Integration of advanced oxidation processes at mild conditions in wet scrubbers for odourous sulphur compounds treatment

The effectiveness of different advanced oxidation processes on the treatment of a multicomponent aqueous solution containing ethyl mercaptan, dimethyl sulphide and dimethyl disulphide (0.5 mg L(-1) of each sulphur compound) was investigated with the objective to assess which one is the most suitable treatment to be coupled in wet scrubbers used in odour treatment facilities. UV/H2O2, Fenton, photo-Fenton and ozone treatments were tested at mild conditions and the oxidation efficiency obtained was compared. The oxidation tests were carried out in magnetically stirred cylindrical quartz reactors using the same molar concentration of oxidants (hydrogen peroxide or ozone). The results show that ozone and photo-Fenton are the most efficient treatments, achieving up to 95% of sulphur compounds oxidation and a mineralisation degree around 70% in 10 min. Furthermore, the total costs of the treatments taking into account the capital and operational costs were also estimated for a comparative purpose. The economic analysis revealed that the Fenton treatment is the most economical option to be integrated in a wet scrubber to remove volatile organic sulphur compounds, as long as there are no space constraints to install the required reactor volume. In the case of reactor volume limitation or retrofitting complexities, the ozone and photo-Fenton treatments should be considered as viable alternatives.

Contemporary wars and their contributions to vascular injury management

INTRODUCTION

Man's inhumanity for man still knows no boundaries, as we continue as a species as a whole to engage in war. According to Kohn's Dictionary of Wars [1], of over 3,700 years of recorded history, there have been a total of 3,010 wars. One is hard pressed to actually find a period of time in which here has not been an active conflict in the globe. The world has experienced two world wars: WWI (1914-1918) and WWII (1939-1945). The total number of military casualties in WWI was over 37 million, while WWII so far, has been the deadliest military conflict in history with over 60 million people killed accounting for slightly over 2.5% of the world's population.

MATERIAL AND METHODS

The purpose of this study is to review contemporary wars and their contributions to vascular injury management. It is precisely wartime contributions that have led to the more precise identification and management of these injuries resulting in countless lives and extremities saved. However, surgeons dealing with vascular injuries have faced a tough and arduous road. Their journey was initiated by surgical mavericks which undaunted, pressed on against all odds guided by William Stewart Halsted's classic statement in 1912: "One of the chief fascinations in surgery is the management of wounded vessels."

CONCLUSION

Contemporary wars of the XX-XXI centuries gave birth, defined and advanced the field of vascular injury management.

Atom-light interactions in photonic crystals

The integration of nanophotonics and atomic physics has been a long-sought goal that would open new frontiers for optical physics, including novel quantum transport and many-body phenomena with photon-mediated atomic interactions. Reaching this goal requires surmounting diverse challenges in nanofabrication and atomic manipulation. Here we report the development of a novel integrated optical circuit with a photonic crystal capable of both localizing and interfacing atoms with guided photons. Optical bands of a photonic crystal waveguide are aligned with selected atomic transitions. From reflection spectra measured with average atom number N=1.1+/-0.4, we infer that atoms are localized within the waveguide by optical dipole forces. The fraction of single-atom radiative decay into the waveguide is Γ1D/Γ'≃(0.32±0.08), where Γ1D is the rate of emission into the guided mode and Γ' is the decay rate into all other channels. Γ1D/Γ' is unprecedented in all current atom-photon interfaces.

Reduction of residual amplitude modulation to 1 × 10⁻⁶ for frequency modulation and laser stabilization

Active control and cancellation of residual amplitude modulation (RAM) in phase modulation of an optical carrier is one of the key technologies for achieving the ultimate stability of a laser locked to an ultrastable optical cavity. Furthermore, such techniques are versatile tools in various frequency modulation-based spectroscopy applications. In this Letter we report a simple and robust approach to actively stabilize RAM in an optical phase modulation process. We employ a waveguide-based electro-optic modulator (EOM) to provide phase modulation and implement an active servo with both DC electric field and temperature feedback onto the EOM to cancel both the in-phase and quadrature components of the RAM. This technique allows RAM control on the parts-per-million level where RAM-induced frequency instability is comparable to or lower than the fundamental thermal noise limit of the best available optical cavities.

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

The Gene Ontology Consortium (GOC) is a major bioinformatics project that provides structured controlled vocabularies to classify gene product function and location. GOC members create annotations to gene products using the Gene Ontology (GO) vocabularies, thus providing an extensive, publicly available resource. The GO and its annotations to gene products are now an integral part of functional analysis, and statistical tests using GO data are becoming routine for researchers to include when publishing functional information. While many helpful articles about the GOC are available, there are certain updates to the ontology and annotation sets that sometimes go unobserved. Here we describe some of the ways in which GO can change that should be carefully considered by all users of GO as they may have a significant impact on the resulting gene product annotations, and therefore the functional description of the gene product, or the interpretation of analyses performed on GO datasets. GO annotations for gene products change for many reasons, and while these changes generally improve the accuracy of the representation of the underlying biology, they do not necessarily imply that previous annotations were incorrect. We additionally describe the quality assurance mechanisms we employ to improve the accuracy of annotations, which necessarily changes the composition of the annotation sets we provide. We use the Universal Protein Resource (UniProt) for illustrative purposes of how the GO Consortium, as a whole, manages these changes.

2'-fucosyllactose: an abundant, genetically determined soluble glycan present in human milk

Lactose is the preeminent soluble glycan in milk and a significant source of energy for most newborn mammals. Elongation of lactose with additional monosaccharides gives rise to a varied repertoire of free soluble glycans such as 2'-fucosyllactose (2'-FL), which is the most abundant oligosaccharide in human milk. In infants, 2'-FL is resistant to digestion and reaches the colon where it is partially fermented, behaving as soluble prebiotic fiber. Evidence also suggests that portions of small soluble milk glycans, including 2'-FL, are absorbed, thus raising the possibility of systemic biological effects. 2'-FL bears an epitope of the Secretor histo-blood group system; approximately 70-80% of all milk samples contain 2'-FL, since its synthesis depends on a fucosyltransferase that is not uniformly expressed. The fact that some infants are not exposed to 2'-FL has helped researchers to retrospectively probe for biological activities of this glycan. This review summarizes the attributes of 2'-FL in terms of its occurrence in mammalian phylogeny, its postulated biological activities, and its variability in human milk.

