BatAlign: an incremental method for accurate alignment of sequencing reads

Structural variations (SVs) play a crucial role in genetic diversity. However, the alignments of reads near/across SVs are made inaccurate by the presence of polymorphisms. BatAlign is an algorithm that integrated two strategies called ‘Reverse-Alignment’ and ‘Deep-Scan’ to improve the accuracy of read-alignment. In our experiments, BatAlign was able to obtain the highest F-measures in read-alignments on mismatch-aberrant, indel-aberrant, concordantly/discordantly paired and SV-spanning data sets. On real data, the alignments of BatAlign were able to recover 4.3% more PCR-validated SVs with 73.3% less callings. These suggest BatAlign to be effective in detecting SVs and other polymorphic-variants accurately using high-throughput data. BatAlign is publicly available at https://goo.gl/a6phxB.     

Efficacy and safety of once-daily fluticasone furoate 50 mcg in adults with persistent asthma: a 12-week randomized trial

Background

Fluticasone furoate (FF) is a novel, once-daily inhaled corticosteroid (ICS) that has been shown to improve lung function vs. placebo in asthma patients. This study evaluated the efficacy and safety of FF 50 mcg compared with placebo in asthma patients uncontrolled by non-ICS therapy.

Methods

This 12-week, multicentre, randomized, double-blind, placebo-controlled, parallel-group, phase III study randomized 248 patients (aged ≥12 years) to once-daily FF 50 mcg administered via the ELLIPTA™^a dry powder inhaler or placebo. The primary endpoint was change from baseline in pre-dose evening trough forced expiratory volume in one second (FEV₁). Secondary endpoints were change from baseline in percentage of rescue-free 24-h periods (powered), evening and morning peak expiratory flow, symptom-free 24-h periods and withdrawals due to lack of efficacy. Other endpoints included Asthma Control Test™, Asthma Quality of Life Questionnaire and ELLIPTA ease of use questions. Safety was assessed throughout the study.

Results

There was a significant difference in evening trough FEV₁ between FF 50 mcg and placebo (treatment difference: 120 mL; p = 0.012). There was also a significant difference in rescue-free 24-h periods (11.6%; p = 0.004) vs. placebo. There were numerically greater improvements with FF vs. placebo for all remaining secondary endpoints. The incidence of adverse events was lower with FF (31%) than with placebo (38%); few were treatment-related (FF 50 mcg: n = 1, <1%; placebo: n = 4, 3%).

Conclusion

FF 50 mcg once daily significantly improved FEV₁ and percentage of rescue-free 24-h periods experienced over 12 weeks vs. placebo, and was well tolerated.

Trial registration

www.clinicaltrials.gov, registration number: {"type":"clinical-trial","attrs":{"text":"NCT01436071","term_id":"NCT01436071"}}NCT01436071     

The Salford Lung Study protocol: a pragmatic,randomised phase III real-world effectiveness trial in chronic obstructive pulmonary disease

Background

New treatments need to be evaluated in real-world clinical practice to account for co-morbidities, adherence and polypharmacy.

Methods

Patients with chronic obstructive pulmonary disease (COPD), ≥40 years old, with exacerbation in the previous 3 years are randomised 1:1 to once-daily fluticasone furoate 100 μg/vilanterol 25 μg in a novel dry-powder inhaler versus continuing their existing therapy. The primary endpoint is the mean annual rate of COPD exacerbations; an electronic medical record allows real-time collection and monitoring of endpoint and safety data.

Conclusions

The Salford Lung Study is the world’s first pragmatic randomised controlled trial of a pre-licensed medication in COPD.

Trial registration

Clinicaltrials.gov identifier {"type":"clinical-trial","attrs":{"text":"NCT01551758","term_id":"NCT01551758"}}NCT01551758.     

SPOROS: A pipeline to analyze DISE/6mer seed toxicity

microRNAs (miRNAs) are (18-22nt long) noncoding short (s)RNAs that suppress gene expression by targeting the 3’ untranslated region of target mRNAs. This occurs through the seed sequence located in position 2-7/8 of the miRNA guide strand, once it is loaded into the RNA induced silencing complex (RISC). G-rich 6mer seed sequences can kill cells by targeting C-rich 6mer seed matches located in genes that are critical for cell survival. This results in induction of Death Induced by Survival gene Elimination (DISE), through a mechanism we have called 6mer seed toxicity. miRNAs are often quantified in cells by aligning the reads from small (sm)RNA sequencing to the genome. However, the analysis of any smRNA Seq data set for predicted 6mer seed toxicity requires an alternative workflow, solely based on the exact position 2–7 of any short (s)RNA that can enter the RISC. Therefore, we developed SPOROS, a semi-automated pipeline that produces multiple useful outputs to predict and compare 6mer seed toxicity of cellular sRNAs, regardless of their nature, between different samples. We provide two examples to illustrate the capabilities of SPOROS: Example one involves the analysis of RISC-bound sRNAs in a cancer cell line (either wild-type or two mutant lines unable to produce most miRNAs). Example two is based on a publicly available smRNA Seq data set from postmortem brains (either from normal or Alzheimer’s patients). Our methods (found at https://github.com/ebartom/SPOROS and at Code Ocean: https://doi.org/10.24433/CO.1732496.v1) are designed to be used to analyze a variety of smRNA Seq data in various normal and disease settings.     

