Development of an online, patient-centred decision aid for patients with oropharyngeal cancer in the transoral robotic surgery era.

BACKGROUND: Radiotherapy (rt) has been the standard treatment for early oropharyngeal cancer, achieving excellent outcomes, but with significant toxicities. Transoral robotic surgery (tors) has emerged as a promising alternative. A decision aid (da) can help to establish patient treatment preferences. METHODS: A da was developed and piloted in 40 healthy adult volunteers. Assuming equal oncologic outcomes of the treatments, participants indicated their preference. The treatment trade-off point was then established, and participant perceptions were elicited. RESULTS: More than 80% of participants initially selected tors for treatment, regardless of facilitator background. For all participants, the treatment trade-off point changed after an average 15% cure benefit. Treatment toxicities, duration, novelty, and perceptions all influenced treatment selection. All subjects valued the da. CONCLUSIONS: A da developed for early oropharyngeal cancer treatment holds promise in the era of shared decision-making. Assuming equal cure rates, tors was preferred over rt by healthy volunteers.

Structural diversity of the core oligosaccharide domain of Pseudomonas aeruginosa lipopolysaccharide.

Pseudomonas aeruginosa is a Gram-negative bacterium that is ubiquitous in the environment and generally considered to be a saprophyte, but it is also an important opportunistic human pathogen. Pseudomonas aeruginosa elaborates a variety of virulence factors, one of which is lipopolysaccharide (LPS). LPS of P. aeruginosa is composed of three distinct regions: lipid A, core oligosaccharide (OS), and the long-chain O antigen. The core OS of P. aeruginosa is composed of L-glycero-D-manno-heptose, 3-deoxy-D-manno-oct-2-ulosonic acid, D-galactosamine, D-glucose, and L-rhamnose. Non-carbohydrate substituents are also found in the core OS including phosphate, 2-aminoethyl (di)phosphate, acetyl, alanyl and carbamoyl groups. Pseudomonas aeruginosa simultaneously synthesizes two core glycoforms, namely, capped and uncapped core. The capped core is covalently attached to an O antigen, whereas the uncapped core is devoid of O antigen. Although the core of P. aeruginosa LPS is relatively conserved, strain-to-strain variability of its structure exists. This includes phosphorylation pattern, the level of O-acetylation, and the presence or absence of a fourth glucose residue at the distal end of the uncapped core. A number of studies have been reported on the structures of unique truncated core OS with unusual modifications. This mini-review summarizes the diversity of P. aeruginosa complete and truncated core OS structures published over the past fifteen years.

Preventing transition "regret": An institutional ethnography of gender-affirming medical care assessment practices in Canada.

When a person openly "regrets" their gender transition or "detransitions" this bolsters within the medical community an impression that transgender and non-binary (trans) people require close scrutiny when seeking hormonal and surgical interventions. Despite the low prevalence of "regretful" patient experiences, and scant empirical research on "detransition", these rare transition outcomes profoundly organize the gender-affirming medical care enterprise. Informed by the tenets of institutional ethnography, we examined routine gender-affirming care clinical assessment practices in Canada. Between 2017 and 2018, we interviewed 11 clinicians, 2 administrators, and 9 trans patients (total n = 22), and reviewed 14 healthcare documents pertinent to gender-affirming care in Canada. Through our analysis, we uncovered pervasive regret prevention techniques, including requirements that trans patients undergo extensive psychosocial evaluations prior to transitioning. Clinicians leveraged psychiatric diagnoses as a proxy to predict transition regret, and in some cases delayed or denied medical treatments. We identified cases of patient dissatisfaction with surgical results, and a person who detransitioned. These accounts decouple transition regret and detransition, and no participants endorsed stricter clinical assessments. We traced the clinical work of preventing regret to cisnormativity and transnormativity in medicine which together construct regret as "life-ending", and in turn drives clinicians to apply strategies to mitigate the perceived risk of malpractice legal action when treating trans people, specifically. Yet, attempts to prevent these outcomes contrast with the material healthcare needs of trans people. We conclude that regret and detransitioning are unpredictable and unavoidable clinical phenomena, rarely appearing in "life-ending" forms. Critical research into the experiences of people who detransition is necessary to bolster comprehensive gender-affirming care that recognizes dynamic transition trajectories, and which can address clinicians' fears of legal action-cisgender anxieties projected onto trans patients who are seeking medical care.

