Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethylene Synthesis and Regulated Expression of Recombinant Protein in Synechocystis sp. PCC 6803

The ethylene-forming enzyme (EFE) from Pseudomonas syringae catalyzes the synthesis of ethylene which can be easily detected in the headspace of closed cultures. A synthetic codon-optimized gene encoding N-terminal His-tagged EFE (EFEh) was expressed in Synechocystis sp. PCC 6803 (Synechocystis) and Escherichia coli (E. coli) under the control of diverse promoters in a self-replicating broad host-range plasmid. Ethylene synthesis was stably maintained in both organisms in contrast to earlier work in Synechococcus elongatus PCC 7942. The rate of ethylene accumulation was used as a reporter for protein expression in order to assess promoter strength and inducibility with the different expression systems. Several metal-inducible cyanobacterial promoters did not function in E. coli but were well-regulated in cyanobacteria, albeit at a low level of expression. The E. coli promoter Ptrc resulted in constitutive expression in cyanobacteria regardless of whether IPTG was added or not. In contrast, a Lac promoter variant, PA1lacO-1, induced EFE-expression in Synechocystis at a level of expression as high as the Trc promoter and allowed a fine level of IPTG-dependent regulation of protein-expression. The regulation was tight at low cell density and became more relaxed in more dense cultures. A synthetic quorum-sensing promoter system was also constructed and shown to function well in E. coli, however, only a very low level of EFE-activity was observed in Synechocystis, independent of cell density.
An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding1

Premise of the study: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. Methods: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms. We used this reference library, along with the existing bioinformatics pipeline and ITS2 reference library, to identify species in an artificial mixture of nine species of pollen. We have made this database publicly available in multiple formats, to allow use with multiple bioinformatics pipelines, now and in the future. Results: Using the rbcL database, in addition to the ITS2 database, we succeeded in making species-level identifications for eight species and a family-level identification of the ninth species. This is an improvement on ITS2 sequence alone. Discussion: The reference library described here will assist with identification of plant species using rbcL. By making another gene region available for standard barcoding, this will increase the resolution and accuracy of identifications.
Situational Awareness and Health Protective Responses to Pandemic Influenza A (H1N1) in Hong Kong: A Cross-Sectional Study

Background Whether information sources influence health protective behaviours during influenza pandemics or other emerging infectious disease epidemics is uncertain. Methodology Data from cross-sectional telephone interviews of 1,001 Hong Kong adults in June, 2009 were tested against theory and data-derived hypothesized associations between trust in (formal/informal) information, understanding, self-efficacy, perceived susceptibility and worry, and hand hygiene and social distancing using Structural Equation Modelling with multigroup comparisons. Principal Findings Trust in formal (government/media) information about influenza was associated with greater reported understanding of A/H1N1 cause (β = 0.36) and A/H1N1 prevention self-efficacy (β = 0.25), which in turn were associated with more hand hygiene (β = 0.19 and β = 0.23, respectively). Trust in informal (interpersonal) information was negatively associated with perceived personal A/H1N1 susceptibility (β = −0.21), which was negatively associated with perceived self-efficacy (β = −0.42) but positively associated with influenza worry (β = 0.44). Trust in informal information was positively associated with influenza worry (β = 0.16) which was in turn associated with greater social distancing (β = 0.36). Multigroup comparisons showed gender differences regarding paths from trust in formal information to understanding of A/H1N1 cause, trust in informal information to understanding of A/H1N1 cause, and understanding of A/H1N1 cause to perceived self-efficacy. Conclusions/Significance Trust in government/media information was more strongly associated with greater self-efficacy and handwashing, whereas trust in informal information was strongly associated with perceived health threat and avoidance behaviour. Risk communication should consider the effect of gender differences.
Electronic consumer interaction, technology-enabled encroachment, and channel power: the changing balance between manufacturers electronic distribution and established retailers