Correlating changes in lung function with patient outcomes in chronic obstructive pulmonary disease: a pooled analysis

Background

Relationships between improvements in lung function and other clinical outcomes in chronic obstructive pulmonary disease (COPD) are not documented extensively. We examined whether changes in trough forced expiratory volume in 1 second (FEV₁) are correlated with changes in patient-reported outcomes.

Methods

Pooled data from three indacaterol studies (n = 3313) were analysed. Means and responder rates for outcomes including change from baseline in Transition Dyspnoea Index (TDI), St. George''s Respiratory Questionnaire (SGRQ) scores (at 12, 26 and 52 weeks), and COPD exacerbation frequency (rate/year) were tabulated across categories of ΔFEV₁. Also, generalised linear modelling was performed adjusting for covariates such as baseline severity and inhaled corticosteroid use.

Results

With increasing positive ΔFEV₁, TDI and ΔSGRQ improved at all timepoints, exacerbation rate over the study duration declined (P < 0.001). Individual-level correlations were 0.03-0.18, but cohort-level correlations were 0.79-0.95. At 26 weeks, a 100 ml increase in FEV₁ was associated with improved TDI (0.46 units), ΔSGRQ (1.3-1.9 points) and exacerbation rate (12% decrease). Overall, adjustments for baseline covariates had little impact on the relationship between ΔFEV₁ and outcomes.

Conclusions

These results suggest that larger improvements in FEV₁ are likely to be associated with larger patient-reported benefits across a range of clinical outcomes.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00393458","term_id":"NCT00393458"}}NCT00393458, {"type":"clinical-trial","attrs":{"text":"NCT00463567","term_id":"NCT00463567"}}NCT00463567, and {"type":"clinical-trial","attrs":{"text":"NCT00624286","term_id":"NCT00624286"}}NCT00624286     

Resistance to Erythropoiesis Stimulating Agents in Patients Treated with Online Hemodiafiltration and Ultrapure Low-Flux Hemodialysis: Results from a Randomized Controlled Trial (CONTRAST)

Resistance to erythropoiesis stimulating agents (ESA) is common in patients undergoing chronic hemodialysis (HD) treatment. ESA responsiveness might be improved by enhanced clearance of uremic toxins of middle molecular weight, as can be obtained by hemodiafiltration (HDF). In this analysis of the randomized controlled CONvective TRAnsport STudy (CONTRAST; {"type":"clinical-trial","attrs":{"text":"NCT00205556","term_id":"NCT00205556"}}NCT00205556), the effect of online HDF on ESA resistance and iron parameters was studied. This was a pre-specified secondary endpoint of the main trial. A 12 months'' analysis of 714 patients randomized to either treatment with online post-dilution HDF or continuation of low-flux HD was performed. Both groups were treated with ultrapure dialysis fluids. ESA resistance, measured every three months, was expressed as the ESA index (weight adjusted weekly ESA dose in daily defined doses [DDD]/hematocrit). The mean ESA index during 12 months was not different between patients treated with HDF or HD (mean difference HDF versus HD over time 0.029 DDD/kg/Hct/week [−0.024 to 0.081]; P = 0.29). Mean transferrin saturation ratio and ferritin levels during the study tended to be lower in patients treated with HDF (−2.52% [−4.72 to −0.31]; P = 0.02 and −49 ng/mL [−103 to 4]; P = 0.06 respectively), although there was a trend for those patients to receive slightly more iron supplementation (7.1 mg/week [−0.4 to 14.5]; P = 0.06).In conclusion, compared to low-flux HD with ultrapure dialysis fluid, treatment with online HDF did not result in a decrease in ESA resistance.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00205556","term_id":"NCT00205556"}}NCT00205556     

Different dose regimens of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373) in younger and older adults: A phase 2 randomized placebo-controlled trial

