Contrast-enhanced MRI of the temporomandibular joint: findings in children without juvenile idiopathic arthritis.

BACKGROUND: Contrast-enhanced magnetic resonance imaging (MRI) is highly sensitive for assessing temporomandibular joint (TMJ) involvement in juvenile idiopathic arthritis (JIA), but only sparse data exist on normal TMJ appearance in children. PURPOSE: To determine normal MRI appearance and enhancement pattern of pediatric TMJ as basis for diagnosing early arthritis. MATERIAL AND METHODS: In 27 children (age range, 1.2-16.8 years) without TMJ pathology undergoing head MRI, fat-saturated T2-weighted (T2W) and postcontrast fat-saturated T1-weighted (T1W) images sagittally aligned to the 54 TMJs, besides standard T1W and T2W images, were assessed for bony and soft tissue signal intensity (SI), the amount of perceptible joint fluid, and contrast enhancement (CE). RESULTS: Bone marrow SI and CE of the mandible were consistent with varying degrees of residual red marrow in 96% of joints. The mandibular condyles were mostly isointense to the ramus, but in 9% showed mild edema-like bone marrow SI and CE. Small amounts of intraarticular fluid were detected in 31% on T2W images without fat saturation and in 83% on T2W images with fat saturation as fine lines in the upper or lower joint compartment or as small dots in an articular recess. Seventy-nine percent of all TMJs showed intense joint enhancement on early images restricted to areas of intraarticular fluid. CONCLUSION: Small amounts of joint fluid with intense CE are a common MRI finding in TMJs of children without JIA and therefore should not be considered diagnostic for early arthritis.

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef).

BACKGROUND: Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. RESULTS: The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. CONCLUSIONS: It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.

Development of neuromotor functions in very low birth weight children from six to 10 years of age: patterns of change.

AIM: To assess patterns of change for different neuromotor functions in very low birth weight (VLBW) children during school age and to identify factors associated with improvement. METHODS: In a longitudinal study, we examined 65 prospectively enrolled VLBW children (38 female, 59%) without cerebral palsy at age six and 10 years. Measures included the evaluation of timed motor performance and motor overflow (MO) for the motor components of the Zurich Neuromotor Assessment (pure motor-, adaptive fine- and gross motor tasks, static balance) and a standardized neurological examination. Variables associated with improvement were assessed by multiple regression analyses. RESULTS: Between six and 10 years, adaptive fine motor tasks (40% vs. 17% of children scoring below 10th percentile) and MO (77% vs. 55%) improved significantly (both p<0.01), while all other components remained stable (pure motor 23% vs. 25%, adaptive gross motor 26% vs. 34%, static balance 18% vs. 20%, respectively). Mild neurological abnormalities at 6 years of age were associated with less improvement. CONCLUSION: Neuromotor functions improve in some children potentially reflecting catch up of maturational delay. However, the majority of neuromotor functions remain abnormal in a significant proportion of VLBW children.

Use of intravital microscopy to study the microvascular behavior of microbubble-based ultrasound contrast agents.

PURPOSE: The study describes the use of intravital microscopy (IVM) to assess the behavior of ultrasound contrast agents (UCAs), including targeted UCAs, in the microcirculation of rodents. MATERIALS AND METHODS: IVM was performed on various exteriorized organs: hamster cheek pouch, rat mesentery, liver, spinotrapezius muscle, and mouse cremaster muscle. A dorsal skin-fold chamber with MatBIII tumor cells was also implanted in rats. Nontargeted UCAs (SonoVue(®) and BR14) and targeted UCAs (BR55 and P-selectin targeted microbubbles) were tested. IVM was used to measure microbubble size, determine their persistence, and observe their behavior in the blood circulation. RESULTS: Intravenous and intra-arterial injections of high doses of UCAs did not modify the local microvascular hemodynamics. No microbubble coalescence and no increased size were observed. Adhesion of some microbubbles to leukocytes was observed in various microcirculation models. Microbubbles are captured by Kupffer cells in the liver. Targeted microbubbles were shown to adhere specifically to endothelial receptors without compromising local blood flow. CONCLUSION: These results support the safety of both targeted and nontargeted UCAs as no microvascular flow alteration or plugging of microvessels were observed. They confirm that binding observed with targeted microbubbles are due to the binding of these microbubbles to specific endothelial receptors.