In a wide range of industries alternative electronic distribution channels may permit disintermediation of wholesalers and of retailers. In some cases manufacturers or primary service deliverers may be able to deal directly with their customers, while in other industries existing intermediaries may be able to withstand attempts to bypass them. Two illustrated industries, consumer packaged goods and air travel, are compared. We conclude that consumer packaged goods retailers may for a variety of reasons find it difficult to disintermediate major retailers; alternative competitive strategies for retailers are examined through simulation models.
Hyaluronic-Based Antibacterial Hydrogel Coating for Implantable Biomaterials in Orthopedics and Trauma: From Basic Research to Clinical Applications

Bacterial colonization of implanted biomaterials remains one of the most challenging complications in orthopedics and trauma surgery, with extremely high social and economic costs. Antibacterial coating of implants has been advocated by many experts as a possible solution to reduce the burden of implant-related infection and several different solutions have been proposed in the last decades. However, while most of the investigated technologies have shown their efficacy in vitro and/or in vivo, only few were able to reach the market, due to clinical, industrial, economic and regulatory issues. Hyaluronic acid composites have been previously shown to possess antifouling capabilities and have been used in various clinical settings to reduce bacterial adhesion and mitigate biofilm-related infections. Recently, a fast-resorbable, hyaluronic-based hydrogel coating was developed to protect implanted biomaterials in orthopedics, trauma and maxillofacial surgery. Preclinical and clinical testing did show the safety and efficacy of the device that can be intraoperatively loaded with one or more antibiotics and directly applied by the surgeon to the implant surface, at the time of surgery. Here, we review the current evidence concerning this very first antibacterial coating of implants and outline the economic impact of the possible large-scale application of this technology.
Noninvasive Diagnosis of Hepatic Fibrosis in HIV/HCV-Coinfected Patients

Background: Several serum markers reflecting extracellular matrix status have been correlated with liver fibrosis in non-HIV-infected patients with chronic hepatitis C infection. These indexes have been less examined in HIV/HCV-coinfected individuals. Objective: We aimed to evaluate the predictive value of serum markers for liver fibrosis in HIV-infected patients with chronic hepatitis C virus (HVC). Methods: Serum levels of metalloproteinases 1 and 2 (MMP-1 and -2), tissue inhibitors of matrix metalloproteinases (TIMP-1), procollagen type III N-terminal peptide (PIIINP), and hyaluronic acid (HA) were measured in HIV-infected patients with chronic hepatitis C at the time of obtaining a liver biopsy and before the consideration of anti-hepatitis C therapy. Results: One hundred and nineteen consecutive HIV-HVC coinfected patients were included. TIMP-1 (r = 0.6; P < 0.001), TIMP-1/MMP-1 ratio (r = 0.5; P < 0.001), TIMP-1/MMP-2 ratio (r = 0.3; P < 0.001), MMP-2 (r = 0.2; P = 0.044), PIIINP (r = 0.4; P < 0.001), and HA (r = 0.5; P < 0.001) were positively and significantly correlated with the fibrosis stage. In the multivariate analysis, TIMP-1 (odds ratio [OR] = 1.004, 95% confidence interval [CI]: 1.002 to 1.006, P = 0.001) and HA >95 μg/dL (OR = 6.041, 95% CI: 1.184 to 30.816, P = 0.031) were independently associated with liver fibrosis. The area under the curve of score to discriminate mild (F0-F1) from significant (F2-F4) fibrosis in the received-operating analysis using the variables TIMP-1 and HA was 0.84, with a sensitivity of 72.9% and a specificity of 83.1%. Conclusion: TIMP-1 and HA were quite sensitive and specific for predicting the degree of liver fibrosis in HIV-infected patients with chronic hepatitis C. These parameters may become a noninvasive alternative to liver biopsy when the degree of liver fibrosis needs to be estimated.
Despeckling of TerraSAR-X Data Using Second-Generation Wavelets

This letter presents the despeckling of synthetic aperture radar (SAR) images within the bandelet and contourlet domains. A model-based approach is presented for the despeckling of SAR images. The speckle-reduced estimate is found using the first-order Bayesian inference, and the best model's parameters are estimated using the second-order Bayesian inference. Synthetic and real images are used for evaluating the qualities of the despeckling methods. The experimental results showed that the combination of Bayesian inference and bandelet transform outperforms the contourlet-based despeckling algorithm using synthetic data and objective measurements.
In vitro evaluation of endotracheal tubes with intrinsic suction.

