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Background: Epistasis, the interaction between genetic loci where the effect of one locus is influenced by one or more other loci, plays a crucial role in the genetic architecture of complex traits. However, as the number of loci considered increases, the investigation of epistasis becomes exponentially more complex, making the selection of key features vital for effective downstream analyses. Relief-Based Algorithms (RBAs) are often employed for this purpose due to their reputation as "interaction-sensitive" algorithms and uniquely non-exhaustive approach. However, the limitations of RBAs in detecting interactions, particularly those involving multiple loci, have not been thoroughly defined. This study seeks to address this gap by evaluating the efficiency of RBAs in detecting higher-order epistatic interactions. Motivated by previous findings that suggest some RBAs may rank predictive features involved in higher-order epistasis negatively, we explore the potential of absolute value ranking of RBA feature weights as an alternative approach for capturing complex interactions. In this study, we assess the performance of ReliefF, MultiSURF, and MultiSURFstar on simulated genetic datasets that model various patterns of genotype-phenotype associations, including 2-way to 5-way genetic interactions, and compare their performance to two control methods: a random shuffle and mutual information., Results: Our findings indicate that while RBAs effectively identify lower-order (2 to 3-way) interactions, their capability to detect higher-order interactions is significantly limited, primarily by large feature count but also by signal noise. Specifically, we observe that RBAs are successful in detecting fully penetrant 4-way XOR interactions using an absolute value ranking approach, but this is restricted to datasets with only 20 total features., Conclusions: These results highlight the inherent limitations of current RBAs and underscore the need for the development of Relief-based approaches with enhanced detection capabilities for the investigation of epistasis, particularly in datasets with large feature counts and complex higher-order interactions., (© 2024. The Author(s).)

Background: Ambulatory surgery is often followed by the development of nausea and/or vomiting (N/V). Although risk factors for postoperative nausea and vomiting (PONV) are frequently discussed, the distinction between PONV and postdischarge nausea and vomiting (PDNV) is unclear. This is especially troublesome given the potential consequences of postdischarge nausea and vomiting (PDNV), which include major discomfort and hospital readmission., Methods: In this retrospective cohort study, data from 10,231 adult patients undergoing ambulatory ophthalmology or otolaryngology procedures with general anesthesia were collected and analyzed. Binary and multinomial logistic regression was used to assess the association between patient and anesthetic characteristics (including age, body mass index (BMI), American Society of Anesthesiologists Physical Status (ASA P/S) classification, current smoker status, and intra- and postoperative opioid usage) and the odds ratios of experiencing only PDNV, only PONV, or both PONV and PDNV, as compared to not experiencing N/V at all., Results: We found that 17.8% of all patients developed N/V (PONV and/or PDNV). Patients who experienced PONV had a 2.79 (95% confidence interval 2.24-3.46) times greater risk of reporting PDNV. Binary logistic regression found that younger age, opioid use, and female sex were associated with an increased likelihood of experiencing any N/V. Increased use of nitrous oxide and a higher ASA P/S class was associated with elevated likelihood of PONV, but not PDNV or PONV plus PDNV., Conclusions: Patients experiencing N/V in the PACU are observed to develop PDNV disproportionately by a factor of 2.79. The patients have distinct predictors, indicating important opportunities for care improvements beyond current guidelines., (© 2024. The Author(s).)

