An improved model averaging scheme for logistic regression

Recently, penalized regression methods have attracted much attention in the statistical literature. In this article, we argue that such methods can be improved for the purposes of prediction by utilizing model averaging ideas. We propose a new algorithm that combines penalized regression with model averaging for improved prediction. We also discuss the issue of model selection versus model averaging and propose a diagnostic based on the notion of generalized degrees of freedom. The proposed methods are studied using both simulated and real data.

Impact of nitrate addition on biofilm properties and activities in rising main sewers

Anaerobic sewer biofilm is a composite of many different microbial populations, including sulfate reducing bacteria (SRB), methanogens and heterotrophic bacteria. Nitrate addition to sewers in an attempt to control hydrogen sulfide concentrations affects the behaviour of these populations, which in turn impacts on wastewater characteristics. Experiments were carried out on a laboratory reactor system simulating a rising main to determine the impact of nitrate addition on the microbial activities of anaerobic sewer biofilm. Nitrate was added to the start of the rising main during sewage pump cycles at a concentration of 30 mg-N L(-1) for over 5 months. While it reduced sulfide levels at the outlet of the system by 66%, nitrate was not toxic or inhibitory to SRB activity and did not affect the dominant SRB populations in the biofilm. Long-term nitrate addition in fact stimulated additional SRB activity in downstream biofilm. Nitrate addition also stimulated the activity of nitrate reducing, sulfide oxidizing bacteria that appeared to be primarily responsible for the prevention of sulfide build up in the wastewater in the presence of nitrate. A short adaptation period of three to four nitrate exposure events (approximately 10 h) was required to stimulate biological sulfide oxidation, beyond which no sulfide accumulation was observed under anoxic conditions. Nitrate addition effectively controlled methane concentrations in the wastewater. The nitrate uptake rate of the biofilm increased with repeated exposure to nitrate, which in turn increased the consumption of biodegradable COD in the wastewater. These results provide a comprehensive understanding of the impact of nitrate addition on wastewater composition and sewer biofilm microbial activities, which will facilitate optimization of nitrate dosing for effective sulfide control in rising main sewers.

A muscle-targeting peptide displayed on AAV2 improves muscle tropism on systemic delivery

Adeno-associated virus (AAV) has become a leading gene transfer vector for striated muscles. However, the AAV vectors also exhibit broad tropisms after systemic delivery. In an attempt to improve muscle tropism, we inserted a 7-amino-acid (ASSLNIA) muscle-targeting peptide (MTP) in the capsids of AAV2 at residue 587 or 588, generating AAV₅₈₇MTP and AAV₅₈₈MTP. In vitro studies showed that both viruses diminished their infectivity on non-muscle cell lines as well as on un-differentiated myoblasts, however, preserved or enhanced their infectivity on differentiated myotubes. AAV₅₈₇MTP, but not AAV₅₈₈MTP, also abolished its heparin-binding capacity and infected myotubes in a heparin-independent manner. Furthermore, in vivo studies by intravenous vector administration in mice showed that AAV₅₈₇MTP enhanced its tropism to various muscles and particularly to the heart (24.3 fold of unmodified AAV2), whereas reduced its tropism to the non-muscle tissues such as the liver, lungs and spleen, etc. This alteration of tissue tropism is not simply due to the loss of heparin-binding, since a mutant AAV2 (AAVHBSMut) containing heparin-binding site mutations lost infectivity on both non-muscle and muscle cells. Furthermore, free MTP peptide, but not the scrambled control peptide, competitively inhibited AAV₅₈₇MTP infection on myotubes. These results suggest that AAV2 could be re-targeted to the striated muscles by a muscle-targeting peptide inserted after residue 587 of the capsids. This proof of principle study showed first evidence of peptide-directed muscle targeting upon systemic administration of AAV vectors.

