Miracle-dz/UniFAR-FTUs huggingface dataset:
A second branched-chain alpha-keto acid dehydrogenase gene cluster (bkdFGH) from Streptomyces avermitilis: its relationship to avermectin biosynthesis and the construction of a bkdF mutant suitable for the production of novel antiparasitic avermectins

A second cluster of genes encoding the E1 alpha, E1 beta, and E2 subunits of branched-chain alpha-keto acid dehydrogenase (BCDH), bkdFGH, has been cloned and characterized from Streptomyces avermitilis, the soil microorganism which produces anthelmintic avermectins. Open reading frame 1 (ORF1) (bkdF, encoding E1 alpha), would encode a polypeptide of 44,394 Da (406 amino acids). The putative start codon of the incompletely sequenced ORF2 (bkdG, encoding E1 beta) is located 83 bp downstream from the end of ORF1. The deduced amino acid sequence of bkdF resembled the corresponding E1 alpha subunit of several prokaryotic and eukaryotic BCDH complexes. An S. avermitilis bkd mutant constructed by deletion of a genomic region comprising the 5' end of bkdF is also described. The mutant exhibited a typical Bkd- phenotype: it lacked E1 BCDH activity and had lost the ability to grow on solid minimal medium containing isoleucine, leucine, and valine as sole carbon sources. Since BCDH provides an alpha-branched-chain fatty acid starter unit, either S(+)-alpha-methylbutyryl coenzyme A or isobutyryl coenzyme A, which is essential to initiate the synthesis of the avermectin polyketide backbone in S. avermitilis, the disrupted mutant cannot make the natural avermectins in a medium lacking both S(+)-alpha-methylbutyrate and isobutyrate. Supplementation with either one of these compounds restores production of the corresponding natural avermectins, while supplementation of the medium with alternative fatty acids results in the formation of novel avermectins. These results verify that the BCDH-catalyzed reaction of branched-chain amino acid catabolism constitutes a crucial step to provide fatty acid precursors for antibiotic biosynthesis in S. avermitilis.
Robotic versus Open Partial Nephrectomy: A Systematic Review and Meta-Analysis

Objectives To critically review the currently available evidence of studies comparing robotic partial nephrectomy (RPN) and open partial nephrectomy (OPN). Materials and Methods A comprehensive review of the literature from Pubmed, Web of Science and Scopus was performed in October 2013. All relevant studies comparing RPN with OPN were included for further screening. A cumulative meta-analysis of all comparative studies was performed and publication bias was assessed by a funnel plot. Results Eight studies were included for the analysis, including a total of 3418 patients (757 patients in the robotic group and 2661 patients in the open group). Although RPN procedures had a longer operative time (weighted mean difference [WMD]: 40.89; 95% confidence interval [CI], 14.39–67.40; p = 0.002), patients in this group benefited from a lower perioperative complication rate (19.3% for RPN and 29.5% for OPN; odds ratio [OR]: 0.53; 95%CI, 0.42–0.67; p<0.00001), shorter hospital stay (WMD: −2.78; 95%CI, −3.36 to −1.92; p<0.00001), less estimated blood loss(WMD: −106.83; 95%CI, −176.4 to −37.27; p = 0.003). Transfusions, conversion to radical nephrectomy, ischemia time and estimated GFR change, margin status, and overall cost were comparable between the two techniques. The main limitation of the present meta-analysis is the non-randomization of all included studies. Conclusions RPN appears to be an efficient alternative to OPN with the advantages of a lower rate of perioperative complications, shorter length of hospital stay and less blood loss. Nevertheless, high quality prospective randomized studies with longer follow-up period are needed to confirm these findings.
Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs

Background Evaluation of the prolonged impact of weaning diet on ileal mucosa bacteria and during periods of reduced and improved growth was conducted using 454 pyrosequencing. Methodology/Principal Findings Weaned pigs were fed HIGH or LOW complexity diets, with or without antibiotics, for 6 weeks, followed by a common grower diet. Pigs were killed at 2 (n = 4 or 5) and 8 (n = 6) weeks post-weaning (periods of reduced and improved growth, respectively). Mucosal bacteria were removed; DNA was extracted and amplified using the V1–V3 region of the 16S rRNA gene. Mucosal bacteria clustered more closely by week post-weaning than diet but 44% of bacterial species did not change from week 2 to 8. There was no effect of diet complexity or antibiotic inclusion on indices of bacterial diversity. Firmicutes made up 91 and 96% of total reads at week 2 and 8, respectively. The proportion of Clostridium paraputrificum increased (P = 0.003) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH; whereas Clostridium leptum decreased (P = 0.02) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH. The proportion of Sarcina genus was 3-fold higher in pigs fed A+ compared to A− at week 2 and 5-fold higher at week 8 despite the lack of in-feed antibiotics at that time. Conclusions/Significance Shifts in mucosal bacteria populations may be related to dietary induced changes in growth performance during reduced and improved growth but further studies are required to confirm causative relationship. Weaning diet results in species specific prolonged alterations in mucosal bacteria, particularly where high levels of in-feed antibiotics are used. A considerable portion of ileal mucosal bacteria colonize early and remain stable over time despite changes in diet.
Delay-Dependent Global Exponential Stability for Delayed Recurrent Neural Networks

This paper deals with the global exponential stability for delayed recurrent neural networks (DRNNs). By constructing an augmented Lyapunov–Krasovskii functional and adopting the reciprocally convex combination approach and Wirtinger-based integral inequality, delay-dependent global exponential stability criteria are derived in terms of linear matrix inequalities. Meanwhile, a general and effective method on global exponential stability analysis for DRNNs is given through a lemma, where the exponential convergence rate can be estimated. With this lemma, some global asymptotic stability criteria of DRNNs acquired in previous studies can be generalized to global exponential stability ones. Finally, a frequently utilized numerical example is carried out to illustrate the effectiveness and merits of the proposed theoretical results.
Marinopyrrole Derivatives as Potential Antibiotic Agents against Methicillin-Resistant Staphylococcus aureus (I)

Infections caused by drug-resistant pathogens are on the rise. The ongoing spread of methicillin-resistant Staphylococcus aureus (MRSA) strains exemplifies the urgent need for new antibiotics. The marine natural product, marinopyrrole A, was previously shown to have potent antibiotic activity against Gram-positive pathogens, including MRSA. However, its minimum inhibitory concentration (MIC) against MRSA was increased by >500 fold in the presence of 20% human serum, thus greatly limiting therapeutic potential. Here we report our discovery of a novel derivative of marinopyrrole A, designated 1a, featuring a 2–4 fold improved MIC against MRSA and significantly less susceptibility to serum inhibition. Importantly, compound 1a displayed rapid and concentration-dependent killing of MRSA. Compared to the natural product counterpart, compound 1a provides an important natural product based scaffold for further Structure Activity Relationship (SAR) and optimization.
Some Overlooked Features of Tropical Atlantic Climate Leading to a New Niño-Like Phenomenon*

Abstract The Atlantic Nino, an equatorial zonal mode akin to the Pacific El Nino–Southern Oscillation (ENSO), is phase-locked to boreal summer when the equatorial easterly winds intensify and the thermocline shoals in the Gulf of Guinea. A suite of satellite and in situ observations reveals a new mode of tropical Atlantic variability that displays many characteristics of the zonal mode but instead peaks in November–December (ND). This new mode is found to be statistically independent from both the Atlantic Nino in the preceding summer and the Pacific ENSO. The origin of this ND zonal mode lies in an overlooked aspect of the seasonal cycle in the equatorial Atlantic. In November the equatorial easterly winds intensify for the second time, increasing upwelling and lifting the thermocline in the Gulf of Guinea. An analysis of high-resolution climatological data shows that these dynamical changes induce a noticeable SST cooling in the central equatorial Atlantic. The shoaling thermocline and increased upwelli.
Parallel Markov Chain Monte Carlo computation for varying-dimension signal analysis