Background: Mental wellbeing encompasses life satisfaction, social connectedness, agency and resilience. In adolescence, mental wellbeing reduces sexual health risk behaviours, substance use and violence; improves educational outcomes; and protects mental health in adulthood. Mental health promotion seeks to improve mental wellbeing and can include activities to engage participants in sport. However, few high-quality trials of mental health promotion interventions have been conducted with adolescents, especially in low- and middle-income countries. We sought to address this gap by testing SMART (Sports-based Mental heAlth pRomotion for adolescenTs) in a pilot cluster-randomised controlled trial (cRCT) in Bardiya, Nepal., Methods: The objectives of the trial are to assess the acceptability and feasibility of SMART, test trial procedures, explore outcome distributions in intervention and control clusters and calculate the total annual cost of the intervention and unit cost per adolescent. The trial design is a parallel-group, two-arm superiority pilot cRCT with a 1:1 allocation ratio and two cross-sectional census surveys with adolescents aged 12-19, one pre-intervention (baseline) and one post-intervention (endline). The study area is four communities of approximately 1000 population (166 adolescents per community). Each community represents one cluster. SMART comprises twice weekly football, martial arts and dance coaching, open to all adolescents in the community, led by local sports coaches who have received psychosocial training. Sports melas (festivals) and theatre performances will raise community awareness about SMART, mental health and the benefits of sport. Adolescents in control clusters will participate in sport as usual. In baseline and endline surveys, we will measure mental wellbeing, self-esteem, self-efficacy, emotion regulation, social support, depression, anxiety and functional impairment. Using observation checklists, unstructured observation and attendance registers from coaching sessions, and minutes of meetings between coaches and supervisors, we will assess intervention fidelity, exposure and reach. In focus group discussions and interviews with coaches, teachers, caregivers and adolescents, we will explore intervention acceptability and mechanisms of change. Intervention costs will be captured from monthly project accounts, timesheets and discussions with staff members., Discussion: Findings will identify elements of the intervention and trial procedures requiring revision prior to a full cRCT to evaluate the effectiveness of SMART., Trial Registration: ISRCTN, ISRCTN15973986 , registered on 6 September 2022; ClinicalTrials.gov, NCT05394311 , registered 27 May 2022., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Background: The messages used to communicate about harm reduction are critical in garnering public support for adoption of harm reduction interventions. Despite the demonstrated effectiveness of harm reduction interventions at reducing overdose deaths and disease transmission, the USA has been slow to adopt harm reduction to scale. Implementation of evidence-based interventions has been hindered by a historical framing of drug use as a moral failure and related stigmatizing attitudes among the public toward people who use drugs. Understanding how professional harm reduction advocates communicate to audiences about the benefits of harm reduction is a critical step to designing persuasive messaging strategies., Methods: We conducted qualitative interviews with a purposively recruited sample of U.S. professional harm reduction advocates (N = 15) to examine their perspectives on which types of messages are effective in persuading U.S. audiences on the value of harm reduction. Participants were professionals working in harm reduction advocacy at national- or state-level organizations promoting and/or implementing harm reduction. Semi-structured interviews were audio-recorded, transcribed, and analyzed using a hybrid inductive/deductive approach., Results: Interviewees agreed that messages about the scientific evidence demonstrating the effectiveness of harm reduction approaches are important but insufficient, on their own, to persuade audiences. Interviewees identified two overarching messaging strategies they perceived as persuasive: using messages about harm reduction that align with audience-specific values, for example centering the value of life or individual redemption; and positioning harm reduction as part of the comprehensive solution to current issues audiences are facing related to drug use and overdose in their community. Interviewees discussed tailoring messages strategies to four key audiences: policymakers; law enforcement; religious groups; and the family and friends of people who use, or have used, drugs. For example, advocates discussed framing messages to law enforcement from the perspective of public safety., Conclusions: Interviewees viewed messages as most persuasive when they align with audience values and audience-specific concerns related to drug use and overdose death. Future research should test effectiveness of tailored messaging strategies to audiences using experimental approaches., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Background: Hypermobile Ehlers-Danlos syndrome (hEDS) and hypermobility spectrum disorders (HSD) are debilitating conditions. Diagnosis is currently clinical in the absence of biomarkers, and criteria developed for adults are difficult to use in children and biologically immature adolescents. Generalized joint hypermobility (GJH) is a prerequisite for hEDS and generalized HSD. Current literature identifies a large proportion of children as hypermobile using a Beighton score ≥ 4 or 5/9, the cut off for GJH in adults. Other phenotypic features from the 2017 hEDS criteria can arise over time. Finally, many comorbidities described in hEDS/HSD are also seen in the general pediatric and adolescent population. Therefore, pediatric specific criteria are needed. The Paediatric Working Group of the International Consortium on EDS and HSD has developed a pediatric diagnostic framework presented here. The work was informed by a review of the published evidence., Observations: The framework has 4 components, GJH, skin and tissue abnormalities, musculoskeletal complications, and core comorbidities. A Beighton score of ≥ 6/9 best identifies children with GJH at 2 standard deviations above average, based on published general population data. Skin and soft tissue changes include soft skin, stretchy skin, atrophic scars, stretch marks, piezogenic papules, and recurrent hernias. Two symptomatic groups were agreed: musculoskeletal and systemic. Emerging comorbid relationships are discussed. The framework generates 8 subgroups, 4 pediatric GJH, and 4 pediatric generalized hypermobility spectrum disorders. hEDS is reserved for biologically mature adolescents who meet the 2017 criteria, which also covers even rarer types of Ehlers-Danlos syndrome at any age., Conclusions: This framework allows hypermobile children to be categorized into a group describing their phenotypic and symptomatic presentation. It clarifies the recommendation that comorbidities should be defined using their current internationally accepted frameworks. This provides a foundation for improving clinical care and research quality in this population., (© 2023. The Author(s).)

Purpose: To compare the effectiveness and safety of phacoemulsification combined with endoscopic cyclophotocoagulation (phaco/ECP), phacoemulsification combined with MicroPulse transscleral cyclophotocoagulation (phaco/MP-TSCPC), and phacoemulsification alone (phaco) in the treatment of coexisting cataract and glaucoma., Methods: Retrospective cohort study of consecutive cases at Massachusetts Eye & Ear. The main outcome measures were the cumulative probabilities of failure between the phaco/ECP group, phaco/MP-TSCPC group, and the phaco alone group with failure defined as reaching NLP vision at any point postoperatively, undergoing additional glaucoma surgery, or the inability to maintain ≥ 20% IOP reduction from baseline with IOP between 5-18 mmHg while maintaining ≤ baseline medications. Additional outcome measures included changes in average IOP, number of glaucoma medications, and complication rates., Results: Sixty-four eyes from 64 patients (25 phaco/ECP, 20 phaco/MPTSCPC, 19 phaco alone) were included in this study. The groups did not differ in age (mean 71.04 ± 6.7 years) or length of follow-up time. Baseline IOPs were significantly different between groups (15.78 ± 4.7 mmHg phaco/ECP, 18.37 ± 4.6 mmHg phaco/MP-TSCPC, 14.30 ± 4.2 mmHg phaco alone, p = 0.02). Primary open-angle glaucoma was the most common type of glaucoma in the phaco alone (42%) and phaco/ECP (48%) groups while mixed-mechanism glaucoma was the most common type in the phaco/MP-TSCPC group (40%). Surgical failure was less likely in eyes in the phaco/MP-TSCPC (3.40 times, p = 0.005) and phaco/ECP (1.40 times, p = 0.044) groups compared to phaco alone based on the Kaplan-Meier survival criteria. These differences maintained statistical significance when differences in preoperative IOP were taken into account using the Cox PH model (p = 0.011 and p = 0.004, respectively). Additionally, surgical failure was 1.98 times less likely following phaco/MP-TSCPC compared to phaco/ECP (p = 0.038). This difference only approached significance once differences in preoperative IOP were accounted for (p = 0.052). There was no significant difference in IOP reduction at 1 year between groups. Mean IOP reductions at 1 year were 3.07 ± 5.3 mmHg from a baseline of 15.78 ± 4.7 in the phaco/ECP group, 6.0 ± 4.3 mmHg from a baseline of 18.37 ± 4.6 in the phaco/MP-TSCPC group and 1.0 ± 1.6 from a baseline of 14.30 ± 4.2 mmHg in the phaco alone group. There were no differences in complication rates among the three groups., Conclusions: Both Phaco/MP-TSCPC and phaco/ECP appear to provide superior efficacy for IOP control when compared to phaco alone. All three procedures had similar safety profiles., (© 2023. The Author(s).)

