New and simple algorithms for stable flow problems

Stable flows generalize the well-known concept of stable matchings to markets in which transactions may involve several agents, forwarding flow from one to another. An instance of the problem consists of a capacitated directed network, in which vertices express their preferences over their incident edges. A network flow is stable if there is no group of vertices that all could benefit from rerouting the flow along a walk. Fleiner established that a stable flow always exists by reducing it to the stable allocation problem. We present an augmenting-path algorithm for computing a stable flow, the first algorithm that achieves polynomial running time for this problem without using stable allocation as a black-box subroutine. We further consider the problem of finding a stable flow such that the flow value on every edge is within a given interval. For this problem, we present an elegant graph transformation and based on this, we devise a simple and fast algorithm, which also can be used to find a solution to the stable marriage problem with forced and forbidden edges. Finally, we study the stable multicommodity flow model introduced by Kir\'{a}ly and Pap. The original model is highly involved and allows for commodity-dependent preference lists at the vertices and commodity-specific edge capacities. We present several graph-based reductions that show equivalence to a significantly simpler model. We further show that it is NP-complete to decide whether an integral solution exists

Improving community ambulation after stroke: the AMBULATE trial

<p>Abstract</p> <p>Background</p> <p>It has been reported that following rehabilitation, only 7% of stroke survivors are able to walk at a level commensurate with community participation. Previous research indicates that treadmill and overground walking training can improve walking capacity in people living in the community after stroke. The main objectives of the AMBULATE trial are to determine (i) whether a 4-month treadmill walking program is more effective than a 2-month program, compared to control, in improving walking capacity, health and community participation and (ii) the "threshold" walking speed that results in sufficient walking capacity that makes walking self-sustaining.</p> <p>Methods/Design</p> <p>A prospective randomised controlled trial of unsupported treadmill training with a 12 month follow-up with concealed allocation and blinded assessment will be conducted. 210 community-dwelling people after stroke who are able to walk independently but slowly will be recruited and randomly allocated to either a 4 month training group, 2 month training group or the control (no intervention) group. Intervention for the two training groups will occur 3 days per week for 30 minutes each session. Measurements of walking, health and community participation will be taken at baseline, 2 months, 4 months, 6 months and 12 months. This study has obtained ethical approval from the relevant Human Research Ethics Committees.</p> <p>Discussion</p> <p>By improving stroke survivors' walking ability, it is likely also to improve their general wellbeing by promoting better health and greater community participation. Furthermore, if stroke survivors can reach a point where their walking and community participation is self-sustaining, this will reduce the burden of care on family and friends as well as the economic burden on the health system. Given the major demographic shift in developed nations involving significant growth in the aged population, this research will make an important evidence-based contribution to the promotion of healthy ageing.</p> <p>Trial registration</p> <p>This trial is registered with the Australian New Zealand Clinical Trials Registry, (ACTRN012607000227493)</p

Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism.

Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data

Characteristics of starch-based films plasticised by glycerol and by the ionic liquid 1-ethyl-3-methylimidazolium acetate: A comparative study

This paper reports the plasticisation effect of the ionic liquid, 1-ethyl-3-methylimidazolium acetate ([Emim][OAc]), as compared with the traditionally used plasticiser, glycerol, on the characteristics of starch-based films. For minimising the additional effect of processing, a simple compression moulding process (which involves minimal shear) was used for preparation of starch-based films. The results show that [Emim][OAc] was favourable for plasticisation, i.e., disruption of starch granules (by scanning electron microscopy), and could result in a more amorphous structure in the starch-based materials (by X-ray diffraction and dynamic mechanical analysis). 13C CP/MAS and SPE/MAS NMR spectroscopy revealed that not only was the crystallinity reduced by [Emim][OAc], but also the amorphous starch present was plasticised to a more mobile form as indicated by the appearance of amorphous starch in the SPE/MAS spectrum. Mechanical results illustrate that, when either glycerol or [Emim][OAc] was used, a higher plasticiser content could contribute to higher flexibility. In spite of the accelerated thermal degradation of starch by [Emim][OAc] as shown by thermogravimetric analysis, the biodegradation study revealed the antimicrobial effect of [Emim][OAc] on the starch-based materials. Considering the high-amylose starch used here which is typically difficult to gelatinise in a traditional plasticiser (water and/or glycerol), [Emim][OAc] is demonstrated to be a promising plasticiser for starch to develop “green” flexible antimicrobial materials for novel applications

Assessing Walking Ability in People with HTLV-1-Associated Myelopathy Using the 10 Meter Timed Walk and the 6 Minute Walk Test