Parallel implementation of Markov Chain Monte Carlo (MCMC) algorithms for Bayesian inference has been effective but is usually restricted to the case where the dimension of the parameter vector is fixed. We propose an efficient parallel solution for the varying-dimension problem by constructing multiple within-model MCMC chains and then combining the separate results to analyze the posterior distribution of dimensionality. We aim for parallel speed-up by reducing the length of the burn-in period and the individual chains in comparison with a serial, reversible jump MCMC (RJMCMC) algorithm. The parallel methodology is illustrated with application to a benchmarking, change point problem.
Studying the chaos of code development

As large software systems evolve, controlling their complexityis a major challenge for many companies, as they striveto deliver future releases on time and within budget. Severalsource code based metrics have been proposed to assist indetermining the complexity of code to help control developmentcosts and outcome.In this paper we offer a novel view on the problem of complexityin software. We present a complexity metric that isbased on the process followed by the developers to producethe code instead of on the code directly. We conjecture thata chaotic/complex development process negatively affect itsoutcome, the source code. We validate our hypothesis empiricallyusing data derived from the development processhistory of six large open source projects (three operatingsystems: NetBSD, FreeBSD, OpenBSD; a window manager:KDE; an office productivity suite: KOffice; and a databasemanagement system: Postgres).
Seizure Duration Determined by Subdural Electrode Recordings in Adult Patients with Intractable Focal Epilepsy

Background and Purpose: To investigate the duration of seizures and its relationship to seizure type, epilepsy syndrome, and seizure clustering. Methods: We examined 1,251 seizures from 152 patients who underwent video-electrocorticographic monitoring with subdural electrodes. Their seizure duration, seizure types, epilepsy syndromes, and seizure clusters were analyzed. Results: The median seizure duration was 91.5s (4–1016s). There were 34 (2.7%) seizures lasting > 5 minutes in 20 (13.2%) patients. There was a significant difference in seizure duration according to seizure types (p < 0.0001), but not to epilepsy syndromes. There were 99 seizure clusters in 67 (44.1%) patients. The first seizure in a cluster of seizures tended to last longer than non-cluster seizures (median 98s versus 89s, p = 0.033). Seizure duration was significantly longer in mesial temporal lobe epilepsy than in neocortical lobe epilepsy (median 103s versus 87s, p = 0.041). Rate of seizure cluster was lower in mTLE (38.0%) than in NLE (47.1%), but this difference was not significant. Conclusions: Seizure durations were different among seizure types. Seizure clustering also differ between patients with mTLE and those with NLE, which suggests different seizure generation and propagation among different epileptogenic foci. This study has implications for the identification of abnormally prolonged seizures.
National patterns in antidepressant medication treatment.

CONTEXT Antidepressants have recently become the most commonly prescribed class of medications in the United States. OBJECTIVE To compare sociodemographic and clinical patterns of antidepressant medication treatment in the United States between 1996 and 2005. DESIGN Analysis of antidepressant use data from the 1996 (n = 18 993) and 2005 (n = 28 445) Medical Expenditure Panel Surveys. SETTING Households in the United States. PARTICIPANTS Respondents aged 6 years or older who reported receiving at least 1 antidepressant prescription during that calendar year. MAIN OUTCOME MEASURES Rate of antidepressant use and adjusted rate ratios (ARRs) of year effect on rate of antidepressant use adjusted for age, sex, race/ethnicity, annual family income, self-perceived mental health, and insurance status. RESULTS The rate of antidepressant treatment increased from 5.84% (95% confidence interval [CI], 5.47-6.23) in 1996 to 10.12% (9.58-10.69) in 2005 (ARR, 1.68; 95% CI, 1.55-1.81), or from 13.3 to 27.0 million persons. Significant increases in antidepressant use were evident across all sociodemographic groups examined, except African Americans (ARR, 1.13; 95% CI, 0.89-1.44), who had comparatively low rates of use in both years (1996, 3.61%; 2005, 4.51%). Although antidepressant treatment increased for Hispanics (ARR, 1.75; 95% CI, 1.60-1.90), it remained comparatively low (1996, 3.72%; 2005, 5.21%). Among antidepressant users, the percentage of patients treated for depression did not significantly change (1996, 26.25% vs 2005, 26.85%; ARR, 0.95; 95% CI, 0.83-1.07), although the percentage of patients receiving antipsychotic medications (5.46% vs 8.86%; ARR, 1.77; 95% CI, 1.31-2.38) increased and those undergoing psychotherapy declined (31.50% vs 19.87%; ARR, 0.65; 95% CI, 0.56-0.72). CONCLUSIONS From 1996 to 2005, there was a marked and broad expansion in antidepressant treatment in the United States, with persisting low rates of treatment among racial/ethnic minorities. During this period, individuals treated with antidepressants became more likely to also receive treatment with antipsychotic medications and less likely to undergo psychotherapy.
A model for transition from pediatric to adult care in cystic fibrosis.

