Organisation of information in a digital library: challenges and possibilities

Cilj ovoga rada je proučiti organizaciju informacija u digitalnim knjižnicama pošto su informacijske tehnologije revolucionizirale samu ulogu knjižnica. Za uvod u temu, prvotno će se objasniti što su digitalne knjižnice i koje su njihove zadaće, što ih razlikuje od tradicionalnih knjižnica te s kojim izazovima se suočavaju. Proučiti će se bibliografska i informacijska organizacija općenito u digitalnim knjižnicama, koja se kasnije nadovezuje na organizaciju mrežnih izvora odnosno sustava za organizaciju znanja. Naposljetku će se sve to pokušati ujediniti i prikazati na primjeru organizacije informacija Smithsonian digitalne knjižnice

Bacteria of the genus Clostridium

Bakterije roda Clostridium rasprostranjene su u prirodi, stoga se mogu pronaći u vodi, zraku, tlu, prašini te u ljudskom probavnom sustavu. Clostridium perfringens, Clostridiumbotulinum, Clostridium difficile,Clostridium tetani najznačajniji su pripadnici ovog roda. Kontaminacija ovim sporogenim bakterijama predstavlja veliku prijetnju za ljudsko zdravlje, posebno ako se kozumira higijenski neispravna, termički dovoljno neobrađena hrana ili podgrijavana hrana. Osim toga, konzumacija dimljene ribe, kobasica, pršuta i drugih suhomesnatih proizvoda predstavlja potencijalni rizik. U ovom radu opisuju se najznačajnije vrste bakterija roda Clostridium njihova svojstva i uvjeti potrebni za rast, spore i toksini te bolesti koje izazivaju.Bacteria of the genus Clostridium are widespread in nature, so we can find them in water, air, soil, dust, and in the human digestive trackt . Clostridium perfringens, Clostridium botulinum, Clostridium difficile and Clostridium tetani are the most significant members of this genus. Food contamination with this sporogenic bacteria presents a great threat for human health, especially if the food consumed is unhygienic, insufficiently thermally processed or warmed up. Additionally, consummation of smoked fish, sausages, persuto and other dehydrated meat products presents a potential risk. In this paper the most common species of genus Clostridium, their characteristics, growth requirements, spores, toxins and illnesses they cause are described

Organisation of information in a digital library: challenges and possibilities

Cilj ovoga rada je proučiti organizaciju informacija u digitalnim knjižnicama pošto su informacijske tehnologije revolucionizirale samu ulogu knjižnica. Za uvod u temu, prvotno će se objasniti što su digitalne knjižnice i koje su njihove zadaće, što ih razlikuje od tradicionalnih knjižnica te s kojim izazovima se suočavaju. Proučiti će se bibliografska i informacijska organizacija općenito u digitalnim knjižnicama, koja se kasnije nadovezuje na organizaciju mrežnih izvora odnosno sustava za organizaciju znanja. Naposljetku će se sve to pokušati ujediniti i prikazati na primjeru organizacije informacija Smithsonian digitalne knjižnice

Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a nonfunctional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20 % better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a give

Testing of SNS-032 in a panel of human neuroblastoma cell lines with acquired resistance to a broad range of drugs

Novel treatment options are needed for the successful therapy of patients with high-risk neuroblastoma. Here, we investigated the cyclindependent kinase (CDK) inhibitor SNS-032 in a panel of 109 neuroblastoma cell lines consisting of 19 parental cell lines and 90 sublines with acquired resistance to 14 different anticancer drugs. Seventy-three percent of the investigated neuroblastoma cell lines and all four investigated primary tumor samples displayed concentrations that reduce cell viability by 50% in the range of the therapeutic plasma levels reported for SNS-032 (<754 nM). Sixty-two percent of the cell lines and two of the primary samples displayed concentrations that reduce cell viability by 90% in this concentration range. SNS-032 also impaired the growth of the multidrug-resistant cisplatin-adapted UKF-NB-3 subline UKF-NB-3rCDDP1000 in mice. ABCB1 expression (but not ABCG2 expression) conferred resistance to SNS-032. The antineuroblastoma effects of SNS-032 did not depend on functional p53. The antineuroblastoma mechanism of SNS-032 included CDK7 and CDK9 inhibition–mediated suppression of RNA synthesis and subsequent depletion of antiapoptotic proteins with a fast turnover rate including X-linked inhibitor of apoptosis (XIAP), myeloid cell leukemia sequence 1 (Mcl-1), baculoviral IAP repeat containing 2 (BIRC2; cIAP-1), and survivin. In conclusion, CDK7 and CDK9 represent promising drug targets and SNS-032 represents a potential treatment option for neuroblastoma including therapy-refractory cases

Predicting P-Glycoprotein-Mediated Drug Transport Based On Support Vector Machine and Three-Dimensional Crystal Structure of P-glycoprotein

Human P-glycoprotein (P-gp) is an ATP-binding cassette multidrug transporter that confers resistance to a wide range of chemotherapeutic agents in cancer cells by active efflux of the drugs from cells. P-gp also plays a key role in limiting oral absorption and brain penetration and in facilitating biliary and renal elimination of structurally diverse drugs. Thus, identification of drugs or new molecular entities to be P-gp substrates is of vital importance for predicting the pharmacokinetics, efficacy, safety, or tissue levels of drugs or drug candidates. At present, publicly available, reliable in silico models predicting P-gp substrates are scarce. In this study, a support vector machine (SVM) method was developed to predict P-gp substrates and P-gp-substrate interactions, based on a training data set of 197 known P-gp substrates and non-substrates collected from the literature. We showed that the SVM method had a prediction accuracy of approximately 80% on an independent external validation data set of 32 compounds. A homology model of human P-gp based on the X-ray structure of mouse P-gp as a template has been constructed. We showed that molecular docking to the P-gp structures successfully predicted the geometry of P-gp-ligand complexes. Our SVM prediction and the molecular docking methods have been integrated into a free web server (http://pgp.althotas.com), which allows the users to predict whether a given compound is a P-gp substrate and how it binds to and interacts with P-gp. Utilization of such a web server may prove valuable for both rational drug design and screening