Optical spectrum analyzer with quantum-limited noise floor

Interactions between atoms and lasers provide the potential for unprecedented control of quantum states. Fulfilling this potential requires detailed knowledge of frequency noise in optical oscillators with state-of-the-art stability. We demonstrate a technique that precisely measures the noise spectrum of an ultrastable laser using optical lattice-trapped 87Sr atoms as a quantum projection noise-limited reference. We determine the laser noise spectrum from near dc to 100 Hz via the measured fluctuations in atomic excitation, guided by a simple and robust theory model. The noise spectrum yields a 26(4) mHz linewidth at a central frequency of 429 THz, corresponding to an optical quality factor of 1.6×10(16). This approach improves upon optical heterodyne beats between two similar laser systems by providing information unique to a single laser and complements the traditionally used Allan deviation which evaluates laser performance at relatively long time scales. We use this technique to verify the reduction of resonant noise in our ultrastable laser via feedback from an optical heterodyne beat. Finally, we show that knowledge of our laser's spectrum allows us to accurately predict the laser-limited stability for optical atomic clocks.

Comparison of two independent Sr optical clocks with 1×10(-17) stability at 10(3) s

Many-particle optical lattice clocks have the potential for unprecedented measurement precision and stability due to their low quantum projection noise. However, this potential has so far never been realized because clock stability has been limited by frequency noise of optical local oscillators. By synchronously probing two ^{87}Sr lattice systems using a laser with a thermal noise floor of 1×10(-15), we remove classically correlated laser noise from the intercomparison, but this does not demonstrate independent clock performance. With an improved optical oscillator that has a 1×10(-16) thermal noise floor, we demonstrate an order of magnitude improvement over the best reported stability of any independent clock, achieving a fractional instability of 1×10(-17) in 1000 s of averaging time for synchronous or asynchronous comparisons. This result is within a factor of 2 of the combined quantum projection noise limit for a 160 ms probe time with ~10(3) atoms in each clock. We further demonstrate that even at this high precision, the overall systematic uncertainty of our clock is not limited by atomic interactions. For the second Sr clock, which has a cavity-enhanced lattice, the atomic-density-dependent frequency shift is evaluated to be -3.11×10(-17) with an uncertainty of 8.2×10(-19).

Full phase stabilization of a Yb:fiber femtosecond frequency comb via high-bandwidth transducers

We present full phase stabilization of an amplified Yb:fiber femtosecond frequency comb using an intracavity electro-optic modulator and an acousto-optic modulator. These transducers provide high servo bandwidths of 580 kHz and 250 kHz for f(rep) and f(ceo), producing a robust and low phase noise fiber frequency comb. The comb was self-referenced with an f-2f interferometer and phase locked to an ultrastable optical reference used for the JILA Sr optical clock at 698 nm, exhibiting 0.21 rad and 0.47 rad of integrated phase errors (over 1 mHz-1 MHz), respectively. Alternatively, the comb was locked to two optical references at 698 nm and 1064 nm, obtaining 0.43 rad and 0.14 rad of integrated phase errors, respectively.

The impact of focused Gene Ontology curation of specific mammalian systems

The Gene Ontology (GO) resource provides dynamic controlled vocabularies to provide an information-rich resource to aid in the consistent description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). System-focused projects, such as the Renal and Cardiovascular GO Annotation Initiatives, aim to provide detailed GO data for proteins implicated in specific organ development and function. Such projects support the rapid evaluation of new experimental data and aid in the generation of novel biological insights to help alleviate human disease. This paper describes the improvement of GO data for renal and cardiovascular research communities and demonstrates that the cardiovascular-focused GO annotations, created over the past three years, have led to an evident improvement of microarray interpretation. The reanalysis of cardiovascular microarray datasets confirms the need to continue to improve the annotation of the human proteome.

AVAILABILITY

GO ANNOTATION DATA IS FREELY AVAILABLE FROM: ftp://ftp.geneontology.org/pub/go/gene-associations/

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.

A tripartite complex composed of ETV6-NTRK3, IRS1 and IGF1R is required for ETV6-NTRK3-mediated membrane localization and transformation

ETV6-NTRK3 (EN), a chimeric tyrosine kinase generated by t(12;15) translocations, is a dominantly acting oncoprotein in diverse tumor types. We previously showed that insulin-like growth factor 1 receptor (IGF1R) is essential for EN-mediated oncogenesis and that insulin receptor substrate 1 (IRS1) is constitutively tyrosine phosphorylated and bound by EN in transformed cells. Given that IRS1 is also an adapter for IGF1R, we hypothesized that IRS1 might localize EN to IGF1R at the membrane to activate phosphatidylinositol 3-kinase (PI3K)-Akt, which is critical for EN oncogenesis. In this study, we examined EN/IRS1/IGF1R complexes in detail. We find that both IRS1 and kinase active IGF1R are required for EN transformation, that tyrosine phosphorylated IRS1 is present in high molecular weight complexes with EN and IGF1R, and that EN colocalizes with IGF1R at the plasma membrane. Both IGF1R kinase activity and an intact cytoplasmic Y950 residue, the IRS1-docking site of IGF1R, are required, confirming the importance of the IGF1R/IRS1 interaction for EN oncogenesis. The dual specificity IGF1R and insulin receptor (INSR) inhibitor, BMS-536924, blocks EN transformation activity, cell survival and its interaction with IRS proteins, and induces a striking shift of EN proteins to smaller sized molecular complexes. We conclude that a tripartite complex of EN, IRS1 and IGF1R localizes EN to the membrane and that this is essential for EN-mediated transformation. These findings provide an explanation for the observed IGF1R dependency of EN transformation. Blocking IGF1R kinase activity may, therefore, provide a tractable therapeutic strategy for the many tumor types driven by the EN oncoprotein.

Gastric anti-ulcer activity of silymarin, a lipoxygenase inhibitor, in rats

Oral treatment with silymarin was found to be effective in the prevention of gastric ulceration induced by cold-restraint stress, in rats. Statistically significant ulcer index values with respect to the control group, were observed. In 6 h pyloric-ligated animals silymarin showed a significant reduction in the number and severity of the ulcers; however, it did not alter the gastric secretion volume or acidity although histamine concentration was significantly decreased. In absolute ethanol-induced ulcers, treatment with silymarin 1 or 2 h before the anti-ulcerogenic agent, did not prevent the formation of gastric lesions. Furthermore, the hexosamine content was decreased significantly, but the total protein output was enhanced, showing similar values to those with the standard drug, carbenoxolone. These results suggest that the anti-ulcerogenic effect of silymarin could be related to its inhibitory mechanism of enzymatic peroxidation by the lipoxygenase pathway, avoiding leukotriene synthesis.

