MaxMin Linear Initialization for Fuzzy C-Means

International audienceClustering is an extensive research area in data science. The aim of clustering is to discover groups and to identify interesting patterns in datasets. Crisp (hard) clustering considers that each data point belongs to one and only one cluster. However, it is inadequate as some data points may belong to several clusters, as is the case in text categorization. Thus, we need more flexible clustering. Fuzzy clustering methods, where each data point can belong to several clusters, are an interesting alternative. Yet, seeding iterative fuzzy algorithms to achieve high quality clustering is an issue. In this paper, we propose a new linear and efficient initialization algorithm MaxMin Linear to deal with this problem. Then, we validate our theoretical results through extensive experiments on a variety of numerical real-world and artificial datasets. We also test several validity indices, including a new validity index that we propose, Transformed Standardized Fuzzy Difference (TSFD)

Safety and Immunogenicity of a Recombinant Plasmodium falciparum AMA1 Malaria Vaccine Adjuvanted with Alhydrogel™, Montanide ISA 720 or AS02

Contains fulltext : 71100.pdf (publisher's version ) (Open Access)BACKGROUND: Plasmodium falciparum Apical Membrane Antigen 1 (PfAMA1) is a candidate vaccine antigen expressed by merozoites and sporozoites. It plays a key role in red blood cell and hepatocyte invasion that can be blocked by antibodies. METHODOLOGY/PRINCIPAL FINDINGS: We assessed the safety and immunogenicity of recombinant PfAMA1 in a dose-escalating, phase Ia trial. PfAMA1 FVO strain, produced in Pichia pastoris, was reconstituted at 10 microg and 50 microg doses with three different adjuvants, Alhydrogel, Montanide ISA720 and AS02 Adjuvant System. Six randomised groups of healthy male volunteers, 8-10 volunteers each, were scheduled to receive three immunisations at 4-week intervals. Safety and immunogenicity data were collected over one year. Transient pain was the predominant injection site reaction (80-100%). Induration occurred in the Montanide 50 microg group, resulting in a sterile abscess in two volunteers. Systemic adverse events occurred mainly in the AS02 groups lasting for 1-2 days. Erythema was observed in 22% of Montanide and 59% of AS02 group volunteers. After the second dose, six volunteers in the AS02 group and one in the Montanide group who reported grade 3 erythema (>50 mm) were withdrawn as they met the stopping criteria. All adverse events resolved. There were no vaccine-related serious adverse events. Humoral responses were highest in the AS02 groups. Antibodies showed activity in an in vitro growth inhibition assay up to 80%. Upon stimulation with the vaccine, peripheral mononuclear cells from all groups proliferated and secreted IFNgamma and IL-5 cytokines. CONCLUSIONS/SIGNIFICANCE: All formulations showed distinct reactogenicity profiles. All formulations with PfAMA1 were immunogenic and induced functional antibodies. TRIAL REGISTRATION: (Clinicaltrials.gov) NCT00730782

New Human Papilloma Virus E2 Transcription Factor Mimics: A Tripyrrole-Peptide Conjugate with Tight and Specific DNA-Recognition

BACKGROUND: Human papillomavirus (HPV) is the main causative agent of cervical cancer, particularly high risk strains such us HPV-16, -18 and -31. The viral encoded E2 protein acts as a transcriptional modulator and exerts a key role in viral DNA replication. Thus, E2 constitutes an attractive target for developing antiviral agents. E2 is a homodimeric protein that interacts with the DNA target through an α-helix of each monomer. However, a peptide corresponding to the DNA recognition helix of HPV-16 E2 binds DNA with lower affinity than its full-length DNA binding domain. Therefore, in an attempt to promote the DNA binding of the isolated peptide, we have designed a conjugate compound of the E2 α-helix peptide and a derivative of the antibiotic distamycin, which involves simultaneous minor- and major-groove interactions. METHODOLOGY/PRINCIPAL FINDINGS: An E2 α-helix peptide-distamycin conjugate was designed and synthesized. It was characterized by NMR and CD spectroscopy, and its DNA binding properties were investigated by CD, DNA melting and gel shift experiments. The coupling of E2 peptide with distamycin does not affect its structural properties. The conjugate improves significantly the affinity of the peptide for specific DNA. In addition, stoichiometric amounts of specific DNA increase meaningfully the helical population of the peptide. The conjugate enhances the DNA binding constant 50-fold, maintaining its specificity. CONCLUSIONS/SIGNIFICANCE: These results demonstrate that peptide-distamycin conjugates are a promising tool to obtain compounds that bind the E2 target DNA-sequences with remarkable affinity and suggest that a bipartite major/minor groove binding scaffold can be a useful approach for therapeutic treatment of HPV infection