Quantification and monitoring of inflammation in murine inflammatory bowel disease with targeted contrast-enhanced US.

PURPOSE: To evaluate ultrasonography (US) by using contrast agent microbubbles (MBs) targeted to P-selectin (MB(P-selectin)) to quantify P-selectin expression levels in inflamed tissue and to monitor response to therapy in a murine model of chemically induced inflammatory bowel disease (IBD). MATERIALS AND METHODS: All procedures in which laboratory animals were used were approved by the institutional administrative panel on laboratory animal care. Binding affinity and specificity of MB(P-selectin) were tested in cell culture experiments under flow shear stress conditions and compared with control MBs (MB(Control)). In vivo binding specificity of MB(P-selectin) to P-selectin was tested in mice with trinitrobenzenesulfonic acid-induced colitis (n = 22) and control mice (n = 10). Monitoring of anti-tumor necrosis factor α antibody therapy was performed over 5 days in an additional 30 mice with colitis by using P-selectin-targeted US imaging, by measuring bowel wall thickness and perfusion, and by using a clinical disease activity index score. In vivo targeted contrast material-enhanced US signal was quantitatively correlated with ex vivo expression levels of P-selectin as assessed by quantitative immunofluorescence. RESULTS: Attachment of MB(P-selectin) to endothelial cells was significantly (P = .0001) higher than attachment of MB(Control) and significantly (ρ = 0.83, P = .04) correlated with expression levels of P-selectin on endothelial cells. In vivo US signal in mice with colitis was significantly higher (P = .0001) with MB(P-selectin) than with MB(Control). In treated mice, in vivo US signal decreased significantly (P = .0001) compared with that in nontreated mice and correlated well with ex vivo P-selectin expression levels (ρ = 0.69; P = .04). Colonic wall thickness (P ≥ .06), bowel wall perfusion (P ≥ .85), and clinical disease activity scoring (P ≥ .06) were not significantly different between treated and nontreated mice at any time. CONCLUSION: Targeted contrast-enhanced US imaging enables noninvasive in vivo quantification and monitoring of P-selectin expression in inflammation in murine IBD.

Cationic versus neutral microbubbles for ultrasound-mediated gene delivery in cancer.

PURPOSE: To test whether plasmid-binding cationic microbubbles (MBs) enhance ultrasound-mediated gene delivery efficiency relative to control neutral MBs in cell culture and in vivo tumors in mice. MATERIALS AND METHODS: Animal studies were approved by the institutional animal care committee. Cationic and neutral MBs were characterized in terms of size, charge, circulation time, and DNA binding. Click beetle luciferase (CBLuc) reporter plasmids were mixed with cationic or neutral MBs. The ability of cationic MBs to protect bound plasmids from nuclease degradation was tested by means of a deoxyribonuclease (DNase) protection assay. Relative efficiencies of ultrasound-mediated transfection (ultrasound parameters: 1 MHz, 1 W/cm(2), 20% duty cycle, 1 minute) of CBLuc to endothelial cells by using cationic, neutral, or no MBs were compared in cell culture. Ultrasound-mediated gene delivery to mouse hind limb tumors was performed in vivo (n = 24) with insonation (1 MHz, 2 W/cm(2), 50% duty cycle, 5 minutes) after intravenous administration of CBLuc with cationic, neutral, or no MBs. Tumor luciferase activity was assessed by means of serial in vivo bioluminescence imaging and ex vivo analysis. Results were compared by using analysis of variance. RESULTS: Cationic MBs (+15.8 mV; DNA binding capacity, 0.03 pg per MB) partially protected bound DNA from DNase degradation. Mean CBLuc expression of treated endothelial cells in culture was 20-fold higher with cationic than with neutral MBs (219.0 relative light units [RLUs]/µg protein ± 92.5 [standard deviation] vs 10.9 RLUs/µg protein ± 2.7, P = .001) and was significantly higher (P < .001) than that in the no MB and no ultrasound control groups. Serial in vivo bioluminescence of mouse tumors was significantly higher with cationic than with neutral MBs ([5.9 ± 2.2] to [9.3 ± 5.2] vs [2.4 ± 0.8] to [2.9 ± 1.1] × 10(4) photons/sec/cm(2)/steradian, P < .0001) and versus no MB and no ultrasound controls (P < .0001). Results of ex vivo analysis confirmed these results (ρ = 0.88, P < .0001). CONCLUSION: Plasmid-binding cationic MBs enhance ultrasound-mediated gene delivery efficiency relative to neutral MBs in both cell culture and mouse hind limb tumors.