BACKGROUND Endotracheal tube (ETT) intubation impairs mucus clearance, which can lead to respiratory compromise. We compared three ETTs that have intrinsic capacity to aspirate secretions pooling above the cuff. METHODS We evaluated the ability of three ETTs with suction, Hi-Lo Evac, Teleflex ISIS, and Portex Blue Line SACETT, to aspirate saliva and mucus simulants at continuous or intermittent vacuum pressures. We also evaluated the potential for a flexible tracheal membrane to obstruct the ETT suction port with applied vacuum. We measured the dimensions of the suction tubing at critical points to calculate differences in flow. RESULTS In a rigid tracheal model, the ISIS aspirated saliva simulant more quickly with continuous low pressure suction than Evac (P = .0006) and SACETT (P < .0001) as well as with intermittent high pressure suction (P < .0001). For mucus simulant, the ISIS aspirated stimulant better than the other ETTs at high intermittent suction (P < .0001); the Evac was more effective than the SACETT (P = .0019). For low and continuous suction, suction ports in all ETTs occluded with mucus, except for ISIS, at the highest continuous suction tested. In a trachea model with a flexible posterior membrane, this membrane either partially or completely occluded the suction port of all tubes at high continuous or intermittent suction. The ISIS was more prone to obstruction by the flexible membrane than the Evac. We found large differences in suction tubing cross-sectional area between the ISIS and the other tubes, and flow calculations using the Hagen-Poiseuille equation can explain the observed differences in volumes aspirated and tendency toward lumen obstruction. CONCLUSIONS The ISIS transmits suction pressure to the tube orifice more powerfully than the Evac and SACETT. This feature makes the ISIS less prone to obstruction by mucus but more likely to obstruct by tissue suction.
Using partial differential equations to model TCP mice and elephants in large IP networks

Fluid models of IP networks have been recently proposed as a way to break the scalability barrier of traditional discrete state-space models, both simulative (e.g., ns-2) and analytical (e.g., queues and Markov chains). Fluid models adopt an abstract deterministic description of the average network dynamics through a set of ordinary differential equations that are then solved numerically, obtaining estimates of the time-dependent network behavior. However, an important limit of the fluid model approaches presented so far in the literature is their unnatural representation of scenarios comprising the short-lived TCP flows that dominate in today's Internet. In this paper we propose a new fluid model approach in which a different description of the dynamics of traffic sources is adopted, exploiting partial differential equations. This new description of the source dynamics allows the natural representation of short-lived as well as long-lived TCP connections, with little sacrifice in the scalability of the model. In addition, the use of partial differential equations permits the description of distributions, instead of averages, thus providing better accuracy in the results. The comparison between the performance estimates obtained with fluid models and with ns simulations proves the accuracy of the proposed modeling approach.
Pre-targeted radioimmunotherapy of human colon cancer xenografts in athymic mice using streptavidin-CC49 monoclonal antibody and 90Y-DOTA-biotin

