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PubMed2005

Cloning, characterization and primary function study of a novel gene, Cymg1, related to family 2 cystatins.

Cystatins are cysteine proteinase inhibitors. We found two expression sequence tags (ESTs), CA463109 and AV042522, from a mouse testis library using Digital differential display (DDD). By electrical hybridization, a novel gene, Cymg1 (GenBank accession No. AY600990), which has a full length of 0.78 kb, and contains four exons and three introns, was cloned from a mouse testis cDNA library. The gene is located in the 2G3 area of chromosome 2. The full cDNA encompasses the entire open reading frame, encoding 141 amino acid residues. The protein has a cysteine protease inhibitor domain that is related to the family 2 cystatins but lacks critical consensus sites important for cysteine protease inhibition. These characteristics are seen in the CRES subfamily, which are related to the family 2 cystatins and are expressed specifically in the male reproductive tract. CYMG1 has a 44% (48/108) identity with mouse CRES and 30% (42/140) identity with mouse cystatin C. Northern blot analysis showed that the Cymg1 is specifically expressed in adult mouse testes. Cell location studies showed that the GFP-tagged CYMG1 protein was localized in the cytoplasm of HeLa cells. Immunohistochemistry revealed that the CYMG1 protein was expressed in mouse testes spermatogonium, spermatocytes, round spermatids, elongating spermatids and spermatozoa. RT-PCR results also showed that Cymg1 was expressed in mouse testes and spermatogonium. The Cymg1 expression level varied in different developmental stages: it was low 1 week postpartum, steadily increased 2 to 5 weeks postpartum, and was highest 7 weeks postpartum. The expression level at 5 weeks postpartum was maintained during 13 to 57 weeks postpartum. The Cymg1 expression level in the testes over different developmental stages correlates with the mouse spermatogenesis and sexual maturation process. All these indicate that Cymg1 might play an important role in mouse spermatogenesis and sexual maturation.

Amino Acid Sequence↗
PubMed2000

Library outreach: addressing Utah's "Digital Divide".

A "Digital Divide" in information and technological literacy exists in Utah between small hospitals and clinics in rural areas and the larger health care institutions in the major urban area of the state. The goals of the outreach program of the Spencer S. Eccles Health Sciences Library at the University of Utah address solutions to this disparity in partnership with the National Network of Libraries of Medicine-- Midcontinental Region, the Utah Department of Health, and the Utah Area Health Education Centers. In a circuit-rider approach, an outreach librarian offers classes and demonstrations throughout the state that teach information-access skills to health professionals. Provision of traditional library services to unaffiliated health professionals is integrated into the library's daily workload as a component of the outreach program. The paper describes the history, methodology, administration, funding, impact, and results of the program.

Area Health Education Centers↗
PubMed2004

Comparative evaluation of eight docking tools for docking and virtual screening accuracy.

Eight docking programs (DOCK, FLEXX, FRED, GLIDE, GOLD, SLIDE, SURFLEX, and QXP) that can be used for either single-ligand docking or database screening have been compared for their propensity to recover the X-ray pose of 100 small-molecular-weight ligands, and for their capacity to discriminate known inhibitors of an enzyme (thymidine kinase) from randomly chosen "drug-like" molecules. Interestingly, both properties are found to be correlated, since the tools showing the best docking accuracy (GLIDE, GOLD, and SURFLEX) are also the most successful in ranking known inhibitors in a virtual screening experiment. Moreover, the current study pinpoints some physicochemical descriptors of either the ligand or its cognate protein-binding site that generally lead to docking/scoring inaccuracies.

Computer Graphics↗
PubMed1997

A method for detecting microcalcifications in digital mammograms.

Microcalcification clusters are often an important indicator for the detection of malignancy in mammograms. In many cases, microcalcifications are the only indication of a malignancy. However, the detection of microcalcifications can be a difficult process. They are small and can be embedded in dense tissue. This paper presents a method for automatically detecting microcalcifications. We utilize a high-boost filter to suppress background clutter enabling segmentation even in very dense breast tissue. We then use a threshholding and region growing technique to extract candidate microcalcifications. Likely microcalcifications are then identified by a linear classifier. We apply this method to images selected from the LLNL/UCSF Digital Mammogram Library, and produce a receiver operating characteristic (ROC) curves to detail the trade-off between probability of detection and false alarms. Finally, we exam the ability to properly select a threshold to achieve a desired probability of detection based upon a training set. This is a US government work. There are no restrictions on its use.

Breast Neoplasms↗
PubMed2005

Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators.