Five to ten million persons, are infected by HTLV-1 of which 3% will develop HTLV-1-associated myelopathy (HAM) a chronic, disabling inflammation of the spinal cord. Walking, a fundamental, complex, multi-functional task is demanding of multiple body systems. Restricted walking ability compromises activity and participation levels in people with HAM (pwHAM). Therapy aims to improve mobility but validated measures are required to assess change.Prospective observational study.To explore walking capacity in pwHAM, walking endurance using the 6 minute walk (6MW), and gait speed, using the timed 10m walk (10mTW).Out-patient setting in an inner London Teaching hospital.Prospective documentation of 10mTW and 6MW distance; walking aid usage and pain scores measured twice, a median of 18 months apart.Data analysis was completed for twenty-six pwHAM, (8♂; 18♀; median age: 57.8 years; median disease duration: 8 years). Median time at baseline to: complete 10m was 17.5 seconds, versus 21.4 seconds at follow up; 23% completed the 6MW compared to 42% at follow up and a median distance of 55m was covered compared to 71m at follow up. Using the 10mTW velocity to predict the 6MW distance, overestimated the distance walked in 6 minutes (p<0.01). Functional decline over time was captured using the functional ambulation categories.The 10mTW velocity underestimated the degree of disability. Gait speed usefully predicts functional domains, shows direction of functional change and comparison with published healthy age matched controls show that these patients have significantly slower gait speeds. The measured differences over 18 months were sufficient to reliably detect change and therefore these assessments can be useful to detect improvement or deterioration within broader disability grades. Walking capacity in pwHAM should be measured using the 10mTW for gait speed and the 6MW for endurance

Rucaparib for patients with platinum-sensitive, recurrent ovarian carcinoma (ARIEL3): post-progression outcomes and updated safety results from a randomised, placebo-controlled, phase 3 trial

BACKGROUND: In ARIEL3, rucaparib maintenance treatment significantly improved progression-free survival versus placebo. Here, we report prespecified, investigator-assessed, exploratory post-progression endpoints and updated safety data. METHODS: In this ongoing (enrolment complete) randomised, placebo-controlled, phase 3 trial, patients aged 18 years or older who had platinum-sensitive, high-grade serous or endometrioid ovarian, primary peritoneal, or fallopian tube carcinoma and an Eastern Cooperative Oncology Group performance status of 0 or 1 who had received at least two previous platinum-based chemotherapy regimens and responded to their last platinum-based regimen were randomly assigned (2:1) to oral rucaparib (600 mg twice daily) or placebo in 28-day cycles using a computer-generated sequence (block size of six with stratification based on homologous recombination repair gene mutation status, progression-free interval following penultimate platinum-based regimen, and best response to most recent platinum-based regimen). Patients, investigators, site staff, assessors, and the funder were masked to assignments. The primary endpoint of investigator-assessed progression-free survival has been previously reported. Prespecified, exploratory outcomes of chemotherapy-free interval (CFI), time to start of first subsequent therapy (TFST), time to disease progression on subsequent therapy or death (PFS2), and time to start of second subsequent therapy (TSST) and updated safety were analysed (visit cutoff Dec 31, 2017). Efficacy analyses were done in all patients randomised to three nested cohorts: patients with BRCA mutations, patients with homologous recombination deficiencies, and the intention-to-treat population. Safety analyses included all patients who received at least one dose of study treatment. This trial is registered with ClinicalTrials.gov, NCT01968213. FINDINGS: Between April 7, 2014, and July 19, 2016, 564 patients were enrolled and randomly assigned to rucaparib (n=375) or placebo (n=189). Median follow-up was 28·1 months (IQR 22·0-33·6). In the intention-to-treat population, median CFI was 14·3 months (95% CI 13·0-17·4) in the rucaparib group versus 8·8 months (8·0-10·3) in the placebo group (hazard ratio [HR] 0·43 [95% CI 0·35-0·53]; p<0·0001), median TFST was 12·4 months (11·1-15·2) versus 7·2 months (6·4-8·6; HR 0·43 [0·35-0·52]; p<0·0001), median PFS2 was 21·0 months (18·9-23·6) versus 16·5 months (15·2-18·4; HR 0·66 [0·53-0·82]; p=0·0002), and median TSST was 22·4 months (19·1-24·5) versus 17·3 months (14·9-19·4; HR 0·68 [0·54-0·85]; p=0·0007). CFI, TFST, PFS2, and TSST were also significantly longer with rucaparib than placebo in the BRCA-mutant and homologous recombination-deficient cohorts. The most frequent treatment-emergent adverse event of grade 3 or higher was anaemia or decreased haemoglobin (80 [22%] patients in the rucaparib group vs one [1%] patient in the placebo group). Serious treatment-emergent adverse events were reported in 83 (22%) patients in the rucaparib group and 20 (11%) patients in the placebo group. Two treatment-related deaths have been previously reported in this trial; there were no new treatment-related deaths. INTERPRETATION: In these exploratory analyses over a median follow-up of more than 2 years, rucaparib maintenance treatment led to a clinically meaningful delay in starting subsequent therapy and provided lasting clinical benefits versus placebo in all three analysis cohorts. Updated safety data were consistent with previous reports. FUNDING: Clovis Oncology