BackgroundNVX-CoV2373 is a recombinant severe acute respiratory coronavirus 2 (rSARS-CoV-2) nanoparticle vaccine composed of trimeric full-length SARS-CoV-2 spike glycoproteins and Matrix-M1 adjuvant.Methods and findingsThe phase 2 component of our randomized, placebo-controlled, phase 1 to 2 trial was designed to identify which dosing regimen of NVX-CoV2373 should move forward into late-phase studies and was based on immunogenicity and safety data through Day 35 (14 days after the second dose). The trial was conducted at 9 sites in Australia and 8 sites in the United States. Participants in 2 age groups (aged 18 to 59 and 60 to 84 years) were randomly assigned to receive either 1 or 2 intramuscular doses of 5-μg or 25-μg NVX-CoV2373 or placebo, 21 days apart. Primary endpoints were immunoglobulin G (IgG) anti-spike protein response, 7-day solicited reactogenicity, and unsolicited adverse events. A key secondary endpoint was wild-type virus neutralizing antibody response. After enrollment, 1,288 participants were randomly assigned to 1 of 4 vaccine groups or placebo, with 1,283 participants administered at least 1 study treatment. Of these, 45% were older participants 60 to 84 years. Reactogenicity was predominantly mild to moderate in severity and of short duration (median <3 days) after first and second vaccination with NVX-CoV2373, with higher frequencies and intensity after second vaccination and with the higher dose. Reactogenicity occurred less frequently and was of lower intensity in older participants. Both 2-dose regimens of 5-μg and 25-μg NVX-CoV2373 induced robust immune responses in younger and older participants. For the 2-dose regimen of 5 μg, geometric mean titers (GMTs) for IgG anti-spike protein were 65,019 (95% confidence interval (CI) 55,485 to 76,192) and 28,137 (95% CI 21,617 to 36,623) EU/mL and for wild-type virus neutralizing antibody (with an inhibitory concentration of 50%—MN_50%) were 2,201 (95% CI 1,343 to 3,608) and 981 (95% CI 560 to 1,717) titers for younger and older participants, respectively, with seroconversion rates of 100% in both age groups. Neutralizing antibody responses exceeded those seen in a panel of convalescent sera for both age groups. Study limitations include the relatively short duration of safety follow-up to date and current lack of immune persistence data beyond the primary vaccination regimen time point assessments, but these data will accumulate over time.ConclusionsThe study confirmed the phase 1 findings that the 2-dose regimen of 5-μg NVX-CoV2373 is highly immunogenic and well tolerated in younger adults. In addition, in older adults, the 2-dose regimen of 5 μg was also well tolerated and showed sufficient immunogenicity to support its use in late-phase efficacy studies.Trial registrationClinicalTrials.gov{"type":"clinical-trial","attrs":{"text":"NCT04368988","term_id":"NCT04368988"}}NCT04368988.

In a phase 2 randomized placebo-controlled trial, Neil Formica and coauthors investigate the immunogenicity and safety of different dose regimens of a SARS-CoV-2 recombinant spike protein vaccine in younger and older adults in USA and Australia.     

On the Calculation of TCID50 for Quantitation of Virus Infectivity

正Dear Editor The most important property of a virus is its infectivity. To measure infectivity, one can assay viral replication in cells to obtain a titer for a given virus stock. A titer is defined as a given number of infectious viral units per unit volume,and an infectious unit is the smallest amount of virus that produces recognizable effects [e.g., cytopathic effect(CPE), dot blot immunoreactivity]. The median tissue culture infectious dose (TCID_(50)) is defined as the dilution of a virus required to infect 50%of a given cell culture.     

Virus Shedding and Potential for Interspecies Waterborne Transmission of Highly Pathogenic H5N1 Influenza Virus in Sparrows and Chickens