Dendritic cells retrovirally transduced with a model antigen gene are therapeutically effective against established pulmonary metastases.

Dendritic cells (DCs) are bone marrow-derived leukocytes that function as potent antigen presenting cells capable of initiating T cell-dependent responses from quiescent lymphocytes. DC pulsed with tumor-associated antigen (TAA) peptide or protein have recently been demonstrated to elicit antigen-specific protective antitumor immunity in a number of murine models. Transduction of DCs with TAA genes may allow stable, prolonged antigen expression as well as the potential for presentation of multiple, or unidentified, epitopes in association with major histocompatibility complex class I and/or class II molecules. To evaluate the potential efficacy of retrovirally transduced DCs, bone marrow cells harvested from BALB/c mice were transduced with either a model antigen gene encoding beta-galactosidase (beta-gal) or a control gene encoding rat HER-2/neu (Neu) by coculture with irradiated ecotropic retroviral producer lines. Bone marrow cells were differentiated into DC in vitro using granulocyte/macrophage colony-stimulating factor and interleukin-4. After 7 d in culture, cells were 45-78% double positive for DC phenotypic cell surface markers by FACS(R) analysis, and DC transduced with beta-gal were 41-72% positive for beta-gal expression by X-gal staining. In addition, coculture of beta-gal transduced DC with a beta-gal-specific T cell line (CTLx) resulted in the production of large amounts of interferon-gamma, demonstrating that transduced DCs could process and present endogenously expressed beta-gal. DC transduced with beta-gal and control rat HER-2/neu were then used to treat 3-d lung metastases in mice bearing an experimental murine tumor CT26.CL25, expressing the model antigen, beta-gal. Treatment with beta-gal-transduced DC significantly reduced the number of pulmonary metastatic nodules compared with treatment with Hank's balanced salt solution or DCs transduced with rat HER-2/neu. In addition, immunization with beta-gal-transduced DCs resulted in the generation of antigen-specific cytotoxic T lymphocytes (CTLs), which were significantly more reactive against relevant tumor targets than CTLs generated from mice immunized with DCs pulsed with the Ld-restricted beta-gal peptide. The results observed in this rapidly lethal tumor model suggest that DCs transduced with TAA may be a useful treatment modality in tumor immunotherapy.

Genetics of O-antigen biosynthesis in Pseudomonas aeruginosa.

Pathogenic bacteria produce an elaborate assortment of extracellular and cell-associated bacterial products that enable colonization and establishment of infection within a host. Lipopolysaccharide (LPS) molecules are cell surface factors that are typically known for their protective role against serum-mediated lysis and their endotoxic properties. The most heterogeneous portion of LPS is the O antigen or O polysaccharide, and it is this region which confers serum resistance to the organism. Pseudomonas aeruginosa is capable of concomitantly synthesizing two types of LPS referred to as A band and B band. The A-band LPS contains a conserved O polysaccharide region composed of D-rhamnose (homopolymer), while the B-band O-antigen (heteropolymer) structure varies among the 20 O serotypes of P. aeruginosa. The genes coding for the enzymes that direct the synthesis of these two O antigens are organized into two separate clusters situated at different chromosomal locations. In this review, we summarize the organization of these two gene clusters to discuss how A-band and B-band O antigens are synthesized and assembled by dedicated enzymes. Examples of unique proteins required for both A-band and B-band O-antigen synthesis and for the synthesis of both LPS and alginate are discussed. The recent identification of additional genes within the P. aeruginosa genome that are homologous to those in the A-band and B-band gene clusters are intriguing since some are able to influence O-antigen synthesis. These studies demonstrate that P. aeruginosa represents a unique model system, allowing studies of heteropolymeric and homopolymeric O-antigen synthesis, as well as permitting an examination of the interrelationship of the synthesis of LPS molecules and other virulence determinants.

