Enzymatic hydrolysis of wood: an engineering assessment

Eucalyptus wood samples were delignified with HCl-catalysed acetic acid solutions under selected experimental conditions and treated with NaClO solutions. The solid residues obtained were employed as substrates for enzymatic hydrolysis. The NaClO concentration used in the pretreatment step, the liquor/solid ratio and the enzyme/substrate ratio were considered as operational variables. The experimental data allowed the development of generalized kinetic models which provided the necessary information for design calculations. The operational conditions were compared from an engineering viewpoint on the basis of economic estimates. Optimum conditions were established from these estimates.     

Development of a target component extraction method from GC-MS data with an in-house program for metabolite profiling

After gas chromatography-mass spectrometry (GC-MS) analysis, data processing, including retention time correction, spectral deconvolution, peak alignment, and normalization prior to statistical analysis, is an important step in metabolomics. Several commercial or free software packages have been introduced for data processing, but most of them are vendor dependent. To design a simple method for Agilent GC/MS data processing, we developed an in-house program, "CompExtractor", using Microsoft Visual Basic. We tailored the macro modules of an Agilent Chemstation and implanted them in the program. To verify the performance of CompExtractor processing, 30 samples from the three species of the genus Papaver were analyzed with Agilent 5973 MSD GC-MS. The results of CompExtractor processing were compared with those of AMDIS-SpectConnect processing by hierarchical cluster analysis (HCA) and principal component analysis (PCA). The two methods showed good classification according to their species in HCA. The PC1+PC2 scores were 54.32-63.62% for AMDIS-SpectConnect and 56.65-85.92% for CompExtractor in PCA. Although the CompExtractor processing method is an Agilent GC-MS-specific application and the target compounds must be selected first, it can extract the target compounds more precisely in the raw data file with batch mode and simultaneously assemble the matrix text file.     

Tissue engineering: generation of differentiated artificial tissues for biomedical applications

A new field in biomedical science has been established. Cell biologists, engineers, and surgeons now work within a team. Artificial connective, epithelial, or neuronal tissues are being constructed using living cells and different kinds of biomaterials. Numerous companies and laboratories are presenting dynamic developments in this field. Prognoses predict that, at the beginning of the coming century, the industry of tissue engineering will reach the importance of the present genetic technology. An enormous demand for organ and tissue transplants motivates research activities and drives the acquisition of innovative techniques and creative solutions. At the front of this development is the creation of artificial skin for severely burned patients and the generation of artificial cartilage for implantation in articular joint diseases. Future challenges are the construction of liver organoids and the development of an artificial kidney on the basis of cultured cells. In this paper we show strategies, needs, tools, and equipment for tissue engineering. The presupposition for all projects is the induction, development, and maintenance of differentiation within the tissue under in vitro conditions. As experiments in conventional culture dishes continued to fail, new cell and tissue culture methods had to be developed. Tissues are cultured under conditions as close as possible to their natural environment. To optimize adherence or embedding, cells are grown on novel tissue carriers and on individually selected biomatrices or scaffolds. The tissues are subsequently transferred into different types of containers for permanent perfusion with fresh culture medium. This guarantees constant nutrition of the developing tissue and prevents the accumulation of harmful metabolites. An organo-typical environment for epithelial cells, for example, is obtained in gradient containers, which are permanently superfused at the apical and basal sides with different media. Long term experiments result in cultured tissues in a quality thus far unreached.     

Breaking out of the echo chamber: missed opportunities for genetics at conservation conferences

Genetic approaches have proven useful for addressing various conservation problems, but genetics remains poorly integrated into conservation practice. Multidisciplinary conservation conferences present excellent opportunities for bridging the conservation-genetics gap and facilitating cross-disciplinary projects. We hypothesize that there is a tendency for presentations featuring genetic approaches to be siloed into approach specific sessions, creating an “echo chamber”; geneticists are left talking amongst themselves, hindering collaboration across disciplines. To test this, we reviewed abstracts from the past six Society for Conservation Biology conferences and assessed how presentations featuring genetics/genomics were distributed throughout the respective programs. We found that: the segregation of presentations featuring genetics varied widely between conferences (22–78 %); that no other method or approach was segregated to the same degree; and that the vast majority (99 %) of presentations featuring genetics had broader applications that made them appropriate for other sessions. We argue that segregating genetics at conservation conferences in this way is unhelpful and serves to strengthen the idea that genetics is not relevant to a wider conservation audience. We recommend that; (1) conference organisers endeavour to facilitate the integration of genetics into sessions based on the conservation questions addressed, rather than the methods used to address them; and (2) geneticists make the practical application of their work clear at abstract submission and during presentations. These recommendations are not novel, but our data illustrate a clear need for them to be implemented to better facilitate integration of genetic research that will benefit conservation outcomes.     