Rucaparib maintenance treatment for recurrent ovarian carcinoma: the effects of progression-free interval and prior therapies on efficacy and safety in the randomized phase III trial ARIEL3

INTRODUCTION: In ARIEL3 (NCT01968213), the poly(adenosine diphosphate-ribose) polymerase inhibitor rucaparib significantly improved progression-free survival versus placebo regardless of biomarker status when used as maintenance treatment for recurrent ovarian cancer. The aim of the current analyses was to evaluate the efficacy and safety of rucaparib in subgroups based on progression-free interval following penultimate platinum, number of prior chemotherapies, and prior use of bevacizumab. METHODS: Patients were randomized 2:1 to rucaparib 600 mg twice daily or placebo. Within subgroups, progression-free survival was assessed in prespecified, nested cohorts: BRCA-mutant, homologous recombination deficient (BRCA-mutant or wild-type BRCA/high genomic loss of heterozygosity), and the intent-to-treat population. RESULTS: In the intent-to-treat population, median investigator-assessed progression-free survival was 8.2 months with rucaparib versus 4.1 months with placebo (n=151 vs n=76; HR 0.33, 95% CI 0.24 to 0.46, p12 months. Median progression-free survival was 10.4 versus 5.4 months (n=231 vs n=124; HR 0.42, 95% CI 0.32 to 0.54, p<0.0001) for patients who had received two prior chemotherapies, and 11.1 versus 5.3 months (n=144 vs n=65; HR 0.28, 95% CI 0.19 to 0.41, p<0.0001) for those who had received ≥3 prior chemotherapies. Median progression-free survival was 10.3 versus 5.4 months (n=83 vs n=43; HR 0.42, 95% CI 0.26 to 0.68, p=0.0004) for patients who had received prior bevacizumab, and 10.9 versus 5.4 months (n=292 vs n=146; HR 0.35, 95% CI 0.28 to 0.45, p<0.0001) for those who had not. Across subgroups, median progression-free survival was also significantly longer with rucaparib versus placebo in the BRCA-mutant and homologous recombination deficient cohorts. Safety was consistent across subgroups. CONCLUSIONS: Rucaparib maintenance treatment significantly improved progression-free survival versus placebo irrespective of progression-free interval following penultimate platinum, number of lines of prior chemotherapy, and previous use of bevacizumab

Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism.

Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells

Fluorosis risk from early exposure to fluoride toothpaste

Swallowed fluoride toothpaste in the early years of life has been postulated to be a risk factor for fluorosis, but the epidemiological evidence is weakened by the fact that most of the relevant studies were done in developed countries where an individual is exposed to multiple sources of fluoride. Objectives: To quantify the risk of fluorosis from fluoride toothpaste in a population whose only potential source of fluoride was fluoride toothpaste. Methods: Case-control analyses were conducted to test the hypothesis that fluoride toothpaste use before the age of 6 years increased an individual's risk of fluorosis. Data came from a cross-sectional clinical dental examination of schoolchildren and a self-administered questionnaire to their parents. The study was conducted in Goa, India. The study group consisted of 1189 seventh grade children with a mean age of 12.2 years. Results: The prevalence of fluorosis was 12.9% using the TF index. Results of the crude, stratified, and logistic regression analyses showed that use of fluoride toothpaste before the age of 6 years was a risk indicator for fluorosis (OR 1.83, 95% CI 1.05–3.15). Among children with fluorosis, beginning brushing before the age of 2 years increased the severity of fluorosis significantly ( P < 0.001). Other factors associated with the use of fluoride toothpaste, such as eating or swallowing fluoride toothpaste and higher frequency of use, did not show a statistically significant increased risk for prevalence or severity of fluorosis. Conclusions: Fluoride toothpaste use before the age of 6 years is a risk indicator for fluorosis in this study population.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75437/1/j.1600-0528.1998.tb01957.x.pd