Biodegradation of mixed wastes : basic kinetics and reaction engineering for cyclic reactor operation

This study dealt with the determination of the detailed kinetics of the biodegradation of mixed substrates by pure cultures, and with reaction engineering studies of bioreactors employed in treatment of substitutable substrates under cyclic operation. In the first part of the study the degradation of phenol and 4-chlorophenol (4-CP) by two strains of Pseudomonas species was investigated. Strain P. putida 0 was found to be capable of utilizing both phenol and 4-CP as sole carbon and energy sources. This suggests that this strain follows the ortho-cleavage pathway for the aromatic ring. Strain P. putida N could grow on phenol, and in its presence, could transform 4-CP to intermediates which are long-lived and do not serve as carbon and/or energy sources for the culture. These results suggest that P. putida N follows the meta-cleavage pathway for the aromatic ring. The second part of the study dealt with the kinetics of glucose and phenol utilization by a pure culture of P. putida OR. It was found that the two substrates could serve as carbon and energy sources for the culture. The two substrates were used simultaneously, but were involved in a cross-inhibitory uncompetitive kinetic interaction. Inhibition from glucose on phenol removal was stronger. The kinetics were described by detailed mathematical expressions. Based on the kinetic expressions obtained in the second part of the study, a detailed model describing biodegradation of phenol/glucose mixtures in a continuously operated cyclic reactor was derived. The dynamics of the system were studied numerically with computer codes based on the bifurcation theory for forced systems. The results, presented in the form of two-dimensional operating diagrams, show that there are regions in the parameter space where multistability occurs. The theoretical predictions were tested in experiments with a fully automated laboratory-scale unit. The experimental data validated the theoretical predictions. The quantitative agreement between theory and experiments was excellent. The experimentally validated model can be used in design and process optimization studies

Fast subcellular localization by cascaded fusion of signal-based and homology-based methods

<p>Abstract</p> <p>Background</p> <p>The functions of proteins are closely related to their subcellular locations. In the post-genomics era, the amount of gene and protein data grows exponentially, which necessitates the prediction of subcellular localization by computational means.</p> <p>Results</p> <p>This paper proposes mitigating the computation burden of alignment-based approaches to subcellular localization prediction by a cascaded fusion of cleavage site prediction and profile alignment. Specifically, the informative segments of protein sequences are identified by a cleavage site predictor using the information in their N-terminal shorting signals. Then, the sequences are truncated at the cleavage site positions, and the shortened sequences are passed to PSI-BLAST for computing their profiles. Subcellular localization are subsequently predicted by a profile-to-profile alignment support-vector-machine (SVM) classifier. To further reduce the training and recognition time of the classifier, the SVM classifier is replaced by a new kernel method based on the perturbational discriminant analysis (PDA).</p> <p>Conclusions</p> <p>Experimental results on a new dataset based on Swiss-Prot Release 57.5 show that the method can make use of the best property of signal- and homology-based approaches and can attain an accuracy comparable to that achieved by using full-length sequences. Analysis of profile-alignment score matrices suggest that both profile creation time and profile alignment time can be reduced without significant reduction in subcellular localization accuracy. It was found that PDA enjoys a short training time as compared to the conventional SVM. We advocate that the method will be important for biologists to conduct large-scale protein annotation or for bioinformaticians to perform preliminary investigations on new algorithms that involve pairwise alignments.</p

High and Increasing Oxa-51 DNA Load Predict Mortality in Acinetobacter baumannii Bacteremia: Implication for Pathogenesis and Evaluation of Therapy

BACKGROUND: While quantification of viral loads has been successfully employed in clinical medicine and has provided valuable insights and useful markers for several viral diseases, the potential of measuring bacterial DNA load to predict outcome or monitor therapeutic responses remains largely unexplored. We tested this possibility by investigating bacterial loads in Acinetobacter baumannii bacteremia, a rapidly increasing nosocomial infection characterized by high mortality, drug resistance, multiple and complicated risk factors, all of which urged the need of good markers to evaluate therapeutics. METHODS AND FINDINGS: We established a quantitative real-time PCR assay based on an A. baumannii-specific gene, Oxa-51, and conducted a prospective study to examine A. baumannii loads in 318 sequential blood samples from 51 adults patients (17 survivors, 34 nonsurvivors) with culture-proven A. baumannii bacteremia in the intensive care units. Oxa-51 DNA loads were significantly higher in the nonsurvivors than survivors on day 1, 2 and 3 (P=0.03, 0.001 and 0.006, respectively). Compared with survivors, nonsurvivors had higher maximum Oxa-51 DNA load and a trend of increase from day 0 to day 3 (P<0.001), which together with Pitt bacteremia score were independent predictors for mortality by multivariate analysis (P=0.014 and 0.016, for maximum Oxa-51 DNA and change of Oxa-51 DNA, respectively). Kaplan-Meier analysis revealed significantly different survival curves in patients with different maximum Oxa-51 DNA and change of Oxa-51 DNA from day 0 to day 3. CONCLUSIONS: High Oxa-51 DNA load and its initial increase could predict mortality. Moreover, monitoring Oxa-51 DNA load in blood may provide direct parameters for evaluating new regimens against A. baumannii in future clinical studies

STAR: Boosting Low-Resource Event Extraction by Structure-to-Text Data Generation with Large Language Models