Structure of a preternary complex involving a prokaryotic NHEJ DNA polymerase

In many prokaryotes, a specific DNA primase/polymerase (PolDom) is required for nonhomologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs). Here, we report the crystal structure of a catalytically active conformation of Mycobacterium tuberculosis PolDom, consisting of a polymerase bound to a DNA end with a 3' overhang, two metal ions, and an incoming nucleotide but, significantly, lacking a primer strand. This structure represents a polymerase:DNA complex in a preternary intermediate state. This polymerase complex occurs in solution, stabilizing the enzyme on DNA ends and promoting nucleotide extension of short incoming termini. We also demonstrate that the invariant Arg(220), contained in a conserved loop (loop 2), plays an essential role in catalysis by regulating binding of a second metal ion in the active site. We propose that this NHEJ intermediate facilitates extension reactions involving critically short or noncomplementary DNA ends, thus promoting break repair and minimizing sequence loss during DSB repair.

Abstract P5-10-17: Bevacizumab (Bev) in Combination with Docetaxel (T) and Cyclophosphamide (C) as Adjuvant Treatment (AdjRx) for Patients (pts) with Early Stage (ES) Breast Cancer (BrCa) and Normal HER-2 Status. A Pilot Evaluation

In random assignment trials, the combination of Bev+ chemotherapy has been shown to produce superior response rates and progression free survival compared to chemotherapy alone, providing a rationale for the study of Bev in the AdjRx of pts with ESBrCa. As a principal side effect of Bev is hypertension (HTN), anthracycline-containing (Anth) AdjRx may pose additional cardiovascular risks. The role of Anth in Her2 normal ESBC is uncertain. TC is a standard non-Anth AdjRx. We performed a single arm pilot study to evaluate the feasibility and toxicity of TC+Bev in pts with ESBC in preparation for participation in a random assignment trial. Methods: Eligibility criteria included: ESBC which was HER-2 normal, node-positive or >2 cm and receptor negative, or >3 cm and receptor positive, normal cardiac ejection fraction (EF), no active or uncontrolled cardiovascular disease, normal organ and marrow function. Treatment consisted of four 3 weekly cycles of docetaxel 75 mg/m2 together with cyclophosphamide 600 mg/m2. Patients commenced bevacizumab 15 mg/kg i.v. on day 1, and q 3 weeks to a total of 19 treatments. Pts were monitored clinically, with echocardiograms and with serial estimations of BNP and troponin.

Results: A total of 105 female pts were accrued in 9 ICORG sites between Dec 2008 and June 2010. Ages ranged from 26-86 (median 55). At June 2010, 33 have completed all phases of therapy, 54 are still on treatment. Eighteen pts have been removed from study due to: HTN -7, intestinal perforation -2, withdrew consent-4, proteinuia-1, anaphylaxis-1, infection-3. The perforations occurred at cycles 9 and 19. Neither pt. with perforation had prior abdominal surgery. The median number of cycles achieved by the discontinued pts was 9. HTN requiring Rx occurred in 25 pts. Among 12 with HTN who have completed Bev, 2 are off HTN meds, and 9 are on reducing doses. The median EF at base line was 67%, at 13 cycles (42 pts) 63%, 18 cycles (27 pts) 66%. Six pts had EF drop >10%, in 3 of these EF fell below 50% as last recorded value. There were no episodes of clinical cardiac failure. Troponin and BNP levels were normal in all 57 pts with serial measurements. Thirteen pts required treatment for neutropenia-related infection or for abscess.

Conclusions: The spectrum and frequency of bevacizumab toxicity in our population of healthy adjuvant pts is similar to that reported for pts with metastatic BC and other malignancies. Hypertension is the principal cause of treatment discontinuation, but cardiac toxicity appears to be limited, with this non-anth chemotherapy +Bev. Intestinal perforation can also occur in pts with ESBC. These toxicities can occur in the post chemotherapy phase of Bev therapy. Pts enrolled on random assignment trials of Bev containing AdjRx require careful monitoring for toxicity.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-10-17.

Infrastructure for the life sciences: design and implementation of the UniProt website

BACKGROUND

The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website http://www.uniprot.org was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008.

DESCRIPTION

The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. These tools include full text and field-based text search, similarity search, multiple sequence alignment, batch retrieval and database identifier mapping. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.http://www.uniprot.org/ is open for both academic and commercial use. The site was built with open source tools and libraries. Feedback is very welcome and should be sent to help@uniprot.org.

CONCLUSION

The new UniProt website makes accessing and understanding UniProt easier than ever. The two main lessons learned are that getting the basics right for such a data provider website has huge benefits, but is not trivial and easy to underestimate, and that there is no substitute for using empirical data throughout the development process to decide on what is and what is not working for your users.

Apnoeic and obstructive nonapnoeic sleep respiratory events

Obstructive nonapnoeic event (ONE) scoring is shrouded in confusion. This is important in patients with mild disease, in whom precision is crucial. The aims of the present study were: 1) to identify ONEs using oesophageal pressure (OP) (OP-ONEs) and a noninvasive (NI) method (NI-ONEs); 2) to compare both methods of scoring; and 3) to determine the contribution of ONE definitions to clinical findings. Patients with suspected sleep apnoeas (respiratory disturbance index <or=10) during a first polysomnography were subjected to a second with an OP measurement. OP-ONEs and NI-ONEs were defined as an increase in OP or discernible reduction in the amplitude of thoracoabdominal bands with both desaturation and/or arousal. Bland-Altman analysis established agreement. Comparisons were made between OP-ONEs, NI-ONEs and clinical findings. In our sample (n = 90), the addition of an arousal to the NI-ONEs or OP-ONEs with only desaturation increased the number of NI-ONEs by 329 and 362%, respectively. NI-ONEs with arousal and/or desaturation detected 91% of OP-ONEs. The association with sleepiness depended on the incorporation of arousal into the definition of ONEs. In patients with mild disease, the addition of an arousal to ONEs, with only desaturation, markedly increased respiratory disturbance index, with probable therapeutic implications. Scoring respiratory events as apnoea and ONEs is easier and sufficiently accurate.