To elucidate the role of sparrows as intermediate hosts of highly pathogenic avian influenza H5N1 viruses, we assessed shedding and interspecies waterborne transmission of A/duck/Laos/25/06 in sparrows and chickens. Inoculated birds shed virus at high titers from the oropharynx and cloaca, and infection was fatal. Waterborne transmission from inoculated sparrows to contact chickens was absent, while 25% of sparrows were infected via waterborne transmission from chickens. The viral shedding and susceptibility to infection we observed in sparrows, coupled with their presence in poultry houses, could facilitate virus spread among poultry and wild birds in the face of an H5N1 influenza virus outbreak.The H5N1 influenza A viruses remain a major global concern because of their rapid evolution, genetic diversity, broad host range, and ongoing circulation in wild and domestic birds. H5N1 influenza viruses have swept through poultry flocks across Asia and have spread westward through Eastern Europe to India and Africa since 2003 (1). Sixty-two countries have reported H5N1 influenza virus in domestic poultry/wild birds during the time period 2003 to 2009 (http://www.oie.int/eng/info_ev/en_AI_factoids_2.htm), and to date, more than 400 human infections have been documented in 16 countries, with a mortality rate of ∼61% (http://www.who.int/csr/disease/avian_influenza/country/cases_table_2009_05_22/en/index.html). Most human cases of H5N1 influenza have occurred after contact with infected poultry (13).Some of the more recent isolates of H5N1 highly pathogenic avian influenza (HPAI) virus do not cause overt disease in certain species of domestic and wild ducks; however, these viruses are 100% lethal to chickens and gallinaceous poultry. Because of ducks’ ability to “silently” spread H5N1 HPAI virus and their unresolved role as a reservoir, they are the focus of much research (5, 6, 11). In contrast, the possible role of passerine birds has received little attention, despite their widespread interaction with poultry at many sites worldwide (http://www.searo.who.int/LinkFiles/Publication_PHI-prevention-control-AI.pdf). The order Passeriformes includes more than half of all bird species, including sparrows. Since 2001, several outbreaks of H5N1 influenza virus infection have been reported in passerine birds in eastern Asia, often near infected poultry farms (15). Interestingly, the only confirmed presence of asymptomatic infection with HPAI H5N1 in wild birds was in tree sparrows in Henan Province, China. Both tree and house sparrows (Passer montanus and Passer domesticus, respectively) are members of the Old World sparrow family Passeridae, and in fact, the tree sparrow was not recognized as a species separate from that of the house sparrow until 1713 (http://www.arkive.org/tree-sparrow/passer-montanus/info.html?displayMode=factsheet). The four avian influenza virus isolates obtained from these asymptomatic infections were of the A/Goose/Guangdong/1/96 lineage and were highly pathogenic to experimentally infected chickens (4, 8).Under experimental conditions, passerine species have shown varied susceptibility to HPAI H5N1 viruses. Among sparrows, starlings, and pigeons inoculated with HPAI H5N1 virus isolates, only sparrows experienced lethal infection, and transmission to contact birds was extremely rare (2). Similarly, in sparrows and starlings inoculated with the H5N1 HPAI A/chicken/Hong Kong/220/97 virus, clinical signs were observed only in sparrows, and no deaths occurred (9).To assess the duration and routes of virus shedding and the waterborne virus transmission of HPAI H5N1 virus between sparrows and chickens, we inoculated groups of birds with A/duck/Laos/25/06, which had caused extremely high morbidity and mortality in domestic ducks (7) and was highly pathogenic to chickens, geese, and quail (J.-K. Kim and R. G. Webster, unpublished data). The virus was obtained from our collaborators in Lao People''s Democratic Republic and was grown in the allantoic cavities of 10-day-old embryonated chicken eggs (eggs) for 36 to 48 h at 35°C. The allantoic fluid was harvested, titrated (50% egg infective dose [EID₅₀] per milliliter), and stored at −80°C. All experiments were approved by the U.S. Department of Agriculture and the U.S. Centers for Disease Control and Prevention and were performed in biosafety level 3+ facilities at St. Jude Children''s Research Hospital. Wild house sparrows (Passer domesticus) were captured locally (Memphis, TN), and specific-pathogen-free outbred White Leghorn chickens (Gallus domesticus) were purchased from Charles River Laboratories (North Franklin, CT). All animal experiments were approved by the St. Jude Animal Care and Use Committee and complied with the policies of the National Institutes of Health and the Animal Welfare Act.Before inoculation, oropharyngeal and cloacal swabs were collected from sparrows, and baseline blood samples were collected from chickens to exclude preexisting H5N1 influenza virus infection. Eight sparrows were inoculated intranasally with 10⁶ EID₅₀ of virus in a volume of 100 μl, and five chickens were inoculated with 10² EID₅₀ of virus in a volume of 1 ml (0.5 ml intranasally, 0.5 ml intratracheally, and 1 drop per eye). All birds in each experimental group were housed in a single cage. Inoculated sparrows were provided with 1 liter of water in a shallow stainless steel pan at the bottom of the cage, and chickens were given 3 liters of water in a trough inside the cage. Twenty-four hours after inoculation, 1 liter of water was removed from the inoculated chickens’ cage and placed undiluted in a cage housing 8 contact sparrows; similarly, 1 liter of water was taken from the inoculated sparrows’ cage, mixed with 2 liters of fresh water, and placed in a cage housing 5 contact chickens. Clinical disease signs, including depression, huddling at the cage bottom, and ruffled feathers, were monitored through daily observation, and oropharyngeal and cloacal swabs obtained from all birds were collected daily for 14 days. Swab samples were titrated in eggs and expressed as log₁₀ EID₅₀/ml (10). The lower limit of detection was 0.75 log₁₀ EID₅₀/ml.Blood samples were taken from all surviving contact birds on day 14 of the study. Sera were treated with a receptor-destroying enzyme (Denka Seiken, Campbell, CA), as instructed by the manufacturer, and heat inactivated at 56°C for 30 min. Hemagglutination inhibition (HI; using 0.5% packed chicken red blood cells) titers were determined as the reciprocal of the highest serum dilution that inhibited 4 hemagglutinating units of virus. HI titers of ≥10 were considered suggestive of recent influenza virus infection.Inoculation with A/duck/Laos/25/06 was lethal to all birds (Table ​(Table1).1). While chickens succumbed to infection within 2 days postinoculation (p.i.), the mean time until death for sparrows was 4.1 days; mortality occurred rapidly (overnight) without prior observation of clinical signs. Expected clinical signs, should they have occurred, included moderate to severe depression, huddling at the cage bottom, and ruffled feathers (9). All inoculated birds shed virus from the oropharynx and, to a lesser extent, from the cloaca (Fig. 1A and B). The mean virus titers of inoculated chickens and sparrows were comparable on day 1 p.i.; however, on day 2 p.i., the mean oropharyngeal and cloacal viral titers of chickens were approximately 2 and 2.5 times greater, respectively, than those of sparrows (Fig. 1A and B). The virus titer in water used by inoculated sparrows was 10^0.75 EID₅₀/ml at 1 day p.i. and peaked at 10^1.75 EID₅₀/ml on days 2 and 4 p.i. (Fig. ​(Fig.1C).1C). No virus was detected in water from the inoculated chickens’ cage.Open in a separate windowFIG. 1.Mean oropharyngeal and cloacal virus titers in sparrows (A) and chickens (B) inoculated with a lethal dose of A/duck/Laos/25/06 (H5N1) virus. (C) Virus titers in the drinking water of inoculated sparrows. Sparrows were inoculated with 10⁶ EID₅₀/ml of virus, and chickens were inoculated with 10² EID₅₀/ml of virus. The lower limit of detection was 0.75 log₁₀ EID₅₀/ml.