Impact of pegylated liposomal doxorubicin (PLD) plus docetaxel (D) versus single-agent D on health-related quality of life (HRQOL) of patients with advanced breast cancer (BC) previously treated with neoadjuvant-adjuvant anthracycline

e20522

Background: A randomized, multicenter phase 3 trial of PLD+D showed a significant improvement in the primary endpoint of time to progression (TTP) compared with D alone but with increased Grade 3/4 hand-foot syndrome (HFS: 24% vs. 0%) and mucositis/stomatitis (M/S: 12% vs. 1%) in patients (pts) with advanced breast cancer (BC). (Sparano JA et al. SABCS 2008. #80) This analysis evaluated HRQOL in these pts. Methods: Pts were randomized to D 75 mg/m2 (N=373) or PLD 30 mg/m2 + D 60 mg/m2 (N=378) on Day 1 every 21 days until progression or unacceptable toxicity. HRQOL was assessed using the Functional Assessment of Cancer Therapy - Breast (FACT-B) at baseline and at every cycle during treatment. FACT-B has 4 primary domains: physical, social/family, emotional, and functional, plus a BC-specific subscale. The primary analysis was a t-test comparison of change in the trial outcome index (TOI) from baseline to the last evaluation. TOI combined physical/functional domain scores with BC-specific scores. Other FACT-B endpoints analyzed included FACT-B total score and individual subscales. Also, % pts meeting an established minimally important difference (MID) of HRQOL improvement in TOI was assessed. Results: Median number of cycles was 6 for both arms. TOI was available for 97.9% of all scheduled assessments for both treatment groups. At baseline, mean FACT-B and TOI scores were similar for PLD+D vs D arms (94.2±18.6 vs 95.3±18.7 and 59.7±13.8 vs 60.2±13.4, respectively); other FACT-B domains were also similar. PLD+D vs D arms showed similar mean change from baseline to last evaluation in TOI (-4.6±12.2 vs -6.0±12.4; P=0.13). Other FACT-B subscales showed 1–2 point differences across domains over time. Likewise, % pts reaching MID was similar across arms. Pts in both arms experienced similar FACT-B declines as disease progressed. Conclusions: Despite increased HFS and M/S with PLD+D vs D alone, HRQOL was comparable for both arms.

[Table: see text]

Modelling using rRNA-structured biomass models

Models currently used have been developed to describe the storage response in the activated sludge process. In these models the distribution of the substrate flux between growth and storage is an empirical function. rRNA-structured biomass models are proposed to describe the metabolic status of cells in view of predicting the growth response (dmicro/dt) of cells in activated sludge process. The autocatalytic reaction rate of the synthesis of the PSS component (rRNA) can provide a mechanistic explanation for the growth response and the growth lag phase. The proposed models were able to describe and predict properly the growth response of the biomass in various types of reactor. Such models could be more widely applicable by using intrinsic model parameters. This would be a key improvement for as it would lead to improved models for design.

Cohort differences in the progression of developmental pathways: evidence for period effects on secular trends of violence in males

BACKGROUND

Rates of violence in the USA have fluctuated widely over the past few decades. Theorists have examined period and cohort effects, but there appear to be no studies examining these effects on progression in developmental pathways towards violence.

OBJECTIVE

To assess whether differences in progression among individuals in the Pittsburgh Youth Study are consistent with period or cohort effects.

DESIGN

Multivariate logistic regression was conducted to examine differences between cohorts in the odds of progressing through the developmental pathway towards violence. Adjusted and unadjusted odds ratios (ORs) and corresponding 95% CI are reported.

SETTING

Pittsburgh Pennsylvania, from 1987 to 2000.

SUBJECTS

Two cohorts of male adolescents from the Pittsburgh Youth Study. The youngest cohort (n = 503) was followed from median ages 7 to 20, and the oldest cohort (n = 506) was followed up from median ages 13 to 25.

MAIN OUTCOME MEASURE

The odds of progression along a developmental pathway towards violence.

RESULTS

There was no statistically significant difference between the cohorts in progression from minor aggression to physical fighting (OR = 1.13, 95% CI 0.77 to 1.65). However, after adjustment for major risk factors, the oldest cohort was significantly more likely to progress from physical fighting to violence (OR = 2.34, 95% CI 1.39 to 3.92).

CONCLUSIONS

These results provide initial evidence that cohort effects, which would be present early in development, do not contribute significantly to later differences in reported violence and raises the possibility of whether period effects can explain these differences.

