomposite. The stretch mode of the carboxylic group (C=O) and (C=C) was present in the band range about ~1635 cm –1 for the C20, but it was ranging between 1640 to 1664 cm –1 for the B30 of the nanocomposite. It was observed that the decomposition was different for each type of organoclay and the temperature peaked at 30 to 800 °C, to measure the degradation points at 5, 10, and 50%. Comparison results for FTIR and TGA showed that the best nanocomposite was found in the C20 (3%) case.
Spectral efficiency of a cellular MC/DS‐CDMA system in Rayleigh fading

The spectral efficiency of a multicarrier direct‐sequence code‐division multiple‐access (MC/DS‐CDMA) cellular system, operating in a mobile radio environment with Rayleigh fading, is investigated and evaluated in terms of channel capacity (in the Shannon sense) per user, estimated in an average sense. The analysis is based on the combination of path‐diversity reception, achieved by a conventional coherent maximal‐ratio combining (MRC) RAKE receiver and the physical frequency diversity potential provided by orthogonal frequency division multiplexing (OFDM). As shown, a closed‐form expression for the achieved spectral efficiency of the considered system's operation is derived following a recently presented general method. Copyright © 2005 John Wiley & Sons, Ltd.
Morphologies of z ∼ 0.7 AGN host galaxies in CANDELS: no trend of merger incidence with AGN luminosity

The processes that trigger active galactic nuclei (AGN) remain poorly understood. While lower luminosity AGN may be triggered by minor disturbances to the host galaxy, stronger disturbances are likely required to trigger luminous AGN. Major wet mergers of galaxies are ideal environments for AGN triggering since they provide large gas supplies and galaxy scale torques. There is however little observational evidence for a strong connection between AGN and major mergers. We analyse the morphological properties of AGN host galaxies as a function of AGN and host galaxy luminosity and compare them to a carefully matched sample of control galaxies. AGN are X-ray selected in the redshift range 0.5 < z < 0.8 and have luminosities 41 ≲ log (L_X [erg s^(−1)]) ≲ 44.5. ‘Fake AGN’ are simulated in the control galaxies by adding point sources with the magnitude of the matched AGN. We find that AGN host and control galaxies have comparable asymmetries, Sersic indices and ellipticities at rest frame ∼950 nm. AGN host galaxies show neither higher average asymmetries nor higher fractions of very disturbed objects. There is no increase in the prevalence of merger signatures with AGN luminosity. At 95 per cent confidence we find that major mergers are responsible for <6 per cent of all AGN in our sample as well as <40 per cent of the highest luminosity AGN (log (L_X [erg s^(−1)]) ∼ 43.5). Major mergers therefore either play only a very minor role in the triggering of AGN in the luminosity range studied or time delays are too long for merger features to remain visible.
Spinal microcircuits comprising dI3 interneurons are necessary for motor functional recovery following spinal cord transection

The spinal cord has the capacity to coordinate motor activities such as locomotion. Following spinal transection, functional activity can be regained, to a degree, following motor training. To identify microcircuits involved in this recovery, we studied a population of mouse spinal interneurons known to receive direct afferent inputs and project to intermediate and ventral regions of the spinal cord. We demonstrate that while dI3 interneurons are not necessary for normal locomotor activity, locomotor circuits rhythmically inhibit them and dI3 interneurons can activate these circuits. Removing dI3 interneurons from spinal microcircuits by eliminating their synaptic transmission left locomotion more or less unchanged, but abolished functional recovery, indicating that dI3 interneurons are a necessary cellular substrate for motor system plasticity following transection. We suggest that dI3 interneurons compare inputs from locomotor circuits with sensory afferent inputs to compute sensory prediction errors that then modify locomotor circuits to effect motor recovery. DOI: http://dx.doi. org/10.7554/eLife.21715. 001
Clinical significance of diffusely increased splenic uptake on FDG-PET

Diffusely increased uptake is more commonly observed than focal uptake in the spleen on a whole-body [18F] fluorodeoxyglucose-positron emission tomography/computed tomography. The significance of diffusely increased splenic uptake varies in different clinical settings. On a pre-therapeutic scan for lymphoma, splenic uptake, greater than hepatic uptake, is a relative reliable indication of lymphomatous involvement of the spleen, unless the patient has a history of recent cytokine administration. In HIV infection, increased splenic uptake is usually noted in the early stage of the disease, which could reflect massive stimulation of B-cells in the spleen by nonreplicating antigenic material. Diffusely increased splenic uptake may also be present in sarcoidosis, malaria, and many inflammatory or hematopoietic diseases. Therapeutic-related reactive splenic uptake concurrent with bone marrow uptake is often secondary to administration of granulocyte colony-stimulating factor for myelosuppression or high-dose interferon-&agr;-2b adjuvant therapy for melanoma.
The effect of maternal depression and marital adjustment on young children's internalizing and externalizing behaviour problems.