Expanding fungal pathogenesis: Cryptococcus breaks out of the opportunistic box

Cryptococcus neoformans is generally considered to be an opportunistic fungal pathogen because of its tendency to infect immunocompromised individuals, particularly those infected with HIV. However, this view has been challenged by the recent discovery of specialized interactions between the fungus and its mammalian hosts, and by the emergence of the related species Cryptococcus gattii as a primary pathogen of immunocompetent populations. In this Review, we highlight features of cryptococcal pathogens that reveal their adaptation to the mammalian environment. These features include not only remarkably sophisticated interactions with phagocytic cells to promote intracellular survival, dissemination to the central nervous system and escape, but also surprising morphological and genomic adaptations such as the formation of polyploid giant cells in the lung.     

Adolescent self harm patients: audit of assessment in an accident and emergency department.

OBJECTIVE--To examine the assessment of adolescent self harm patients attending an accident and emergency department. DESIGN--Retrospective assessment of case notes. SETTING--Accident and emergency department, Leicester Royal Infirmary. PATIENTS--210 adolescent patients (aged 9-19 years) attending the department during 1 January 1989-31 December 1989 after deliberate self poisoning; records were available for 200. MAIN OUTCOME MEASURES--Numbers of admissions, discharges from department without either a psychiatric consultation or some form of follow up, and discharges with either of these; scoring of adequacy of psychiatric and social assessment by accident and emergency doctor. RESULTS--89 patients were admitted (mean score 5.1, excluding 22 patients too drowsy or unforthcoming for proper assessment), 80 were discharged without specific psychiatric consultation or other follow up (mean score 5.4), and 31 were discharged with psychiatric consultation or other follow up (mean score 9.1). The percentage of patients in each group whose assessment by the accident and emergency doctor was considered to be adequate or better than adequate over 10 headings ranged from 0%-40% for admitted patients, 0%-50% for those discharged without psychiatric assessment, and 0%-61% in the remaining group. Overall, in almost half (49%, 54/111) of all of those discharged documentation of the suicidal state was inadequate. CONCLUSION--The assessment of many adolescent self harm patients in this clinic was unsatisfactory. IMPLICATIONS--Doctors working in accident and emergency departments should be encouraged to liaise with child psychiatrists before discharging such patients.     

Design and integration of a problem-based biofabrication course into an undergraduate biomedical engineering curriculum

Background

The rapidly evolving discipline of biological and biomedical engineering requires adaptive instructional approaches that teach students to target and solve multi-pronged and ill-structured problems at the cutting edge of scientific research. Here we present a modular approach to designing a lab-based course in the emerging field of biofabrication and biological design, leading to a final capstone design project that requires students to formulate and test a hypothesis using the scientific method.

Results

Students were assessed on a range of metrics designed to evaluate the format of the course, the efficacy of the format for teaching new topics and concepts, and the depth of the contribution this course made to students training for biological engineering careers. The evaluation showed that the problem-based format of the course was well suited to teaching students how to use the scientific method to investigate and uncover the fundamental biological design rules that govern the field of biofabrication.

Conclusions

We show that this approach is an efficient and effective method of translating emergent scientific principles from the lab bench to the classroom and training the next generation of biological and biomedical engineers for careers as researchers and industry practicians.

     

Infections requiring hospitalization in the abatacept clinical development program: an epidemiological assessment

Introduction  

Patients with rheumatoid arthritis (RA) have an increased risk of infection and this risk appears to be higher with anti-TNF (tumor necrosis factor) agents. We pooled data from the cumulative abatacept RA clinical development program, both double-blind and open-label periods, to estimate the incidence rates (IRs) of infections requiring hospitalization including pneumonia and opportunistic infections, in comparison with RA patients treated with non-biologic disease-modifying antirheumatic drugs (DMARDs) from several reference cohorts.     