Retroviral transduction of human dendritic cells with a tumor-associated antigen gene.

Dendritic cells (DCs) are potent antigen-presenting cells that can activate quiescent T lymphocytes. When pulsed with tumor-associated antigen (TAA) peptide or protein, murine DCs can provide antitumor immunity. We reasoned that DCs retrovirally transduced with TAA genes might have important advantages over peptide- or protein-pulsed DCs, including long-term TAA presentation in vivo, and presentation of important but undefined epitopes. Therefore, we attempted to retrovirally transduce human DCs with a melanoma TAA gene (MART-1) and determine whether these transduced DCs could raise a specific antitumor response from quiescent autologous T lymphocytes. After retroviral transduction, human CD34+ cells were differentiated into DCs in vitro using granulocyte macrophage colony-stimulating factor, tumor necrosis factor alpha, and stem cell factor. This method consistently yielded a population of DCs as analyzed by morphology, phenotype, and MLR. Flow cytometric analysis revealed that 22-28% of cells expressing the DC phenotype also expressed a transduced marker gene. When DCs were transduced with the gene encoding MART-1, they stimulated much higher levels of cytokine release by MART-1-specific tumor-infiltrating lymphocytes than control DCs transduced with an irrelevant gene. In vitro stimulation using MART-1-transduced DCs but not control-transduced DCs raised specific antitumor CTLs from autologous quiescent T cells. These results provide evidence that human DCs can be retrovirally transduced with a TAA gene and that these transduced cells can raise a specific antitumor immune response in vitro. Transduced DCs may be useful for in vivo immunization against TAA.

Pseudomonas aeruginosa antigens as potential vaccines.

Pseudomonas aeruginosa is one of the most important opportunistic bacterial pathogens in humans and animals. This organism is ubiquitous and has high intrinsic resistance to antibiotics due to the low permeability of the outer membrane and the presence of numerous multiple drug efflux pumps. Various cell-associated and secreted antigens of P. aeruginosa have been the subject of vaccine development. Among pseudomonas antigens, the mucoid substance, which is an extracellular slime consisting predominantly of alginate, was found to be heterogenous in terms of size and immunogenicity. High molecular mass alginate components (30-300 kDa) appear to contain conserved epitopes while lower molecular mass alginate components (10-30 kDa) possess conserved epitopes in addition to unique epitopes. Surface-exposed antigens including O-antigens (O-specific polysaccharide of LPS) or H-antigens (flagellar antigens) have been used for serotyping due to their highly immunogenic nature. Chemical structures of repeating units of O-specific polysaccharides have been elucidated and these data allowed the identification of 31 chemotypes of P. aeruginosa. Conserved epitopes among all serotypes of P. aeruginosa are located in the core oligosaccharide and the lipid A region of LPS and immunogens containing these epitopes induce cross-protective immunity in mice against different P. aeruginosa immunotypes. To examine the protective properties of OM proteins, a vaccine containing P. aeruginosa OM proteins of molecular masses ranging from 20 to 100 kDa has been used in pre-clinical and clinical trials. This vaccine was efficacious in animal models against P. aeruginosa challenge and induced high levels of specific antibodies in human volunteers. Plasma from human volunteers containing anti-P. aeruginosa antibodies provided passive protection and helped the recovery of 87% of patients with severe forms of P. aeruginosa infection. Vaccines prepared from P. aeruginosa ribosomes induced protective immunity in mice, but the efficacy of ribosomal vaccines in humans is not yet known. A number of recent studies indicated the potential of some P. aeruginosa antigens that deserve attention as new vaccine candidates. The outer core of LPS was implicated to be a ligand for binding of P. aeruginosa to airway and ocular epithelial cells of animals. However, heterogeneity exists in this outer core region among different serotypes. Epitopes in the inner core are highly conserved and it has been demonstrated to be surface-accessible, and not masked by O-specific polysaccharide. The use of an in vivo selection/expression technology (IVET) by a group of researchers identified a number of P. aeruginosa proteins that are expressed in vivo and essential for virulence. Two of these in vivo-expressed proteins are FptA (ferripyochelin receptor protein) and a homologue of an LPS biosynthetic enzyme. Our laboratory has identified a highly conserved protein, WbpM, and P. aeruginosa with a deficiency in this protein produces only rough LPS and became serum sensitive. Results from these studies have provided the foundation for a variety of vaccine formulations.

