NamesforLife Semantic Resolution Services for the Life Sciences

A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. 

To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others who use biological data in their routine work), we developed a generalizable semantic model that represents names, concepts, and exemplars (representations of biological entities) as distinct objects. By identifying each object with a Digital Object Identifier (DOI) it becomes possible to place forward-pointing links in the published literature, in databases, and vector graphics that can be used as part of a mechanism for resolving ambiguities, thereby “future proofing” a nomenclature or terminology. A full implementation of the N4L model for the _Bacteria_ and _Archaea_ was released in April, 2010. The system is professionally curated and represents a Tier III resource in Parkhill’s view of bioinformatic services. A variety of tools and web services have been developed for readers, publishers, and others (N4L Guide, N4L Autotagger, N4L Semantic Search, N4L Taxonomic Abstracts) and we are incorporating other taxonomies into the N4L data model, as well as adding additional phenotypic, genotypic, and genomic information to the existing exemplars to add greater value to end users

The IPD-IMGT/HLA Database

It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community

Process analytical technology in food biotechnology

Biotechnology is an area where precision and reproducibility are vital. This is due to the fact that products are often in form of food, pharmaceutical or cosmetic products and therefore very close to the human being. To avoid human error during the production or the evaluation of the quality of a product and to increase the optimal utilization of raw materials, a very high amount of automation is desired. Tools in the food and chemical industry that aim to reach this degree of higher automation are summarized in an initiative called Process Analytical Technology (PAT). Within the scope of the PAT, is to provide new measurement technologies for the purpose of closed loop control in biotechnological processes. These processes are the most demanding processes in regards of control issues due to their very often biological rate-determining component. Most important for an automation attempt is deep process knowledge, which can only be achieved via appropriate measurements. These measurements can either be carried out directly, measuring a crucial physical value, or if not accessible either due to the lack of technology or a complicated sample state, via a soft-sensor.Even after several years the ideal aim of the PAT initiative is not fully implemented in the industry and in many production processes. On the one hand a lot effort still needs to be put into the development of more general algorithms which are more easy to implement and especially more reliable. On the other hand, not all the available advances in this field are employed yet. The potential users seem to stick to approved methods and show certain reservations towards new technologies.Die Biotechnologie ist ein Wissenschaftsbereich, in dem hohe Genauigkeit und Wiederholbarkeit eine wichtige Rolle spielen. Dies ist der Tatsache geschuldet, dass die hergestellten Produkte sehr oft den Bereichen Nahrungsmitteln, Pharmazeutika oder Kosmetik angehöhren und daher besonders den Menschen beeinflussen. Um den menschlichen Fehler bei der Produktion zu vermeiden, die Qualität eines Produktes zu sichern und die optimale Verwertung der Rohmaterialen zu gewährleisten, wird ein besonders hohes Maß an Automation angestrebt. Die Werkzeuge, die in der Nahrungsmittel- und chemischen Industrie hierfür zum Einsatz kommen, werden in der Process Analytical Technology (PAT) Initiative zusammengefasst. Ziel der PAT ist die Entwicklung zuverlässiger neuer Methoden, um Prozesse zu beschreiben und eine automatische Regelungsstrategie zu realisieren. Biotechnologische Prozesse gehören hierbei zu den aufwändigsten Regelungsaufgaben, da in den meisten Fällen eine biologische Komponente der entscheidende Faktor ist. Entscheidend für eine erfolgreiche Regelungsstrategie ist ein hohes Maß an Prozessverständnis. Dieses kann entweder durch eine direkte Messung der entscheidenden physikalischen, chemischen oder biologischen Größen gewonnen werden oder durch einen SoftSensor. Zusammengefasst zeigt sich, dass das finale Ziel der PAT Initiative auch nach einigen Jahren des Propagierens weder komplett in der Industrie noch bei vielen Produktionsprozessen angekommen ist. Auf der einen Seite liegt dies mit Sicherheit an der Tatsache, dass noch viel Arbeit in die Generalisierung von Algorithmen gesteckt werden muss. Diese müsse einfacher zu implementieren und vor allem noch zuverlässiger in der Funktionsweise sein. Auf der anderen Seite wurden jedoch auch Algorithmen, Regelungsstrategien und eigne Ansätze für einen neuartigen Sensor sowie einen Soft-Sensors vorgestellt, die großes Potential zeigen. Nicht zuletzt müssen die möglichen Anwender neue Strategien einsetzen und Vorbehalte gegenüber unbekannten Technologien ablegen

Integrated municipal waste management systems: An indicator to assess their environmental and economic sustainability

Tools based on Life Cycle Thinking (LCT) are routinely used to assess the environmental and economic performance of integrated municipal solid waste (MSW) management systems. Life Cycle Assessment (LCA) is used to quantify the environmental impacts, whereas Life Cycle Costing (LCC) allows financial and economic assessments. These tools require specific experience and knowledge, and a large amount of data. The aim of this project is the definition of an indicator for the assessment of the environmental and economic sustainability of integrated MSW management systems. The challenge is to define a simple but comprehensive indicator that may be calculated also by local administrators and managers of the waste system and not only by scientists or LCT experts. The proposed indicator is a composite one, constituted by three individual indicators: two of them assess the environmental sustainability of the system by quantifying the achieved material and energy recovery levels, while the third one quantifies the costs. The composite indicator allows to compare different integrated MSW management systems in an objective way, and to monitor the performance of a system over time. The calculation of the three individual indicators has been tested on the integrated MSW management systems of the Lombardia Region (Italy) as well as on four of its provinces (Milano, Bergamo, Pavia, and Mantova)

