Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective Removal of Aberrant Extender Units by a Type II Thioesterase for Efficient FR-008/Candicidin Biosynthesis in Streptomyces sp. Strain FR-008

ABSTRACT Gene fscTE, encoding a putative type II thioesterase (TEII), was associated with the FR-008/candicidin gene cluster. Deletion of fscTE reduced approximately 90% of the FR-008/candicidin production, while the production level was well restored when fscTE was added back to the mutant in trans. FscTE was unable to compensate for the release of the maturely elongated polyketide as site-directed inactivation of the type I thioesterase (TEI) totally abolished FR-008/candicidin production. Direct biochemical analysis of FscTE in parallel with its homologue TylO from the tylosin biosynthetic pathway demonstrated their remarkable preferences for acyl-thioesters (i.e., propionyl-S-N-acetylcysteamine [SNAC] over methylmalonyl-SNAC and acetyl-SNAC over malonyl-SNAC) and thus concluded that TEII could maintain effective polyketide biosynthesis by selectively removing the nonelongatable residues bound to acyl carrier proteins. Overexpression of FscTE under the strong constitutive ermE*p promoter in the wild-type strain did not suppress FR-008/candicidin formation, which confirmed its substrate specificity in vivo. Furthermore, successful complementation of the fscTE mutant was obtained with fscTE and tylO, whereas no complementation was detected with nonribosomal peptide synthetase (NRPS) TEII tycF and srfAD, reflecting substrate specificities of TEIIs distinctive from those of either polyketide synthases or NRPSs.
Functional Analysis of a Novel β-(1,3)-Glucanase from Corallococcus sp. Strain EGB Containing a Fascin-Like Module

ABSTRACT A novel β-(1,3)-glucanase gene designated lamC, cloned from Corallococcus sp. strain EGB, contains a fascin-like module and a glycoside hydrolase family 16 (GH16) catalytic module. LamC displays broad hydrolytic activity toward various polysaccharides. Analysis of the hydrolytic products revealed that LamC is an exo-acting enzyme on β-(1,3)(1,3)- and β-(1,6)-linked glucan substrates and an endo-acting enzyme on β-(1,4)-linked glucan and xylan substrates. Site-directed mutagenesis of conserved catalytic Glu residues (E304A and E309A) demonstrated that these activities were derived from the same active site. Excision of the fascin-like module resulted in decreased activity toward β-(1,3)(1,3)-linked glucans. The carbohydrate-binding assay showed that the fascin-like module was a novel β-(1,3)-linked glucan-binding module. The functional characterization of the fascin-like module and catalytic module will help us better understand these enzymes and modules. IMPORTANCE In this report of a bacterial β-(1,3)(1,3)-glucanase containing a fascin-like module, we reveal the β-(1,3)(1,3)-glucan-binding function of the fascin-like module present in the N terminus of LamC. LamC displays exo-β-(1,3)/(1,6)-glucanase and endo-β-(1,4)-glucanase/xylanase activities with a single catalytic domain. Thus, LamC was identified as a novel member of the GH16 family.
Abstract S2-01: The PRIME II trial: Wide local excision and adjuvant hormonal therapy ± postoperative whole breast irradiation in women ≥ 65 years with early breast cancer managed by breast conservation