Inhibition of murine renal carcinoma pulmonary metastases by systemic administration of interferon gamma: mechanism of action and potential for combination with interleukin 4.

We have previously demonstrated that IFN-gamma causes cell growth inhibition and up-regulation of MHC antigens in human renal cell carcinoma cell lines. In this study, we have investigated the therapeutic potential of IFN-gamma for the treatment of 5-day established pulmonary metastases induced by i.v. injection of Renca cells, a murine renal adenocarcinoma. We found that systemic injections of IFN-gamma significantly reduced the number of lung metastases in a dose-dependent manner and increased mouse survival. Histological evaluation of IFN-gamma-treated lungs showed residual small tumor nodules containing extensive necrosis and mononuclear infiltrates. Immunohistochemistry studies on lung sections showed macrophage infiltration into tumor nodules, and in vivo depletion of macrophages partially inhibited IFN-gamma antitumor effect, suggesting a role for the macrophages in tumor destruction. Lymphocyte depletion of either natural killer (NK) cells or CD4+ or CD8+ T-cell subsets or both T-cell subsets did not affect the IFN-gamma effect, whereas depletion of both NK and T cells decreased the antitumor activity of IFN-gamma. These data indicate that neither T cells nor NK cells are essential for this activity but that either lymphocyte population can contribute to the IFN-gamma effect. An optimal dose of IFN-gamma inhibited by 60% the growth of Renca cells treated for 3 days in vitro, but this effect was transient and less pronounced in a long-term colony assay, suggesting that IFN-gamma direct growth inhibition may play a role but may not be sufficient to mediate its antitumor effect in vivo. In vitro, IFN-gamma caused up-regulation of class I MHC antigens and induction of class II antigen expression in Renca cells, an effect that may enhance Renca immunogenicity but may be relevant only when a T-cell response is elicited. A sequential administration of IFN-gamma followed by interleukin 4 was therapeutically better than IFN-gamma alone for the treatment of advanced pulmonary metastases, probably due to different antitumor mechanisms induced by these two cytokines.

Improved gene transfer into human lymphocytes using retroviruses with the gibbon ape leukemia virus envelope.

Gene-modified lymphocytes have a potential role in the therapy of cancer, infectious diseases, and genetic disorders of the immune system. Current gene therapy protocols involving gene transfer into lymphocytes utilize retroviruses with amphotropic envelope proteins. However, transduction efficiencies in lymphocytes using these viruses are relatively low. A potential strategy to improve gene transfer efficiency is the utilization of alternative retroviral envelopes that target unique receptors on the cell surface. One such alternative retroviral envelope, the gibbon ape leukemia virus (GALV) envelope, targets a distinct surface receptor (GLVR-1) that is 60% homologous but not cross-reactive to the amphotropic receptor (GLVR-2/RAM-1). Understanding the relationship between receptor expression and transduction efficiency is important for designing new strategies to improve gene transfer. Therefore, we compared GLVR-1 and GLVR-2 mRNA levels in lymphocytes and found that GLVR-1 was expressed 8- to 19-fold higher than GLVR-2. We then analyzed whether this enhanced expression of GLVR-1 correlated with increased infectivity of lymphocytes by retroviral vectors that utilize the GALV envelope compared to those that use the amphotropic envelope. We evaluated retroviral vectors packaged with either PA317 or PG13, which express the amphotropic and GALV envelopes, respectively. Lymphocyte transduction with PG13-packaged vectors was 4- to 18-fold higher than that with PA317-packaged vectors. These findings suggest that receptor expression level is an important factor in retroviral-target interactions and that gene transfer into human T lymphocytes should be performed with retroviruses that use the GALV envelope as opposed to retroviruses that use the amphotropic envelope.