Based on the structural characters of PPAR modulators, a virtual combinatorial library containing 1226,625 compounds was constructed using SMILES strings. Selected ADME filters were employed to compel compounds having poor drug-like properties from this library. This library was converted to sdf and mol2 files by CONCORD 4.0, and was then docked to PPARgamma by DOCK 4.0 to identify new chemical entities that may be potential drug leads against type 2 diabetes and other metabolic diseases. The method to construct virtual combinatorial library using SMILES strings was further visualized by Visual Basic.net that can facilitate the needs of generating other type virtual combinatorial libraries.

Combinatorial Chemistry Techniques↗
PubMed2006

Using argumentation to extract key sentences from biomedical abstracts.

PROBLEM: key word assignment has been largely used in MEDLINE to provide an indicative "gist" of the content of articles and to help retrieving biomedical articles. Abstracts are also used for this purpose. However with usually more than 300 words, MEDLINE abstracts can still be regarded as long documents; therefore we design a system to select a unique key sentence. This key sentence must be indicative of the article's content and we assume that abstract's conclusions are good candidates. We design and assess the performance of an automatic key sentence selector, which classifies sentences into four argumentative moves: PURPOSE, METHODS, RESULTS and CONCLUSION METHODS: we rely on Bayesian classifiers trained on automatically acquired data. Features representation, selection and weighting are reported and classification effectiveness is evaluated on the four classes using confusion matrices. We also explore the use of simple heuristics to take the position of sentences into account. Recall, precision and F-scores are computed for the CONCLUSION class. For the CONCLUSION class, the F-score reaches 84%. Automatic argumentative classification using Bayesian learners is feasible on MEDLINE abstracts and should help user navigation in such repositories.

Abstracting and Indexing↗
PubMed2006

An exploration of on-line access by non-traditional students in higher education: a case study.

The nature of Higher Education (HE) has seen many changes throughout the last decade. The agenda for widening participation in HE has led to an increase in the number of students with a broader range of educational backgrounds. At the same time there has been a surge in the development of digitalisation and the convergence of computing and telecommunications technologies available for use in education. This paper discusses the outcomes of a case study, conducted in a School of Health Studies within a northern English University, which identified the extent to which 'non-traditional' students access on-line learning facilities, such as virtual learning environments and library networks, and what factors enhanced or formed barriers to access. 'Non-traditional' students, for the purpose of this study, were defined as mature students who were returning to higher education after a considerable break. The outcomes indicated that skill deficit is a major obstacle for many 'non-traditional' students. The paper explores this issue in depth and suggests potential ways forward for the delivery of technology supported learning for 'non-traditional' students in Higher Education.

Adult↗
PubMed2005

Neuroethology application for the study of human temporal lobe epilepsy: from basic to applied sciences.

The aim of this investigation was to apply neuroethology to the study of human temporal lobe epilepsy (TLE). For this purpose, 42 seizures in 7 patients recorded during video/EEG monitoring (1997-1998) were analyzed by means of a behavioral glossary containing all behaviors. Video recordings were reobserved, and all patients' behaviors were annotated second-by-second. Data were analyzed using Ethomatic software and displayed as flowcharts including frequency, mean duration, and sequential statistic interaction of behavioral items (chi2 > or = 10.827, P<0.001). Flowcharts of (1) a group of seizures from a single patient, (2) the sum of four seizures per patient of two patients with right and five patients with left TLE, and (3) the comparison of left versus right TLE are shown. Well-established data in the literature were confirmed, such as aura (especially epigastric), contralateral lateralization value of dystonia and version, consciousness and language alterations in ictal and postictal periods, mostly with respect to dominant hemisphere involvement, among others. Less well established data such as awakening seizures in TLE patients, lateralization value of facial wiping (ipsilateral to the focus), statistically significant associations between behavioral pairs (dyads), and new behavioral sequences in TLE were also observed. We suggest that neuroethology also has great potential in the study of human epilepsy semiology. This work had an important role in method standardization for human epilepsy, setting the basis for the development of future clinical studies including correlation with other diagnostic methods (EEG, magnetic resonance, and SPECT). The next step will be the comparative study of seizures of patients with left and right TLE, with a greater number of patients, and the development of a digital video library.

Automatism↗
PubMed2002

Exhaustive identification of human class II basic helix-loop-helix proteins by virtual library screening.

Cellular proliferation, specification and differentiation in developing tissues are tightly coordinated by groups of transcription factors in response to extrinsic and intrinsic signals. Furthermore, renewable pools of stem cells in adult tissues are subject to similar regulation. Basic helix-loop-helix (bHLH) proteins are a group of transcription factors that exert such a determinative influence on a variety of developmental pathways from C. elegans to humans, and we wished to exclusively identify novel members from within the whole human bHLH family. We have, therefore, developed an 'empirical custom fingerprint', to define the class II bHLH domain and exclusively identify these proteins in silico. We have identified nine previously uncharacterised human class II proteins, four of which were novel, by interrogating conceptual translations of the GenBank HTGS database. RT-PCR and mammalian 2-hybrid analysis of a subset of the factors demonstrated that they were indeed expressed, and were able to interact with an appropriate binding partner in vitro. Thus, we are now approaching an almost complete listing of human class II bHLH factors.