TABLE 1.

Transmission rates, mortality rates, and mean peak titers of A/duck/Laos/25/06 (H5N1) virus in inoculated and contact birds

Determination of the effective diffusion coefficient of oxygen in gel materials in relation to gel concentration

Summary The effective diffusion coefficient of oxygen, ID_e, was determined in different gel support materials (calcium alginate, -carrageenan, gellan gum, agar and agarose) which are generally used for immobilization of cells. The method used was based upon fitting Crank's model on the experimental data. The model describes the solute diffusion from a well-stirred solution into gel beads which are initially free of solute. The effect of the gel concentration on ID_e of oxygen in the gel was investigated. The results showed a decreasing ID_e for both agar and agarose at increasing gel concentration. In case of calcium alginate and gellan gum, a maximum in ID_e at the intermediate gel concentration was observed. It is hypothesized that this phenomenon is due to a changing gelpore structure at increasing gel concentrations. The ID_e of oxygen in calcium alginate, -carrageenan and gellan gum varied from 1.5^*10^–9 to 2.1^*10^–9 m²s^–1 in the gel concentration range of 0.5 to 5% (w/v).     

Measuring respiratory symptoms of COPD: performance of the EXACT- Respiratory Symptoms Tool (E-RS) in three clinical trials

Background

Symptomatic relief is an important treatment goal for patients with COPD. To date, no diary for evaluating respiratory symptoms in clinical trials has been developed and scientifically-validated according to FDA and EMA guidelines. The EXACT – Respiratory Symptoms (E-RS) scale is a patient-reported outcome (PRO) measure designed to address this need. The E-RS utilizes 11 respiratory symptom items from the existing and validated 14-item EXACT, which measures symptoms of exacerbation. The E-RS total score quantifies respiratory symptom severity, and 3 domains assess breathlessness, cough and sputum, and chest symptoms.

Methods

This study examined the performance of the E-RS in each of 3 controlled trials with common and unique validation variables: one 6-month (N = 235, US) and two 3-month (N = 749; N = 597; international). Subjects completed the E-RS as part of a daily eDiary. Tests of reliability, validity, and responsiveness were conducted in each dataset.

Results

In each study, RS-Total score was internally consistent (Cronbach α) (0.88, 0.92, 0.92) and reproducible (intra-class correlation) in stable patients (2 days apart: 0.91; 7 days apart: 0.71, 0.74). RS-Total scores correlated significantly with the following criterion variables (Spearman’s rho; p < 0.01, all comparisons listed here): FEV₁% predicted (−0.19, −0.14, −0.15); St. George’s Respiratory Questionnaire (SGRQ) (0.65, 0.52, 0.51); Breathlessness, Cough, and Sputum Scale (BCSS) (0.89, 0.89); modified Medical Research Council dyspnoea scale (mMRC) (0.40); rescue medication use (0.43, 0.42); Functional Performance Inventory Short-Form (FPI-SF) (0.43); 6-minute walk distance (6-MWT) (−0.30, −0.14) and incremental shuttle walk (ISWT) (−0.18) tests. Correlations between these variables and RS-Breathlessness, RS-Cough and Sputum, RS-Chest Symptoms scores supported subscale validity. RS-Total, RS-Breathlessness, and RS-Chest Symptoms differentiated mMRC levels of breathlessness severity (p < 0.0001). RS-Total and domain scores differentiated subjects with no rescue medication use and 3 or more puffs (p < 0.0001). Sensitivity to changes in health status (SGRQ), symptoms (BCSS), and exercise capacity (6MWT, ISWT) were also shown and responder definitions using criterion- and distribution-based methods are proposed.

