A Computational Comparison of Optimization Methods for the Golomb Ruler Problem

The Golomb ruler problem is defined as follows: Given a positive integer n, locate n marks on a ruler such that the distance between any two distinct pair of marks are different from each other and the total length of the ruler is minimized. The Golomb ruler problem has applications in information theory, astronomy and communications, and it can be seen as a challenge for combinatorial optimization algorithms. Although constructing high quality rulers is well-studied, proving optimality is a far more challenging task. In this paper, we provide a computational comparison of different optimization paradigms, each using a different model (linear integer, constraint programming and quadratic integer) to certify that a given Golomb ruler is optimal. We propose several enhancements to improve the computational performance of each method by exploring bound tightening, valid inequalities, cutting planes and branching strategies. We conclude that a certain quadratic integer programming model solved through a Benders decomposition and strengthened by two types of valid inequalities performs the best in terms of solution time for small-sized Golomb ruler problem instances. On the other hand, a constraint programming model improved by range reduction and a particular branching strategy could have more potential to solve larger size instances due to its promising parallelization features

Electron temperature in the cusp as measured with the SCIFER-2 sounding rocket

It is expected that energy deposited by soft auroral electron precipitation in the ionosphere should result in heating of ionospheric electrons in that location, and this heating is an important step in the ion outflow process. We present coordinated observations from the SCIFER-2 sounding rocket in the cusp region overflying optical observing sites in Svalbard. The rocket payload included a sensor which is designed to measure the temperature of thermal electrons. We show that elevated electron temperatures measured in situ are correlated with electron precipitation as inferred from auroral emissions during the 60–120 s preceding the passage of the rocket. This integrated “cooking time” is an important factor in determining the origin and resulting flux of outflowing ions

EFSUMB Guidelines on Interventional Ultrasound (INVUS), Part III - Abdominal Treatment Procedures (Short Version)

Publisher Copyright: © Georg Thieme Verlag KG Stuttgart · New York ·.The third part of the European Federation of Societies for Ultrasound in Medicine and Biology (EFSUMB) Guidelines on Interventional Ultrasound assesses the evidence for ultrasound-guided and assisted interventions in abdominal treatment procedures. Recommendations for clinical practice are presented covering indications, contraindications, safety and efficacy of the broad variety of these techniques. In particular, drainage of abscesses and fluid collections, interventional tumor ablation techniques, interventional treatment of symptomatic cysts and echinococcosis, percutaneous transhepatic cholangiography and drainage, percutaneous gastrostomy, urinary bladder drainage, and nephrostomy are addressed (short version; a long version is published online).publishersversionPeer reviewe

Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution

A birth-death process is a continuous-time Markov chain that counts the number of particles in a system over time. In the general process with $n$ current particles, a new particle is born with instantaneous rate $\lambda_n$ and a particle dies with instantaneous rate $\mu_n$. Currently no robust and efficient method exists to evaluate the finite-time transition probabilities in a general birth-death process with arbitrary birth and death rates. In this paper, we first revisit the theory of continued fractions to obtain expressions for the Laplace transforms of these transition probabilities and make explicit an important derivation connecting transition probabilities and continued fractions. We then develop an efficient algorithm for computing these probabilities that analyzes the error associated with approximations in the method. We demonstrate that this error-controlled method agrees with known solutions and outperforms previous approaches to computing these probabilities. Finally, we apply our novel method to several important problems in ecology, evolution, and genetics

EFSUMB Guidelines on Interventional Ultrasound (INVUS), Part III - Abdominal Treatment Procedures (Long Version)

Publisher Copyright: © Georg Thieme Verlag KG Stuttgart. New York .The third part of the European Federation of Societies for Ultrasound in Medicine and Biology (EFSUMB) Guidelines on Interventional Ultrasound (INVUS) assesses the evidence for ultrasound-guided and assisted interventions in abdominal treatment procedures. Recommendations for clinical practice are presented covering indications, contraindications, and safe and effective performance of the broad variety of these techniques. In particular, drainage of abscesses and fluid collections, interventional tumor ablation techniques, interventional treatment of symptomatic cysts and echinococcosis, percutaneous transhepatic cholangiography and drainage, percutaneous gastrostomy, urinary bladder drainage, and nephrostomy are addressed (long version).publishersversionPeer reviewe

Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization

Ciliopathies are a large group of clinically and genetically heterogeneous disorders caused by defects in primary cilia. Here we identified mutations in TRAF3IP1 (TNF Receptor-Associated Factor Interacting Protein 1) in eight patients from five families with nephronophthisis (NPH) and retinal degeneration, two of the most common manifestations of ciliopathies. TRAF3IP1 encodes IFT54, a subunit of the IFT-B complex required for ciliogenesis. The identified mutations result in mild ciliary defects in patients but also reveal an unexpected role of IFT54 as a negative regulator of microtubule stability via MAP4 (microtubule-associated protein 4). Microtubule defects are associated with altered epithelialization/polarity in renal cells and with pronephric cysts and microphthalmia in zebrafish embryos. Our findings highlight the regulation of cytoplasmic microtubule dynamics as a role of the IFT54 protein beyond the cilium, contributing to the development of NPH-related ciliopathies