Background. Local Recurrence rates after breast conserving surgery (BCS) are falling because of increasing use of effective systemic therapy. The question of whether whole breast radiotherapy (WBRT) can be omitted in carefully defined groups of older patients receiving appropriate systemic therapy has not been addressed. PRIME II is an International phase III RCT addressing this question. Methods. Between April 2003 and December 2009, 1326 patients were randomised to receive (n = 658) or nor receive (n = 668) radiotherapy (RT). Eligiblity criteria were ≥65 years, T1-2 (up to 3cm), N0, M0, hormone receptor positive, clear excision margins (≥ 1mm), axillary node negative women in receipt of adjuvant hormone therapy. Patients could have Grade 3 tumours or lympho-vascular invasion but not both. An accrual of 1300 was planned to detect a difference based on estimates of local recurrence of 2% in RT group and 5% in no RT arm at 5 years, with 80% power and 5% significance. The primary endpoint was ipsilateral breast tumour recurrence (IBTR). Secondary endpoints were regional recurrence, contralateral breast cancer, distant metastases and overall survival (OS). Median follow up is 5.0 years. Results IBTR at 5 years was 4.1% (95% CI 2.4, 5.7%) without RT, 1.3% (95% CI 0.2, 2.3%) with RT. The hazard ratio for IBTR in those IBTR receiving radiotherapy was 4.34 (1.79, 10.55) (p = 0.001). Overall actuarial survival at 5 years was 93.8% (95% CI 91.6, 95.9%) without RT and 94.2% (95% CI 92.2, 96.3%) with RT, (p = 0.24). No significant differences in regional recurrence (1.4% no RT vs 0.5% RT), contralateral breast cancer (0.9% no RT vs 1.5% RT), nor distant metastases (1.0% vs 0.3%) were seen. Breast cancer-free survival was 94.6% (95% CI 92.7, 96.5%)for no RT and 97.3% (95% CI 95.9, 98.8%) for those receiving RT (p = 0.003): this difference was due to the greater IBTR in no RT group. The majority of deaths were not linked to breast cancer (35 no RT vs 29 RT from a total of 87 deaths), with no influence of omission of RT (p = 0.27). Conclusions The randomised International Trial has shown that • Omission of RT in women ≥65 year of age with N0, ER positive breast cancer receiving endocrine therapy results in only a 4.1% 5 year IBTR • Although RT reduces IBTR significantly, the absolute reduction in this study is very small. • RT does not reduce the rate of regional recurrence, distant metastases or affect overall survival. • Omission of postoperative WBRT in this population based on the 5 year rate of IBTR appears safe, especially in the presence of comorbidities. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S2-01.
Path following with an underactuated self-balancing spherical-wheel mobile robot

Reactive methods for motion planning offer robustness advantages in the presence of large disturbances for robotic systems. Unfortunately, it is difficult to generalize these reactive methods to underactuated systems and existing research predominantly focuses on solutions based on the high-gain tracking of dynamically feasible trajectories. Self-balancing mobile robots with spherical wheels, BallBot platforms, are rich examples of such underactuated mechanisms where motion planning has traditionally been done through trajectory tracking on actuated system states with little explicit feedback on external states that are not directly controlled. In this paper, we propose a reactive path-following controller for external states of such platforms, eliminating the need to follow time-parameterized state trajectories. We first define the path-following problem in general, and present how it can be realized through a parallel composition of existing, two-dimensional controllers for the BallBot morphology. We then show in simulation how this idea can be used to achieve asymptotic convergence to a linear path with a constant forward velocity. We also show how the basic idea can be generalized to more complex path shapes such as circles, towards an eventual deployment in a more complete motion planning framework based on sequential composition.
Inverse Scattering for Monochromatic Phaseless Measurements

An inverse method and measurement setup for profile and constitutive parameters reconstruction from monochromatic phaseless information is presented. The method is based on the minimization of a cost function that relates the measured field with the one scattered by a model of the object under test (OUT), where the position, contour, and constitutive parameters are the unknowns. As a result, phaseless information is directly related to the inverse problem unknowns, thus avoiding the need of an intermediate phase retrieval step. Due to the nonlinear nature of the cost function, global optimization techniques, such as the particle swarm optimization and differential evolution algorithms, have been considered for cost function minimization. An exhaustive analysis of the cost function behavior as a function of the electric size of the OUT is presented, discussing the optimal OUT size where the proposed methodology provides accurate profile and constitutive parameters reconstruction. The proposed methodology is conceived to use it together with a simple, low-cost measurement setup for fast characterization of perfect electric conductor and dielectric objects. Measurement examples are presented aiming to prove the feasibility of the described measurement setup.
Particle Learning Framework for Estimating the Remaining Useful Life of Lithium-Ion Batteries