Removal of odour-causing compounds using carbonaceous adsorbents/catalysts prepared from sewage sludge

This paper discusses H(2)S, NH(3) and VOCs removal by sewage-sludge-derived materials with outstanding chemical and textural properties. These materials were obtained from different precursors using different chemical and thermal treatments. Results show that the H(2)S removal process entailed a catalytic conversion of H(2)S to S or SO(4) (2-) species. On the other hand, adsorption is the main mechanism governing the performance of sludge-based materials for NH(3) and VOCs. Retention capacities (x/M values) obtained for some of the sludge-based adsorbents/catalysts are similar to those obtained with commercial activated carbons selected as reference materials.

Sr lattice clock at 1 x 10(-16) fractional uncertainty by remote optical evaluation with a Ca clock

Optical atomic clocks promise timekeeping at the highest precision and accuracy, owing to their high operating frequencies. Rigorous evaluations of these clocks require direct comparisons between them. We have realized a high-performance remote comparison of optical clocks over kilometer-scale urban distances, a key step for development, dissemination, and application of these optical standards. Through this remote comparison and a proper design of lattice-confined neutral atoms for clock operation, we evaluate the uncertainty of a strontium (Sr) optical lattice clock at the 1 x 10(-16) fractional level, surpassing the current best evaluations of cesium (Cs) primary standards. We also report on the observation of density-dependent effects in the spin-polarized fermionic sample and discuss the current limiting effect of blackbody radiation-induced frequency shifts.

The Universal Protein Resource (UniProt): an expanding universe of protein information

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at or downloaded at .

Dried sludges and sludge-based chars for H2S removal at low temperature: influence of sewage sludge characteristics

The use of sewage sludge as a precursor of adsorbent/ catalyst materials for environmental applications has been encouraged during the past few years. Due to the heterogeneous nature of sludges, there exists a lack of information regarding the characteristics of these low-cost precursors and how their physicochemical properties affect the final performance of materials prepared from them. In this work, three sewage-sludges collected at WWTPs with assorted sludge/wastewater treatment schemes were used as precursors of adsorbents/catalysts for H2S removal at room temperature. All the solidswere characterized to establish their textural properties and chemical composition, including the speciation of the adsorbents/ catalysts inorganic fraction. Thermal treatment (gasification) of the raw (dried) sludges increased the H2S removal ability in all cases. For these thermally treated materials, catalytic conversion to elemental sulfur and sulfate moieties was found to be the main route of H2S removal. Results indicate that adsorbents based on an iron/calcium-containing sludge were the most reactive and exhibited the highest capacities for H2S retention. Forthis particulartype of sludge, a reasonably good performance was observed even when the dried (raw) sludge was used as adsorbent/ catalyst. Alternatively, the oxidation of H2S by chars obtained from the other two sludges under study was related to their textural properties.

A novel mathematical model identifies potential factors regulating bone apposition

The development of pharmaceutical treatments for bone disease can be enhanced by mathematical models that predict their effects on matrix apposition during cancellous bone remodelling. Therefore, a mathematical model was constructed to simulate the rate of focal bone formation from the number of osteoid-forming osteoblasts at one microsite and their rate of activity. The number of mature osteoid-forming cells was simulated from a relationship describing the proliferation of preosteoblasts. Osteoblast activity was described by Michaelis-Menten enzyme kinetic equations adapted to describe cellular activity. The model incorporates the negative feedback effects on the rates of bone apposition due to the reduction in size of mature osteoblasts with continuing differentiation and the reduction in number of osteoid-forming cells with apoptosis and osteocyte formation. In addition, the rate of mineralisation is limited according to osteoid substrate availability. Results of sensitivity analysis revealed the amount of bone formed at one microsite to be more sensitive to changes in factors that controlled cell growth during proliferation and the number of mature osteoid-forming osteoblasts than to those that determined cellular activity. Matrix and osteocyte signalling were shown to have potentially important roles in controlling rates of osteoid apposition in normal, healthy bone. This simple model supports the critical role of controlled mitotic growth in normal bone apposition. It can also help to explain how the homeostatic processes of bone resorption and apposition during remodelling can be disrupted by growth factors that affect the mitotic fraction and division time of proliferative preosteoblast cells.

Evolution of human-chimpanzee differences in malaria susceptibility: relationship to human genetic loss of N-glycolylneuraminic acid

Chimpanzees are the closest evolutionary cousins of humans, sharing >99% identity in most protein sequences. Plasmodium falciparum is the major worldwide cause of malaria mortality. Plasmodium reichenowi, a morphologically identical and genetically very similar parasite, infects chimpanzees but not humans. Conversely, experimental P. falciparum infection causes brief moderate parasitization and no severe infection in chimpanzees. This surprising host specificity remains unexplained. We modified and enhanced traditional methods for measuring sialic acid (Sia)-dependent recognition of glycophorins by merozoite erythrocyte-binding proteins, eliminating interference caused by endogenous Sias on transfected cells, and by using erythroleukemia cells to allow experimental manipulation of Sia content. We present evidence that these remarkable differences among such closely related host-parasite pairs is caused by species-specific erythrocyte-recognition profiles, apparently related to the human-specific loss of the common primate Sia N-glycolylneuraminic acid. The major merozoite-binding protein erythrocyte-binding antigen-175 of P. falciparum apparently evolved to take selective advantage of the excess of the Sia N-acetylneuraminic acid (the precursor of N-glycolylneuraminic acid) on human erythrocytes. The contrasting preference of P. reichenowi erythrocyte-binding antigen-175 for N-glycolylneuraminic acid is likely the ancestral condition. The surprising ability of P. falciparum to cause disease in New World Aotus monkeys (geographically isolated from P. falciparum until arrival of peoples from the Old World) can be explained by parallel evolution of a human-like Sia expression pattern in these distantly related primates. These results also have implications for the prehistory of hominids and for the genetic origins and recent emergence of P. falciparum as a major human pathogen.

Human embryonic stem cells express an immunogenic nonhuman sialic acid

Human embryonic stem cells (HESC) can potentially generate every body cell type, making them excellent candidates for cell- and tissue-replacement therapies. HESC are typically cultured with animal-derived 'serum replacements' on mouse feeder layers. Both of these are sources of the nonhuman sialic acid Neu5Gc, against which many humans have circulating antibodies. Both HESC and derived embryoid bodies metabolically incorporate substantial amounts of Neu5Gc under standard conditions. Exposure to human sera with antibodies specific for Neu5Gc resulted in binding of immunoglobulin and deposition of complement, which would lead to cell killing in vivo. Levels of Neu5Gc on HESC and embryoid bodies dropped after culture in heat-inactivated anti-Neu5Gc antibody-negative human serum, reducing binding of antibodies and complement from high-titer sera, while allowing maintenance of the undifferentiated state. Complete elimination of Neu5Gc would be likely to require using human serum with human feeder layers, ideally starting with fresh HESC that have never been exposed to animal products.

