Topological Machine Learning with Persistence Indicator Functions

Techniques from computational topology, in particular persistent homology, are becoming increasingly relevant for data analysis. Their stable metrics permit the use of many distance-based data analysis methods, such as multidimensional scaling, while providing a firm theoretical ground. Many modern machine learning algorithms, however, are based on kernels. This paper presents persistence indicator functions (PIFs), which summarize persistence diagrams, i.e., feature descriptors in topological data analysis. PIFs can be calculated and compared in linear time and have many beneficial properties, such as the availability of a kernel-based similarity measure. We demonstrate their usage in common data analysis scenarios, such as confidence set estimation and classification of complex structured data.Comment: Topology-based Methods in Visualization 201

Is there still a place for the concept of therapeutic regression in psychoanalysis?

The author uses his own failure to find a place for the idea of therapeutic regression in his clinical thinking or practice as the basis for an investigation into its meaning and usefulness. He makes a distinction between three ways the term ‘regression’ is used in psychoanalytic discourse: as a way of evoking a primitive level of experience; as a reminder in some clinical situations of the value of non-intervention on the part of the analyst; and as a description of a phase of an analytic treatment with some patients where the analyst needs to put aside normal analytic technique in order to foster a regression in the patient. It is this third meaning, which the author terms “therapeutic regression” that this paper examines, principally by means of an extended discussion of two clinical examples of a patient making a so-called therapeutic regression, one given by Winnicott and the other by Masud Khan. The author argues that in these examples the introduction of the concept of therapeutic regression obscures rather than clarifies the clinical process. He concludes that, as a substantial clinical concept, the idea of therapeutic regression has outlived its usefulness. However he also notes that many psychoanalytic writers continue to find a use for the more generic concept of regression, and that the very engagement with the more particular idea of therapeutic regression has value in provoking questions as to what is truly therapeutic in psychoanalytic treatment

On Arrangements of Orthogonal Circles

In this paper, we study arrangements of orthogonal circles, that is, arrangements of circles where every pair of circles must either be disjoint or intersect at a right angle. Using geometric arguments, we show that such arrangements have only a linear number of faces. This implies that orthogonal circle intersection graphs have only a linear number of edges. When we restrict ourselves to orthogonal unit circles, the resulting class of intersection graphs is a subclass of penny graphs (that is, contact graphs of unit circles). We show that, similarly to penny graphs, it is NP-hard to recognize orthogonal unit circle intersection graphs.Comment: Appears in the Proceedings of the 27th International Symposium on Graph Drawing and Network Visualization (GD 2019

Thermal infrared emission reveals the Dirac point movement in biased graphene

Graphene is a 2-dimensional material with high carrier mobility and thermal conductivity, suitable for high-speed electronics. Conduction and valence bands touch at the Dirac point. The absorptivity of single-layer graphene is 2.3%, nearly independent of wavelength. Here we investigate the thermal radiation from biased graphene transistors. We find that the emission spectrum of single-layer graphene follows that of a grey body with constant emissivity (1.6 \pm 0.8)%. Most importantly, we can extract the temperature distribution in the ambipolar graphene channel, as confirmed by Stokes/anti-Stokes measurements. The biased graphene exhibits a temperature maximum whose location can be controlled by the gate voltage. We show that this peak in temperature reveals the spatial location of the minimum in carrier density, i.e. the Dirac point.Comment: Accepted in principle at Nature Nanotechnolog

Telomere disruption results in non-random formation of de novo dicentric chromosomes involving acrocentric human chromosomes

Copyright: © 2010 Stimpson et al.Genome rearrangement often produces chromosomes with two centromeres (dicentrics) that are inherently unstable because of bridge formation and breakage during cell division. However, mammalian dicentrics, and particularly those in humans, can be quite stable, usually because one centromere is functionally silenced. Molecular mechanisms of centromere inactivation are poorly understood since there are few systems to experimentally create dicentric human chromosomes. Here, we describe a human cell culture model that enriches for de novo dicentrics. We demonstrate that transient disruption of human telomere structure non-randomly produces dicentric fusions involving acrocentric chromosomes. The induced dicentrics vary in structure near fusion breakpoints and like naturally-occurring dicentrics, exhibit various inter-centromeric distances. Many functional dicentrics persist for months after formation. Even those with distantly spaced centromeres remain functionally dicentric for 20 cell generations. Other dicentrics within the population reflect centromere inactivation. In some cases, centromere inactivation occurs by an apparently epigenetic mechanism. In other dicentrics, the size of the alpha-satellite DNA array associated with CENP-A is reduced compared to the same array before dicentric formation. Extrachromosomal fragments that contained CENP-A often appear in the same cells as dicentrics. Some of these fragments are derived from the same alpha-satellite DNA array as inactivated centromeres. Our results indicate that dicentric human chromosomes undergo alternative fates after formation. Many retain two active centromeres and are stable through multiple cell divisions. Others undergo centromere inactivation. This event occurs within a broad temporal window and can involve deletion of chromatin that marks the locus as a site for CENP-A maintenance/replenishment.This work was supported by the Tumorzentrum Heidelberg/Mannheim grant (D.10026941)and by March of Dimes Research Foundation grant #1-FY06-377 and NIH R01 GM069514