A comparison of the efficiency in serotyping of Pseudomonas aeruginosa from cystic fibrosis patients using monoclonal and polyclonal antibodies.

A well-known problem in serotyping Pseudomonas aeruginosa strains from cystic fibrosis patients using polyclonal sera is that more than half of the strains cannot be assigned to a single O-serogroup because of the high occurrence of polyagglutinable strains and nontypable strains. In the present study, the efficiency of a set of O-specific monoclonal antibodies in the simple slide agglutination test was compared with polyclonal sera for the serotyping of 243 isolates of P. aeruginosa from cystic fibrosis patients. Using the monoclonal antibodies, 213 (88%) strains were found to be typable and only 30 (12%) strains were nontypable. In contrast, when the polyclonal sera from Statens Seruminstitut were used, only 53 (22%) strains were typable. Similar results were obtained when polyclonal sera manufactured by Difco were used where only 61 (25%) strains were typable. We also investigated the consistency of each set of antibodies in typing of the same isolates on different days and found that the polyclonal sera showed higher reproducibility. The Statens Seruminstitut sera were found to have an 86% reproducibility while the Difco sera scored 81%; however, the percentage of strains that are nontypable remains below 25% despite the highly reproducible results obtained. The monoclonal antibodies were found to score a 75% reproducibility when the serotyping of the same strains was done both in the laboratories of Copenhagen and of Guelph. However, it should be noted that although the reproducibility was somewhat lower with the monoclonal antibodies, these highly specific antibodies are still clearly superior when compared with polyclonal sera used because more than 80% of the strains from cystic fibrosis can now be assigned to a single O-serogroup.

Typing of polyagglutinable Pseudomonas aeruginosa isolates from cystic fibrosis patients.

The study assesses the reproducibility, typability and discriminatory power of several typing methods for Pseudomonas aeruginosa isolated from cystic fibrosis patients. 178 polyagglutinable Pseudomonas aeruginosa isolates from cystic fibrosis patients were serotyped using polyclonal sera and monoclonal antibodies, phage typed, pyocin typed and reverse phage typed. 31 of these polyagglutinable isolates, six monoagglutinable isolates and three nontypable isolates were also typed by means of hybridization using a DNA probe. In a comparison of the methods used, on polyagglutinable isolates only, typability was 0% with polyclonal sera, 90% with monoclonal sera, 94% with phage typing, 85% with pyocin typing, 36% with reverse phage typing and 100% with DNA-prope typing. Using monoclonal antibodies, the reproducibility was 75%, while that of phage typing was 88%, pyocin typing 53% and reverse phage typing 62%. Typing with the DNA probe was not repeated. using polyclonal sera, repeated typing showed that 94% of the isolates were polyagglutinable. Using phage typing, 40% of the isolates belonged to phage type 31, while 60% were distributed amongst 32 phage types. Using monoclonal antibodies, 71% of the isolates belonged to 0-group 3, and these isolates showed 16 different phage types. Subdivision of the phage types was further achieved by both pyocin typing and reverse phage typing. The DNA probe typing made it possible in some cases to discriminate between isolates which were otherwise found identical with the conventional typing methods, while in other cases typing with the DNA probe recorded as identical isolates which conventional methods had typed as being different. These differences may be due to a high mutation rate caused by the selection pressure of antibiotics, and by the host immune response. According to our results, investigations of reproducibility and typability of old and new typing methods are essential when they are used in clinical situations. The low reproducibility of some of the typing methods in the present study affects the reliability of epidemiological investigations in cystic fibrosis patients. Usage of only one method may not be sufficient in cases of polyagglutinable strains from cystic fibrosis patients.