As an important part of prognostics and health management, accurate remaining useful life (RUL) prediction for lithium (Li)-ion batteries can provide helpful reference for when to maintain the batteries in advance. This paper presents a novel method to predict the RUL of Li-ion batteries. This method is based on the framework of improved particle learning (PL). The PL framework can prevent particle degeneracy by resampling state particles first with considering the current measurement information and then propagating them. Meanwhile, PL is improved by adjusting the number of particles at each iteration adaptively to reduce the running time of the algorithm, which makes it suitable for online application. Furthermore, the kernel smoothing algorithm is fused into PL to keep the variance of parameter particles invariant during recursive propagation with the battery prediction model. This entire method is referred to as PLKS in this paper. The model can then be updated by the proposed method when new measurements are obtained. Future capacities are iteratively predicted with the updated prediction model until the predefined threshold value is triggered. The RUL is calculated according to these predicted capacities and the predefined threshold value. A series of case studies that demonstrate the proposed method is presented in the experiment.
Infliximab regulates lamina propria T lymphocytes in patients with Crohn's disease

The immune system is a major determinant of the pathophysiological inflammation, which may lead to gastrointestinal mucosal injury in patients with Crohn's disease. Cytokines such as tumour necrosis factor‐alpha are well‐known mediators of the immune system, and treatment with a chimeric anti‐tumour necrosis factor‐alpha antibody (infliximab) has been shown to be highly effective in patients with Crohn's disease. Recent evidence indicates that infliximab induces apoptosis in lamina propria T lymphocytes in these patients. To better understand the mechanisms of infliximab's effect on gastrointestinal inflammation, we investigated changes in the serum level of cytokines after treatment in these patients, and the effect of infliximab in inducing the apoptosis of T lymphocytes.
Six physical education lessons a week can reduce cardiovascular risk in school children aged 6–13 years: A longitudinal study

Aims: Cardiovascular disease (CVD) originates during childhood and adolescence. Schools are potentially effective settings for early public health prevention strategies. The aim of this study was to evaluate the effect of six physical education (PE) lessons on children’s CVD risk. Methods: This longitudinal study in 10 public schools (1218 children, aged 6–13 years), 6 intervention and 4 control schools evaluates a natural experiment, where intervention schools tripled PE to six lessons per week compared to the mandatory two PE lessons in the control schools. Baseline (2008) and 2-year follow-up measures were anthropometrics, cardiorespiratory fitness, blood pressure and blood samples providing lipids and measures for insulin resistance. Based on these variables, a composite risk score was calculated and used for further analysis. Multivariate multilevel mixed effect regression models were used to estimate effect of intervention taking the hierarchical structure of data into account. Individual, class and school were considered random effects. Intra class correlation (ICC) was calculated. Results: Intervention significantly lowered mean of composite risk score with 0.17 SD (95% CI: −0.34 to −0.01). Six PE lessons per week had a beneficial effect on triglycerides (TG) levels (−0.18 SD, 95% CI: −0.36 to 0.00), systolic blood pressure (SBP) (−0.22 SD, 95% CI: −0.42 to −0.02) and insulin resistance (HOMA-IR) (−0.17 SD, 95% CI: −0.34 to 0.01). Conclusions: Six PE lessons at school can reduce children’s CVD risk measured as a composite risk score. The changes in risk score are considered substantial in the perspective of public health strategy for preventing CVD in later life.
Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC

ABSTRACT Limonene, a major component of citrus peel oil, has a number of applications related to microbiology. The antimicrobial properties of limonene make it a popular disinfectant and food preservative, while its potential as a biofuel component has made it the target of renewable production efforts through microbial metabolic engineering. For both applications, an understanding of microbial sensitivity or tolerance to limonene is crucial, but the mechanism of limonene toxicity remains enigmatic. In this study, we characterized a limonene-tolerant strain of Escherichia coli and found a mutation in ahpC, encoding alkyl hydroperoxidase, which alleviated limonene toxicity. We show that the acute toxicity previously attributed to limonene is largely due to the common oxidation product limonene hydroperoxide, which forms spontaneously in aerobic environments. The mutant AhpC protein with an L-to-Q change at position 177 (AhpCL177Q) was able to alleviate this toxicity by reducing the hydroperoxide to a more benign compound. We show that the degree of limonene toxicity is a function of its oxidation level and that nonoxidized limonene has relatively little toxicity to wild-type E. coli cells. Our results have implications for both the renewable production of limonene and the applications of limonene as an antimicrobial.
Two Novel Class II Hydrophobins from Trichoderma spp. Stimulate Enzymatic Hydrolysis of Poly(Ethylene Terephthalate) when Expressed as Fusion Proteins