Conclusions

Results suggest the E-RS is a reliable, valid, and responsive measure of respiratory symptoms of COPD suitable for use in natural history studies and clinical trials.

Trial registration

MPEX: {"type":"clinical-trial","attrs":{"text":"NCT00739648","term_id":"NCT00739648"}}NCT00739648; AZ1: {"type":"clinical-trial","attrs":{"text":"NCT00949975","term_id":"NCT00949975"}}NCT00949975; AZ 2: {"type":"clinical-trial","attrs":{"text":"NCT01023516","term_id":"NCT01023516"}}NCT01023516

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-014-0124-z) contains supplementary material, which is available to authorized users.     

Efficacy and safety of once-daily aclidinium in chronic obstructive pulmonary disease

Background

The long-term efficacy and safety of aclidinium bromide, a novel, long-acting muscarinic antagonist, were investigated in patients with moderate to severe chronic obstructive pulmonary disease (COPD).

Methods

In two double-blind, 52-week studies, ACCLAIM/COPD I (n = 843) and II (n = 804), patients were randomised to inhaled aclidinium 200 μg or placebo once-daily. Patients were required to have a post-bronchodilator forced expiratory volume in 1 second (FEV₁)/forced vital capacity ratio of ≤70% and FEV₁ <80% of the predicted value. The primary endpoint was trough FEV₁ at 12 and 28 weeks. Secondary endpoints were health status measured by St George''s Respiratory Questionnaire (SGRQ) and time to first moderate or severe COPD exacerbation.

Results

At 12 and 28 weeks, aclidinium improved trough FEV₁ versus placebo in ACCLAIM/COPD I (by 61 and 67 mL; both p < 0.001) and ACCLAIM/COPD II (by 63 and 59 mL; both p < 0.001). More patients had a SGRQ improvement ≥4 units at 52 weeks with aclidinium versus placebo in ACCLAIM/COPD I (48.1% versus 39.5%; p = 0.025) and ACCLAIM/COPD II (39.0% versus 32.8%; p = 0.074). The time to first exacerbation was significantly delayed by aclidinium in ACCLAIM/COPD II (hazard ratio [HR] 0.7; 95% confidence interval [CI] 0.55 to 0.92; p = 0.01), but not ACCLAIM/COPD I (HR 1.0; 95% CI 0.72 to 1.33; p = 0.9). Adverse events were minor in both studies.

Conclusion

Aclidinium is effective and well tolerated in patients with moderate to severe COPD.

Trial registration

ClinicalTrials.gov: {"type":"clinical-trial","attrs":{"text":"NCT00363896","term_id":"NCT00363896"}}NCT00363896 (ACCLAIM/COPD I) and {"type":"clinical-trial","attrs":{"text":"NCT00358436","term_id":"NCT00358436"}}NCT00358436 (ACCLAIM/COPD II).     

Do Sustained Lung Inflations during Neonatal Resuscitation Affect Cerebral Blood Volume in Preterm Infants? A Randomized Controlled Pilot Study

Background

Sustained lung inflations (SLI) during neonatal resuscitation may promote alveolar recruitment in preterm infants. While most of the studies focus on respiratory outcome, the impact of SLI on the brain hasn’t been investigated yet.

Objective

Do SLI affect cerebral blood volume (CBV) in preterm infants?

Methods

Preterm infants of gestation 28 weeks 0 days to 33 weeks 6 days with requirement for respiratory support (RS) were included in this randomized controlled pilot trial. Within the first 15 minutes after birth near-infrared spectroscopy (NIRS) measurements using ‘NIRO-200-NX’ (Hamamatsu, Japan) were performed to evaluate changes in CBV and cerebral tissue oxygenation. Two groups were compared based on RS: In SLI group RS was given by applying 1–3 SLI (30 cmH₂O for 15 s) continued by respiratory standard care. Control group received respiratory standard care only.

Results

40 infants (20 in each group) with mean gestational age of 32 weeks one day (±2 days) and birth weight of 1707 (±470) g were included. In the control group ΔCBV was significantly decreasing, whereas in SLI group ΔCBV showed similar values during the whole period of 15 minutes. Comparing both groups within the first 15 minutes ΔCBV showed a tendency toward different overall courses (p = 0.051).

Conclusion

This is the first study demonstrating an impact of SLI on CBV. Further studies are warranted including reconfirmation of the present findings in infants with lower gestational age. Future investigations on SLI should not only focus on respiratory outcome but also on the consequences on the developing brain.