Spinal arachnoid cysts: A case series & systematic review of the literature.

Introduction: Spinal arachnoid cysts (SACs) are rare lesions with challenging and controversial management. Research question: We analyzed our experiences from a case series and provide a systematic review to determine 1) Demographic and clinical features of SACs, 2) Optimal imaging for diagnosis and operative planning, 3) Optimal management of SACs, and 4) Clinical outcomes following surgery. Materials and methods: A single-institution, ambispective analysis of patients with symptomatic SACs surgically managed between May 2005 and May 2019 was performed. Data were collected as per local ethics committee stipulations. A systematic review of SACs in adults was performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and a preapproved protocol. Results: Our series consisted of 11 patients, M:F 8:3, mean age 47.8 years (range 18-73 years). Mean follow-up was 19 months (range 5-36 months). SACs were excised or marsupialised (7), fenestrated (3) or partially excised (1). Eight patients had expansile duroplasty, 3 primary dural closure. One patient had a cystoperitoneal shunt. All patients were AIS D preoperatively; 4 remained unchanged and 7 improved to AIS E at follow-up. Our systematic search retrieved 725 citations. Fourteen case series met the inclusion criteria. There was no evidence to support superiority of one surgical strategy over another. Surgery for symptomatic patients resulted in positive clinical outcomes. Discussion and conclusions: Symptomatic SACs require surgical intervention. Limited evidence suggests that decompressing the cord, breakdown of arachnoid adhesions, and establishing CSF flow by consideration of expansile duroplasty are important for positive outcomes.

Prevalence of Neck Pain in Patients with Degenerative Cervical Myelopathy and Short-Term Response After Operative Treatment: A Cohort Study of 664 Patients From 26 Global Sites.

STUDY DESIGN: Ambispective cohort study. OBJECTIVES: 1) To define the prevalence of neck pain in patients with degenerative cervical myelopathy (DCM). 2) To identify associated factors of preoperative neck pain in patients with DCM. 3) To assess the neck pain response to surgical intervention. METHODS: 757 patients with DCM were enrolled at 26 global sites from 2005 to 2011. A total of 664 patients had complete neck pain scores preoperatively (Neck Disability Index, NDI). The prevalence and severity of neck pain preoperatively and at the 6-months follow-up was summarized. Functional assessments of individuals with and without pain were compared. Associations of preoperative neck pain and related factors were evaluated. RESULTS: Preoperatively, 79.2% of patients reported neck pain while 20.8% had no neck pain. Of individuals with neck pain, 20.2% rated their pain as very mild, 27.9% as moderate, 19.6% as fairly severe, 9.6% as very severe and 1.9% as the worst imaginable. Functional status (mJOA), number of stenotic levels, age, and duration of symptoms did not significantly differ in patients with and without pain. Factors associated with the presence of neck pain were female gender, BMI ≥27 kg/m2, rheumatologic and gastrointestinal comorbidities, and age <57 years. Neck pain improved significantly from the preoperative examination to the 6-months postoperative follow-up (P < .0001). CONCLUSION: Here, we demonstrate a high prevalence of neck pain in patients with DCM as well as a link between gender, body weight, comorbidity and age. We highlight a significant reduction in neck pain 6 months after surgery.