Nitrite effectively inhibits sulfide and methane production in a laboratory scale sewer reactor

The production and emission of hydrogen sulfide and methane by anaerobic microoganisms in sewer systems is a well-documented problem. The effectiveness of nitrite in controlling sulfide and methane production was tested in a laboratory scale sewer reactor. Nitrite was continuously dosed in the reactor for 25 days at concentrations of 20-140mgN/L. No sulfide and methane accumulation was observed in the reactor in the presence of nitrite. A significant reduction was observed in the sulfate reduction and methane production capabilities of the biofilm. Nitrite also stimulated biological sulfide oxidation within the biofilm. The nitrite uptake rate of the reactor increased over the nitrite dosing period and nitrous oxide production was observed within the biofilm. When nitrite addition was stopped, sulfate reduction and methane production gradually resumed, and reached pre-nitrite addition levels after 2.5 months. The slow recovery suggests that nitrite can be applied intermittently for sulfide and methane control, which represents a key advantage over similar chemicals such as nitrate and oxygen. The study demonstrates nitrite addition as a promising and effective strategy for the management of sulfide and methane in sewers. Further investigation and optimization are still required before application in the field.

Torsional ultrasound modality for hard nucleus phacoemulsification cataract extraction

AIM

To evaluate the efficacy and safety of phacoemulsification using torsional modality with different parameter settings for hard nucleus cataract extraction.

DESIGN

A prospective, randomised clinical study.

METHODS

A clinical practice study conducted at the Cataract Service, Zhongshan Ophthalmic Center, Sun-Yat-Sen University, and Guangzhou. One eye each from 198 consecutive patients with cataract density grade IV according to the Emery-Little system classification system, requiring phacoemulsification and intraocular lens implantation, was included. Eyes were randomly assigned to the Linear Torsional combined with Ultrasound power group (Linear Tor+US group, n = 66), 100% Fixed Torsional group (Fixed Tor group, n = 65) and conventional Ultrasound burst group (US group, n = 67). All surgeries were performed by a single experienced surgeon and outcomes evaluated by another surgeon masked to treatment. Intraoperative parameters were Ultrasound Time (UST), Cumulative Dissipated Energy (CDE) and surgical complications. Patients were examined on post-op days 1, 7 and 30. Postoperative outcomes were final best corrected visual acuity (BCVA), average central and incisional corneal thickness and central endothelial cell counts.

RESULTS

The mean UST was lower in the Fixed Tor group than in the US group and in the Lin US+Tor group (p0.01), greater average central corneal and incisional thickness on days 1, 7 (p0.01), and higher average corneal endothelial cell losses on day 7 and 30 days (p

CONCLUSIONS

Torsional combined with ultrasound power or high fixed torsional amplitude can yield more effective hard nucleus phacoemulsification than conventional ultrasound modality.

Collapse

Key Words Collapse

MESH Headings

• Aged
• Aged, 80 and over
• Cornea/pathology
• Endothelium, Corneal/pathology
• Female
• Humans
• Lens Nucleus, Crystalline/surgery
• Male
• Middle Aged
• Phacoemulsification/methods
• Prospective Studies
• Tomography, Optical Coherence
• Treatment Outcome
• Ultrasonic Therapy/methods
• Visual Acuity

Collapse

Grants Collapse

A phase I study of the safety and pharmacokinetics of trabectedin in combination with pegylated liposomal doxorubicin in patients with advanced malignancies

BACKGROUND

To determine the maximum tolerated dose (MTD), safety, potential pharmacokinetic (PK) interactions, and effect on liver histology of trabectedin in combination with pegylated liposomal doxorubicin (PLD) for advanced malignancies.

PATIENTS AND METHODS

Entry criteria for the 36 patients included normal liver function, prior doxorubicin exposure <250 mg/m(2), and normal cardiac function. A 1-h PLD (30 mg/m(2)) infusion was followed immediately by one of six trabectedin doses (0.4, 0.6, 0.75, 0.9, 1.1, and 1.3 mg/m(2)) infused over 3 h, repeated every 21 days until evidence of complete response (CR), disease progression, or unacceptable toxicity. Plasma samples were obtained to assess PK profiles.

RESULTS

The MTD of trabectedin was 1.1 mg/m(2). Drug-related grade 3 and 4 toxic effects were neutropenia (31%) and elevated transaminases (31%). Six patients responded (one CR, five partial responses), with an overall response rate of 16.7%, and 14 had stable disease (less than a 50% reduction and less than a 25% increase in the sum of the products of two perpendicular diameters of all measured lesions and the appearance of no new lesions) >4 months (39%). Neither drug had its PK affected significantly by concomitant administration compared with trabectedin and PLD each given as a single agent.