A new paradigm for graduate research and training in the biomedical sciences and engineering

98Emphasis on the individual investigator has fostered discovery for centuries, yet it is now recognized that the complexity of problems in the biomedical sciences and engineering requires collaborative efforts from individuals having diverse training and expertise. Various approaches can facilitate interdisciplinary interactions, but we submit that there is a critical need for a new educational paradigm for the way that we train biomedical engineers, life scientists, and mathematicians. We cannot continue to train graduate students in isolation within single disciplines, nor can we ask any one individual to learn all the essentials of biology, engineering, and mathematics. We must transform how students are trained and incorporate how real-world research and development are done-in diverse, interdisciplinary teams. Our fundamental vision is to create an innovative paradigm for graduate research and training that yields a new generation of biomedical engineers, life scientists, and mathematicians that is more diverse and that embraces and actively pursues a truly interdisciplinary, team-based approach to research based on a known benefit and mutual respect. In this paper, we describe our attempt to accomplish this via focused training in biomechanics, biomedical optics, mathematics, mechanobiology, and physiology. The overall approach is applicable, however, to most areas of biomedical research.     

Mitochondrial gene therapy: an arena for the biomedical use of inteins

Mitochondrial DNA (mtDNA) mutations underlie many rare diseases and might also contribute to human ageing. Gene therapy is a tempting future possibility for intervening in mitochondriopathies. Expression of the 13 mtDNA-encoded proteins from nuclear transgenes (allotopic expression) might be the most effective gene-therapy strategy. Its only confirmed difficulty is the extreme hydrophobicity of these proteins, which prevents their import into mitochondria from the cytosol. Inteins (self-splicing 'protein introns') might offer a solution to this problem: their insertion into such transgenes could greatly reduce the encoded proteins' hydrophobicity, enabling import, with post-import excision restoring the natural amino acid sequence.     

Development and application of an in-house reverse hybridization method for Chlamydia trachomatis genotyping

Aim

To develop and evaluate an in‐house reverse hybridization technique for Chlamydia trachomatis genotype identification.

Methods and Results

The evaluation of the developed and optimized reverse hybridization method on reference strains showed the specific detection of all genotypes. This technique showed its ability to type one inclusion‐forming unit of C. trachomatis genotype E and equivalent sensitivity to the Cobas TaqMan assay. It was also able to detect mixed infections in vitro. Application of the reverse hybridization method on 38 isolated C. trachomatis strains and their respective swabs allowed the detection of six urogenital genotypes D, E, F, G, H and K and one trachoma genotype B. Genotype E was the most prevalent, detected in 73% of the swab samples. Mixed infections were detected in 26% of swab cases.

Conclusion

The reverse hybridization technique is simple and does not require specialized instruments. It is powerful in the diagnosis of mixed infections and is suitable for use in epidemiological studies.

Significance and Impact of the Study

This technique allowed rapid C. trachomatis genotype identification.     

Regionalization of agri-food life cycle assessment: a review of studies in Portugal and recommendations for the future

Purpose

One of the main trends in life cycle assessment (LCA) today is towards increased regionalization in inventories and impact assessment methods. LCA studies require the collection of activity data but also of increasingly region-specific background data to accurately depict supply chain processes and enable the application of an increasing number of geographically explicit impact assessment models. This is particularly important for agri-food products. In this review, we assess progress in Portugal towards this goal and provide recommendations for future developments.

Methods

We perform a comprehensive review of available LCA studies conducted for Portuguese agri-food products, in order to evaluate the current state of Portuguese agri-food LCA. Among other issues, we assess availability of data, methods used, level of regionalization, impact assessment model relevance and coherence for inter-product comparability. We also provide conclusions and recommendations based on recent developments in the field.

Results and discussion

We found 22 LCA studies, covering 22 different products. The analysis of these studies reveals limitations in inter-study comparability. The main challenges have to do with a lack of country-specific foreground data sources applied consistently in the studies found, with discrepancies in impact assessment categories, and with the use of simple functional units that may misrepresent the product analyzed.