Molecular and functional ultrasound imaging in differently aggressive breast cancer xenografts using two novel ultrasound contrast agents (BR55 and BR38).

OBJECTIVES: To characterise clinically translatable long-circulating (BR38) and VEGFR2-targeted (BR55) microbubbles (MB) and to assess their ability to discriminate breast cancer models with different aggressiveness. METHODS: The circulation characteristics of BR38 and BR55 were investigated in healthy mice. The relative blood volume (rBV) of MDA-MB-231 (n = 5) or MCF-7 (n = 6) tumours was determined using BR38. In the same tumours in-vivo binding specificity of BR55 was tested and VEGFR2 expression assessed. Data validation included quantitative immunohistological analysis. RESULTS: BR38 had a longer blood half-life than BR55 (>600 s vs. 218 s). BR38-enhanced ultrasound showed greater vascularisation in MDA-MB-231 tumours (p = 0.022), which was in line with immunohistology (p = 0.033). In-vivo competitive binding experiments proved the specificity of BR55 to VEGFR2 (p = 0.027). Binding of BR55 was significantly higher in MDA-MB-231 than in MCF-7 tumours (p = 0.049), which corresponded with the VEGFR2 levels found histologically (p = 0.015). However, differences became smaller when normalising the levels of BR55 to the rBV. CONCLUSIONS: BR38 and BR55 are well suited to characterising and distinguishing breast cancers with different angiogenesis and aggressiveness. Long-circulating BR38 MB allow extensive 3-dimensional examinations of larger or several organs. BR55 accumulation faithfully reflects the VEGFR2 status in tumours and depicts even small differences in angiogenesis.

Antiangiogenic cancer therapy: monitoring with molecular US and a clinically translatable contrast agent (BR55).

PURPOSE: To develop and test human kinase insert domain receptor (KDR)-targeted microbubbles (MBs) (MB(KDR)) for imaging KDR at the molecular level and for monitoring antiangiogenic therapy in a human colon cancer xenograft tumor model in mice. MATERIALS AND METHODS: Animal studies were approved by the Institutional Administrative Panel on Laboratory Animal Care. A heterodimeric peptide that binds to human KDR with low nanomolar affinity (K(D) = 0.5 nmol/L) was coupled onto the surface of perfluorobutane-containing lipid-shelled MBs (MB(KDR)). Binding specificity of MB(KDR) to human KDR and cross-reactivity with murine vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2) were tested in cell culture under flow shear stress conditions (at 100 sec(-1)). In vivo binding specificity of MB(KDR) to VEGFR2 was tested in human LS174T colon cancer xenografts in mice with a 40-MHz ultrasonographic (US) transducer. Targeted contrast material-enhanced US imaging signal by using MB(KDR) was longitudinally measured during 6 days in tumors with (n = 6) and without (n = 6) antiangiogenic treatment (anti-VEGF antibody). Ex vivo VEGFR2 staining and microvessel density analysis were performed. Significant differences were evaluated (t, Mann-Whitney, or Wilcoxon test). RESULTS: Cell culture experiments showed four times greater binding specificity of MB(KDR) to human KDR and cross-reactivity to murine VEGFR2 (P < or = .01). In vivo imaging signal was more than three times higher (P = .01) with MB(KDR) compared with control MBs and decreased significantly (approximately fourfold lower, P = .03) following in vivo receptor blocking with anti-VEGFR2 antibody. One day after initiation of antiangiogenic therapy, imaging signal was significantly decreased (approximately 46% lower, P = .02) in treated versus untreated tumors; it remained significantly lower (range, 46%-84% decreased; P = .038) during the following 5 days. Microvessel density was significantly reduced (P = .04) in treated (mean, 7.3 microvessels per square millimeter +/- 4.7 [standard deviation]) versus untreated tumors (mean, 22.0 microvessels per square millimeter +/- 9.4); VEGFR2 expression was significantly decreased (>50% lower, P = .03) in treated tumors. CONCLUSION: Human MB(KDR) allow in vivo imaging and longitudinal monitoring of VEGFR2 expression in human colon cancer xenografts.