Trial Registration

German Clinical Trials Register DRKS00005161 https://drks-neu.uniklinik-freiburg.de/drks_web/setLocale_EN.do     

The effectiveness of the peer-delivered Thinking Healthy PLUS (THPP+) Program for maternal depression and child socioemotional development in Pakistan: study protocol for a randomized controlled trial

BackgroundThe negative effects of perinatal depression on the mother and child start early and persist throughout the lifecourse (Lancet 369(9556):145–57, 2007; Am J Psychiatry 159(1):43-7, 2002; Arch Dis Child 77(2):99–101, 1997; J Pak Med Assoc 60(4):329; J Psychosoma Res 49(3):207–16, 2000; Clin Child Fam Psychol Rev 14(1):1–27, 2011). Given that 10–35 % of children worldwide are exposed to perinatal depression in their first year of life (Int Rev Psychiatry 8(1):37–54, 1996), mitigating this intergenerational risk is a global public health priority (Perspect Public Health 129(5):221–7, 2009; Trop Med Int Health 13(4):579–83, 2008; Br Med Bull 101(1):57–79, 2012). However, it is not clear whether intervention with depressed women can have long-term benefits for the mother and/or her child. We describe a study of the effectiveness of a peer-delivered depression intervention delivered through 36 postnatal months, the Thinking Healthy Program Peer-delivered PLUS (THPP+) for women and their children in rural Pakistan.Methods/designThe THPP+ study aims are: (1) to evaluate the effects of an extended 36-month perinatal depression intervention on maternal and index child outcomes using a cluster randomized controlled trial (c-RCT) and (2) to determine whether outcomes among index children of perinatally depressed women in the intervention arm converge with those of index children born to perinatally nondepressed women. The trial is designed to recruit 560 pregnant women who screened positive for perinatal depression (PHQ-9 score ≥10) from 40 village clusters, of which 20 receive the THPP+ intervention. An additional reference group consists of 560 perinatally nondepressed women from the same 40 clusters as the THPP+ trial. The women in the nondepressed group are not targeted to receive the THPP+ intervention; but, by recruiting pregnant women from both intervention and control clusters, we are able to evaluate any carryover effects of the THPP+ intervention on the women and their children. Perinatally depressed women in the THPP+ intervention arm receive bimonthly group-based sessions. Primary outcomes are 3-year maternal depression and 3-year child development indicators. Analyses are intention-to-treat and account for the clustered design.DiscussionThis trial, together with the reference group, has the potential to further our understanding of the early developmental lifecourse of children of both perinatally depressed and perinatally nondepressed women in rural Pakistan and to determine whether intervening with women’s depression in the perinatal period can mitigate the negative effects of maternal depression on 36-month child development.

Trial registration

THPP-P ClinicalTrials.gov Identifier: {"type":"clinical-trial","attrs":{"text":"NCT02111915","term_id":"NCT02111915"}}NCT02111915 (registered on 9 April 2014).THPP+ ClinicalTrials.gov Identifier: {"type":"clinical-trial","attrs":{"text":"NCT02658994","term_id":"NCT02658994"}}NCT02658994 (registered on 21 January 2016).Sponsor: Human Development Research Foundation (HDRF).

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-016-1530-y) contains supplementary material, which is available to authorized users.     

Could dual G-protein coupling explain [d-Met]FMRFamide's mixed action in vivo?

In vitro studies have demonstrated that FMRFamide-related peptide receptors can be coupled to different G-proteins, mediating opposite stimulatory and inhibitory effects. The present study tested whether this duality might extend to effects in vivo. Antinociception in mice of ICV [d-Met²]FMRFamide, which produced agonist [ED₅₀ = 36.3 μg (61.6 nmol)] and antagonist [ID₅₀ = 0.72 μg (1.22 nmol)] actions, was attenuated by 24-h pretreatment with ICV pertussis toxin (ID₅₀ = 0.55 μg) or cholera toxin (ID₅₀ = 0.09 μg), suggesting that [d-Met²]FMRFamide in vivo effects might also be explained by dual coupling.     

A 12-Week Exercise Program for Pregnant Women with Obesity to Improve Physical Activity Levels: An Open Randomised Preliminary Study

Objective

To evaluate whether a 12-week supervised exercise program promotes an active lifestyle throughout pregnancy in pregnant women with obesity.

Methods

In this preliminary randomised trial, pregnant women (body mass index ≥ 30 kg/m²) were allocated to either standard care or supervised training, from 15 to 27 weeks of gestation. Physical activity was measured by accelerometry at 14, 28 and 36 weeks, while fitness (oxygen consumption (VO₂) at the anaerobic threshold), nutrition (caloric intake and macronutrients percentage) and anthropometry were assessed at 14 and 28 weeks of gestation. Analyses were performed using repeated measures ANOVA.