Pseudomonas aeruginosa B-band lipopolysaccharide genes wbpA and wbpI and their Escherichia coli homologues wecC and wecB are not functionally interchangeable.

The O antigen unit of Pseudomonas aeruginosa serotype O5 is a complex trisaccharide containing 2-acetamido-3-acetiminido-2, 3-dideoxy-beta-D-mannuronic acid, 2-acetimido-3-acetimido-2, 3-dideoxy-beta-D-mannuronic acid, and 2-acetimido-2, 6-deoxy-beta-D-galactosamine. Specific knockout mutations in the putative UDP-D-N-acetylglucosamine (UDP-D-GlcNAc) epimerase gene, wbpI, or the putative UDP-D-N-acetylmannosamine dehydrogenase gene, wbpA, resulted in strains that no longer produced B-band lipopolysaccharide, confirming the essential roles of these genes in B-band O antigen synthesis. Despite approximately 50% similarity of wbpI and wbpA to the Escherichia coli genes wecB (rffE) and wecC (rffD) involved in enterobacterial common antigen synthesis, cross-complementation experiments were not successful. These results imply that the P. aeruginosa UDP-D-GlcNAc precursor may be di-N-acetylated prior to further modification, preventing the E. coli enzymes from recognizing it as a substrate.

Pseudomonas aeruginosa rfc genes of serotypes O2 and O5 could complement O-polymerase-deficient semi-rough mutants of either serotype.

Using a gene-replacement strategy and a mutated copy of the Pseudomonas aeruginosa O5 rfc gene, we were able to generate a rfc mutant in P. aeruginosa serotype O2. This mutant, which exhibits the semi-rough (SR) LPS phenotype, was used to isolate the O2 rfc gene. Mobilization of the O2 and O5 rfc genes into SR mutants of the heterologous serotype resulted in 'cross-polymerization' of O-repeat units, indicating that the genes are functionally exchangeable. Analysis of the nucleotide sequence of the rfc genes revealed that the two Rfc proteins are identical. The results of this study have enabled us to propose the linkage catalyzed by the O5 O-polymerase enzyme.

Genetic and biochemical characterization of an operon involved in the biosynthesis of 3-deoxy-D-manno-octulosonic acid in Pseudomonas aeruginosa.

A Pseudomonas aeruginosa serotype O5 (PAO1) genomic DNA fragment that was able to complement a temperature-sensitive mutation in the 3-deoxy-D-manno-octulosonic acid (Kdo) 8-P synthase gene (kdsA) of Salmonella enterica serovar typhimurium was cloned. Nucleotide sequence analysis revealed the presence of a potential operon with the gene order pyrG, kdsA, eno. PyrG catalyzes the synthesis of the nucleotide cytidine triphosphate, while Eno catalyzes the formation of phosphoenolpyruvate from phosphoglycerate during glycolysis. Phosphoenolpyruvate is one of the substrates for Kdo-8-P biosynthesis by KdsA and cytidine triphosphate is the nucleotide used to activate Kdo prior to its transfer to lipid A. pyrG and eno are important for many metabolic pathways and it is interesting to find them linked to kdsA. A sigma 70-like promoter was found upstream of pyrG and evidence was provided to show that this promoter was responsible for the initiation of transcription of the genes in this operon. These genes mapped to 28.2-29.9 min on the 75-min PAO1 chromosome, unlinked to other lipopolysaccharide biosynthetic gene clusters.

Effects of order of magnesium exposure on the postantibiotic effect and bactericidal activity of ciprofloxacin.