Background: Lupus nephritis (LN) is an inflammatory disease of the kidneys affecting patients with systemic lupus erythematosus. Current immunosuppressive and cytotoxic therapies are associated with serious side effects and fail to protect 20-40% of LN patients from end-stage renal disease. In this study, we investigated whether a small heat shock protein, HSPB5, can reduce kidney inflammation and the clinical manifestations of the disease in NZB/W F1 mice. Furthermore, we investigated whether HSPB5 can enhance the effects of methylprednisolone, a standard-of-care drug in LN, in an endotoxemia mouse model., Methods: NZB/W F1 mice were treated with HSPB5, methylprednisolone, or vehicle from 23 to 38 weeks of age. Disease progression was evaluated by weekly proteinuria scores. At the end of the study, the blood, urine, spleens, and kidneys were collected for the assessment of proteinuria, blood urea nitrogen, kidney histology, serum IL-6 and anti-dsDNA levels, immune cell populations, and their phenotypes, as well as the transcript levels of proinflammatory chemokine/cytokines in the kidneys. HSPB5 was also evaluated in combination with methylprednisolone in a lipopolysaccharide-induced endotoxemia mouse model; serum IL-6 levels were measured at 24 h post-endotoxemia induction., Results: HSPB5 significantly reduced terminal proteinuria and BUN and substantially improved kidney pathology. Similar trends, although to a lower extent, were observed with methylprednisolone treatment. Serum IL-6 levels and kidney expression of BAFF, IL-6, IFNγ, MCP-1 (CCL2), and KIM-1 were reduced, whereas nephrin expression was significantly preserved compared to vehicle-treated mice. Lastly, splenic Tregs and Bregs were significantly induced with HSPB5 treatment. HSPB5 in combination with methylprednisolone also significantly reduced serum IL-6 levels in endotoxemia mice., Conclusions: HSPB5 treatment reduces kidney inflammation and injury, providing therapeutic benefits in NZB/W F1 mice. Given that HSPB5 enhances the anti-inflammatory effects of methylprednisolone, there is a strong interest to develop HSBP5 as a therapeutic for the treatment of LN., (© 2022. The Author(s).)

Background: Many assisted reproductive technology (ART) centers utilize satellite clinics to expand reach and access to clinical services, but their contribution to lowering geographic barriers in access to care has not been examined. This study's purpose is to determine the extent to which satellite clinics impact geographic access to ART and estimate the percentage of reproductive-age women who have geographic access to ART services., Methods: A systematic web-search collected the locations of all main and satellite ART clinics in the United States (US). Driving times were calculated between satellite clinics and main clinics. The percentage of women with geographic access to care was characterized by clinic type using US Census Core Based Statistical Areas (CBSAs). Logistic regression was used to statistically model the presence of main and satellite clinics as a function of CBSA median income and female reproductive-age population., Results: Four hundred sixty-nine main clinics with embryology labs and 583 satellite clinics were found in the US. Practices with satellite clinics tend to perform more ART cycles. Satellite clinics are located on average 66 minutes from their practice's main clinic and 31 minutes from any main clinic. 22% of satellite clinics were in CBSAs without a main clinic. 46 M (72%) US reproductive-age women live in a CBSA with a main clinic, 5.1 M (8%) women live in a CBSA without a main clinic but at least one satellite clinic, and 13 M (20%) women live in an area with no ART clinic of either type. Female reproductive-age population was found to be a more important predictor of clinic presence than median income., Conclusions: The majority of satellite clinics in the US are positioned in relative proximity to a main clinic. 85% of satellite clinics are located closer to the main clinic of other practices than to their own main clinic. Less than a quarter of ART satellite clinics expand geographic access to ART services by being located in areas without a main clinic, and the vast majority of practices with satellite clinics position their satellite clinics close to another practice's main clinic., Trial Registration: Not applicable., (© 2022. The Author(s).)

Background: Radium-223 is used for the treatment of osseous metastases in castrate-resistant prostate cancer, and has been shown to increase time to the first skeletal-related event, reduce the rate of hospitalization, and improve quality of life. It is well tolerated, with hematologic toxicity as the main adverse event. Thus far, no ocular complication has been reported in the literature after initial administration of radium-223 with a single case reported of ocular complications after a patient's second course of radium-223., Case Presentations: We present three cases of ocular complications after the use of radium-223 in patients with metastatic prostatic adenocarcinoma. Ocular complications presented as blurry vision, and formal diagnosis included uveitis and hyphema., Conclusions: Documentation of adverse events is exceedingly important due to the high incidence of metastatic prostate cancer and increasing interest for the use of radium-223 in other osteoblastic disease. The authors postulate that these ocular complications may be a result of radiation's potential effect on neovascularization, polypharmacy, or the biomolecular effects of radium-223 on integral signaling proteins, potentially coupled with poor underlying ocular health., (© 2022. The Author(s).)

Background: Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms., Methods: To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years., Results: Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment., Conclusions: Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks., (© 2022. The Author(s).)

Background: The coronavirus disease 2019 (COVID-19) pandemic caused significant disruption to in-office and surgical procedures in the field of ophthalmology. The magnitude of the impact of the pandemic on surgical training among ophthalmology residents is not known. This study aims to quantify changes in average case logs among United States (U.S.) ophthalmology residency graduates prior to and during the COVID-19 pandemic., Methods: Retrospective, cross-sectional analysis of aggregate, national data on case logs of U.S. ophthalmology residency graduates from 2012 to 2020. The yearly percent change in the average number of procedures performed in the Accreditation Council for Graduate Medical Education (ACGME) ophthalmology resident case logs were analyzed using linear regression on log-transformed dependent variables. The average percent change from 2019 to 2020 was compared to the average yearly percent change from 2012 to 2019 for procedures performed as the primary surgeon, and primary surgeon and surgical assistant (S + A), as well as procedures for which there are ACGME minimum graduating numbers., Results: Across all procedures and roles, average case logs in 2020 were lower than the averages in 2019. While average total cases logged as primary surgeon increased yearly by 3.2% (95% CI: 2.7, 3.8%, p < 0.001) from 2012 to 2019, total primary surgeon case logs decreased by 11.2% from 2019 to 2020. Cataract (-22.0%) and keratorefractive (-21.1%) surgery experienced the greatest percent decrease in average primary surgeon cases logged from 2019 to 2020. Average total cases logged as S + A experienced an average yearly increase by 1.2% (95% CI: 0.9,1.6%, p < 0.001) prior to 2020, but decreased by 9.6% from 2019 to 2020. For ACGME minimum requirements, similar changes were observed. Specifically, the average case logs in YAG, SLT, filtering (glaucoma), and intravitreal injections had been increasing significantly prior to 2020 (p < 0.05 for all) but decreased in 2020., Conclusions: These findings demonstrate the vulnerability of ophthalmology residency programs to a significant interruption in surgical volume. There is a critical need for development of competency-based, rather than volume-based, requirements to evaluate readiness for independent practice., (© 2022. The Author(s).)