Poly(ethylene terephthalate) (PET) can be functionalized and/or recycled via hydrolysis by microbial cutinases. The rate of hydrolysis is however low. Here, we tested whether hydrophobins (HFBs), small secreted fungal proteins containing eight positionally conserved cysteine residues, are able to enhance the rate of enzymatic hydrolysis of PET. Species of the fungal genus Trichoderma have the most proliferated arsenal of class II hydrophobin-encoding genes among fungi. To this end, we studied two novel class II HFBs (HFB4 and HFB7) of Trichoderma. HFB4 and HFB7, produced in Escherichia coli as fusions to the C terminus of glutathione S-transferase, exhibited subtle structural differences reflected in hydrophobicity plots that correlated with unequal hydrophobicity and hydrophily, respectively, of particular amino acid residues. Both proteins exhibited a dosage-dependent stimulation effect on PET hydrolysis by cutinase from Humicola insolens, with HFB4 displaying an adsorption isotherm-like behavior, whereas HFB7 was active only at very low concentrations and was inhibitory at higher concentrations. We conclude that class II HFBs can stimulate the activity of cutinases on PET, but individual HFBs can display different properties. The present findings suggest that hydrophobins can be used in the enzymatic hydrolysis of aromatic-aliphatic polyesters such as PET.
Biodegradation of 2-Ethylhexyl Nitrate by Mycobacterium austroafricanum IFP 2173

ABSTRACT 2-Ethyhexyl nitrate (2-EHN) is a major additive of fuel that is used to increase the cetane number of diesel. Because of its wide use and possible accidental release, 2-EHN is a potential pollutant of the environment. In this study, Mycobacterium austroafricanum IFP 2173 was selected from among several strains as the best 2-EHN degrader. The 2-EHN biodegradation rate was increased in biphasic cultures where the hydrocarbon was dissolved in an inert non-aqueous-phase liquid, suggesting that the transfer of the hydrophobic substrate to the cells was a growth-limiting factor. Carbon balance calculation, as well as organic-carbon measurement, indicated a release of metabolites in the culture medium. Further analysis by gas chromatography revealed that a single metabolite accumulated during growth. This metabolite had a molecular mass of 114 Da as determined by gas chromatography/mass spectrometry and was provisionally identified as 4-ethyldihydrofuran-2(3H)-one by liquid chromatography-tandem mass spectrometry analysis. Identification was confirmed by analysis of the chemically synthesized lactone. Based on these results, a plausible catabolic pathway is proposed whereby 2-EHN is converted to 4-ethyldihydrofuran-2(3H)-one, which cannot be metabolized further by strain IFP 2173. This putative pathway provides an explanation for the low energetic efficiency of 2-EHN degradation and its poor biodegradability.
Fuzzy impedance control for robots in complex spatial edge following

In automating manufacturing process of aircraft wings, one of the most difficult tasks is to apply sealant onto its edge surfaces. This is mainly due to the fact that the wing edge surfaces are in complex spatial forms. If a robot is to be employed to perform such a task, position control alone for robots will not be sufficient. A passive or active force control strategy has to be employed. In this paper a fuzzy logic based impedance control algorithm is introduced for this application. The performance of this fuzzy impedance control is compared with that of the neural impedance and conventional impedance control. Simulation results are used to show the effectiveness of using such a fuzzy impedance controller.
A Novel Bacillus thuringiensis Cry-Like Protein from a Rare Filamentous Strain Promotes Crystal Localization within the Exosporium

ABSTRACT Mutation of a novel cry-like gene (cry256) from Bacillus thuringiensis resulted in a protein crystal, normally located within the spore's exosporium, being found predominately outside the exosporium. The cry256 gene codes for a 3-domain Cry-like protein that does not correspond to any of the known Cry protein holotypes.
Death Becomes Them: Bacterial Community Dynamics and Stilbene Antibiotic Production in Cadavers of Galleria mellonella Killed by Heterorhabditis and Photorhabdus spp