Searches for Gravitational Waves from Binary Neutron Stars: A Review

A new generation of observatories is looking for gravitational waves. These waves, emitted by highly relativistic systems, will open a new window for ob- servation of the cosmos when they are detected. Among the most promising sources of gravitational waves for these observatories are compact binaries in the final min- utes before coalescence. In this article, we review in brief interferometric searches for gravitational waves emitted by neutron star binaries, including the theory, instru- mentation and methods. No detections have been made to date. However, the best direct observational limits on coalescence rates have been set, and instrumentation and analysis methods continue to be refined toward the ultimate goal of defining the new field of gravitational wave astronomy.Comment: 30 pages, 5 Figures, to appear in "Short-Period Binary Stars: Observations, Analyses, and Results", Ed.s Eugene F. Milone, Denis A. Leahy, David W. Hobil

Factorial validity and internal consistency of the PRAFAB questionnaire in women with stress urinary incontinence

<p>Abstract</p> <p>Background</p> <p>To investigate the factor structure, dimensionality and construct validity of the (5-item) PRAFAB questionnaire score in women with stress urinary incontinence (stress UI).</p> <p>Methods</p> <p>A cross validation study design was used in a cohort of 279 patients who were randomly divided into Sample A or B. Sample A was used for preliminary exploratory factor analyses with promax rotation. Sample B provided an independent sample for confirming the premeditated and proposed factor structure and item retention. Internal consistency, item-total and subscale correlations were determined to assess the dimensionality. Construct validity was assessed by comparing factor-based scale means by clinical characteristics based on known relationships.</p> <p>Results</p> <p>Factor analyses resulted in a two-factor structure or subscales: items related to 'leakage severity' (protection, amount and frequency) and items related to its 'perceived symptom impact' or consequences of stress UI on the patient's life (adjustment and body (or self) image). The patterns of the factor loadings were fairly identical for both study samples. The two constructed subscales demonstrated adequate internal consistency with Cronbach's alphas in a range of 0.78 and 0.84 respectively. Scale scores differed by clinical characteristics according to the expectations and supported the construct validity of the scales.</p> <p>Conclusion</p> <p>The findings suggest a two-factorial structure of the PRAFAB questionnaire. Furthermore the results confirmed the internal consistency and construct validity as demonstrated in our previous study. The best description of the factorial structure of the PRAFAB questionnaire was given by a two-factor solution, measuring the stress UI leakage severity items and the perceived symptom impact items. Future research will be necessary to replicate these findings in different settings, type of UI and non-white women and men.</p

Phase Structure and Compactness

In order to study the influence of compactness on low-energy properties, we compare the phase structures of the compact and non-compact two-dimensional multi-frequency sine-Gordon models. It is shown that the high-energy scaling of the compact and non-compact models coincides, but their low-energy behaviors differ. The critical frequency $\beta^2 = 8\pi$ at which the sine-Gordon model undergoes a topological phase transition is found to be unaffected by the compactness of the field since it is determined by high-energy scaling laws. However, the compact two-frequency sine-Gordon model has first and second order phase transitions determined by the low-energy scaling: we show that these are absent in the non-compact model.Comment: 21 pages, 5 figures, minor changes, final version, accepted for publication in JHE

Functional gait rehabilitation in elderly people following a fall-related hip fracture using a treadmill with visual context: design of a randomized controlled trial

