Compressed Genotyping

Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, largely due to the relatively tedious and expensive process of DNA sequencing. Since the genetic polymorphisms that underlie these disorders are relatively rare in the human population, the presence or absence of a disease-linked polymorphism can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies, and assembled a mathematical framework that has some important distinctions from 'traditional' compressed sensing ideas in order to address different biological and technical constraints.Comment: Submitted to IEEE Transaction on Information Theory - Special Issue on Molecular Biology and Neuroscienc

Improving the surgical consenting process for patients with acute hip fractures: a pilot quality improvement project

Abstract Background: Consenting patients for trauma procedures following hip fracture is a key stage in the treatment pathway from admission to the operating theatre. Errors in this process can result in delayed procedures which may negatively impact patient recovery. The aim of this project was to identify and reduce errors in our consenting process for patients with capacity. Methods: Consent forms for all adult patients with capacity admitted for surgical repair of traumatic hip fracture were reviewed over a 4-week period. The baseline measurement (n = 24), identified errors in three key process measures: clarity of documentation, failure to record procedure-specific risks and not offering a copy of the consent form to the patient. Pre-printed stickers and targeted teaching were then introduced as quality improvement measures. Their impact was evaluated over subsequent 4-week review of the same patient demographic, with further refinement of these interventions being carried out and re-evaluated for a final cycle. Results: Cycle 1 (n = 26) following targeted teaching demonstrated a reduction in abbreviations from 38 to 20%, while doubling the documentation of discussion of procedure-specific risks from 31 to 72%. More patients were offered a copy of their consent form, rising from 12 to 48%. Cycle 2 (n = 24) saw the introduction of pre-printed “risk of procedure” stickers. Although clarity measures continued to improve, quality of pre-procedure risk documentation remained static while the number of forms being offered to patients fell to 8%. Conclusions: Our project would suggest that while pre-printed stickers can be useful memory aids, specific teaching on consenting produces the greatest benefit. The usage of such tools should therefore be limited, as adjuncts only to specific training. Keywords: Checklists, Control charts/run charts, Reminders, Surger

Rapid re-identification of human samples using portable DNA sequencing

DNA re-identification is used for a broad suite of applications, ranging from cell line authentication to forensics. However, current re-identification schemes suffer from high latency and limited access. Here, we describe a rapid, inexpensive, and portable strategy to robustly re-identify human DNA called 'MinION sketching'. MinION sketching requires as few as 3 min of sequencing and 60-300 random SNPs to re-identify a sample enabling near real-time applications of DNA re-identification. Our method capitalizes on the rapidly growing availability of genomic reference data for cell lines, tissues in biobanks, and individuals. This empowers the application of MinION sketching in research and clinical settings for periodic cell line and tissue authentication. Importantly, our method enables considerably faster and more robust cell line authentication relative to current practices and could help to minimize the amount of irreproducible research caused by mix-ups and contamination in human cell and tissue cultures

Completeness of algebraic CPS simulations

The algebraic lambda calculus and the linear algebraic lambda calculus are two extensions of the classical lambda calculus with linear combinations of terms. They arise independently in distinct contexts: the former is a fragment of the differential lambda calculus, the latter is a candidate lambda calculus for quantum computation. They differ in the handling of application arguments and algebraic rules. The two languages can simulate each other using an algebraic extension of the well-known call-by-value and call-by-name CPS translations. These simulations are sound, in that they preserve reductions. In this paper, we prove that the simulations are actually complete, strengthening the connection between the two languages.Comment: In Proceedings DCM 2011, arXiv:1207.682

Weak localization in disordered systems at the ballistic limit

The weak localization (WL) contribution to the two-level correlation function is calculated for two-dimensional disordered conductors. Our analysis extends to the nondiffusive (ballistic) regime, where the elastic mean path is of order of the size of the system. In this regime the structure factor (the Fourier transform of the two-point correlator) exhibits a singular behavior consisting of dips superimposed on a smooth positive background. The strongest dips appear at periods of the periodic orbits of the underlying clean system. Somewhat weaker singularities appear at times which are sums of periods of two such orbits. The results elucidate various aspects of the weak localization physics of ballistic chaotic systems.Comment: 13 pages, 13 figure