Objective: Deep extubation refers to endotracheal extubation performed while a patient is deeply anesthetized and without airway reflexes. After deep extubation, patients are sent to the post-anesthesia care unit (PACU) to recover, an area with notably different management and staffing than the operating room (OR). One of the most frequent and concerning complications to occur in the PACU is hypoxemia. As such, this study seeks to evaluate the incidence of desaturation, defined by SpO2 < 90% for longer than 10 s, in the PACU following deep extubation. Additionally, we hope to assess the consequence of desaturation on perioperative workflow by comparing PACU recovery times., Results: Following deep extubation, 4.3% of patients (13/300) experienced desaturation in the PACU. Every episode was notably minor, with patients reverting to normal saturation levels within a minute. Of the 26 case factors assessed, 24 had no significant association desaturation in the PACU, including the amount of time spent in the PACU. History of asthma was the only statistically significant factor found to be positively associated with desaturation. We find that PACU desaturation episodes following deep extubation are rare. Our findings suggest that deep extubation is a viable and safe option for patients without significant respiratory tract pathology.

Background: Stigma, both enacted and internalized, is part of the illness experience of many chronic conditions / diseases and has been found to increase psychological distress, lower self-esteem, and impact social engagement lowering quality of life (QOL). Stigma among pediatric patients is of particular concern due to its potential impact on identity formation. Using patient data from the online FD/MAS Alliance Patient Registry (FDMASAPR), this study seeks to 1) determine levels of enacted and self-stigma in a pediatric population of fibrous dysplasia (FD) / McCune Albright syndrome (MAS) patients and 2) to explore the relationship between stigma and anxiety and depression., Methods: This is a cross sectional analysis of deidentified self-report data from 18 pediatric patients. Key analytic variables include the Neuro-QOL stigma short form, the Hospital Anxiety and Depression Scale (HADS), diagnostic category and craniofacial involvement, and select demographics. Sample means and score distributions are examined. Bivariate relationships between stigma, anxiety and depression and patient's personal and medical characteristics are established through analysis of variance and correlation., Results: Composite stigma levels for FD/MAS pediatric patients were comparable to those of children with multiple sclerosis, epilepsy, and muscular dystrophy. Self-stigma was more frequently reported than enacted/felt stigma, but few patients indicated complete freedom from either type of stigma. Diagnosis was significantly related to self-stigma. Significant bivariate relationships were found between depression and enacted/felt and self-stigma and between anxiety and self-stigma., Conclusions: This study establishes the illness experience of pediatric patients with FD / MAS is impacted by stigma and suggests they should be regularly screened for stigma and psychological distress. It supports the integration of clinical psychologists/ therapists in regular patient care, referral of families to advocacy organizations, and indicates that rare disease patient registries can be a useful tool in efforts to improve the QOL of patients.

Background: Endotracheal extubation is the most crucial step during emergence from general anesthesia and is usually carried out when patients are awake with return of airway reflexes. Alternatively, extubations can also be accomplished while patients are deeply anesthetized, a technique known as "deep extubation", in order to provide a "smooth" emergence from anesthesia. Deep extubation is seldomly performed in adults, even in appropriate circumstances, likely due to concerns for potential respiratory complications and limited research supporting its safety. It is in this context that we designed our prospective study to understand the factors that contribute to the success or failure of deep extubation in adults., Methods: In this prospective observational study, 300 patients, age ≥ 18, American Society of Anesthesiologists Physical Status (ASA PS) Classification I - III, who underwent head-and-neck and ocular surgeries. Patients' demographic, comorbidity, airway assessment, O 2 saturation, end tidal CO 2 levels, time to exit OR, time to eye opening, and respiratory complications after deep extubation in the OR were analyzed., Results: Forty (13%) out of 300 patients had at least one complication in the OR, as defined by persistent coughing, desaturation SpO 2  < 90% for longer than 10s, laryngospasm, stridor, bronchospasm and reintubation. When comparing the complication group to the no complication group, the patients in the complication group had significantly higher BMI (30 vs 26), lower O 2 saturation pre and post extubation, and longer time from end of surgery to out of OR (p < 0.05)., Conclusions: The complication rate during deep extubation in adults was relatively low compared to published reports in the literature and all easily reversible. BMI is possibly an important determinant in the success of deep extubation.