Background: Walking requires gait adjustments in order to walk safely in continually changing environments. Gait adaptability is reduced in older adults, and (near) falls, fall-related hip fractures and fear of falling are common in this population. Most falls occur due to inaccurate foot placement relative to environmental hazards, such as obstacles. The C-Mill is an innovative, instrumented treadmill on which visual context (e. g., obstacles) is projected. The C-Mill is well suited to train foot positioning relative to environmental properties while concurrently utilizing the high-intensity practice benefits associated with conventional treadmill training. The present protocol was designed to examine the efficacy of C-Mill gait adaptability treadmill training for improving walking ability and reducing fall incidence and fear of falling relative to conventional treadmill training and usual care. We hypothesize that C-Mill gait adaptability treadmill training and conventional treadmill training result in better walking ability than usual care due to the enhanced training intensity, with superior effects for C-Mill gait adaptability treadmill training on gait adaptability aspects of walking given the concurrent focus on practicing step adjustments. Methods/design: The protocol describes a parallel group, single-blind, superiority randomized controlled trial with pre-tests, post-tests, retention-tests and follow-up. Hundred-twenty-six older adults with a recent fall-related hip fracture will be recruited from inpatient rehabilitation care and allocated to six weeks of C-Mill gait adaptability treadmill training (high-intensity, adaptive stepping), conventional treadmill training (high-intensity, repetitive stepping) or usual care physical therapy using block randomization, with allocation concealment by opaque sequentially numbered envelopes. Only data collectors are blind to group allocation. Study parameters related to walking ability will be assessed as primary outcome pre-training, post-training, after 4 weeks retention and 12 months follow-up. Secondary study parameters are measures related to fall incidence, fear of falling and general health. Discussion: The study will shed light on the relative importance of adaptive versus repetitive stepping and practice intensity for effective intervention programs directed at improving walking ability and reducing fall risk and fear of falling in older adults with a recent fall-related hip fracture, which may help reduce future fall-related health-care costs

The Hubble Constant

I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give $H_0$ values of around 72-74km/s/Mpc , with typical errors of 2-3km/s/Mpc. This is in mild discrepancy with CMB-based measurements, in particular those from the Planck satellite, which give values of 67-68km/s/Mpc and typical errors of 1-2km/s/Mpc. The size of the remaining systematics indicate that accuracy rather than precision is the remaining problem in a good determination of the Hubble constant. Whether a discrepancy exists, and whether new physics is needed to resolve it, depends on details of the systematics of the object-based methods, and also on the assumptions about other cosmological parameters and which datasets are combined in the case of the all-sky methods.Comment: Extensively revised and updated since the 2007 version: accepted by Living Reviews in Relativity as a major (2014) update of LRR 10, 4, 200

Investigations on a clinically and functionally unusual and novel germline p53 mutation

This report describes an individual with a rare choroid plexus papilloma in adulthood (age 29) after earlier having an osteosarcoma (age 22). The results from this study, and others, suggest that it may be advisable to consider the possibility of a germline p53 mutation in adults presenting with choroid plexus tumours. In the current study automated DNA sequencing of genomic DNA detected a novel germline 7 base pair insertion in exon 5 of the p53 gene in this patient. The alteration in frame would produce amino acid substitutions beginning with alanine to glycine at position 161 and a stop codon at position 182 in the mutated protein. Surprisingly two assays of p53 function gave apparently wild-type results on peripheral blood lymphocytes from this individual. These results led us to carry out more detailed functional tests on the mutant protein. The mutant allele was expressed either at very low levels or not at all in phytohaemagglutinin stimulated lymphocytes. Further, the mutant protein was completely non-functional in terms of its ability to transactivate a series of p53-responsive genes (p21WAF1, bax, PIG3), to transrepress a target gene and to inhibit colony growth in transfected Saos-2 cells. However, surprisingly, data from irradiated peripheral blood lymphocytes and transfected Saos-2 cells, suggested that this truncated, mutant protein retains significant ability to induce apoptosis