Dynamic visualization of lymphatic channels and sentinel lymph nodes using intradermal microbubbles and contrast-enhanced ultrasound in a swine model and patients with breast cancer.

OBJECTIVE: Sentinel lymph node (SLN) identification using intradermal micro-bubbles and contrast-enhanced ultrasound (CEUS) has been recently reported in swine models and patients with breast cancer. The objective of this study was to investigate the dynamics of intradermally administered microbubbles as they travel to draining SLNs in pigs. We also performed a detailed study of the passage of microbubbles through breast lymphatic channels in a small group of patients with breast cancer. METHODS: Nine anesthetized healthy pigs were used for the study, and 5 female patients with primary breast cancer were recruited. Pigs received intradermal injections of a microbubble contrast agent in several territories to access lymphatic drainage to regional lymph nodes. Patients had periareolar intradermal injection of the microbubble contrast agent. Ultrasound examination was performed in the real-time contrast pulse sequencing mode with a commercial scanner. RESULTS: Sentinel lymph nodes were identified rapidly (<1 minute) and consistently in pigs. Intradermal microbubble injection and CEUS were found to have perfect concordance with the Evans blue dye method in locating swine SLNs. In all 5 patients with breast cancer, the microbubble contrast agent entered breast lymphatic channels and traveled to draining ipsilateral axillary SLNs within 3 minutes. CONCLUSIONS: Intradermally injected microbubbles traverse readily though lymphatic channels in pigs and human breast tissue. The ability to rapidly identify SLNs in the diagnostic period would enable targeted biopsy and may facilitate preoperative axillary staging in patients with early breast cancer.

The ultrasound-assisted oxidative scission of monoenic fatty acids by ruthenium tetroxide catalysis: influence of the mixture of solvents.

Carboxylic acids and diacids were synthesized from monoenic fatty acids by using RuO4 catalysis, under ultrasonic irradiation, in various mixtures of solvents. Ultrasound associated with Aliquat 336 have promoted in water, the quantitative oxidative cleavage of the CH=CH bond of oleic acid. A design of experiment (DOE) shows that the optimal mixture of solvents (H2O/MeCN, ratio 1/1, 2.2% RuCl3/4.1 eq. NaIO4) gives 81% azelaic acid and 97% pelargonic acid. With the binary heterogeneous mixture H2O/AcOEt, the oxidation of the oleic acid leads to a third product, the alpha-dione 9,10-dioxostearic acid.

Molecular imaging and ultrasound-assisted drug delivery.

Ultrasound imaging is undergoing a major revolution, about to bring this modality well beyond its established role as a low-cost noninvasive real-time imaging modality. Particularly important has been the commercial availability of microbubble-based contrast agents. Several new indications for contrast ultrasound have been developed and have entered clinical practice. The characterization of focal liver lesions and the follow-up of antiangiogenic therapy are two applications that will have a major impact in medical practice. Others, such as prostate cancer diagnosis, are still under investigation and need to be clinically validated. Thanks to its outstanding sensitivity, contrast-enhanced ultrasound is also geared to become the preferred modality for molecular imaging of diseases occurring at the vascular level. Angiogenesis, inflammation, and other endothelial dysfunctions are important targets that can be imaged and investigated with targeted microbubbles. In the field of prostate cancer, targeted agents will facilitate detection and provide additional information on tumor size, and hopefully on aggressiveness as well. Ultrasound can also play a role to deliver drugs or genes locally. This is an exciting area that has become an important field of research. Imaging and drug delivery can be performed simultaneously, thereby achieving the release of a drug, at the site where it is needed, in a most efficient way.