Background: Salmonella enterica serotype Typhimurium is a nontyphoidal and common foodborne pathogen that causes serious threat to humans. There is no licensed vaccine to prevent the nontyphoid bacterial infection caused by S. Typhimurium., Methods: To develop conjugate vaccines, the bacterial lipid-A free lipopolysaccharide (LFPS) is prepared as the immunogen and used to synthesize the LFPS-linker-protein conjugates 6a-9b. The designed bifunctional linkers 1-5 comprising either an o-phenylenediamine or amine moiety are specifically attached to the exposed 3-deoxy-D-manno-octulosonic acid (Kdo), an α-ketoacid saccharide of LFPS, via condensation reaction or decarboxylative amidation. In addition to bovine serum albumin and ovalbumin, the S. Typhimurium flagellin (FliC) is also used as a self-adjuvanting protein carrier., Results: The synthesized conjugate vaccines are characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and fast performance liquid chromatography (FPLC), and their contents of polysaccharides and protein are determined by phenol-sulfuric acid assay and bicinchoninic acid assay, respectively. Enzyme-linked immunosorbent assay (ELISA) shows that immunization of mouse with the LFPS-linker-protein vaccines at a dosage of 2.5 μg is sufficient to elicit serum immunoglobulin G (IgG) specific to S. Typhimurium lipopolysaccharide (LPS). The straight-chain amide linkers in conjugates 7a-9b do not interfere with the desired immune response. Vaccines 7a and 7b derived from either unfractionated LFPS or the high-mass portion show equal efficacy in induction of IgG antibodies. The challenge experiments are performed by oral gavage of S. Typhimurium pathogen, and vaccine 7c having FliC as the self-adjuvanting protein carrier exhibits a high vaccine efficacy of 74% with 80% mice survival rate at day 28 post the pathogen challenge., Conclusions: This study demonstrates that lipid-A free lipopolysaccharide prepared from Gram-negative bacteria is an appropriate immunogen, in which the exposed Kdo is connected to bifunctional linkers to form conjugate vaccines. The decarboxylative amidation of Kdo is a novel and useful method to construct a relatively robust and low immunogenic straight-chain amide linkage. The vaccine efficacy is enhanced by using bacterial flagellin as the self-adjuvanting carrier protein.

Historical controls (HCs) can be used for model parameter estimation at the study design phase, adaptation within a study, or supplementation or replacement of a control arm. Currently on the latter, there is no practical roadmap from design to analysis of a clinical trial to address selection and inclusion of HCs, while maintaining scientific validity. This paper provides a comprehensive roadmap for planning, conducting, analyzing and reporting of studies using HCs, mainly when a randomized clinical trial is not possible. We review recent applications of HC in clinical trials, in which either predominantly a large treatment effect overcame concerns about bias, or the trial targeted a life-threatening disease with no treatment options. In contrast, we address how the evidentiary standard of a trial can be strengthened with optimized study designs and analysis strategies, emphasizing rare and pediatric indications. We highlight the importance of simulation and sensitivity analyses for estimating the range of uncertainties in the estimation of treatment effect when traditional randomization is not possible. Overall, the paper provides a roadmap for using HCs.

Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements., Results: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged., Conclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.

Background: Most data on mortality and prognostic factors of universal healthcare waiting lists come from North America, Australasia, and Europe, with little information from South America. We aimed to determine the relationship between medical center-specific waiting time and waiting list mortality in Chile., Method: Using data from all new patients listed in medical specialist waitlists for non-prioritized health problems from 2008 to 2015 in three geographically distant regions of Chile, we constructed hierarchical multivariate survival models to predict mortality risk at two years after registration for each medical center. Kendall rank correlation analysis was used to measure the association between medical center-specific mortality hazard ratio and waiting times., Result: There were 987,497 patients waiting for care at 77 medical centers, including 33,546 (3.40%) who died within two years after registration. Male gender (hazard ratio [HR] = 1.17, 95% confidence interval [CI] 1.1-1.24), older age (HR = 2.88, 95% CI 2.72-3.05), urban residence (HR = 1.19, 95% CI 1.09-1.31), tertiary care (HR = 2.2, 95% CI 2.14-2.26), oncology (HR = 3.57, 95% CI 3.4-3.76), and hematology (HR = 1.6, 95% CI 1.49-1.73) were associated with higher risk of mortality at each medical center with large region-to-region variations. There was a statistically significant association between waiting time variability and death (Z = 2.16, P = 0.0308)., Conclusion: Patient wait time for non-prioritized health conditions was associated with increased mortality in Chilean hospitals.

Background: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization., Results: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization., Conclusions: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .

Background: Australia's only island state, Tasmania, experiences one of the nation's highest incidences of non-urgent emergency department (ED) presentations in a healthcare system regularly faced with service demands that exceed resource availability. Service-demand mismatches are acknowledged to contribute to ED crowding which in turn, has been documented to have a correlation with poorer patient outcomes. Crowding within EDs is complex, non-urgent presentations alone are not the primary cause, but have been reported to be a contributing factor. In 2015-16 Tasmania recorded over 153,000 ED attendances, 55% of these fell into the two least urgent triage categories. Recent research in the State's North established that 29% of non-urgent presentations were referred, formally or informally, from primary healthcare providers and that, for many patients (39%), the ED was not their first choice of service provider. This study aims to identify the service needs of patients referred to a regional Australian ED and subsequently triaged as non-urgent., Method: In order to achieve this aim, three objectives have been identified. The first two objectives use an explanatory sequential mixed-method approach while the third objective will incorporate an implementation science approach. These three objectives are: first, a retrospective analysis of seven years of routinely collected hospital data to identify trends in referral of patients with non-urgent conditions; second, focus group interviews with patients and primary care providers to further understand perceived need and service requirements of those referred to the ED, and third, translation of findings into local health service recommendations., Discussion: Identification of the needs of patients referred to the ED with non-urgent conditions will inform future service planning aiming to facilitate access to the right service at the right time and in the right place.