With improved medical technology, many chronic medical conditions of childhood are now recognized as conditions of childhood onset. Appropriate treatment of these conditions in the adult patient is required. The pediatric setting is not appropriate in terms of philosophy, service delivery, and relationship with the patient. To design a suitable transition protocol, a survey of teenage patients with cystic fibrosis was carried out and the process was discussed with the relevant clinicians. The results of the survey indicated that young people identified transition to an adult service as necessary and accepted, provided that good preparation is given from the pediatric setting. This article provides a detailed example of a model of transition for cystic fibrosis services to encourage practice and evaluation of provision.
UNINTENTIONAL AND UNCONSCIOUS ANALOGIES BETWEEN SUPERFICIALLY DISSIMILAR BUT RELATIONALLY SIMILAR SIMPLE STRUCTURES

This research addresses empirically the issue of the possibility for making unconscious analogies. It demonstrates unconscious and unintentional analogies between structurally similar but superficially dissimilar word pairs. Experiment 1 demonstrated spontaneous unconscious analogical transfer between analogous word pairs. Experiment 2 ruled out the potential semantic priming explanation for the findings reported in the first experiment.
Indicators of Optimal Lung Volume During High-Frequency Oscillatory Ventilation in Infants*

Objectives:During high-frequency oscillatory ventilation, an understanding of the relationship between lung volume and lung mechanics may help clinicians better apply ventilation. The objectives of this study were: 1) to describe the relationship between lung volume and lung function parameters during mapping of the deflation limb of the pressure–volume relationship in infants receiving high-frequency oscillatory ventilation, and 2) to determine whether these parameters might be useful in targeting an optimal volume to apply ventilation. Design:Observational physiological study. Setting:Tertiary neonatal intensive care unit in a pediatric hospital. Patients:Fifteen infants receiving high-frequency oscillatory ventilation and muscle relaxants. Interventions:The deflation limb of the pressure–volume relationship was mapped in each infant, after recruitment to total lung capacity, using stepwise airway pressure decrements. Total lung capacity and closing volume were defined by oxygenation response. Measurements and Main Results:Lung volume (respiratory inductive plethysmography), oxygen saturation, transcutaneous carbon dioxide, and indicators of lung mechanics were recorded at each pressure. A distinct bell-shaped relationship between lung volume and carbon dioxide, minute ventilation, and tidal volume (both at airway opening and by inductive plethysmography) could be identified on the deflation limb, with an improvement of 21.6 mm Hg (CO2), 168 mL2/sec (minute ventilation), 0.25 mL/kg (airway opening tidal volume), and 13.7% (plethysmography tidal volume) compared with total lung capacity levels. The mean (SD) optimal volumes and pressures for these parameters were significantly lower than total lung capacity, occurring at volumes between 38.6 (39.8)% and 62.8 (31.1)% of total lung capacity, and 28 (36.3)% and 41.3 (38.7)% of pressure at total lung capacity (p < 0.05; Bonferroni post-test). These coincided with the lowest pressure and volumes that maintained the oxygenation benefit of recruitment. Conclusions:Transcutaneous carbon dioxide, tidal volume, and minute ventilation may assist in refining strategies to identify optimal lung volume.
Compression Failure of Aluminum Plates Exposed to Constant Heat Flux