The Universal Protein Resource (UniProt)

The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

Sensitivity analysis of a novel mathematical model identifies factors determining bone resorption rates

The development of pharmaceutical treatments for bone disease can be enhanced by computational models that predict their effects on resorption and rates of remodeling. Therefore, a simple mathematical model was formulated to simulate erosion depth and duration of resorption, using Michaelis-Menten (M-M) equations to describe changing rates of cellular activity during the two phases of bone resorption. The model was based on histomorphometric data and cellular interactions that occur in the bone microenvironment cited from the literature. Availability of bone substrate for osteoclastic activity during Phase I was assumed to be limited by the ratio of RANKL (ligand for receptor activator for nuclear factor kappaB) to osteoprotegerin (OPG) ('effective RANKL'). The required presence of marrow stromal cell produced macrophage-colony stimulating factor (M-CSF) for osteoclast action was represented as a factor equal to 1 for healthy bone. Growth factors released from the matrix during Phase I were assumed to cause two negative feedback effects: (1) the inhibitory effect of transforming growth factor-beta1 (TGFbeta1)-induced production of OPG by marrow osteoblast stromal cells, reducing effective RANKL; (2) the apoptosis of osteoclast nuclei assumed to occur at high concentrations of TGFbeta. This signaled the end of Phase I. During Phase II, cellular activity to remove the collagen fibrils left behind by osteoclasts was also simulated by Michaelis-Menten kinetic equations. Results of sensitivity analysis revealed variation in resorption depth and duration to fluctuate within 6% and 7% of the baseline value for changes in most input parameters. However, resorption depth was reduced and the duration of resorption lengthened by both a decrease in matrix TGFbeta and an increase the apoptotic threshold. Furthermore, the duration of resorption, but not erosion depth, was sensitive to changes in the maximum rate of cellular activity during removal of collagen fibrils. This mathematical model, which simulates the changing rates of cellular activity, has identified factors that reduce the duration and depth of resorption. It also suggests new targets for modeling therapeutic intervention to slow the rate of bone remodeling.

A prospective randomized multi-center study for the treatment of lumbar spinal stenosis with the X STOP interspinous implant: 1-year results

Patients suffering from neurogenic intermittent claudication secondary to lumbar spinal stenosis have historically been limited to a choice between a decompressive laminectomy with or without fusion or a regimen of non-operative therapies. The X STOP Interspinous Process Distraction System (St. Francis Medical Technologies, Concord, Calif.), a new interspinous implant for patients whose symptoms are exacerbated in extension and relieved in flexion, has been available in Europe since June 2002. This study reports the results from a prospective, randomized trial of the X STOP conducted at nine centers in the U.S. Two hundred patients were enrolled in the study and 191 were treated; 100 received the X STOP and 91 received non-operative therapy (NON OP) as a control. The Zurich Claudication Questionnaire (ZCQ) was the primary outcomes measurement. Validated for lumbar spinal stenosis patients, the ZCQ measures physical function, symptom severity, and patient satisfaction. Patients completed the ZCQ upon enrollment and at follow-up periods of 6 weeks, 6 months, and 1 year. Using the ZCQ criteria, at 6 weeks the success rate was 52% for X STOP patients and 10% for NON OP patients. At 6 months, the success rates were 52 and 9%, respectively, and at 1 year, 59 and 12%. The results of this prospective study indicate that the X STOP offers a significant improvement over non-operative therapies at 1 year with a success rate comparable to published reports for decompressive laminectomy, but with considerably lower morbidity.

Quantitation of PGE9509924, a novel, nonfluorinated quinolone, in rat plasma using liquid chromatography electrospray-tandem mass spectrometry following solid-phase extraction sample clean-up in a 96-well format

PGE9509924, a novel nonfluorinated quinolone, is a potent antibacterial agent with a broad spectrum of activity. A semi-automated method using 96-well format, solid-phase extraction has been developed for quantitating PGE9509924 in rat plasma. The Waters Oasis HLB extraction plate containing a polymeric packing material was found to give the best overall recoveries. All liquid transfer steps other than aliquoting the plasma are accomplished using a 96-channel pipettor. Reverse-phase HPLC with electrospray/MS/MS detection using selective reaction monitoring is used to quantitate the samples. Stable isotopically labeled PGE9509924 is used as the internal standard. The assay is linear over the range from 0.01 to 10 ug/ml. Excellent precision is obtained within a single run and between multiple runs performed on different days. CVs of <6% were observed. The combination of the semi-automated, 96-well parallel sample processing and the short runtime on the LC/MS/MS results in a high throughput assay with reduced operator interaction.

Comparing bacterial genomes through conservation profiles

We constructed two-dimensional representations of profiles of gene conservation across different genomes using the genome of Escherichia coli as a model. These profiles permit both the visualization at the genome level of different traits in the organism studied and, at the same time, reveal features related to the genomes analyzed (such as defective genomes or genomes that lack a particular system). Conserved genes are not uniformly distributed along the E. coli genome but tend to cluster together. The study of gene distribution patterns across genomes is important for the understanding of how sets of genes seem to be dependent on each other, probably having some functional link. This provides additional evidence that can be used for the elucidation of the function of unannotated genes. Clustering these patterns produces families of genes which can be arranged in a hierarchy of closeness. In this way, functions can be defined at different levels of generality depending on the level of the hierarchy that is studied. The combined study of conservation and phenotypic traits opens up the possibility of defining phenotype/genotype associations, and ultimately inferring the gene or genes responsible for a particular trait.

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org.

Development of a chiral assay for a novel, nonfluorinated quinolone, PGE-9509924, in dog plasma using high performance liquid chromatography with electrospray tandem mass spectrometry or fluorescence detection

PGE-9509924 is a nonfluorinated quinolone and is active against a variety of susceptible and drug resistant bacteria in vitro and in animal infection models. A method for determining both enantiomers of PGE-9509924 in dog plasma has been developed. The enantiomers are derivatized with a chiral derivatizing agent, (-)-1-(9-fluorenyl)ethyl chloroformate (FLEC) and the resulting diastereomers are separated by reverse phase chromatography. Plasma samples are prepared via solid phase extraction (SPE) in a 96-well format prior to being derivatized. Samples are then analyzed by electrospray-LC/MS/MS with multiple reaction monitoring or by HPLC with fluorescence detection. Results of a side-by-side validation of the method with LC/MS/MS and HPLC/Fl detection are presented. Over the range selected for validation (0.025-10 micro g/ml), both methods give similar results with identical limits of quantitation. Due to the selectivity of LC/MS/MS and the use of a stable-isotopically labeled internal standard, significantly shorter chromatographic runtimes are achieved with LC/MS/MS, making it the method of choice for sample analysis.