Background: Postoperative complications and delayed physical recovery are significant problems following emergency abdominal surgery. Physiotherapy aims to aid recovery and prevent complications in the acute phase after surgery and is commonplace in most first-world hospitals. Despite ubiquitous service provision, no well-designed, adequately powered, parallel-group, randomised controlled trial has investigated the effect of physiotherapy on the incidence of respiratory complications, paralytic ileus, rate of physical recovery, ongoing need for formal sub-acute rehabilitation, hospital length of stay, health-related quality of life, and mortality following emergency abdominal surgery. We hypothesise that an enhanced physiotherapy care package of additional education, breathing exercises, and early rehabilitation prevents postoperative complications and improves physical recovery following emergency abdominal surgery compared to standard care alone., Methods: The Incidence of Complications following Emergency Abdominal surgery: Get Exercising (ICEAGE) trial is a pragmatic, investigator-initiated, multicentre, patient- and assessor-blinded, parallel-group, active-placebo controlled randomised trial, powered for superiority. ICEAGE will compare standard care physiotherapy to an enhanced physiotherapy care package in 288 participants admitted for emergency abdominal surgery at three Australian hospitals. Participants will be randomised using concealed allocation to receive either standard care physiotherapy (education, single session of coached breathing exercises, and daily early ambulation for 15 min) or an enhanced physiotherapy care package (education, twice daily coached breathing exercises for a minimum 2 days, and 30 min of daily supervised early rehabilitation for minimum five postoperative days). The primary outcome is a respiratory complication within the first 14 postoperative hospital days assessed daily with standardised diagnostic criteria. Secondary outcomes include referral for sub-acute rehabilitation services, discharge destination, paralytic ileus, hospital length of stay and costs, intensive care unit utilisation, 90-day patient-reported complications and health-related quality of life and physical capacity, and mortality at 30 days and at 1 year following surgery., Discussion: The morbidity, mortality, and fiscal burdens following emergency abdominal surgery are some of the worst within surgery. Physiotherapy may be an effective, low-cost, minimal harm intervention to improve outcomes and reduce hospital utilisation following this surgery type. ICEAGE will test the benefits of this commonly provided intervention within a methodologically robust, multicentre, double-blinded, active-placebo controlled randomised trial., Trial Registration: ACTRN 12615000318583. Registered 8 April 2015., Competing Interests: This trial’s protocol including obtaining written informed consent following randomisation has been approved by each participating hospital’s institutional review board and relevant ethics committee (Human Research Ethics Committee (Tasmania) Network, Tasmania, Australia (H0013666), Metro South Human Research Ethics Committee (17/QPAH/786), Northeast Health Wangaratta Human Research Ethics Committee (185), and Monash University Human Research Ethics Committee (CF15/2550-2015001039)).Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The correct title of the article [1] should be "Integrating multiple data sources (MUDS) for meta-analysis to improve patient-centered outcomes research: a protocol".

Background: The information content of genomes plays a crucial role in the existence and proper development of living organisms. Thus, tremendous effort has been dedicated to developing DNA sequencing technologies that provide a better understanding of the underlying mechanisms of cellular processes. Advances in the development of sequencing technology have made it possible to sequence genomes in a relatively fast and inexpensive way. However, as with any measurement technology, there is noise involved and this needs to be addressed to reach conclusions based on the resulting data. In addition, there are multiple intermediate steps and degrees of freedom when constructing genome assemblies that lead to ambiguous and inconsistent results among assemblers., Methods: Here we introduce HiMMe, an HMM-based tool that relies on genetic patterns to score genome assemblies. Through a Markov chain, the model is able to detect characteristic genetic patterns, while, by introducing emission probabilities, the noise involved in the process is taken into account. Prior knowledge can be used by training the model to fit a given organism or sequencing technology., Results: Our results show that the method presented is able to recognize patterns even with relatively small k-mer size choices and limited computational resources., Conclusions: Our methodology provides an individual quality metric per contig in addition to an overall genome assembly score, with a time complexity well below that of an aligner. Ultimately, HiMMe provides meaningful statistical insights that can be leveraged by researchers to better select contigs and genome assemblies for downstream analysis.

Background: This cluster randomised controlled trial aimed to determine if a 6- month home-based intervention could improve the physical activity and dietary behaviours of adults aged 60 to 80 years living in retirement villages located in Perth, Western Australia., Methods: Participants (n = 363) from 38 retirement villages were recruited into the trial and allocated to the intervention (n = 197: 17 sites) or control (n = 166: 21 sites) group and were blinded. Previously validated instruments-Fat and Fibre Barometer and International Physical Activity Questionnaire, along with anthropometric measures (weight, height, waist and hip circumferences) and blood pressure were collected at baseline and 6 -month time period. Comparisons between intervention and control groups were undertaken pre- and post- intervention using univariate chi-square and t-tests. Multi-level mixed regression analyses were then conducted to ascertain the effects of the intervention on changes in the outcome variables over time and between groups., Results: A total of 139 (70.5%) intervention and 141 (84.9%) control group participants completed the program and post-test assessments. The intervention group demonstrated significant increases in time (80 min more per week on average) devoted to moderate-intensity physical activity, engagement in strength exercises (from 23.7% to 48.2%), frequency of fruit consumed as well as fat avoidance and fibre intake scores, in addition to a 0.5 kg mean reduction in weight post program, whereas no apparent changes were observed in the control group. Mixed regression results further confirmed statistically significant improvements in weight loss (p < 0.05), engagement in strength exercises (p < 0.001) and fruit intake (p = 0.012) by the intervention participants at post-test relative to their controls., Conclusions: Retirement offers a time to reassess lifestyle, and adopt positive health enhancing physical activity and dietary behaviours. This intervention was successful in improving weight, engagement in strength exercises, increasing levels of moderate-intensity physical activity and consumption of fruit among retirement village residents. Further investigation is needed on how to better engage retirement village managers in such programs., Trial Registration: Australia and New Zealand Clinical Trial Registry (ACTRN12612001168842) registered November 2, 2012.

Background: Several techniques have been tailored to the quantification of microRNA expression, including hybridization arrays, quantitative PCR (qPCR), and high-throughput sequencing. Each of these has certain strengths and limitations depending both on the technology itself and the algorithm used to convert raw data into expression estimates. Reliable quantification of microRNA expression is challenging in part due to the relatively low abundance and short length of the miRNAs. While substantial research has been devoted to the development of methods to quantify mRNA expression, relatively little effort has been spent on microRNA expression., Results: In this work, we focus on the Life Technologies TaqMan OpenArray(Ⓡ) system, a qPCR-based platform to measure microRNA expression. Several algorithms currently exist to estimate expression from the raw amplification data produced by qPCR-based technologies. To assess and compare the performance of these methods, we performed a set of dilution/mixture experiments to create a benchmark data set. We also developed a suite of statistical assessments that evaluate many different aspects of performance: accuracy, precision, titration response, number of complete features, limit of detection, and data quality. The benchmark data and software are freely available via two R/Bioconductor packages, miRcomp and miRcompData. Finally, we demonstrate use of our software by comparing two widely used algorithms and providing assessments for four other algorithms., Conclusions: Benchmark data sets and software are crucial tools for the assessment and comparison of competing algorithms. We believe that the miRcomp and miRcompData packages will facilitate the development of new methodology for microRNA expression estimation.