Radioimmunotherapy of solid malignancies using directly labelled 90Y-monoclonal antibodies has been associated in clinical trials with dose-limiting bone marrow toxicity. Our objective in this study was to evaluate the efficacy and toxicity of an alternative two-step pre-targeted radioimmunotherapy protocol for the treatment of human colon cancer. The two-step protocol consisted of administration of the tumour-associated glycoprotein (TAG-72) monoclonal antibody CC49 conjugated to streptavidin, followed by administration of 90Y-DOTA-biotin. Swiss nu/nu athymic mice bearing subcutaneous LS174T human colon cancer xenografts were injected intraperitoneally with streptavidin-CC49 (250 μg), followed 40 h later by an intravenous injection of 90Y-DOTA-biotin (900 μCi, 40 μg). Tumour growth was measured over 25 days and compared with that in control mice receiving no treatment. Bone marrow and normal tissue toxicity was determined by peripheral blood leucocyte counts and by monitoring the body weight of the animals. Pre-targeted radioimmunotherapy resulted in a modest (30-40%) decrease in the mean tumour growth rate in treated mice compared to control animals. There was no change in body weight following treatment and peripheral blood leucocyte counts remained within the normal range. Pre-targeted radioimmunotherapy was safe at administered amounts of 90Y radioactivity, which were at least nine-fold higher than those previously determined to be lethal using directly labelled 90Y-monoclonal antibodies. The results of this study are promising for the application of pre-targeted radioimmunotherapy using streptavidin-CC49 and 90Y-DOTA-biotin for the treatment of advanced colorectal cancer in humans.
Improve Glioblastoma Multiforme Prognosis Prediction by Using Feature Selection and Multiple Kernel Learning

Glioblastoma multiforme (GBM) is a highly aggressive type of brain cancer with very low median survival. In order to predict the patient's prognosis, researchers have proposed rules to classify different glioma cancer cell subtypes. However, survival time of different subtypes of GBM is often various due to different individual basis. Recent development in gene testing has evolved classic subtype rules to more specific classification rules based on single biomolecular features. These classification methods are proven to perform better than traditional simple rules in GBM prognosis prediction. However, the real power behind the massive data is still under covered. We believe a combined prediction model based on more than one data type could perform better, which will contribute further to clinical treatment of GBM. The Cancer Genome Atlas (TCGA) database provides huge dataset with various data types of many cancers that enables us to inspect this aggressive cancer in a new way. In this research, we have improved GBM prognosis prediction accuracy further by taking advantage of the minimum redundancy feature selection method (mRMR) and Multiple Kernel Machine (MKL) learning method. Our goal is to establish an integrated model which could predict GBM prognosis with high accuracy.
Lung Cancer: Understanding Its Molecular Pathology and the 2015 WHO Classification

Lung cancer is the leading cause of cancer-related death worldwide due to late diagnoses and limited treatment interventions. Recently, comprehensive molecular profiles of lung cancer have been identified. These novel characteristics have enhanced the understanding of the molecular pathology of lung cancer. The identification of driver genetic alterations and potential molecular targets has resulted in molecular-targeted therapies for an increasing number of lung cancer patients. Thus, the histopathological classification of lung cancer was modified in accordance with the increased understanding of molecular profiles. This review focuses on recent developments in the molecular profiling of lung cancer and provides perspectives on updated diagnostic concepts in the new 2015 WHO classification. The WHO classification will require additional revisions to allow for reliable, clinically meaningful tumor diagnoses as we gain a better understanding of the molecular characteristics of lung cancer.
Metabolic Versatility and Antibacterial Metabolite Biosynthesis Are Distinguishing Genomic Features of the Fire Blight Antagonist Pantoea vagans C9-1

Background Pantoea vagans is a commercialized biological control agent used against the pome fruit bacterial disease fire blight, caused by Erwinia amylovora. Compared to other biocontrol agents, relatively little is currently known regarding Pantoea genetics. Better understanding of antagonist mechanisms of action and ecological fitness is critical to improving efficacy. Principal Findings Genome analysis indicated two major factors contribute to biocontrol activity: competition for limiting substrates and antibacterial metabolite production. Pathways for utilization of a broad diversity of sugars and acquisition of iron were identified. Metabolism of sorbitol by P. vagans C9-1 may be a major metabolic feature in biocontrol of fire blight. Biosynthetic genes for the antibacterial peptide pantocin A were found on a chromosomal 28-kb genomic island, and for dapdiamide E on the plasmid pPag2. There was no evidence of potential virulence factors that could enable an animal or phytopathogenic lifestyle and no indication of any genetic-based biosafety risk in the antagonist. Conclusions Identifying key determinants contributing to disease suppression allows the development of procedures to follow their expression in planta and the genome sequence contributes to rationale risk assessment regarding the use of the biocontrol strain in agricultural systems.
Changes in Cross-Fostered Sprague-Dawley Rat Litters Exposed to Perchlorate