Quinolone antibiotics are known to form chelates with various metal cations. It has also been recognized that the physicochemical properties of the chelated antibiotic differ significantly from its unchelated form, thereby causing a reduction in antimicrobial activity. In addition, the formation of metal chelates is also believed to be the reason for the significant reduction in oral bioavailability for the quinolones when concomitantly dosed with oral cation containing agents. This has prompted the adoption of an alternate dosing regimen by introducing an adequate interval between the two. As a result of this dosing strategy, pathogens are exposed to the quinolones and metal cations in alternate orders. Using magnesium, ciprofloxacin, and Escherichia coli as the test organism, investigations were conducted to study the changes in bactericidal activity and postantibiotic effect (PAE) in relation to the orders of cation/antibiotic exposure. Results showed a parallel decrease in both bactericidal activity and PAE when the test organism was exposed to the two agents simultaneously; however, no apparent influences on these two antimicrobial effects were observed when Mg2+ was presented before or after ciprofloxacin exposure. In line with the current dosing recommendations, the interval spaced between ciprofloxacin and Mg2+ should preserve both the bactericidal activity and PAE exhibited by the antibiotic. How the present data are to be extrapolated to other quinolones and cations should be the subject of future studies.

The porcine gut microbial metagenomic library for mining novel cellulases established from growing pigs fed cellulose-supplemented high-fat diets.

The porcine gut microbiome is a novel genomic resource for screening cellulose-degrading enzymes. A plasmid metagenomic expression library was constructed from the hindgut microbiota of 6 Yorkshire growing pigs (25 to 40 kg) fed a high-fat basal diet supplemented with 10% Solka-Floc for 28 d. Fresh cecal and colonic digesta samples were collected, flash-frozen in liquid N, and stored under -80°C. Metagenomic DNA was extracted, mechanically sheared, and cleaned to remove small DNA fragments (<1.0 kb). The resulting DNA fragments were subjected to blunt-end polishing, fractionation, and purification by using commercial kits. The end-modified DNA fragments were ligated to pCR4Blunt-TOPO vector and transformed into competent Escherichia coli TOPO10 cells. Metagenomic plasmid libraries were screened for carboxymethyl cellulolytic activities by using lysogeny broth agar plates. The average insert size of the resulting library was approximately 4.2 kb. Screening for the ability to hydrolyze carboxymethyl cellulose yielded 14 positive colonies, giving an estimated 430 Mb of metagenomic DNA in the approximately 102,000 E. coli clones with an overall hit rate of 0.14%. The 11 assembled insert sequences included 4 function-related gene clusters, and a total of 18 putative carbohydrate active enzyme genes were identified. This included genes encoding 11 cellulases, 4 hemicellulases, 1 polygalacturonas, 1 glycoside hydrolase family 26 mannanase-family 5 cellulase chimeric enzyme gene, and 1 cellobiose phosphorylase. In conclusion, the coupling of functional metagenomic mining with biochemical characterization of fiber-degrading enzymes is a powerful strategy for exploring the enzymological underpinnings of the anaerobic fermentation of dietary fiber in the complex animal gut environment.

Interferon gamma release assay for differentiating tuberculosis among pneumonia cases in acute healthcare setting.

OBJECTIVES: Early diagnosis of smear-negative tuberculosis remains challenging. The role of an interferon-gamma release assay (IGRA) in discriminating active pulmonary tuberculosis (PTB) among cases of 'pneumonia' was investigated. METHODS: Consecutive patients admitted to an acute hospital in Hong Kong (intermediate TB burden) during 2006-2008 because of pneumonia and suspected PTB were recruited for IGRA (Quantiferon-TB Gold, QFN-G) study. Diagnosis of tuberculosis was confirmed by mycobacterial culture or histology. RESULTS: Altogether 179 patients were recruited (median (IQR) age 59 (44-75), 68.7% male); active PTB was confirmed in 63 (35.2%). Among the AFB-smear-negative 'pneumonias' (n = 152), age>50 (OR 0.27, 95% CI 0.09-0.84), absence of weight loss (OR 0.30, 95% CI 0.10-0.88), and negative IGRA (OR 0.08, 95% CI 0.03-0.25) were independently associated with lower risks of PTB. The overall sensitivity, specificity, positive and negative predictive values for the IGRA in diagnosing active PTB were 60%, 87%, 72% and 80% respectively. Among smear-negative 'pneumonias' (n = 152), the performance values of IGRA were 64%, 87%, 62% and 88% respectively; in the absence of characteristic clinical or radiographic features of PTB, the negative predictive value (NPV) improved to 90-95%. CONCLUSIONS: The high NPV of QFN-G among smear-negative 'pneumonias' can be useful for risk stratification in hospitalized patients suspected of PTB. Further investigation on the role of these assays in patient management is warranted.