Background: Post-operative pulmonary complications are a significant problem following open upper abdominal surgery. Preliminary evidence suggests that a single pre-operative physiotherapy education and preparatory lung expansion training session alone may prevent respiratory complications more effectively than supervised post-operative breathing and coughing exercises. However, the evidence is inconclusive due to methodological limitations. No well-designed, adequately powered, randomised controlled trial has investigated the effect of pre-operative education and training on post-operative respiratory complications, hospital length of stay, and health-related quality of life following upper abdominal surgery., Methods/design: The Lung Infection Prevention Post Surgery - Major Abdominal- with Pre-Operative Physiotherapy (LIPPSMAck POP) trial is a pragmatic, investigator-initiated, bi-national, multi-centre, patient- and assessor-blinded, parallel group, randomised controlled trial, powered for superiority. Four hundred and forty-one patients scheduled for elective open upper abdominal surgery at two Australian and one New Zealand hospital will be randomised using concealed allocation to receive either i) an information booklet or ii) an information booklet, plus one additional pre-operative physiotherapy education and training session. The primary outcome is respiratory complication incidence using standardised diagnostic criteria. Secondary outcomes include hospital length of stay and costs, pneumonia diagnosis, intensive care unit readmission and length of stay, days/h to mobilise >1 min and >10 min, and, at 6 weeks post-surgery, patient reported complications, health-related quality of life, and physical capacity., Discussion: The LIPPSMAck POP trial is a multi-centre randomised controlled trial powered and designed to investigate whether a single pre-operative physiotherapy session prevents post-operative respiratory complications. This trial standardises post-operative assisted ambulation and physiotherapy, measures many known confounders, and includes a post-discharge follow-up of complication rates, functional capacity, and health-related quality of life. This trial is currently recruiting., Trial Registration: Australian New Zealand Clinical Trials Registry number: ACTRN12613000664741 , 19 June 2013.

Background: Systematic reviews should provide trustworthy guidance to decision-makers, but their credibility is challenged by the selective reporting of trial results and outcomes. Some trials are not published, and even among clinical trials that are published partially (e.g., as conference abstracts), many are never published in full. Although there are many potential sources of published and unpublished data for systematic reviews, there are no established methods for choosing among multiple reports or data sources about the same trial., Methods: We will conduct systematic reviews of the effectiveness and safety of two interventions following the Institute of Medicine (IOM) guidelines: (1) gabapentin for neuropathic pain and (2) quetiapine for bipolar depression. For the review of gabapentin, we will include adult participants with neuropathic pain who do not require ventilator support. For the review of quetiapine, we will include adult participants with acute bipolar depression (excluding mixed or rapid cycling episodes). We will compare these drugs (used alone or in combination with other interventions) with placebo or with the same intervention alone; direct comparisons with other medications will be excluded. For each review, we will conduct highly sensitive electronic searches, and the results of the searches will be assessed by two independent reviewers. Outcomes, study characteristics, and risk of bias ratings will be extracted from multiple reports by two individuals working independently, stored in a publicly available database (Systematic Review Data Repository) and analyzed using commonly available statistical software. In each review, we will conduct a series of meta-analyses using data from different sources to determine how the results are affected by the inclusion of data from multiple published sources (e.g., journal articles and conference abstracts) as well as unpublished aggregate data (e.g., "clinical study reports") and individual participant data (IPD). We will identify patient-centered outcomes in each report and identify differences in the reporting of these outcomes across sources., Systematic Review Registration: CRD42015014037 , CRD42015014038.

Background: Tumorigenesis is an evolutionary process by which tumor cells acquire mutations through successive diversification and differentiation. There is much interest in reconstructing this process of evolution due to its relevance to identifying drivers of mutation and predicting future prognosis and drug response. Efforts are challenged by high tumor heterogeneity, though, both within and among patients. In prior work, we showed that this heterogeneity could be turned into an advantage by computationally reconstructing models of cell populations mixed to different degrees in distinct tumors. Such mixed membership model approaches, however, are still limited in their ability to dissect more than a few well-conserved cell populations across a tumor data set., Results: We present a method to improve on current mixed membership model approaches by better accounting for conserved progression pathways between subsets of cancers, which imply a structure to the data that has not previously been exploited. We extend our prior methods, which use an interpretation of the mixture problem as that of reconstructing simple geometric objects called simplices, to instead search for structured unions of simplices called simplicial complexes that one would expect to emerge from mixture processes describing branches along an evolutionary tree. We further improve on the prior work with a novel objective function to better identify mixtures corresponding to parsimonious evolutionary tree models. We demonstrate that this approach improves on our ability to accurately resolve mixtures on simulated data sets and demonstrate its practical applicability on a large RNASeq tumor data set., Conclusions: Better exploiting the expected geometric structure for mixed membership models produced from common evolutionary trees allows us to quickly and accurately reconstruct models of cell populations sampled from those trees. In the process, we hope to develop a better understanding of tumor evolution as well as other biological problems that involve interpreting genomic data gathered from heterogeneous populations of cells.