Amino Acid Sequence↗
PubMedDate not supplied

ZINC--a free database of commercially available compounds for virtual screening.

A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy to access database of purchasable compounds. We have therefore prepared a library of 727,842 molecules, each with 3D structure, using catalogs of compounds from vendors (the size of this library continues to grow). The molecules have been assigned biologically relevant protonation states and are annotated with properties such as molecular weight, calculated LogP, and number of rotatable bonds. Each molecule in the library contains vendor and purchasing information and is ready for docking using a number of popular docking programs. Within certain limits, the molecules are prepared in multiple protonation states and multiple tautomeric forms. In one format, multiple conformations are available for the molecules. This database is available for free download (http://zinc.docking.org) in several common file formats including SMILES, mol2, 3D SDF, and DOCK flexibase format. A Web-based query tool incorporating a molecular drawing interface enables the database to be searched and browsed and subsets to be created. Users can process their own molecules by uploading them to a server. Our hope is that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists.

Databases, Factual↗
PubMedDate not supplied

Pharmacophore identification, in silico screening, and virtual library design for inhibitors of the human factor Xa.

Factor Xa inhibitors are innovative anticoagulant agents that provide a better safety/efficacy profile compared to other anticoagulative drugs. A chemical feature-based modeling approach was applied to identify crucial pharmacophore patterns from 3D crystal structures of inhibitors bound to human factor Xa (Pdb entries 1fjs, 1kns, 1eqz) using the software LIGANDSCOUT and CATALYST. The complex structures were selected regarding the criteria of high inhibitory potency (i.e. all ligands show K(i) values against factor Xa in the subnanomolar range) and good resolution (i.e. at least 2.2 A) in order to generate selective and high quality pharmacophore models. The resulting chemical-feature based hypotheses were used for virtual screening of commercial molecular databases such as the WDI database. Furthermore, a ligand-based molecular modeling approach was performed to obtain common-feature hypotheses that represent the relevant chemical interactions between 10 bioactive factor Xa inhibitors and the protein, respectively. In a next step a virtual combinatorial library was designed in order to generate new compounds with similar chemical and spatial properties as known inhibitors. The software tool ILIB DIVERSE was used for this procedure in order to provide new scaffolds of this group of anticoagulants. Finally we present the combination of these two techniques, hence virtual screening was performed with selective pharmacophore models in a focused virtual combinatorial database. De novo derived molecular scaffolds that were able to adequately satisfy the pharmacophore criteria are revealed and are promising templates for candidates for further development.

Anticoagulants↗
PubMed2006

Colorimetric sensor arrays for the analysis of beers: a feasibility study.

Eighteen commercial beers have been analyzed in both liquid and gas phases using colorimetric sensor arrays made from selected chemically responsive dyes printed on a hydrophobic membrane. Digital imaging of the dye array before and after exposure to the complex analytes in either the liquid phase or the head-gas provides a color change profile as a unique fingerprint for the specific analyte. The digital data libraries generated were analyzed using statistical and chemometric methods, including principal component analysis (PCA) and hierarchical clustering analysis (HCA). In either liquid- or gas-phase experiments, facile identification of specific beers was achieved using comparison of the color change profiles; using HCA statistical analysis the error rate of identification was <3%. Differentiation between even very similar beers proved to be straightforward. In addition, differentiation of pristine beer from the effects of watering or decarbonation proved to be possible. These results suggest that colorimetric sensor arrays may prove to be useful for quality assurance/quality control applications of beers and perhaps other beverages.

Beer↗
PubMed2007

Colorimetric sensor array for soft drink analysis.

Fourteen commercial soft drinks have been analyzed using colorimetric sensor arrays made from a set of 25 chemically responsive dyes printed on a hydrophobic membrane. Digital imaging of the dye array before and after immersion provides a color change profile as a unique fingerprint for each specific analyte. The digital data library generated was analyzed with statistical and chemometric methods, including principal component analysis (PCA) and hierarchical clustering analysis (HCA). Facile identification of all of the soft drinks was readily achieved using comparison of the color change profiles or a PCA score plot. Using a HCA dendrogram, the misclassification rate was <2%, and even very similar sodas were easily differentiated. In addition, the monitoring of soft drinks as they degas or upon dilution also proved to be possible. This work demonstrates the potential of our colorimetric sensor array technology for quality assurance/control applications of sodas and perhaps other beverages as well.

Carbonated Beverages↗