BACKGROUND The present study aimed to clarify the circumstances under which maternal depression is associated with adverse outcomes in pre-school-aged children, and to explore the additional impact of the marital relationship in a socio-economically low-risk sample. METHODS Ninety-two mothers recruited into a longitudinal study were assessed for symptoms of depression when their children were 4, 12 and 15 months, and later at 4 years of age. At 4 years of age, mothers were also asked to report on marital adjustment. Mothers, fathers and pre-school teachers were asked to report on children's internalizing and externalizing behaviour problems. RESULTS Children exposed to chronic maternal depression were rated by their parents as significantly more problematic on internalizing and externalizing behaviours. This association was not mediated or moderated by low marital satisfaction. No parent-reported effects were evident for children exposed to transient depression. Ten per cent of the children had internalizing scores in the clinical range, and 7% had externalizing scores in the clinical range. Almost all of the children with clinically elevated scores had been exposed to chronic maternal depression. Teacher reports of internalizing behaviours corroborated parent reports; however, teachers tended to report significantly lower levels of behaviour problems. Although there was a tendency for teachers to rate children exposed to any depression as more problematic on internalizing behaviours, the subgroup differences were not significant. CONCLUSIONS Findings confirm that depression chronicity is important in determining child behavioural outcomes, and that depression effects cannot be accounted for by low marital adjustment. Results are discussed with reference to transmission of risk models, and treatment implications are considered.
Paranasal Sinus Balloon Catheter Dilation for Treatment of Chronic Rhinosinusitis

Objective Paranasal sinus balloon catheter dilation (BCD) represents a commonly used tool in the management of chronic rhinosinusitis (CRS) for which the indications, utilization, and outcomes have not been well established. A systematic review and meta-analysis were undertaken to evaluate change in quality of life and sinus opacification following paranasal sinus BCD in the treatment of CRS. Data Sources MEDLINE and EMBASE databases. Review Methods Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines were utilized to identify English-language studies reporting patient outcomes following BCD for CRS. Primary outcomes included the impact of BCD on validated measures of quality of life and sinonasal opacification. Results Systematic review identified 17 studies for qualitative analysis. Studies generally included cases with limited disease based on radiographic opacification. Five studies contained extractable data for change in 20-Item Sinonasal Outcome Test (SNOT-20) 1 year following BCD, with significant improvement in self-reported quality of life (P = .04). Five studies reported a significant change in paranasal sinus opacification following BCD (P < .001). Two studies directly compared change in SNOT-20 between BCD and endoscopic sinus surgery, without demonstration of significant difference in outcome (P = .07). Subgroup analysis found that change in SNOT-20 score was greater after BCD in the operating room than in the office (P = .004). Conclusion Current evidence supporting the role of BCD in CRS remains incomplete. Long-term within-group improvements in quality-of-life and sinus opacification scores are demonstrated among a restricted adult population with CRS. Additional study is needed to further evaluate the role for BCD in specific settings and patient subgroups.
Competing values of emergency department performance: balancing multiple stakeholder perspectives.

OBJECTIVE To describe the performance interests of multiple stakeholders associated with the management and delivery of emergency department (ED) care, and to develop a performance framework and set of indicators that reflect these interests. STUDY SETTING Stakeholders (1,100 physicians, nurses, managers, home care providers, and prehospital care personnel) with responsibility for ED patients in hospitals in the Canadian province of Ontario. STUDY DESIGN Sixty-two percent of stakeholders responded to a mail survey regarding the importance of 104 potential ED performance indicators. Descriptive and inferential statistics are used to explore the interests of each stakeholder group and to compare interests across the five groups. PRINCIPAL FINDINGS Emergency department stakeholders are primarily interested in indicators that focus on their role and capacity to provide care. Key differences exist between hospital and nonhospital stakeholders. Physicians mean ratings of the importance on ED performance measures were lower than mean ratings in the other stakeholder groups. CONCLUSIONS Emergency department performance interests are not homogeneous across stakeholder groups, and evaluating performance from the perspective of any one stakeholder group will result in unbalanced assessments. Community-based stakeholders, a group frequently excluded from commenting on ED performance, provide important insights into ED performance related to the external environment and the broader continuum of care.