Positive margins in laparoscopic partial nephrectomy in 855 cases: a multi-institutional survey from the United States and Europe.

PURPOSE: Open partial nephrectomy has emerged as the standard of care in the management of renal tumors smaller than 4 cm. While laparoscopic radical nephrectomy has been shown to be comparable to open radical nephrectomy with respect to long-term outcomes, important questions remain unanswered regarding the oncological efficacy of laparoscopic partial nephrectomy. We examined the practice patterns and pathological outcomes following laparoscopic partial nephrectomy. MATERIALS AND METHODS: A survey was sent to academic medical centers in the United States and in Europe performing laparoscopic partial nephrectomy. The total number of laparoscopic partial nephrectomies, positive margins, indications for intraoperative frozen biopsy as well as tumor size and position were queried. RESULTS: Surveys suitable for analysis were received from 17 centers with a total of 855 laparoscopic partial nephrectomy cases. Mean tumor size was 2.7 cm (+/-0.6). There were 21 cases with positive margins on final pathology, giving an overall positive margin rate of 2.4%. Intraoperative frozen sections were performed selectively at 10 centers based on clinical suspicion of positive margins on excised tumor. Random biopsies were routinely performed on the resection bed at 5 centers. Frozen sections were never performed at 2 centers. Of the 21 cases with positive margins 14 underwent immediate radical nephrectomy based on the frozen section and 7 were followed expectantly. CONCLUSIONS: Early experience with laparoscopic partial nephrectomy in this multicenter study demonstrates oncological efficacy comparable to that of open partial nephrectomy with respect to the incidence of positive margins. The practice of intraoperative frozen sections varied among centers and is not definitive in guiding the optimal surgical treatment.

Selective inhibition of ventral temporal but not dorsal nasal neurites from mouse retinal explants during contact with chondroitin sulphate.

We have determined whether chondroitin sulphate (CS) glycosaminoglycans are sufficient to direct a selective inhibition of neurite growth from ventral temporal (VT) but not from dorsal nasal (DN) retina in mouse embryos; this may underlie the formation of axon divergence in the optic chiasm. Explants from the retinal region of embryonic day-14 mouse were grown on a laminin-polylysine substrate near to a circular spot coated with CS. In control cultures, in which no CS was added to the spot, both VT and DN retinal neurites grew extensively into the coated territory. When presented with spots coated with 10 mg/ml CS, neurite growth from the VT retina into the CS territory was dramatically reduced but that from the DN retina was not significantly affected. The selective inhibition to VT neurites was completely abolished by treatment with chondroitinase ABC, indicating a specific contribution of CS glycosaminoglycan in this regionally specific behaviour. This differential behaviour was not observed in explants presented with a lower or higher concentration of CS or in explants grown on substrate coated with a different laminin concentration. Thus, a critical ratio of CS to laminin seems to be essential to induce this differential behaviour in retinal neurites towards contact with CS. Furthermore, this behavior was not observed in explants cultured directly on a CS-rich substrate, suggesting that contact with growth-promoting molecules is necessary for the selective responses of retinal neurites during subsequent contact with CS. We concluded that CS glycosaminoglycan is sufficient to drive selective inhibition of VT but not DN neurites and that, together with a critical combination of growth-promoting factors, it may control the axon divergence process at the mouse optic chiasm.