Structure prediction tasks such as event extraction require an in-depth understanding of the output structure and sub-task dependencies, thus they still heavily rely on task-specific training data to obtain reasonable performance. Due to the high cost of human annotation, low-resource event extraction, which requires minimal human cost, is urgently needed in real-world information extraction applications. We propose to synthesize data instances given limited seed demonstrations to boost low-resource event extraction performance. We propose STAR, a structure-to-text data generation method that first generates complicated event structures (Y) and then generates input passages (X), all with Large Language Models. We design fine-grained step-by-step instructions and the error cases and quality issues identified through self-reflection can be self-refined. Our experiments indicate that data generated by STAR can significantly improve the low-resource event extraction performance and they are even more effective than human-curated data points in some cases

Asic3−/− Female Mice with Hearing Deficit Affects Social Development of Pups

BACKGROUND: Infant crying is an important cue for mothers to respond adequately. Inappropriate response to infant crying can hinder social development in infants. In rodents, the pup-mother interaction largely depends on pup's calls. Mouse pups emit high frequency to ultrasonic vocalization (2-90 kHz) to communicate with their dam for maternal care. However, little is known about how the maternal response to infant crying or pup calls affects social development over the long term. METHODOLOGY/PRINCIPAL FINDINGS: Here we used mice lacking acid-sensing ion channel 3 (Asic3(-/-)) to create a hearing deficit to probe the effect of caregiver hearing on maternal care and adolescent social development. Female Asic3(-/-) mice showed elevated hearing thresholds for low to ultrasonic frequency (4-32 kHz) on auditory brain stem response, which thus hindered their response to their pups' wriggling calls and ultrasonic vocalization, as well as their retrieval of pups. In adolescence, pups reared by Asic3(-/-) mice showed a social deficit in juvenile social behaviors as compared with those reared by wild-type or heterozygous dams. The social-deficit phenotype in juvenile mice reared by Asic3(-/-) mice was associated with the reduced serotonin transmission of the brain. However, Asic3(-/-) pups cross-fostered to wild-type dams showed rescued social deficit. CONCLUSIONS/SIGNIFICANCE: Inadequate response to pups' calls as a result of ASIC3-dependent hearing loss confers maternal deficits in caregivers and social development deficits in their young

A Large Volume Multi-Anvil Apparatus for the Earth Sciences Community in Taiwan

A modified DIA type multi-anvil apparatus was installed in the Department of Earth Sciences, National Cheng Kung University, Taiwan. This modified DIA multi-anvil system is used with a hydraulic press that generates loads of up to 1000 tons and is the first multi-anvil press installed for geoscience research in Taiwan. In this paper, the geometry of the high-pressure apparatus is briefly described and the pressure calibration performed in the press is reported. The thermal behaviors of various pressure mediums, boron-epoxy, zirconia, and mullite, are also compared. Pressure calibrations at room temperature were performed with different cell designs, paying special attention to the so called ¡§D¡¨ factor, which is defined as the ratio of diagonal length of the cell assembly cube to the diameter of the cavity hole. For a given cell design, the sample-pressure efficiency for the three materials examined was similar. Calibrations with different cell designs showed that increasing the ¡§D¡¨ value results in greater pressure generation efficiency. By comparing the deformation behavior at high temperatures (up to 1200°C), the semi-sintered mullite and zirconia appeared to be better pressure mediums compared to boron-epoxy

Strategically examining the full-genome of dengue virus type 3 in clinical isolates reveals its mutation spectra

BACKGROUND: Previous studies presented the quasispecies spectrum of the envelope region of dengue virus type 3 (DENV-3) from either clinical specimens or field-caught mosquitoes. However, the extent of sequence variation among full genomic sequences of DENV within infected individuals remains largely unknown. RESULTS: Instead of arbitrarily choosing one genomic region in this study, the full genomic consensus sequences of six DENV-3 isolates were used to locate four genomic regions that had a higher potential of sequence heterogeneity at capsid-premembrane (C-prM), envelope (E), nonstructural protein 3 (NS3), and NS5. The extentof sequence heterogeneity revealed by clonal sequencing was genomic region-dependent, whereas the NS3 and NS5 had lower sequence heterogeneity than C-prM and E. Interestingly, the Phylogenetic Analysis by Maximum Likelihood program (PAML) analysis supported that the domain III of E region, the most heterogeneous region analyzed, was under the influence of positive selection. CONCLUSION: This study confirmed previous reports that the most heterogeneous region of the dengue viral genome resided at the envelope region, of which the domain III was under positive selection pressure. Further studies will need to address the influence of these mutations on the overall fitness in different hosts (i.e., mosquito and human) during dengue viral transmission

Phyllanthus urinaria Induces Apoptosis in Human Osteosarcoma 143B Cells via Activation of Fas/FasL- and Mitochondria-Mediated Pathways

Phyllanthus urinaria (P. urinaria), in this study, was used for the treatment of human osteosarcoma cells, which is one of the tough malignancies with few therapeutic modalities. Herein, we demonstrated that P. urinaria inhibited human osteosarcoma 143B cells growth through an apoptotic extrinsic pathway to activate Fas receptor/ligand expression. Both intracellular and mitochondrial reactive oxygen species were increased to lead to alterations of mitochondrial membrane permeability and Bcl-2 family including upregulation of Bid, tBid, and Bax and downregulation of Bcl-2. P. urinaria triggered an intrinsic pathway and amplified the caspase cascade to induce apoptosis of 143B cells. However, upregulation of both intracellular and mitochondrial reactive oxygen species and the sequential membrane potential change were less pronounced in the mitochondrial respiratory-defective 143Bρ0 cells compared with the 143B cells. This study offers the evidence that mitochondria are essential for the anticancer mechanism induced by P. urinaria through both extrinsic and intrinsic pathways