Conditional gene expression in human embryonic stem cells.

Human embryonic stem cells (hESCs) possess unique properties for studying mechanisms controlling cell fate commitment during early mammalian development. Gain of function is a common strategy to study the function of specific genes involved in these mechanisms. However, transgene toxicity can be a major limitation, especially with factors influencing proliferation or differentiation.

Ultra-resolution imaging of a self-assembling biomolecular system using robust carbon nanotube AFM probes.

Nanoscale structural features of a novel self-assembling DNA based nanostructure have been resolved. Image data is of sufficient resolution to allow molecular orientation and the effect of surface adsorption to be characterized. This has been achieved using AFM with probes employing carbon nanotubes attached via a thin film of plasma polymerized hexane.

Study of the resistance of SAMs on aluminium to acidic and basic solutions using dynamic contact angle measurement.

We report the development of a method to determine the aqueous stability of self-assembled monolayers (SAMs) using the Wilhelmy plate dynamic contact angle (DCA) experiment. The DCA is measured in solutions over a range of pH values for alkyl carboxylic and alkyl phosphonic acid SAMs formed on magnetron-sputtered aluminum. The change in DCA on repeated immersion is used as a measure of the degradation of the SAMs by hydrolytic attack.

Controlling protein retention on enzyme-responsive surfaces.

The ability to change the properties of solid surfaces on demand is a key component of a multitude of established and emerging technologies. Stimuli that have previously been used to trigger changes in surface properties include changes in solvent, light, pH, ionic strength, temperature and magnetic or electric fields. We are interested in developing surfaces that can be triggered by the catalytic action of enzymes.

Friction force microscopy of alkylphosphonic acid and carboxylic acids adsorbed on the native oxide of aluminum.

Monolayers of alkylphosphonic acids (APA) and alkylcarboxylic acids (ACA) on magnetron-sputtered aluminum films have been investigated by friction force microscopy (FFM), contact angle measurement, and polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS). Clear evidence has been provided from PM-IRRAS that friction coefficients, determined from FFM data, may be correlated directly with variations in adsorbate molecular structure. The friction coefficient increased with the length of the adsorbate molecule, but reached a limiting value when the alkyl chain of the adsorbate contained eight carbons in the case of APA or 12 carbons in the case of ACA.

Vitelliform macular dystrophy.

Purpose: To investigate and integrate the photographic, angiographic, and tomographic findings from a group of patients with various stages of vitelliform macular dystrophy type 2 (VMD2; also known as Best's disease) and use this information to propose mechanisms of disease pathogenesis.

Design: Retrospective observational case series.

Participants: Nine consecutive patients seen in a private practice referral setting by the authors.

HOXB4 overexpression promotes hematopoietic development by human embryonic stem cells.

Human embryonic stem cells (hESCs) are a potential source of hematopoietic cells for therapeutic transplantation and can provide a model for human hematopoiesis. Culture of hESCs on murine stromal layers or in stromal-free conditions as embryoid bodies results in low levels of hematopoietic cells. Here we demonstrate that overexpression of the transcription factor HOXB4 considerably augments hematopoietic development of hESCs.

Activin/Nodal and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells.

Maintenance of pluripotency is crucial to the mammalian embryo's ability to generate the extra-embryonic and embryonic tissues that are needed for intrauterine survival and foetal development. The recent establishment of embryonic stem cells from human blastocysts (hESCs) provides an opportunity to identify the factors supporting pluripotency at early stages of human development. Using this in vitro model, we have recently shown that Nodal can block neuronal differentiation, suggesting that TGFbeta family members are involved in cell fate decisions of hESCs, including preservation of their pluripotency.

BioCreAtIvE task 1A: gene mention finding evaluation.

Background: The biological research literature is a major repository of knowledge. As the amount of literature increases, it will get harder to find the information of interest on a particular topic. There has been an increasing amount of work on text mining this literature, but comparing this work is hard because of a lack of standards for making comparisons.

Data preparation and interannotator agreement: BioCreAtIvE task 1B.

Background: We prepared and evaluated training and test materials for an assessment of text mining methods in molecular biology. The goal of the assessment was to evaluate the ability of automated systems to generate a list of unique gene identifiers from PubMed abstracts for the three model organisms Fly, Mouse, and Yeast. This paper describes the preparation and evaluation of answer keys for training and testing.

Overview of BioCreAtIvE task 1B: normalized gene lists.

Background: Our goal in BioCreAtIve has been to assess the state of the art in text mining, with emphasis on applications that reflect real biological applications, e.g., the curation process for model organism databases.

Gene name identification and normalization using a model organism database.

Biology has now become an information science, and researchers are increasingly dependent on expert-curated biological databases to organize the findings from the published literature. We report here on a series of experiments related to the application of natural language processing to aid in the curation process for FlyBase. We focused on listing the normalized form of genes and gene products discussed in an article.

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.

Motivation: The biological literature is a major repository of knowledge. Many biological databases draw much of their content from a careful curation of this literature. However, as the volume of literature increases, the burden of curation increases.

Rutabaga by any other name: extracting biological names.

As the pace of biological research accelerates, biologists are becoming increasingly reliant on computers to manage the information explosion. Biologists communicate their research findings by relying on precise biological terms; these terms then provide indices into the literature and across the growing number of biological databases. This article examines emerging techniques to access biological resources through extraction of entity names and relations among them.

Explicating the implicit: the local level and the microprocess of change in the analytic situation.

This paper proposes a method of examining the micro-events of the analytic process that borrows heavily from developmental research. The increasing importance of illuminating the microprocess of interaction to understanding the process of change in analytic treatment is emphasised. A set of constructs and terminology is proposed for the study of the moment-to-moment interactive process in psychoanalytic therapy referred to as the local level.