EFSUMB Guidelines on Interventional Ultrasound (INVUS), Part II : Diagnostic ultrasound-guided interventional procedures (Long Version)

Publisher Copyright: © Georg Thieme Verlag KG Stuttgart New York.This is the second part of the series on interventional ultrasound guidelines of the Federation of Societies for Ultrasound in Medicine and Biology (EFSUMB). It deals with the diagnostic interventional procedure. General points are discussed which are pertinent to all patients, followed by organ-specific imaging that will allow the correct pathway and planning for the interventional procedure. This will allow for the appropriate imaging workup for each individual interventional procedure (Long version).publishersversionPeer reviewe

Forward Technology Solar Cell Experiment First On-Orbit Data

This paper presents first on orbit measured data from the Forward Technology Solar Cell Experiment (FTSCE). FTSCE is a space experiment housed within the 5th Materials on the International Space Station Experiment (MISSE-5). MISSE-5 was launched aboard the Shuttle return to flight mission (STS-114) on July 26, 2005 and deployed on the exterior of the International Space Station (ISS). The experiment will remain in orbit for nominally one year, after which it will be returned to Earth for post-flight testing and analysis. While on orbit, the experiment is designed to measure a 36 point current vs. voltage (IV) curve on each of the experimental solar cells, and the data is continuously telemetered to Earth. The experiment also measures the solar cell temperature and the orientation of the solar cells to the sun. A range of solar cell technologies are included in the experiment including state-of-the-art triple junction InGaP/GaAs/Ge solar cells from several vendors, thin film amorphous Si and CuIn(Ga)Se2 cells, and next-generation technologies like single-junction GaAs cells grown on Si wafers and metamorphic InGaP/InGaAs/Ge triple-junction cells. In addition to FTSCE, MISSE-5 also contains a Thin-Film Materials experiment. This is a passive experiment that will provide data on the effect of the space environment on more than 200 different materials. FTSCE was initially conceived in response to various on-orbit and ground test anomalies associated with space power systems. The Department of Defense (DoD) required a method of rapidly obtaining on orbit validation data for new space solar cell technologies, and NRL was tasked to devise an experiment to meet this requirement. Rapid access to space was provided by the MISSE Program which is a NASA Langley Research Center program. MISSE-5 is a completely self-contained experiment system with its own power generation and storage system and communications system. The communications system, referred to as PCSat, transmits and receives in the Amateur Radio band providing a node on the Amateur Radio Satellite Service. This paper presents an overview of the various aspects of MISSE-5 and a sample of the first measured on orbit data

A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer

Background: miR‑346 was identified as an activator of Androgen Receptor (AR) signalling that associates with DNA damage response (DDR)‑linked transcripts in prostate cancer (PC). We sought to delineate the impact of miR‑346 on DNA damage, and its potential as a therapeutic agent. Methods: RNA‑IP, RNA‑seq, RNA‑ISH, DNA fibre assays, in vivo xenograft studies and bioinformatics approaches were used alongside a novel method for amplification‑free, single nucleotide‑resolution genome‑wide mapping of DNA breaks (INDUCE‑seq). Results: miR‑346 induces rapid and extensive DNA damage in PC cells ‑ the first report of microRNA‑induced DNA damage. Mechanistically, this is achieved through transcriptional hyperactivation, R‑loop formation and replication stress, leading to checkpoint activation and cell cycle arrest. miR‑346 also interacts with genome‑protective lncRNA NORAD to disrupt its interaction with PUM2, leading to PUM2 stabilisation and its increased turnover of DNA damage response (DDR) transcripts. Confirming clinical relevance, NORAD expression and activity strongly correlate with poor PC clinical outcomes and increased DDR in biopsy RNA‑seq studies. In contrast, miR‑346 is associated with improved PC survival. INDUCE‑seq reveals that miR‑346‑induced DSBs occur preferentially at binding sites of the most highly‑transcriptionally active transcription factors in PC cells, including c‑Myc, FOXA1, HOXB13, NKX3.1, and importantly, AR, resulting in target transcript downregulation. Further, RNA‑seq reveals widespread miR‑346 and shNORAD dysregulation of DNA damage, replication and cell cycle processes. NORAD drives target‑directed miR decay (TDMD) of miR‑346 as a novel genome protection mechanism: NORAD silencing increases mature miR‑346 levels by several thousand‑fold, and WT but not TDMD‑mutant NORAD rescues miR‑346‑induced DNA damage. Importantly, miR‑346 sensitises PC cells to DNA‑damaging drugs including PARP inhibitor and chemotherapy, and induces tumour regression as a monotherapy in vivo, indicating that targeting miR‑346:NORAD balance is a valid therapeutic strategy