ABSTRACT Insect larvae killed by entomopathogenic nematodes are thought to contain bacterial communities dominated by a single bacterial genus, that of the nematode's bacterial symbiont. In this study, we used next-generation sequencing to profile bacterial community dynamics in greater wax moth (Galleria mellonella) larvae cadavers killed by Heterorhabditis nematodes and their Photorhabdus symbionts. We found that, although Photorhabdus strains did initially displace an Enterococcus-dominated community present in uninfected G. mellonella insect larvae, the cadaver community was not static. Twelve days postinfection, Photorhabdus shared the cadaver with Stenotrophomonas species. Consistent with this result, Stenotrophomonas strains isolated from infected cadavers were resistant to Photorhabdus-mediated toxicity in solid coculture assays. We isolated and characterized a Photorhabdus-produced antibiotic from G. mellonella cadavers, produced it synthetically, and demonstrated that both the natural and synthetic compounds decreased G. mellonella-associated Enterococcus growth, but not Stenotrophomonas growth, in vitro. Finally, we showed that the Stenotrophomonas strains described here negatively affected Photorhabdus growth in vitro. Our results add an important dimension to a broader understanding of Heterorhabditis-Photorhabdus biology and also demonstrate that interspecific bacterial competition likely characterizes even a theoretically monoxenic environment, such as a Heterorhabditis-Photorhabdus-parasitized insect cadaver. IMPORTANCE Understanding, and eventually manipulating, both human and environmental health depends on a complete accounting of the forces that act on and shape microbial communities. One of these underlying forces is hypothesized to be resource competition. A resource that has received little attention in the general microbiological literature, but likely has ecological and evolutionary importance, is dead/decaying multicellular organisms. Metazoan cadavers, including those of insects, are ephemeral and nutrient-rich environments, where resource competition might shape interspecific macrobiotic and microbiotic interactions. This study is the first to use a next-generation sequencing approach to study the community dynamics of bacteria within a model insect cadaver system: insect larvae parasitized by entomopathogenic nematodes and their bacterial symbionts. By integrating bioinformatic, biochemical, and classic in vitro microbiological approaches, we have provided mechanistic insight into how antibiotic-mediated bacterial interactions may shape community dynamics within insect cadavers.
Pathogenic Enteric Viruses and Microbial Indicators during Secondary Treatment of Municipal Wastewater

ABSTRACT Pathogenic enteric viruses are responsible for a wide range of infections in humans, with diverse symptoms. Raw and partially treated wastewaters are major sources of environmental contamination with enteric viruses. We monitored a municipal secondary wastewater treatment plant (New Orleans, LA) on a monthly basis for norovirus (NoV) GI and GII and enterovirus serotypes using multiplex reverse transcription-quantitative PCR (RT-qPCR) and microbial indicators of fecal contamination using standard plating methods. Densities of indicator bacteria (enterococci, fecal coliforms, and Escherichia coli) did not show monthly or seasonal patterns. Norovirus GII was more abundant than GI and, along with enterovirus serotypes, increased in influent during fall and spring. The highest NoV GI density in influent was in the fall, reaching an average of 4.0 log10 genomic copies/100 ml. Norovirus GI removal (0.95 log10) was lower than that for GII, enterovirus serotypes, and male-specific coliphages (1.48 log10) or for indicator bacteria (4.36 log10), suggesting higher resistance of viruses to treatment. Male-specific coliphages correlated with NoV GII densities in influent and effluent (r = 0.48 and 0.76, respectively) and monthly removal, indicating that male-specific coliphages can be more reliable than indicator bacteria to monitor norovirus GII load and microbial removal. Dominant norovirus genotypes were classified into three GI genotypes (GI.1, GI.3, and GI.4) and four GII genotypes (GII.3, GII.4, GII.13, and GII.21), dominated by GI.1 and GII.4 strains. Some of the seasonal and temporal patterns we observed in the pathogenic enteric viruses were different from those of epidemiological observations.