Preoperative evaluation of chronic alcoholics assessed for surgery of the upper digestive tract

BACKGROUND

Alcoholics are at risk of developing major complications in the postoperative period. Adequate prophylactic treatment, as well as preoperative abstinence, can significantly decrease the rate of complications. However, the preoperative diagnosis of alcoholism is difficult to establish. The purpose of this study was to assess whether three preoperative visits, an alcohol-related questionnaire (CAGE), and the laboratory markers carbohydrate-deficient transferrin (CDT) and gamma-glutamyltransferase (GGT) would increase the rate of detection of chronic alcoholics.

METHODS

The study included the Departments of ENT, Facial and Maxillofacial Surgery, and General Surgery of a university hospital; 705 male patients were assessed for tumor surgery of the upper digestive tract and were allocated to 5 different groups. All patients were seen three times, and five different strategies were used to detect chronic alcoholics. The gold standard was the diagnosis of alcohol misuse made by an experienced (blinded) investigator according to the DSM-III-R. The main outcome measurements were the detection rates of the different test strategies.

RESULTS

By clinical routine alone, only 16% were detected during the first visit and 34% after three visits. If the CAGE questionnaire was added, sensitivity increased to 64%. The further addition of GGT or CDT led to 80 and 85% detections, respectively. A combination of all tests had a sensitivity of 91%.

CONCLUSIONS

To detect more alcoholic patients at risk for major complications, patients should be seen more often, and additional diagnostic tools such as the CAGE, CDT, and GGT should be used before surgery.

Total colonic manometry as a guide for surgical management of functional colonic obstruction: Preliminary results

BACKGROUND/PURPOSE

Functional colonic obstruction (pseudo-obstruction) encompasses a broad group of motility disorders. Medical management of colonic pseudo-obstruction is complex and often fails, leading to surgical referral. In most cases (excepting Hirschsprung's disease) the surgeon is unable to precisely localize the area of functional obstruction. Total colonic manometry can directly measure intraluminal pressures and contractile function along the entire length of the colon. The authors propose that total colonic manometry can be used by the pediatric surgeon to guide the timing and extent of surgical therapy in refractory functional colonic obstruction.

METHODS

Four patients were evaluated for functional colonic obstruction. All underwent barium enema and rectal biopsy with a diagnosis of Hirschsprung's disease in one patient. All patients underwent colonoscopy and total colonic manometry. Manometric tracings were obtained while fasting, after feeding, and after pharmacologic stimulation both preoperatively (n = 4) and postoperatively (n = 3).

RESULTS

Total colonic manometry identified an abrupt end of normal peristalsis in 2 of the non-Hirschsprung's patients (one in the proximal colon and one in the transverse colon). Medical therapy failed in both of these patients, and they underwent diverting ostomy proximal to the loss of normal peristalsis. The third non-Hirschsprung's patient essentially had normal manometry and was able to have her colon decompressed successfully on a laxative regimen. Repeat manometry after colonic decompression showed return of normal peristalsis in 2 of these patients and continued abnormal peristaltic activity in the third. Definitive surgical intervention based on the results of total colonic manometry was performed on the latter. All 3 patients achieved normal continence. A fourth patient had Hirschsprung's disease confirmed by rectal biopsy and underwent a 1-stage neonatal modified Duhamel procedure, which was complicated by postoperative functional obstruction. Manometry showed a lack of peristaltic function beginning in the right colon. An ileostomy was performed, and timing of ileostomy closure was guided by the return of normal colonic peristalsis seen on manometry.

CONCLUSIONS

These initial cases show the utility of total colonic manometry in the management of colonic pseudo-obstruction syndromes. In addition to its diagnostic utility, direct measurement of colonic motor activity can be valuable in deciding the need for and timing of diversion, the extent of resection, and the suitability of the patient for restoring bowel continuity. In Hirschsprung's disease, total colonic manometry can potentially be used to determine suitability for primary neonatal pull-through versus a staged approach. J Pediatr Surg 36:1757-1763.

Issues in system boundary definition for substance flow analysis: the case of nitrogen cycle management in Catalonia

The great complexity of the nitrogen cycle, including anthropogenic contributions, makes it necessary to carry out local studies, which allow us to identify the specific cause-effect links in a particular society. Models of local societies that are based on methods such as Substance Flow Analysis (SFA), which study and characterise the performance of metabolic exchanges between human society and the environment, are a useful tools for directing local policy towards sustainable management of the nitrogen cycle. In this paper, the selection of geographical boundaries for SFA application is discussed. Data availability and accuracy, and the possibility of linking the results with instructions for decision making, are critical aspects for proper scale selection. The experience obtained in the construction of the model for Catalonia is used to draw attention to the difficulties found in regional studies.

A human CD46 transgenic pig model system for the study of discordant xenotransplantation

BACKGROUND

The chronic shortage in the supply of human organs available for allotransplantation has turned attention toward the use of animals as potential donors, with pigs as the most likely species under consideration. Hyperacute rejection, the initial and immediate barrier to a pig-to-primate xenograft, has been addressed by generation of transgenic pigs that express the human membrane-bound complement-regulatory proteins CD59 and/or CD55. Difficulty has been encountered in generation of transgenic animals that express a third membrane-bound complement-regulatory protein, CD46.

METHODS

We have generated transgenic animals by using a large genomic construct that encompasses the entire human CD46 gene.

RESULTS

We report the first description of transgenic mice and pigs that express high levels of human CD46 in a cell and tissue type-specific manner, resembling patterns of endogenous CD46 expression observed in human tissues. Furthermore, when human CD46 transgenic porcine hearts were transplanted into baboons, the grafts did not succumb to hyperacute rejection, and survival extended for up to 23 days. Under the same conditions, nontransgenic grafts underwent hyperacute rejection within 90 min.

CONCLUSIONS

This is the first report to describe generation of transgenic pigs that express human CD46, and the first in vivo demonstration of the ability of human CD46 expressed on pig organs to regulate complement activation and overcome hyperacute rejection upon transplantation of a vascularized organ into nonhuman primates.