Conclusions

We conclude that Portuguese agri-food LCA studies do not have a systematic and country-scale approach in order to guarantee regional accuracy and comparability. We propose a research strategy to engage the Portuguese agri-food LCA community in devising a consistent framework before practical application studies are conducted.

     

Clinical and pharmacogenomic data mining: 4. The FANO program and command set as an example of tools for biomedical discovery and evidence based medicine

The culmination of methodology explored and developed in the preceding three papers is described in terms of the FANO program (also known as CliniMiner) and specifically in terms of the contemporary command set for data mining. This provides a more detailed account of how strategies were implemented in applications described elsewhere, in the previous papers in the series and in a paper on the analysis of 667 000 patient records. Although it is not customary to think of a command set as the output of research, it represents the elements and strategies for data mining biomedical and clinical data with many parameters, that is, in a high dimensional space that requires skilful navigation. The intent is not to promote FANO per se, but to report its science and methodologies. Typical example rules from traditional data mining are that A and B and C associate, or IF A & B THEN C. We need much higher complexity rules for clinical data especially with inclusion of proteomics and genomics. FANO's specific goal is to be able routinely to extract from clinical record repositories and other data not only the complex rules required for biomedical research and the clinical practice of evidence based medicine, but to quantify their uncertainty, that is, their essentially probabilistic nature. The underlying information and number theoretic basis previously described is less of an issue here, being "under the hood", although the fundamental role and use of the Incomplete (generalized) Riemann Zeta Function as a general surprise measure is highlighted, along with its covariance or multivariance analogue, as it appears to be a unique and powerful feature. Another characteristic described is the very general tactic of the metadata operator ':='. It allows decomposition of diverse data types such as trees, spreadsheets, biosequences, sets of objects, amorphous data collections with repeating items, XML structures, and so forth into universally atomic data items with or without metadata, and assists in reconstruction of ontology from the associations and numerical correlations so data mined.     

Education and research in biomedical engineering of the Budapest University of Technology and Economics

Biomedical Engineering is a relatively new interdisciplinary science. This review paper presents the biomedical engineering activity, which is carried out at the Budapest University of Technology and Economics (BUTE) and its partner institutions. In the first parts the main goals and the curriculum of the Biomedical Engineering Education Program is presented. The second part of the paper summarizes the most important biomedical engineering researches most of them carried out in the Biomedical Engineering Laboratory of BUTE.     

Comparison of a commercial and an in-house T cell-based assay for the diagnosis of Mycobacterium tuberculosis infection

Identification of individuals with a tuberculosis infection is a very important element for the control of tuberculosis. The currently used tuberculin skin test has poor sensitivity and specificity. Recently, an important advance in tuberculosis diagnosis occurred with the development of in vitro T cell-based IFN-gamma release assays. The aim of this study was to compare a RD1-based in-house ELISPOT-IFN-gamma assay with a commercial (T-SPOT.TB) assay for the diagnosis of tuberculosis infection. The results showed an almost complete concordance between the two assays, confirming that our restricted but highly selected pool of peptides is sufficient to detect tuberculosis infection.     

Current status of genetic engineering in cotton (Gossypium hirsutum L): an assessment

Abstract

Cotton is considered as the foremost commercially important fiber crop and is deemed as the backbone of the textile industry. The productivity of cotton crop, worldwide, is severely hampered by the occurrence of pests, weeds, pathogens apart from various environmental factors. Several beneficial agronomic traits, viz., early maturity, improved fiber quality, heat tolerance, etc. have been successfully incorporated into cotton varieties employing conventional hybridization and mutation breeding. Crop losses, due to biotic factors, are substantial and may be reduced through certain crop protection strategies. In recent years, pioneering success has been achieved through the adoption of modern biotechnological approaches. Genetically engineered cotton varieties, expressing Bacillus thuringiensis cry genes, proved to be highly successful in controlling the bollworm complex. Various other candidate genes responsible for resistance to insect pests and pathogens, tolerance to major abiotic stress factors such as temperature, drought and salinity, have been introduced into cotton via genetic engineering methods to enhance the agronomic performance of cotton cultivars. Furthermore, genes for improving the seed oil quality and fiber characteristics have been identified and introduced into cotton cultivars. This review provides a brief overview of the various advancements made in cotton through genetic engineering approaches.