Ammonium perchlorate is used as an oxidizer in rocket fuel. It has become a groundwater contaminant, dissociating to ammonium cation and perchlorate anion. The perchlorate ion competes with iodide for uptake into the thyroid, reducing thyroid hormone production. Pregnant Sprague-Dawley rats were given either untreated or perchlorate (1 mg/kg-day) treated drinking water beginning on gestation day 2. One set of control and exposed dams was sacrificed on gestation day 20. The litters from the second set of control and exposed dams were crossed immediately after parturition and were sacrificed at postnatal day 10. Dam serum and thyroid, pooled fetal sera, and male and female pup sera were collected and analyzed for perchlorate, thyroid-stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4). Control pups receiving perchlorate through lactation had serum levels at postnatal day 10 of 0.54 μg/ml and 0.56 μg/ml for male and female pups, respectively, whereas exposed fetuses had serum perchlorate levels of 0.38 ± 0.04 μg/ml. Female pups receiving perchlorate lactationally had significantly lower levels of serum T4 than control pups and prenatally exposed pups. Serum T4 levels in male pups were not affected by perchlorate. Serum thyroid hormone levels from gestational perchlorate exposure were restored to control values by postnatal day 10. In utero perchlorate-exposure decreased serum T4 levels in the fetus. Gestational studies in conjunction with a crossfostering study design helped discern thyroid hormonal changes caused by perchlorate exposure during the perinatal period.
Probing structures in channel flow through SO(3) and SO(2) decomposition

SO(3) and SO(2) decompositions of numerical channel flow turbulence are performed. The decompositions are used to probe, characterize, and quantify anisotropic structures in the flow. Close to the wall, the anisotropic modes are dominant and reveal the flow structures. The dominance of the (j, m) = (2, 1) mode of the SO(3) decomposition in the buffer layer is associated with hairpin vortices. The SO(2) decomposition in planes parallel to the walls allows us also to access the regions very close to the wall. In those regions we have found that the strong enhancement of intermittency can be explained in terms of streaklike structures and their signatures in the m = 2 and m = 4 modes of the SO(2) decomposition.
Performance analysis of the FastICA algorithm and Crame/spl acute/r-rao bounds for linear independent component analysis

The FastICA or fixed-point algorithm is one of the most successful algorithms for linear independent component analysis (ICA) in terms of accuracy and computational complexity. Two versions of the algorithm are available in literature and software: a one-unit (deflation) algorithm and a symmetric algorithm. The main result of this paper are analytic closed-form expressions that characterize the separating ability of both versions of the algorithm in a local sense, assuming a "good" initialization of the algorithms and long data records. Based on the analysis, it is possible to combine the advantages of the symmetric and one-unit version algorithms and predict their performance. To validate the analysis, a simple check of saddle points of the cost function is proposed that allows to find a global minimum of the cost function in almost 100% simulation runs. Second, the Crame/spl acute/r-Rao lower bound for linear ICA is derived as an algorithm independent limit of the achievable separation quality. The FastICA algorithm is shown to approach this limit in certain scenarios. Extensive computer simulations supporting the theoretical findings are included.
Physics at BES-III

This physics book provides detailed discussions on important topics in $\tau$-charm physics that will be explored during the next few years at \bes3 . Both theoretical and experimental issues are covered, including extensive reviews of recent theoretical developments and experimental techniques. Among the subjects covered are: innovations in Partial Wave Analysis (PWA), theoretical and experimental techniques for Dalitz-plot analyses, analysis tools to extract absolute branching fractions and measurements of decay constants, form factors, and CP-violation and \DzDzb-oscillation parameters. Programs of QCD studies and near-threshold tau-lepton physics measurements are also discussed.