Optimization of the indole photodegradation on supported TiO(2): influences of temperature, concentration, TiO(2) amount and flow rate.

This work describes the photodegradation of aqueous indole solutions by using TiO(2) supported on cellulose fibres. Four parameters were studied: the indole concentration; the TiO(2) amount; the temperature and the flow rate. Central composite experimental design was used to determine the influences of the parameters on the indole degradation percentage. We demonstrate that in our experimental domain the quasi complete degradation of indole is in all cases reached and more interestingly that it is possible to find unique values of TiO(2) amount and flow rate leading to optimised photodegradation of indole in the studied domains of temperature and indole concentration.

The Barrow Neurological Institute Grading Scale as a Predictor for Delayed Cerebral Ischemia and Outcome After Aneurysmal Subarachnoid Hemorrhage: Data From a Nationwide Patient Registry (Swiss SOS).

BACKGROUND: The Barrow Neurological Institute (BNI) scale is a novel quantitative scale measuring maximal subarachnoid hemorrhage (SAH) thickness to predict delayed cerebral ischemia (DCI). This scale could replace the Fisher score, which was traditionally used for DCI prediction. OBJECTIVE: To validate the BNI scale. METHODS: All patient data were obtained from the prospective aneurysmal SAH multicenter registry. In 1321 patients, demographic data, BNI scale, DCI, and modified Rankin Scale (mRS) score up to the 1-yr follow-up (1FU) were available for descriptive and univariate statistics. Outcome was dichotomized in favorable (mRS 0-2) and unfavorable (mRS 3-6). Odds ratios (OR) for DCI of Fisher 3 patients (n = 1115, 84%) compared to a control cohort of Fisher grade 1, 2, and 4 patients (n = 206, 16%) were calculated for each BNI grade separately. RESULTS: Overall, 409 patients (31%) developed DCI with a high DCI rate in the Fisher 3 cohort (34%). With regard to the BNI scale, DCI rates went up progressively from 26% (BNI 2) to 38% (BNI 5) and corresponding OR for DCI increased from 1.9 (1.0-3.5, 95% confidence interval) to 3.4 (2.1-5.3), respectively. BNI grade 5 patients had high rates of unfavorable outcome with 75% at discharge and 58% at 1FU. Likelihood for unfavorable outcome was high in BNI grade 5 patients with OR 5.9 (3.9-8.9) at discharge and OR 6.6 (4.1-10.5) at 1FU. CONCLUSION: This multicenter external validation analysis confirms that patients with a higher BNI grade show a significantly higher risk for DCI; high BNI grade was a predictor for unfavorable outcome at discharge and 1FU.

Molecular imaging of human thrombus with novel abciximab immunobubbles and ultrasound.

BACKGROUND AND PURPOSE: Molecular imaging of therapeutic interventions with targeted agents that simultaneously carry drugs or genes for local delivery is appealing. We investigated the ability of a novel microbubble carrier (immunobubble) for abciximab, a glycoprotein IIb/IIIa receptor inhibitor, for ultrasonographic molecular imaging of human clots. METHODS: Human thrombi were incubated with immunobubbles conjugated with abciximab. Control clots were incubated in either saline or with immunobubbles conjugated with nonspecific antibody. We evaluated immunobubble suspensions with variable concentrations of encapsulated gas and measured mean acoustic intensity of the incubated clots. In vivo molecular imaging of human thrombi with abciximab immunobubbles was evaluated in a rat model of carotid artery occlusion. RESULTS: Mean acoustic intensity was significantly higher for abciximab immunobubbles as compared with control immunobubbles under all conditions tested with maximum difference in intensity at a gas volume of 0.2 microL (P=0.0013 for mechanical index 0.05, P=0.0001 for mechanical index 0.7). Binding of abciximab immunobubbles to clots in vitro led to enhanced echogenicity dependent on bubble concentration. In vivo ultrasonic detectability of carotid thrombi was significantly higher for clots targeted with abciximab immunobubbles (P<0.05). Quantification of in vivo contrast enhancement displayed a highly significant increment for abciximab immunobubble-targeted clots compared with nonspecific immunobubble-targeted clots (P<0.0001) and to native clots (P<0.0001). CONCLUSIONS: This study demonstrates the feasibility of using a therapeutic agent for selective targeting in vascular imaging. Abciximab immunobubbles improve visualization of human clots both in vitro and in an in vivo model of acute arterial thrombotic occlusion.