Long-term viability and function of transplanted islets macroencapsulated at high density are achieved by enhanced oxygen supply

Transplantation of encapsulated islets can cure diabetes without immunosuppression, but oxygen supply limitations can cause failure. We investigated a retrievable macroencapsulation device wherein islets are encapsulated in a planar alginate slab and supplied with exogenous oxygen from a replenishable gas chamber. Translation to clinically-useful devices entails reduction of device size by increasing islet surface density, which requires increased gas chamber pO Here we show that islet surface density can be substantially increased safely by increasing gas chamber pO to a supraphysiological level that maintains all islets viable and functional. These levels were determined from measurements of pO profiles in islet-alginate slabs. Encapsulated islets implanted with surface density as high as 4,800 islet equivalents/cm in diabetic rats maintained normoglycemia for more than 7 months and provided near-normal intravenous glucose tolerance tests. Nearly 90% of the original viable tissue was recovered after device explantation. Damaged islets failed after progressively shorter times. The required values of gas chamber pO were predictable from a mathematical model of oxygen consumption and diffusion in the device. These results demonstrate feasibility of developing retrievable macroencapsulated devices small enough for clinical use and provide a firm basis for design of devices for testing in large animals and humans

Mental health needs and services in the West Bank, Palestine

Background Palestine is a low income country with scarce resources, which is seeking independence. This paper discusses the high levels of mental health need found amongst Palestinian people, and examines services, education and research in this area with particular attention paid to the West Bank. Methods CINAHL, PubMed, and Science Direct were used to search for materials. Results and conclusion Evidence from this review is that there is a necessity to increase the availability and quality of mental health care. Mental health policy and services in Palestine need development in order to better meet the needs of service users and professionals. It is essential to raise awareness of mental health and increase the integration of mental health services with other areas of health care. Civilians need their basic human needs met, including having freedom of movement and seeing an end to the occupation. There is a need to enhance the resilience and capacity of community mental health teams. There is a need to increase resources and offer more support, up-to-date training and supervision to mental health teams

Roadmap on optical energy conversion

For decades, progress in the field of optical (including solar) energy conversion was dominated by advances in the conventional concentrating optics and materials design. In recent years, however, conceptual and technological breakthroughs in the fields of nanophotonics and plasmonics combined with a better understanding of the thermodynamics of the photon energy-conversion processes reshaped the landscape of energy-conversion schemes and devices. Nanostructured devices and materials that make use of size quantization effects to manipulate photon density of states offer a way to overcome the conventional light absorption limits. Novel optical spectrum splitting and photon-recycling schemes reduce the entropy production in the optical energy-conversion platforms and boost their efficiencies. Optical design concepts are rapidly expanding into the infrared energy band, offering new approaches to harvest waste heat, to reduce the thermal emission losses, and to achieve noncontact radiative cooling of solar cells as well as of optical and electronic circuitries. Light–matter interaction enabled by nanophotonics and plasmonics underlie the performance of the third- and fourth-generation energy-conversion devices, including up- and down-conversion of photon energy, near-field radiative energy transfer, and hot electron generation and harvesting. Finally, the increased market penetration of alternative solar energy-conversion technologies amplifies the role of cost-driven and environmental considerations. This roadmap on optical energy conversion provides a snapshot of the state of the art in optical energy conversion, remaining challenges, and most promising approaches to address these challenges. Leading experts authored 19 focused short sections of the roadmap where they share their vision on a specific aspect of this burgeoning research field. The roadmap opens up with a tutorial section, which introduces major concepts and terminology. It is our hope that the roadmap will serve as an important resource for the scientific community, new generations of researchers, funding agencies, industry experts, and investors.United States. Department of Energy (DE-AC36-086038308