Food Additives and Processing Aids used in Breadmaking

The main classes of additives used in breadmaking are: (i) oxidants/reductants; (ii) emulsifiers; (iii) hydrocolloids; and (iv) preservatives. The main processing aids used are enzymes. Historically, market trends have developed from the use of ingredients in greater quantities - to obtain specific effects in bread (such as fat for crumb softness) - to the use of additives at much lower levels (max. 1%) and, more recently, to enzymes which are used in parts per million (ppm). According to many regulations, enzymes do not need to be declared on the label of the final product, attending the “clean label” trend. We will describe the food additives used under each class, individually describing their mode of action and effects on dough rheology, during the breadmaking process, and on product quality. We will also describe the main enzymes currently used, dividing them according to the substrate they act on (gluten, starch, lipids, non-starch polysaccharides or NSPS), individually describing their mode of action and effects on dough rheology, during the breadmaking process, and on product quality. Legal aspects will also be addressed. We will conclude with future trends in the use of additives and processing aids in breadmaking

Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)

The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with the proposed Minimum Information about a Bioinformatics investigation (MIABi), proposed in June 2009. Authors of the conference supplements in BMC Bioinformatics, BMC Genomics and Immunome Research have consented to cooperate in this process, which will include the procedures described herein, where appropriate, to ensure data and software persistence and perpetuity, database and resource re-instantiability and reproducibility of results, author and contributor identity disambiguation and MIABi-compliance. Wherever possible, datasets and databases will be submitted to depositories with standardized terminologies. As standards are evolving, this process is intended as a prelude to the 100 BioDatabases (BioDB100) initiative whereby APBioNet collaborators will contribute exemplar databases to demonstrate the feasibility of standards-compliance and participate in refining the process for peer-review of such publications and validation of scientific claims and standards compliance. This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources

Binding and Uptake into Human Hepatocellular Carcinoma Cells of Peptide-Functionalized Gold Nanoparticles

One of the most daunting challenges of nanomedicine is the finding of appropriate targeting agents to deliver suitable payloads precisely to cells affected by malignancies. Even more complex is to achieve the ability to ensure the nanosystems enter those cells. Here we use 2 nm (metal core) gold nanoparticles to target human hepatocellular carcinoma (HepG2) cells stably transfected with the SERPINB3 (SB3) protein. The nanoparticles were coated with a 85:15 mixture of thiols featuring, respectively, a phosphoryl choline, to ensure water solubility and biocompatibility, and a 28-mer peptide corresponding to the amino acid sequence 21-47 of the hepatitis B virus-PreS1 protein (PreS1(21-47)). Conjugation of the peptide was performed via the maleimide-thiol reaction in methanol allowing the use of a limited amount of the targeting molecule. This is an efficient procedure also in the perspective of selecting libraries of new targeting agents. The rationale behind the selection of the peptide is that SB3, which is undetectable in normal hepatocytes, is over-expressed in hepatocellular carcinoma and in hepatoblastoma and has been proposed as a target of the hepatitis B virus (HBV). For the latter the key recognition element is the PreS1(21-47) peptide, which is a fragment of one of the proteins composing the viral envelope. The ability of the conjugated nanoparticles to bind the target protein SB3, expressed in liver cancer cells, was investigated by surface plasmon resonance analysis and in vitro via cellular uptake analysis followed by atomic absorption analysis of digested samples. The results showed that the PreS1(21-47) peptide is a suitable targeting agent for cells overexpressing the SB3 protein. Even more important is the evidence that the gold nanoparticles are internalized by the cells. The comparison between the surface plasmon resonance analysis and the cellular uptake studies suggests the presentation of the protein on cell surface is critical for efficient recognition

Llàgrima artificial lipídica. Estudi clinic i fisicoquímic

Les llàgrimes artificials lipídiques són un tipus de suplements lacrimals formats per lípids, entre d’altres components, amb la finalitat de restaurar la capa lipídica fisiològica de la pel·lícula lacrimal. La capa lipídica s’encarrega de disminuir l’evaporació de la llàgrima, a més de lubricar en el parpelleig, per aquest motiu les llàgrimes lipídiques estan indicades, especialment, en pacients amb ull sec per excessiva taxa d’evaporació de la pel·lícula lacrimal. Un dels components lipídics que s’utilitzen en aquest tipus de llàgrimes artificials és la lecitina de soja. En el present estudi s’han analitzat les propietats fisicoquímiques de tres llàgrimes artificials comercials basades en aquest component, la Zero, l’Optrex i l’Opticalm en format esprai. S’han obtingut les isotermes àrea-pressió superficial i s’ha intentat corroborar l’efectivitat d’aquestes tècniques per estudiar el comportament dels components lipídics de les llàgrimes i extreure conclusions sobre algunes de les seves propietats. A més s’ha complementat el treball amb un estudi clínic amb la finalitat d’intentar establir algun tipus de relació entre els resultats fisicoquímics i els resultats clínics. S’ha vist que l’Opticalm és la llàgrima amb més fluïdesa de les tres estudiades i que l’Opticalm en comparació amb l’Oprex produeix més millora en els resultats de les proves de qualitat de la llàgrima, la qual cosa podria estar relacionada amb la seva major fluïdesa constatada en la primera part de l’estudi

Rice and Water: The Final Frontier

Outlines the threat of diminishing water resources for rice crops, the economic and social dimensions of the droughts' potential effects, and the new cultural systems and adapted rice varieties being pursued as potential solutions