Simulating the growth response of aspen to elevated ozone: a mechanistic approach to scaling a leaf-level model of ozone effects on photosynthesis to a complex canopy architecture

Predicting ozone-induced reduction of carbon sequestration of forests under elevated tropospheric ozone concentrations requires robust mechanistic leaf-level models, scaled up to whole tree and stand level. As ozone effects depend on genotype, the ability to predict these effects on forest carbon cycling via competitive response between genotypes will also be required. This study tests a process-based model that predicts the relative effects of ozone on the photosynthetic rate and growth of an ozone-sensitive aspen clone, as a first step in simulating the competitive response of genotypes to atmospheric and climate change. The resulting composite model simulated the relative above ground growth response of ozone-sensitive aspen clone 259 exposed to square wave variation in ozone concentration. This included a greater effect on stem diameter than on stem height, earlier leaf abscission, and reduced stem and leaf dry matter production at the end of the growing season. Further development of the model to reduce predictive uncertainty is discussed.

Melatonin profiles and sleep characteristics in boys with fragile X syndrome: a preliminary study

Sleep patterns and endogenous melatonin profiles in 13 fragile X boys between the age of 4.7 and 11.0 years were compared to those of 8 age-matched, normal control boys. Parents recorded sleep patterns on a Sleep Diary Chart for 14 consecutive days. Twelve saliva samples were obtained from 8 fragile X participants and all of the controls over 48 hours for the assessment of salivary melatonin profiles. The results showed greater variability in total sleep time and difficulty in sleep maintenance in fragile X boys compared with the control participants. Nocturnal melatonin production, expressed as both peak level and area under the concentration-time curve between 20:00 h and 08:00 h, were found to be significantly larger in fragile X boys than in controls. Additionally, the mean of the minimum daytime melatonin levels recorded was significantly higher for the fragile X group. Elevated levels in some fragile X boys relative to the range seen in controls, occurring either during the day or at night, or in both segments of the secretory profile for some individuals, may be due in part to overactivity of the sympathetic nervous system. Alternative molecular mechanisms leading to changes in melatonin profiles in fragile X are also discussed.

Development of in vivo-matured porcine oocytes following intracytoplasmic sperm injection

The objective of this study was to assess the development of porcine ova fertilized by intracytoplasmic sperm injection (ICSI). Allyl trenbolone (Regumate) was used to synchronize estrus in 13 postpuberal gilts. Gilts were superovulated with pregnant mare serum gonadotropin and hCG. Ova were aspirated from 5- to 8-mm follicles at 36 h after hCG. Cumulus cells were removed by blunt dissection and pipetting in Beltsville embryo culture medium (BECM) supplemented with 0.1% hyaluronidase. Sperm were washed and resuspended in BECM + 8% polyvinylpyrrolidone. Ova (n = 237) that exhibited a polar body were centrifuged at 15 000 x g for 6 min and injected with a single spermatozoon. One hundred fifty-four ova were cultured in NCSU-23 medium in a 5% CO(2) in air environment for 168 h. Ova were fixed in acetic acid/ethanol and stained with 1% orcein. Sixty-nine ICSI ova were cultured for 24 h and transferred (mean = 23) to three recipients. Eighty-one ova (69%) that survived ICSI cleaved within 48 h. Thirty-eight percent (31/81) of these ova became blastocysts (mean +/- SEM = 24.7 +/- 1.1 cells). One recipient gave birth to three pigs. These results demonstrate that porcine embryos derived from ICSI can develop into live pigs.

CD46 transgene expression in pig peripheral blood mononuclear cells does not alter their susceptibility to measles virus or their capacity to downregulate endogenous and transgenic CD46

CD46 (or membrane cofactor protein) protects autologous cells from complement-mediated lysis and has been expressed as a transgene in pigs to overcome complement-mediated hyperacute rejection of porcine organs upon transplantation into primates. Since CD46 has been identified as a receptor for measles virus (MV), the susceptibility of CD46-transgenic (tg) pig peripheral blood mononuclear cells (PBMC) to infection with MV strains which do and do not use CD46 as receptor was investigated. Surprisingly, it was found that MV vaccine strains (e.g. Edmonston) bound to tg as well as non-tg pig PBMC. Phytohaemagglutinin-stimulated CD46-tg and non-tg pig PBMC were equally well infected with MV vaccine strains irrespective of CD46 expression. Upon infection, tg CD46 was downregulated from the cell surface. In contrast, the binding capacity for MV wild-type strains to pig and human PBMC was low, irrespective of CD46 expression. These MV strains did not infect tg or non-tg pig cells. Expression of endogenous pig CD46 was detected with polyclonal sera against human CD46. After infection of pig PBMC with MV strain Edmonston, endogenous pig CD46 was also downregulated. This suggests an interaction between MV Edmonston and pig CD46. However, polyclonal CD46 sera did not inhibit infection with MV Edmonston indicating that CD46 may not exclusively act as a receptor for MV on these cells. Interestingly, similar results were observed using human PBMC. Data suggest that CD46 downregulation after interaction with MV may also occur in porcine organs which express endogenous and/or human CD46 as a means of protection against complement-mediated damage.

The role SWISS-PROT and TrEMBL play in the genome research environment

SWISS-PROT, a curated protein sequence data bank, contains not only sequence data but also annotation relevant to a particular sequence. The annotation added to each entry is done by a team of biologists and comes, primarily, from articles in journals reporting the actual sequencing and sometimes characterisation. Review articles and collaboration with external experts also play a role along with the use of secondary databases like PROSITE and Pfam in addition to a variety of feature prediction methods. Annotation added by these methods is checked for relevance and likelihood to a particular sequence. The onset of genome sequencing has led to a dramatic increase in sequence data to be included in SWISS-PROT. This has led to the production of TrEMBL (Translation of the EMBL database). TrEMBL consists of entries in a SWISS-PROT format that are derived from the translation of all coding sequences in the EMBL nucleotide sequence database, that are not in SWISS-PROT. Unlike SWISS-PROT entries those in TrEMBL are awaiting manual annotation. However, rather than just representing basic sequence and source information, steps have been taken to add features and annotation automatically. In taking these steps it is hoped that TrEMBL entries are enhanced with some indication as to what a protein is, could or may be.