CONCLUSION

Trabectedin combined with PLD is generally well tolerated at therapeutic doses of both drugs in pretreated patients with diverse tumor types and appears to provide clinical benefit. These results support the need for additional studies of this combination in appropriate cancer types.

Characterizing the biochemical activity of full-scale enhanced biological phosphorus removal systems: A comparison with metabolic models

The metabolism of polyphosphate accumulating organisms (PAOs) has been widely studied through the use of lab-scale enrichments. Various metabolic models have been formulated, based on the results from lab-scale experiments using enriched PAO cultures. A comparison between the anaerobic stoichiometry predicted by metabolic models with that exhibited by full-scale sludge in enhanced biological phosphorus removal (EBPR) wastewater treatment plants (WWTPs) was performed in this study. Batch experiments were carried out with either acetate or propionate as the sole carbon source, using sludges from two different EBPR-WWTPs in Australia that achieved different phosphorus removal performances. The results support the hypothesis that the anaerobic degradation of glycogen is the primary source of reducing equivalents generated by PAOs, however, they also suggested a partial contribution of the tricarboxylic acid (TCA) cycle in some cases. The experimental results obtained when acetate was the carbon source suggest the involvement of the modified succinate-propionate pathway for the generation of poly-beta-hydroxyvalerate (PHV). Overall, the batch test results obtained from full-scale EBPR sludge with both substrates were generally well described by metabolic model predictions for PAOs.

Continuous measurement of dissolved sulfide in sewer systems

Sulfides are particularly problematic in the sewage industry. Hydrogen sulfide causes corrosion of concrete infrastructure, is dangerous at high concentrations and is foul smelling at low concentrations. Despite the importance of sulfide monitoring there is no commercially available system to quantify sulfide in waste water. In this article we report on our use of an in situ spectrometer to quantify bisulfide in waste water and additional analysis with a pH probe to calculate total dissolved sulfide. Our results show it is possible to use existing commercially available and field proven sensors to measure sulfide to mg/l levels continuously with little operator intervention and no sample preparation.

Vaccination of sarcoid-bearing donkeys with chimeric virus-like particles of bovine papillomavirus type 1

Equine sarcoids are fibroblastic skin tumours affecting equids worldwide. While the pathogenesis is not entirely understood, infection with bovine papillomavirus (BPV) type 1 (and less commonly type 2) has been implicated as a major factor in the disease process. Sarcoids very seldom regress and in fact often recrudesce following therapy. Nothing is known about the immune response of the equine host to BPV. Given that the viral genes are expressed in sarcoids, it is reasonable to assume that vaccination of animals against the expressed viral proteins would lead to the induction of an immune response against the antigens and possible tumour rejection. To this end we vaccinated sarcoid-bearing donkeys in a placebo-controlled trial using chimeric virus-like particles (CVLPs) comprising BPV-1 L1 and E7 proteins. The results show a tendency towards enhanced tumour regression and reduced progression in the vaccinated group compared to control animals. Although promising, further studies are required with larger animal groups to definitely conclude that vaccination with CVLPs is a potential therapy for the induction of sarcoid regression.

Activating transcription factor 3 up-regulated by c-Jun NH(2)-terminal kinase/c-Jun contributes to apoptosis induced by potassium deprivation in cerebellar granule neurons

Cerebellar granule neurons (CGNs) depend on potassium depolarization for survival and undergo apoptosis when deprived of depolarizing concentration of potassium. Activating transcription factor 3 (ATF3), a stress-inducible protein, belongs to the ATF/CREB family of transcription factors family and is involved in cell growth and apoptosis. However, the role of ATF3 in neuronal apoptosis remains unknown. Here, we showed that ATF3 was up-regulated under potassium deprivation in CGNs, and this induction was preceded by a rapid and sustained activation of c-Jun NH(2)-terminal kinase/c-Jun signaling pathway, which plays a fundamental role in neuronal apoptosis. Furthermore, ATF3 up-regulation was abolished by inhibition of JNK or knockdown of c-Jun. Finally, knockdown of ATF3 by RNA interference protected CGNs from potassium deprivation-induced apoptosis. Taken together, our results indicate that ATF3 is a downstream target of JNK/c-Jun pathway and contributes to apoptosis induced by potassium deprivation in rat CGNs.