Results

A total of fifty (50) women were randomised, 25 in each group. There was no time-group interaction for time spent at moderate and vigorous activity (p_interaction = 0.064), but the exercise group’s levels were higher than controls’ at all times (p_{group effect} = 0.014). A significant time-group interaction was found for daily physical activity (p = 0.023); similar at baseline ((22.0 ± 6.7 vs 21.8 ± 7.3) x 10⁴ counts/day) the exercise group had higher levels than the control group following the intervention ((22.8 ± 8.3 vs 19.2 ± 4.5) x 10⁴ counts/day, p = 0.020) and at 36 weeks of gestation ((19.2 ± 1.5 vs 14.9 ± 1.5) x 10⁴ counts/day, p = 0.034). Exercisers also gained less weight than controls during the intervention period despite similar nutritional intakes (difference in weight change = -0.1 kg/week, 95% CI -0.2; -0.02, p = 0.016) and improved cardiorespiratory fitness (difference in fitness change = 8.1%, 95% CI 0.7; 9.5, p = 0.041).

Conclusions

Compared with standard care, a supervised exercise program allows pregnant women with obesity to maintain fitness, limit weight gain and attenuate the decrease in physical activity levels observed in late pregnancy.

Trial Registration

ClinicalTrials.gov NCT01610323     

The Stewart Approach – One Clinician’s Perspective

Peter Stewart added controversy to an already troubled subject when he entered the clinical acid-base arena. His approach puts water dissociation at the centre of the acid-base status of body fluids. It is based on six simultaneous equations, incorporating the Laws of Mass Action, Mass Conservation, and Electrical Neutrality. Together with Gibbs-Donnan equilibria, these equations explain the diagnostically important PaCO₂/pH relationship, and improve understanding of the physiologic basis of traditional acid-base approaches. Spin-offs have included new scanning tools for unmeasured ions, in particular the ‘strong ion gap’ and ‘net unmeasured ions’. The most controversial feature is the designation of pH and bicarbonate concentrations as dependent variables, answerable exclusively to three independent variables. These are the strong ion difference (SID), the total concentration of non-volatile weak acid (A_TOT), and PCO₂. Aspects of this assertion conflict with traditional renal physiology, and with current models of membrane H⁺/base transporters, oxidative phosphorylation, and proton and bicarbonate ionophores. The debate in this area is ongoing. Meanwhile, Stewart-style diagnostic and decision support systems such as the ‘Strong Ion Calculator’ and the web-site www.acidbase.org are now appearing.     

Randomized single oral dose phase 1 study of safety,tolerability, and pharmacokinetics of Iminosugar UV-4 Hydrochloride (UV-4B) in healthy subjects

BackgroundUV-4 (N-(9’-methoxynonyl)-1-deoxynojirimycin, also called MON-DNJ) is an iminosugar small-molecule oral drug candidate with in vitro antiviral activity against diverse viruses including dengue, influenza, and filoviruses and demonstrated in vivo efficacy against both dengue and influenza viruses. The antiviral mechanism of action of UV-4 is through inhibition of the host endoplasmic reticulum-resident α-glucosidase 1 and α-glucosidase 2 enzymes. This inhibition prevents proper glycan processing and folding of virus glycoproteins, thereby impacting virus assembly, secretion, and the fitness of nascent virions.Methodology/Principal findingsHere we report a first-in-human, single ascending dose Phase 1a study to evaluate the safety, tolerability, and pharmacokinetics of UV-4 hydrochloride (UV-4B) in healthy subjects (ClinicalTrials.gov Identifier {"type":"clinical-trial","attrs":{"text":"NCT02061358","term_id":"NCT02061358"}}NCT02061358). Sixty-four subjects received single oral doses of UV-4 as the hydrochloride salt equivalent to 3, 10, 30, 90, 180, 360, 720, or 1000 mg of UV-4 (6 subjects per cohort), or placebo (2 subjects per cohort). Single doses of UV-4 hydrochloride were well tolerated with no serious adverse events or dose-dependent increases in adverse events observed. Clinical laboratory results, vital signs, and physical examination data did not reveal any safety signals. Dose-limiting toxicity was not observed; the maximum tolerated dose of UV-4 hydrochloride in humans has not yet been determined (>1000 mg). UV-4 was rapidly absorbed and distributed after dosing with the oral solution formulation used in this study. Median time to reach maximum plasma concentration ranged from 0.5–1 hour and appeared to be independent of dose. Exposure increased approximately in proportion with dose over the 333-fold dose range. UV-4 was quantifiable in pooled urine over the entire collection interval for all doses.Conclusions/SignificanceUV-4 is a host-targeted broad-spectrum antiviral drug candidate. At doses in humans up to 1000 mg there were no serious adverse events reported and no subjects were withdrawn from the study due to treatment-emergent adverse events. These data suggest that therapeutically relevant drug levels of UV-4 can be safely administered to humans and support further clinical development of UV-4 hydrochloride or other candidate antivirals in the iminosugar class.Trial registrationClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT02061358","term_id":"NCT02061358"}}NCT02061358 https://clinicaltrials.gov/ct2/show/{"type":"clinical-trial","attrs":{"text":"NCT02061358","term_id":"NCT02061358"}}NCT02061358.