Background: Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. Despite active experimental and computational research, relationships among sequence, conservation, and function are still poorly understood., Results: We compared transcription factor occupied segments (TFos) for 116 human and 35 mouse TFs in 546 human and 125 mouse cell types and tissues from the Human and the Mouse ENCODE projects. We based the map between human and mouse TFos on a one-to-one nucleotide cross-species mapper, bnMapper, that utilizes whole genome alignments (WGA). Our analysis shows that TFos are under evolutionary constraint, but a substantial portion (25.1% of mouse and 25.85% of human on average) of the TFos does not have a homologous sequence on the other species; this portion varies among cell types and TFs. Furthermore, 47.67% and 57.01% of the homologous TFos sequence shows binding activity on the other species for human and mouse respectively. However, 79.87% and 69.22% is repurposed such that it binds the same TF in different cells or different TFs in the same cells. Remarkably, within the set of repurposed TFos, the corresponding genome regions in the other species are preferred locations of novel TFos. These events suggest exaptation of some functional regulatory sequences into new function. Despite TFos repurposing, we did not find substantial changes in their predicted target genes, suggesting that CRMs buffer evolutionary events allowing little or no change in the TFos - target gene associations. Thus, the small portion of TFos with strictly conserved occupancy underestimates the degree of conservation of regulatory interactions., Conclusion: We mapped regulatory sequences from an extensive number of TFs and cell types between human and mouse using WGA. A comparative analysis of this correspondence unveiled the extent of the shared regulatory sequence across TFs and cell types under study. Importantly, a large part of the shared regulatory sequence is repurposed on the other species. This sequence, fueled by turnover events, provides a strong case for exaptation in regulatory elements.

Background: Whole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of specific variants and genes that contribute to human disease., Results: We have developed the Variant Effect Scoring Tool (VEST), a supervised machine learning-based classifier, to prioritize rare missense variants with likely involvement in human disease. The VEST classifier training set comprised ~ 45,000 disease mutations from the latest Human Gene Mutation Database release and another ~45,000 high frequency (allele frequency >1%) putatively neutral missense variants from the Exome Sequencing Project. VEST outperforms some of the most popular methods for prioritizing missense variants in carefully designed holdout benchmarking experiments (VEST ROC AUC = 0.91, PolyPhen2 ROC AUC = 0.86, SIFT4.0 ROC AUC = 0.84). VEST estimates variant score p-values against a null distribution of VEST scores for neutral variants not included in the VEST training set. These p-values can be aggregated at the gene level across multiple disease exomes to rank genes for probable disease involvement. We tested the ability of an aggregate VEST gene score to identify candidate Mendelian disease genes, based on whole-exome sequencing of a small number of disease cases. We used whole-exome data for two Mendelian disorders for which the causal gene is known. Considering only genes that contained variants in all cases, the VEST gene score ranked dihydroorotate dehydrogenase (DHODH) number 2 of 2253 genes in four cases of Miller syndrome, and myosin-3 (MYH3) number 2 of 2313 genes in three cases of Freeman Sheldon syndrome., Conclusions: Our results demonstrate the potential power gain of aggregating bioinformatics variant scores into gene-level scores and the general utility of bioinformatics in assisting the search for disease genes in large-scale exome sequencing studies. VEST is available as a stand-alone software package at http://wiki.chasmsoftware.org and is hosted by the CRAVAT web server at http://www.cravat.us.

Background: Nonsense-mediated mRNA decay (NMD) is an mRNA quality control mechanism that selectively recognizes and targets for degradation mRNAs containing premature termination codons. Retroviral full-length RNA is presented to the host translation machinery with characteristics rarely observed among host cell mRNAs: a long 3' UTR, retained introns, and multiple open reading frames. As a result, the viral RNA is predicted to be recognized by the host NMD machinery and degraded. In the case of the Rous sarcoma virus (RSV), we identified a stability element (RSE), which resides immediately downstream of the gag termination codon and facilitates NMD evasion., Results: We defined key RNA features of the RSE through directed mutagenesis of the virus. These data suggest that the minimal RSE is 155 nucleotides (nts) and functions independently of the nucleotide sequence of the stop codon or the first nucleotide following the stop codon. Further data suggested that the 3'UTRs of the RSV pol and src may also function as stability elements., Conclusions: We propose that these stability elements in RSV may be acting as NMD insulators to mask the preceding stop codon from the NMD machinery.

Background: Gradients of morphogens pattern cell fate - a phenomenon that is especially important during development. A simple model system for studying how morphogens pattern cell behavior would overcome difficulties inherent in the study of natural morphogens in vivo. A synthetic biology approach to building such a system is attractive., Results: Using an externally-tunable band-pass filter paradigm, we engineered Escherichia coli cells to function as a model system for the study of how multiple morphogens can pattern cell behavior. We demonstrate how our system exhibits behavior such as morphogen crosstalk and how the cells' growth and fluorescence can be patterned in a number of complex patterns. We extend our cell patterning from 2D cultures on the surface of plates to 3D cultures in soft agarose medium., Conclusion: Our system offers a convenient, well-defined model system for fundamental studies on how multiple morphogen gradients can affect cell fate and lead to pattern formation. Our design principles could be applied to eukaryotic cells to develop other models systems for studying development or for enabling the patterning of cells for applications such as tissue engineering and biomaterials.

Background: There is evidence that dyslipidemia is associated with chronic kidney disease (CKD). Experimental studies have established that lipids are damaging to the kidney and animal intervention studies show statins attenuate this damage. Small clinical trials, meta-analyses, observational studies and post-hoc analyses of cardiovascular intervention studies all support the concept that statins can reduce kidney damage in humans. Based on this background, a double blind randomized placebo controlled trial was designed to assess the effectiveness of atorvastatin 10 mg on slowing the progression of kidney disease in a population of patients with CKD., Method/design: The Lipid lowering and Onset of Renal Disease (LORD) trial is a three-year, single center, multi-site, double blind, randomized, placebo controlled trial. The primary outcome measure is kidney function measured by eGFR calculated by both Modification of Diet in Renal Disease (MDRD) and Cockcroft and Gault equations. Secondary outcome measures include kidney function measured by 24-hour urine creatinine clearance and also 24-hour urinary protein excretion, markers of oxidative stress, inflammation and drug safety and tolerability., Discussion: The results of this study will help determine the effectiveness and safety of atorvastatin and establish its effects on oxidative stress and inflammation in patients with CKD., Trial Registration: ANZCTRN012605000693628.