PyScan: Interfacing Laboratory Instruments with Python

Laboratory instruments can be interfaced with and controlled from personal computers. Several programs to scan lasers and acquire data have been written by students in the Polik Lab. However, computer hardware and software change more rapidly (3-5 years) than instrument lifetime (20 years). Thus, programs must be replaced to run on modern computers and operating systems. This can be done to minimize dependence on specific hardware and software. PyScan is a laser instrument interface program intended to replace the Polik Lab’s current software. It allows the user to control the laser, setup a scan, acquire data, and store the data for subsequent analysis. PyScan is written in Python 3 in order to run on various computer platforms and access a variety of data acquisition products. This flexibility insulates it from future hardware and software changes

Single-mode sapphire optical fiber temperature sensor

Sapphire fiber is intrinsically multimoded, resulting in poor precision sensors. We demonstrate a 4-cm single-mode sapphire fiber with a Bragg grating temperature sensor and a standard-fiber tail, operating up to 1200°C

Single-mode sapphire fiber temperature sensor

Sapphire fiber can withstand temperatures of around 2000 °C, but it is multimoded, giving poor precision sensors. We have demonstrated a single-mode sapphire fiber Bragg grating temperature sensor operating up to 1200 °C. A single-mode sapphire fiber was formed by writing a depressed cladding waveguide along the length of a 100-μm diameter sapphire fiber using a femtosecond laser. A second-order Bragg grating sensor was inscribed within the waveguide, achieving a reflectivity of >90% and a narrow bandwidth of <0.5 nm. The single-mode sapphire fiber was fusion spliced to standard silica single-mode fiber. The sensor was vibration-tested over a 10 Hz to 30 kHz range with 30 μm displacement, resulting in minimal Bragg wavelength variation of <30 pm standard deviation. The sensor was furnace-tested to 1200 °C, showing ±0.08% repeatability above 1000 °C. This demonstrates the high precision sensing capability of single-mode sapphire fiber Bragg grating sensors with end-to-end single mode interrogation

High-precision optical fiber sensing beyond 1000{\deg}C

Sapphire fiber can withstand around 2000{\deg}C, but it is multimoded, giving poor precision sensors. We demonstrate a single-mode sapphire fiber Bragg grating temperature sensor operating up to 1200{\deg}C. The repeatability above 1000{\deg}C is within {\pm}0.08%.Comment: 4 Pages, 5 Figure

Ice-stream stability on a reverse bed slope

Marine-based ice streams whose beds deepen inland are thought to be inherently unstable. This instability is of particular concern because significant portions of the marine-based West Antarctic and Greenland ice sheets are losing mass and their retreat could contribute significantly to future sea-level rise. However, the present understanding of ice-stream stability is limited by observational records that are too short to resolve multi-decadal to millennial-scale behaviour or to validate numerical models8. Here we present a dynamic numerical simulation of Antarctic ice-stream retreat since the Last Glacial Maximum (LGM), constrained by geophysical data, whose behaviour is consistent with the geomorphological record. We find that retreat of Marguerite Bay Ice Stream following the LGM was highly nonlinear and was interrupted by stabilizations on a reverse-sloping bed, where theory predicts rapid unstable retreat. We demonstrate that these transient stabilizations were caused by enhanced lateral drag as the ice stream narrowed. We conclude that, as well as bed topography, ice-stream width and long-term retreat history are crucial for understanding decadal- to centennial-scale ice-stream behaviour and marine ice-sheet vulnerability

A second planet transiting LTT 1445A and a determination of the masses of both worlds

K.H. acknowledges support from STFC grant ST/R000824/1.LTT 1445 is a hierarchical triple M-dwarf star system located at a distance of 6.86 pc. The primary star LTT 1445A (0.257 M⊙) is known to host the transiting planet LTT 1445Ab with an orbital period of 5.36 days, making it the second-closest known transiting exoplanet system, and the closest one for which the host is an M dwarf. Using Transiting Exoplanet Survey Satellite data, we present the discovery of a second planet in the LTT 1445 system, with an orbital period of 3.12 days. We combine radial-velocity measurements obtained from the five spectrographs, Echelle Spectrograph for Rocky Exoplanets and Stable Spectroscopic Observations, High Accuracy Radial Velocity Planet Searcher, High-Resolution Echelle Spectrometer, MAROON-X, and Planet Finder Spectrograph to establish that the new world also orbits LTT 1445A. We determine the mass and radius of LTT 1445Ab to be 2.87 ± 0.25 M⊕ and 1.304-0.060+0.067 R⊕, consistent with an Earth-like composition. For the newly discovered LTT 1445Ac, we measure a mass of 1.54-0.19+0.20 M⊕ and a minimum radius of 1.15 R⊕, but we cannot determine the radius directly as the signal-to-noise ratio of our light curve permits both grazing and nongrazing configurations. Using MEarth photometry and ground-based spectroscopy, we establish that star C (0.161 M⊙) is likely the source of the 1.4 day rotation period, and star B (0.215 M⊙) has a likely rotation period of 6.7 days. We estimate a probable rotation period of 85 days for LTT 1445A. Thus, this triple M-dwarf system appears to be in a special evolutionary stage where the most massive M dwarf has spun down, the intermediate mass M dwarf is in the process of spinning down, while the least massive stellar component has not yet begun to spin down.Publisher PDFPeer reviewe

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700