Prediction of the hip joint centre in adults, children, and patients with cerebral palsy based on magnetic resonance imaging

The location of the hip joint centre (HJC) is required for calculations of hip moments, the location and orientation of the femur, and muscle lengths and lever arms. In clinical gait analysis, the HJC is normally estimated using regression equations based on normative data obtained from adult populations. There is limited relevant anthropometric data available for children, despite the fact that clinical gait analysis is predominantly used for the assessment of children with cerebral palsy. In this study, pelvic MRI scans were taken of eight adults (ages 23-40), 14 healthy children (ages 5-13) and 10 children with spastic diplegic cerebral palsy (ages 6-13). Relevant anatomical landmarks were located in the scans, and the HJC location in pelvic coordinates was found by fitting a sphere to points identified on the femoral head. The predictions of three common regression equations for HJC location were compared to those found directly from MRI. Maximum absolute errors of 31 mm were found in adults, 26 mm in children, and 31 mm in the cerebral palsy group. Results from regression analysis and leave-one-out cross-validation techniques on the MRI data suggested that the best predictors of HJC location were: pelvic depth for the antero-posterior direction; pelvic width and leg length for the supero-inferior direction; and pelvic depth and pelvic width for the medio-lateral direction. For single-variable regression, the exclusion of leg length and pelvic depth from the latter two regression equations is proposed. Regression equations could be generalised across adults, children and the cerebral palsy group.

Free ammonia and free nitrous acid inhibition on the anabolic and catabolic processes of Nitrosomonas and Nitrobacter

The inhibitory effects of free ammonia (FA) and free nitrous acid (FNA) on the catabolic and anabolic processes of Nitrosomonas and Nitrobacter were investigated using a method that allows decoupling the growth and energy generation processes. Lab-scale sequencing batch reactors (SBRs) were operated for the enrichment of Nitrosomonas and Nitrobacter. Fluorescent In-Situ Hybridization (FISH) analysis showed that the reactors were 82% and 73% enriched with Nitrosomonas and Nitrobacter, respectively. Batch tests were carried out to measure the oxygen uptake rate (OUR) by the enriched cultures at various FA and FNA levels, in the presence (OUR with CO2 ) or absence (OUR without CO2) of inorganic carbon (CO2, HCO*3 and CO 2*3). FA up to 16.0 mgNH3-N.L(-1) was not found to have any inhibitory effect on either the catabolic or anabolic processes of the Nitrosomonas culture, but both these processes were inhibited by FNA. While an FNA level of 0.40-0.63 mgHNO2-N.L(-1) inhibited the energy production capability of Nitrosomonas by 50%, the growth process of the culture was completely inhibited by FNA at a concentration of 0.40 mgHNO2-N.L(-1). Both FA and FNA were found to have strong inhibition on the anabolic processes of Nitrobacter, but with limited inhibitory effects on the catabolism of this culture. The biosynthesis of Nitrobacter was totally inhibited at an FA level of 6.0 mgNH3-N.L(-1) (or above) or an FNA level of 0.02 mgHNO2-N.L(-1) (or above). At the same level of FA, the energy production capability of Nitrobacter was only inhibited by 12%, whereas an FNA level of up to 0.024 mgHNO2-N.L(-1) did not show any inhibition on the energy production of Nitrobacter. Further, these inhibitory effects appears to be much stronger on Nitrobacter than on Nitrosomonas, supporting that FA and FNA inhibition may play a major role in the elimination of nitrite oxidizing bacteria in processes treating wastewater containing a high level of nitrogen.

A rapid reverse transcription-PCR assay for F+ RNA coliphages to trace fecal pollution in Table Rock Lake on the Arkansas-Missouri border

Source determination of fecal contamination is imperative to efficiently reduce the fecal material load to environmental waters. This study developed primer pairs targeting three F+ RNA bacteriophages and a simple filtration sampling method to enumerate and identify coliphages in environmental waters. Water samples were collected seasonally for one year from the watershed of Table Rock Lake on the Arkansas-Missouri border in areas predisposed to fecal contamination. Collected samples were analyzed quantitatively with most probable number and plaque assays and qualitatively with reverse transcription-PCR. We demonstrated the usefulness of F+ RNA coliphages as an indicator of fecal contamination, but were unable to distinguish between human and non-human sources. F+ coliphage numbers in Table Rock Lake showed seasonal variation with the highest level of coliphage presence during the January sampling event.