UniProtKB/Swiss-Prot.

The Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI), and the Protein Information Resource (PIR) form the Universal Protein Resource (UniProt) consortium. Its main goal is to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB) and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc). (1) UniProtKB is a comprehensive protein sequence knowledgebase that consists of two sections: UniProtKB/Swiss-Prot, which contains manually annotated entries, and UniProtKB/TrEMBL, which contains computer-annotated entries. UniProtKB/Swiss-Prot entries contain information curated by biologists and provide users with cross-links to about 100 external databases and with access to additional information or tools. (2) The UniRef databases (UniRef100, UniRef90, and UniRef50) define clusters of protein sequences that share 100, 90, or 50% identity. (3) The UniParc database stores and maps all publicly available protein sequence data, including obsolete data excluded from UniProtKB. 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 2 weeks. The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry, paying particular attention to the specificities of plant protein annotation. We will also present some of the tools and databases that are linked to each entry.

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.

Hydrodemetallation and Hydrodesulfurization Spent Catalysts Elemental Analysis: Comparison of Wavelength Dispersive X-ray Fluorescence and Atomic Emission Spectrometries.

Petroleum industries continuously consume catalysts on very large scales. The recycling of spent catalysts is thus of major economic and environmental importance and its first step consists of the characterization of the valuable metal content. Wavelength dispersive X-ray fluorescence (WDXRF) analysis is compared with inductively coupled plasma atomic emission spectrometry (ICP-AES) for the analysis of five samples of spent hydrodesulphurization (HDS) and hydrodemetallization (HDM) catalysts. The elements are considered for their economic interest (Co, Ni, Mo, and V) or for the problems that can arise when they are present in the sample in significant quantities (Al, As, P, Fe). First, the systematic comparison of the analysis of known synthetic samples was performed. The originality here is that the samples were first beaded with lithium tetraborate (Li2B4O7) for WDXRF analysis and then dissolved in hot HCl 6M for ICP-AES measurements. With this processing, we were able to clearly identify the origin of analytical problems when they arose. Second, the semi-quantitative protocol of WDXRF is compared with the quantitative procedure. Finally, the analysis of the spent catalysts is presented and the information gained by the systematic comparison of ICP-AES and WDXRF is shared. The interest of the simultaneous determination by the two techniques when such complicated heterogeneous matrices are involved is clearly demonstrated.

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.

UniProt Knowledgebase (UniProtKB) is a publicly available database with access to a vast amount of protein sequence and functional information. To widen the scope of the publications associated with a protein entry, UniProt has introduced the computationally mapped additional bibliography section, which includes literature collected from external sources. In this article, we describe a text mining system, eGenPub, which selects articles that are 'about' specific proteins and allows automatic identification of additional bibliography for given UniProt protein entries. Focusing on plant proteins initially, eGenPub utilizes a gene normalization tool called pGenN, and a trained support vector machine model, which achieves a precision of 95.3%, to predict whether an article, based on its abstract, should be linked to a given UniProt entry. We have conducted a full-scale PubMed processing using eGenPub for eight common plant species. Altogether, 9025 articles are identified as relevant bibliography for 4752 UniProt entries, among which 5252 are additional papers not in the existing publication section. These newly computationally mapped additional bibliography via eGenPub is being integrated in the UniProt production pipeline, and can be accessed via the UniProtKB protein entry publication view.