Aluminum is used as a structural member in marine applications because of its low weight. One challenge is to design against failure of aluminum structures in fire. A parametric study was performed to quantify the effects of parameters on the compression failure of aluminum plates during a fire. A thermo-structural apparatus was designed to perform compression tests on aluminum samples consisting of a compression load frame, a hydraulic system, and electric heaters. The effect of dimensional variation on failure behavior was examined. Aluminum 5083 and 6082 alloys were tested with three thicknesses, two lengths and two widths. Three heat fluxes and various buckling stresses were used. Micro Vicker’s hardness values were measured before and after testing to quantify the effect of heating on the strength of the aluminum. In general, lower applied stress resulted in higher failure temperature and longer time to failure. Dimensional variations had a negligible effect on failure behavior. The 5083 alloy has a minimum stress level of 50% of the buckling stress at 10kW/m 2 and 10% of the buckling stress at 20kW/m 2 , while the 6082 alloy has a minimum stress level of 75% of the buckling stress at 10kW/m 2 and 25% of the buckling stress at 20kW/m 2 . The 6082 failed at higher temperatures and longer failure times than the 5083. The presence of insulation on the exposed surface decreased the temperature rise, resulting in longer failure times. Vicker’s hardness decreased with heating in general. The results describe the effects of parameters of the failure of aluminum.
Regulation of expression of a sheep metallothionein 1a-sheep growth hormone fusion gene in transgenic mice

Transgenic mice containing a sheep metallothionein 1a-sheep growth hormone fusion gene exhibited low, tissue-specific basal levels of transgene mRNA expression, resulting in slightly elevated levels of circulating growth hormone that did not lead to a detectable increase in growth. After zinc stimulation, high levels of transgene mRNA expression were induced in a number of tissues; these levels correlated with increased levels of circulating growth hormone, resulting in growth increases of up to 1.5 times the levels of controls and unstimulated transgenic mice. After removal of the zinc stimulus, transgene expression and circulating growth hormone concentrations returned to basal levels. Additional evidence from the pattern of developmental expression of the transgene suggests that zinc is the main regulator of this promoter in mice. The demonstrated regulation and low basal level of expression of the sheep metallothionein 1a promoter make it a candidate for use in other mouse transgenic studies and for use in transgenic livestock, in which regulation of expression is essential.
Is the relation of systolic blood pressure to risk of cardiovascular disease continuous and graded, or are there critical values?

Because epidemiologic data indicate a continuous incremental risk of cardiovascular disease (CVD) in relation to blood pressure (BP), hypertension treatment guidelines now recommend treating high-normal and mild BP elevations.1 Port and coworkers,2 analyzing Framingham Study data, challenge this assertion. They claim that Framingham data in actuality “contradict the concept that lower pressures imply lower risk and the idea that 140 mm Hg is a useful cut-off value for hypertension for all adults . ” They suggest that there is an age- and sex-dependent threshold for “hypertension” and that a substantial proportion of the population currently deemed at increased risk are, in fact, not. Their conclusion derives from the use of “logistic splines” methodology to examine the relation of systolic blood pressure (SBP) to CVD and all-cause mortality. They contend that previous linear logistic analysis depicting a continuous, graded relation is misleading and that there is actually a threshold at the 70th percentile of SBP for a person at a given age and sex. They also suggest that because BP increases steadily with age, the threshold also increases with age.2 By inference, Port et al seem to suggest that we to return to the discarded concept that a “normal” systolic pressure is, roughly, “100+ years of age mm Hg. ” They focus on all-cause mortality because “it is most free of misclassifications and, importantly the number of events is sufficiently high to allow accurate estimates of the shape of the relation with systolic blood pressure. ” However, the more relevant outcome is CVD mortality and the CVD events promoted by hypertension unconfounded by non-CVD mortality, which could be associated with low BP. Furthermore, even a focus on CVD mortality, excluding the large majority of nonfatal events, needlessly reduces the amount of data on which to determine the shape of the BP–CVD …
Temporal decomposition: a promising approach to low rate wideband speech compression

In this paper, we present new results on Temporal Decomposition (TD) applied to the Line Spectral Frequencies (LSFs) derived for wideband speech. The paper shows that by incorporating a dynamic programming search algorithm into TD, near transparent quantisation of wideband LSFs can be obtained at approximately 1 kbps. We also show that TD performs significantly better than Split Vector Quantisation at low bit rates. We propose that TD is a promising approach to low rate wideband speech coding for applications such as unicast streaming.