PARP inhibitors as P-glyoprotein substrates

The cytotoxicity of PARP inhibitors olaparib, veliparib, and CEP-8983 were investigated in two P-glycoprotein (P-gp) overexpressing drug-resistant cell models (IGROVCDDP and KB-8-5-11). IGROVCDDP and KB-8-5-11 were both resistant to olaparib and resistance was reversible with the P-gp inhibitors elacridar, zosuquidar, and valspodar. In contrast, the P-gp overexpressing models were not resistant to veliparib or CEP-8983. Olaparib and veliparib did not induce protein expression of P-gp in IGROVCDDP or KB-8-5-11 at doses that successfully inhibit PARP. Olaparib therefore appears to be a P-gp substrate. Veliparib and CEP-8983 do not appear to be substrates. Veliparib and CEP-8983 may therefore be more useful in combined chemotherapy regimens with P-gp substrates and may be active in platinum and taxane-resistant ovarian cancer

Contrasting cellular uptake pathways for chlorido and iodido iminopyridine ruthenium arene anticancer complexes

The pathways involved in cellular uptake and accumulation of iminopyridine complexes of general formula [Ru(η6-p-cymene)(N,N-dimethyl-N′-[(E)-pyridine-2-ylmethylidene]benzene-1,4-diamine)X]PF6 bearing two different halido ligands X = Cl or I, have been explored. The ratio of passive/active cellular accumulation of Ru in A2780 human ovarian cancer cells is compared and contrasted with cisplatin. Also, saturation of cellular uptake, time-dependence of cellular influx/efflux equilibria, together with endocytotic pathways such as caveolae and facilitated diffusion are investigated and discussed. Temperature dependence studies of Ru accumulation in the A2780 cells show that in contrast to cisplatin (CDDP) and chlorido complex 1, which are taken up largely through active transport, the iodido complex 2 enters cells via passive transport. The cellular efflux of Ru is slow (ca. 25% retained after 72 h) and is partially inhibited by verapamil, implicating the P-gp protein in the efflux mechanism. Ouabain inhibition experiments suggest that the cellular uptake of these ruthenium complexes relies at least in part on facilitated diffusion, and in particular is dependent on the membrane potential. In addition the finding that depletion of cellular ATP with antimycin A had little effect on cellular Ru accumulation from iodido complex 2 is consistent with passive diffusion. In contrast, ATP depletion caused a major increase in cellular accumulation of ruthenium from chlorido complex 1

VnD: a structure-centric database of disease-related SNPs and drugs

Numerous genetic variations have been found to be related to human diseases. Significant portion of those affect the drug response as well by changing the protein structure and function. Therefore, it is crucial to understand the trilateral relationship among genomic variations, diseases and drugs. We present the variations and drugs (VnD), a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. VnD was built in three steps. First, we integrated various resources systematically to deduce catalogs of disease-related genes, single nucleotide polymorphisms (SNPs), protein mutations and relevant drugs. VnD contains 137 195 disease-related gene records (13 940 distinct genes) and 16 586 genetic variation records (1790 distinct variations). Next, we carried out structure modeling and docking simulation for wild-type and mutant proteins to examine the structural and functional consequences of non-synonymous SNPs in the drug-related genes. Conformational changes in 590 wild-type and 4437 mutant proteins from drug-related genes were included in our database. Finally, we investigated the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs and physico-chemical properties. The VnD database, available at http://vnd.kobic.re.kr:8080/VnD/ or vandd.org, would be a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs

Binding of Tetracycline and Chlortetracycline to the Enzyme Trypsin: Spectroscopic and Molecular Modeling Investigations

Tetracycline (TC) and chlortetracycline (CTC) are common members of the widely used veterinary drug tetracyclines, the residue of which in the environment can enter human body, being potentially harmful. In this study, we establish a new strategy to probe the binding modes of TC and CTC with trypsin based on spectroscopic and computational modeling methods. Both TC and CTC can interact with trypsin with one binding site to form trypsin-TC (CTC) complex, mainly through van der Waals' interactions and hydrogen bonds with the affinity order: TC>CTC. The bound TC (CTC) can result in inhibition of trypsin activity with the inhibition order: CTC>TC. The secondary structure and the microenvironment of the tryptophan residues of trypsin were also changed. However, the effect of CTC on the secondary structure content of trypsin was contrary to that of TC. Both the molecular docking study and the trypsin activity experiment revealed that TC bound into S1 binding pocket, competitively inhibiting the enzyme activity, and CTC was a non-competitive inhibitor which bound to a non-active site of trypsin, different from TC due to the Cl atom on the benzene ring of CTC which hinders CTC entering into the S1 binding pocket. CTC does not hinder the binding of the enzyme substrate, but the CTC-trypsin-substrate ternary complex can not further decompose into the product. The work provides basic data for clarifying the binding mechanisms of TC (CTC) with trypsin and can help to comprehensively understanding of the enzyme toxicity of different members of tetracyclines in vivo