Metabolism of antisense oligonucleotides in rat liver homogenates

Phosphorothioate antisense oligodeoxynucleotides are novel therapeutic agents designed to selectively and specifically inhibit production of various disease-related gene products. In vivo pharmacokinetic experiments indicate that these molecules are widely distributed in many species, with the majority of oligomers accumulating within liver and kidney. To better understand the metabolism of these agents, we studied the stability of several phosphorothioate oligodeoxynucleotides, their congeners, and second generation oligomer chemistries in rat liver homogenates. To examine metabolism, background nuclease activity was characterized in whole liver homogenates by using ISIS 1049, a 21-mer phosphodiester oligodeoxynucleotide. Nuclease activity could readily be detected in liver homogenates. Under optimized conditions, the predominant enzymatic activity was 3'-exonucleolytic and could be influenced by pH and ionic conditions. However, in addition to 3' exonucleases, 5' exo- and endonuclease activities were also observed. Our data indicate that metabolism of phosphorothioate oligodeoxynucleotides was more complex than that of phosphodiesters for many reasons, including phosphorothioate oligodeoxynucleotide inhibition of nucleases and the presence of R(p) and S(p) stereoisomers. The rate of phosphorothioate metabolism also appeared to be influenced by sequence, with pyrimidine-rich compounds being metabolized to a greater extent than purine-rich oligomers. Other factors affecting stability included oligomer chemistry and length. Concomitant experiments performed in rats dosed systemically with the same compounds mimic the activities seen in vitro and suggest that this liver homogenate system is a valuable model with which to study the mechanism of metabolism of antisense oligonucleotides.

13C-urea breath test for the diagnosis of Helicobacter pylori infection before treatment: is citric acid necessary?

AIM

13C-urea breath test is one of the best methods for the diagnosis of Helicobacter pylori infection. Although a citric acid solution is generally used prior to urea intake, the superiority of this strategy has not been sufficiently demonstrated. Thus, our aim was to compare 13C-urea breath test with and without citric acid solution, to evaluate whether 13C-urea breath test can also achieve favourable results when the test meal is omitted.

METHODS

13C-urea breath test with and without citric acid were compared prospectively in 53 subjects without prior Helicobacter pylori eradication therapy prescription. Basal samples and at 15', 30', and 45' after taking 100 mg of 13C-urea were obtained. The gold standard for Helicobacter pylori diagnosis was the 13C-urea breath test result with citric acid at 30', and "Delta Over Baseline" values >5 at that time were considered positive.

RESULTS

The prevalence of Helicobacter pylori infection was 68%. Mean Delta Over Baseline values with citric acid at 15', 30' and 45' were: 29.6+/-39, 30.8+/-37 and 24.6+/-27; whereas respective values without citric acid were lower: 14.9+/-22, 12.2+/-17 and 10D+/-13 (p<O. 001 for all comparisons, Wilcoxon test for paired data). Thus, the area under the curve (constructed with Delta Over Baseline values at different times) with citric acid was 85+/- 102, and 37+/-50 without citric acid [p<0.001). Correlation coefficient between Delta Over Baseline values with and without citric acid at 30' was 0.73 (p<0.0001). The percentage of subjects achieving the highest Delta Over Baseline value at 15', 30' and 45' with citric acid was 51%, 30% and 19%, whereas without citric acid it was 51%, 26% and 23% (non-significant differences). The area under receiver operating characteristic curve for 13C-urea breath test without citric acid was: 0.98 at 15', 1 at 30' and 0.97 at 45'. The best cut-off point for 13C-urea breath test without citric acid at 30' was anywhere between 3. 3 and 3.9 (that is, a lower value than that usually considered with citric acid), with 100% (95% confidence interval, 90-100%) sensitivity and 100% [82-100%) specificity

CONCLUSIONS

13C-urea breath test values with citric acid are higher than those obtained without citric acid, although this difference does not imply a diagnostic superiority in untreated patients when considering 13C-urea breath test without citric acid at 30'. Therefore, for the diagnosis of Helicobacter pylori infection in untreated patients, citric acid solution in 13C-urea breath test protocol can be omitted.

Angiogenic cytokines in mesothelioma: a study of VEGF, FGF-1 and -2, and TGF beta expression

Vascular endothelial growth factor (VEGF), acidic and basic fibroblast growth factors (FGF-1 and -2), and transforming growth factor beta (TGFbeta) are potent angiogenic cytokines. Malignant mesothelioma of the pleura presents with a high intra-tumoural microvascular density (IMD) which also has prognostic relevance. This study was designed to verify the immunohistochemical expression of the angiogenic cytokines in mesothelioma as well as in non-neoplastic human mesothelial cells and to study the individual as well as the combined expression of these cytokines in mesothelioma in relation to both IMD and prognosis. In addition, four mesothelioma cell lines were studied by ELISA for the secretion of VEGF and FGF-2 in their supernatants and were shown to contain high levels of both of these cytokines. Immunohistochemically, VEGF, FGF-1 and -2, and TGFbeta immunoreactivity was present in 81, 67, 92 and 96 per cent of mesotheliomas, and in 20, 50, 40, and 10 per cent of samples of the non-neoplastic mesothelium, respectively. Co-ordinate expression of the cytokines was observed whereby mesotheliomas expressed more than one cytokine. The combined immunohistochemical expression levels for all four cytokines correlated significantly with both IMD (p=0.01) and prognosis (p=0. 0013). When studied individually, high FGF-2 expression correlated best with more tumour aggressiveness and worse prognosis for mesothelioma (p=0.0011). There was no significant correlation between prognosis and immunoexpression of VEGF (p=0.07), FGF-1 (p=0.3), or TGFbeta (p=0.1), or between IMD and any of the cytokines studied individually. These data support the assertion that selective angiogenic cytokines might contribute to the progressive changes of mesothelioma by tumour angiogenesis.

Return of the internal jugular vein--development of collateral drainage following neonatal ligation of the vein

The development of collateral venous drainage in the neck of a child, who as a neonate had undergone ligation and cannulation of the right internal jugular vein, is described. The resultant vessels were of sufficient calibre to be considered as potential sites for vascular access, although it is possible that their course in the thorax may preclude correct placement of a central venous catheter. Nevertheless, we feel that this case further illustrates the benefit of hand-held ultrasonography in visualizing the vascular structures of the neck. Moreover, ligation of a vein in the neonatal period should not be a contraindication to subsequent assessment of that site for vascular access.

Removing redundancy in SWISS-PROT and TrEMBL

SUMMARY

One of the distinguishing criteria of the SWISS-PROT protein sequence data bank is minimal redundancy. The introduction of TrEMBL as a supplementary database ensured the comprehensiveness of SWISS-PROT and TrEMBL but introduced some degree of redundancy. We developed a strategy to identify the redundancy present within and between SWISS-PROT and TrEMBL and its subsequent removal.

AVAILABILITY

The tools mentioned in this paper are available on request.