The clinical features of the piriformis syndrome: a systematic review

Piriformis syndrome, sciatica caused by compression of the sciatic nerve by the piriformis muscle, has been described for over 70 years; yet, it remains controversial. The literature consists mainly of case series and narrative reviews. The objectives of the study were: first, to make the best use of existing evidence to estimate the frequencies of clinical features in patients reported to have PS; second, to identify future research questions. A systematic review was conducted of any study type that reported extractable data relevant to diagnosis. The search included all studies up to 1 March 2008 in four databases: AMED, CINAHL, Embase and Medline. Screening, data extraction and analysis were all performed independently by two reviewers. A total of 55 studies were included: 51 individual and 3 aggregated data studies, and 1 combined study. The most common features found were: buttock pain, external tenderness over the greater sciatic notch, aggravation of the pain through sitting and augmentation of the pain with manoeuvres that increase piriformis muscle tension. Future research could start with comparing the frequencies of these features in sciatica patients with and without disc herniation or spinal stenosis

The oil-dispersion bath in anthroposophic medicine – an integrative review

<p>Abstract</p> <p>Background</p> <p>Anthroposophic medicine offers a variety of treatments, among others the oil-dispersion bath, developed in the 1930s by Werner Junge. Based on the phenomenon that oil and water do not mix and on recommendations of Rudolf Steiner, Junge developed a vortex mechanism which churns water and essential oils into a fine mist. The oil-covered droplets empty into a tub, where the patient immerses for 15–30 minutes. We review the current literature on oil-dispersion baths.</p> <p>Methods</p> <p>The following databases were searched: Medline, Pubmed, Embase, AMED and CAMbase. The search terms were 'oil-dispersion bath' and 'oil bath', and their translations in German and French. An Internet search was also performed using Google Scholar, adding the search terms 'study' and 'case report' to the search terms above. Finally, we asked several experts for gray literature not listed in the above-mentioned databases. We included only articles which met the criterion of a clinical study or case report, and excluded theoretical contributions.</p> <p>Results</p> <p>Among several articles found in books, journals and other publications, we identified 1 prospective clinical study, 3 experimental studies (enrolling healthy individuals), 5 case reports, and 3 field-reports. In almost all cases, the studies described beneficial effects – although the methodological quality of most studies was weak. Main indications were internal/metabolic diseases and psychiatric/neurological disorders.</p> <p>Conclusion</p> <p>Beyond the obvious beneficial effects of warm bathes on the subjective well-being, it remains to be clarified what the unique contribution of the distinct essential oils dispersed in the water can be. There is a lack of clinical studies exploring the efficacy of oil-dispersion baths. Such studies are recommended for the future.</p

A Minimal Threshold of c-di-GMP Is Essential for Fruiting Body Formation and Sporulation in Myxococcus xanthus

Generally, the second messenger bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) regulates the switch between motile and sessile lifestyles in bacteria. Here, we show that c-di-GMP is an essential regulator of multicellular development in the social bacterium Myxococcus xanthus. In response to starvation, M. xanthus initiates a developmental program that culminates in formation of spore-filled fruiting bodies. We show that c-di-GMP accumulates at elevated levels during development and that this increase is essential for completion of development whereas excess c-di-GMP does not interfere with development. MXAN3735 (renamed DmxB) is identified as a diguanylate cyclase that only functions during development and is responsible for this increased c-di-GMP accumulation. DmxB synthesis is induced in response to starvation, thereby restricting DmxB activity to development. DmxB is essential for development and functions downstream of the Dif chemosensory system to stimulate exopolysaccharide accumulation by inducing transcription of a subset of the genes encoding proteins involved in exopolysaccharide synthesis. The developmental defects in the dmxB mutant are non-cell autonomous and rescued by co-development with a strain proficient in exopolysaccharide synthesis, suggesting reduced exopolysaccharide accumulation as the causative defect in this mutant. The NtrC-like transcriptional regulator EpsI/Nla24, which is required for exopolysaccharide accumulation, is identified as a c-diGMP receptor, and thus a putative target for DmxB generated c-di-GMP. Because DmxB can be—at least partially—functionally replaced by a heterologous diguanylate cyclase, these results altogether suggest a model in which a minimum threshold level of c-di-GMP is essential for the successful completion of multicellular development in M. xanthus

Low-value care practice in headache: a Spanish mixed methods research study

Background Headache is one of the most prevalent diseases. The Global Burden of Disease Study ranks it as the seventh most common disease overall and the second largest neurological cause of disability in the world. The "Do Not Do" recommendations are a strategy for increasing the quality of care and reducing the cost of care for headache. This study aimed to identify specific low-value practices in headache care, determine their frequency, and estimate the cost overrun that they represent, in order to establish "Do not Do" recommendations specifically for headache by consensus and according to scientific evidence. Methods This was a mixed methods research study that combined qualitative consensus-building techniques, involving a multidisciplinary panel of experts to define the "Do Not Do" recommendations in headache care, and a retrospective observational study with review of a randomized set of patient records from the past 6 months in four hospitals, to quantify the frequency of these "Do Not Do" practices. We calculated the sum of direct costs of medical consultations, medicines, and unnecessary diagnostic tests. Results Seven "Do Not Do" recommendations were established for headache. In total, 3507 medical records were randomly reviewed. Low-value practices had a highly variable occurrence, depending on the hospital and type of headache. Overall, 34.1% of low-value practices were related to treatment, 21% were related to overuse of imaging in consultation, and 19% were related to emergency care. The estimated cost of low-value practices in the four hospitals was 203,520.47 euros per 1000 patients. Conclusions This study identified low-value headache practices that need to be eradicated and provided data on their frequency and cost overruns