KMOS Data Flow: Reconstructing Data Cubes in One Step

KMOS is a multi-object near-infrared integral field spectrometer with 24 deployable pick-off arms. Data processing is inevitably complex. We discuss specific issues and requirements that must be addressed in the data reduction pipeline, the calibration, the raw and processed data formats, and the simulated data. We discuss the pipeline architecture. We focus on its modular style and show how these modules can be used to build a classical pipeline, as well as a more advanced pipeline that can account for both spectral and spatial flexure as well as variations in the OH background. A novel aspect of the pipeline is that the raw data can be reconstructed into a cube in a single step. We discuss the advantages of this and outline the way in which we have implemented it. We finish by describing how the QFitsView tool can now be used to visualise KMOS data.Comment: Contribution to "Ground-based and Airborne Instrumentation for Astronomy III', SPIE 7735-254 (June 2010). High resolution version can be found at http://spiedl.or

Comparing Energy Cost and Maneuverability for Pushers of Two Pediatric Wheelchairs Designed for Low-income Countries

Summary: Our study compared two pediatric wheelchairs designed for less resourced settings, a wheelchair made by the Association of the Physically Disabled of Kenya and the Regency chair made in the US and distributed globally. The Regency chair outperformed the APDK chair in most aspects measured. Introduction: Many wheelchairs are donated to less-resourced countries by well-meaning organizations without regard to local, cultural, and physical conditions and without ensuring appropriate knowledge, tools, and support are present1. In the last ten years, several organizations have been manufacturing and distributing wheelchairs designed for low-income countries, however few outcomes studies have been done on these chairs. We completed a set of tests to compare two pediatric wheelchairs that are currently distributed in Kenya for children with disabilities. By providing accurate outcomes measures to manufacturers, we hope to enable design improvements2. Materials and Methods: During the 2010-2011 school year, local high school students pushed first graders sitting in the chairs on two surfaces (sidewalk and gravel drive) for six minutes. From heart rate data collected and distance covered, physiological cost indexes were calculated for pushing both chairs and time-walk test comparisons were made. In addition, a series of timed maneuverability tests from the Wheelchair Skills Test were performed, up and down a curb, up and down a ramp, and in a figure eight pattern3. Subject input was obtained by a visual analogue scale question and an opportunity to comment on each test. Results: Paired T tests showed that the APDK chair required significantly more energy to push than the Regency chair on both rough and smooth surfaces, and that the APDK chair was perceived as significantly harder to push on both terrains as well as more difficult to maneuver around tight spaces. Discussion: Results favored the Regency chair in all tests with significant differences. User comments indicated issues with the APDK chair about manufacturing quality control such as wobbling wheels due to lack of alignment and asymmetrically assembled frames. Results from this study as well as from a parallel study in Kenya have been provided to manufactures and on-going discussion is underway

Innate immune cellular therapeutics in transplantation

Successful organ transplantation provides an opportunity to extend the lives of patients with end-stage organ failure. Selectively suppressing the donor-specific alloimmune response, however, remains challenging without the continuous use of non-specific immunosuppressive medications, which have multiple adverse effects including elevated risks of infection, chronic kidney injury, cardiovascular disease, and cancer. Efforts to promote allograft tolerance have focused on manipulating the adaptive immune response, but long-term allograft survival rates remain disappointing. In recent years, the innate immune system has become an attractive therapeutic target for the prevention and treatment of transplant organ rejection. Indeed, contemporary studies demonstrate that innate immune cells participate in both the initial alloimmune response and chronic allograft rejection and undergo non-permanent functional reprogramming in a phenomenon termed “trained immunity.” Several types of innate immune cells are currently under investigation as potential therapeutics in transplantation, including myeloid-derived suppressor cells, dendritic cells, regulatory macrophages, natural killer cells, and innate lymphoid cells. In this review, we discuss the features and functions of these cell types, with a focus on their role in the alloimmune response. We examine their potential application as therapeutics to prevent or treat allograft rejection, as well as challenges in their clinical translation and future directions for investigation

Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019

Background: For years, coagulase-negative staphylococci (CoNS) were not considered a cause of bloodstream infections (BSIs) and were often regarded as contamination. However, the association of CoNS with nosocomial infections is increasingly recognized. The identification of more than 40 different CoNS species has been driven by the introduction of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Yet, treatment guidelines consider CoNS as a whole group, despite increasing antibiotic resistance (ABR) in CoNS. This retrospective study provides an in-depth data analysis of CoNS isolates found in human blood culture isolates between 2013 and 2019 in the entire region of the Northern Netherlands. Methods: In total, 10,796 patients were included that were hospitalized in one of the 15 hospitals in the region, leading to 14,992 CoNS isolates for (ABR) data analysis. CoNS accounted for 27.6% of all available 71,632 blood culture isolates. EUCAST Expert rules were applied to correct for errors in antibiotic test results. Results: A total of 27 different CoNS species were found. Major differences were observed in occurrence and ABR profiles. The top five species covered 97.1% of all included isolates: S. epidermidis, S. hominis, S. capitis, S. haemolyticus, and S. warneri. Regarding ABR, methicillin resistance was most frequently detected in S. haemolyticus (72%), S. cohnii (65%), and S. epidermidis (62%). S. epidermidis and S. haemolyticus showed 50–80% resistance to teicoplanin and macrolides while resistance to these agents remained lower than 10% in most other CoNS species. Conclusion: These differences are often neglected in national guideline development, prompting a focus on ‘ABR-safe’ agents such as glycopeptides. In conclusion, this multi-year, full-region approach to extensively assess the trends in both the occurrence and phenotypic resistance of CoNS species could be used for evaluating treatment policies and understanding more about these important but still too often neglected pathogens

Wave function recombination instability in cold atom interferometers

Cold atom interferometers use guiding potentials that split the wave function of the Bose-Einstein condensate and then recombine it. We present theoretical analysis of the wave function recombination instability that is due to the weak nonlinearity of the condensate. It is most pronounced when the accumulated phase difference between the arms of the interferometer is close to an odd multiple of PI and consists in exponential amplification of the weak ground state mode by the strong first excited mode. The instability exists for both trapped-atom and beam interferometers.Comment: 4 pages, 5 figure

Production of Lightning NO(x) and its Vertical Distribution Calculated from 3-D Cloud-scale Chemical Transport Model Simulations

A 3-D cloud scale chemical transport model that includes a parameterized source of lightning NO(x), based on observed flash rates has been used to simulate six midlatitude and subtropical thunderstorms observed during four field projects. Production per intracloud (P(sub IC) and cloud-to-ground (P(sub CG)) flash is estimated by assuming various values of P(sub IC) and P(sub CG) for each storm and determining which production scenario yields NO(x) mixing ratios that compare most favorably with in-cloud aircraft observations. We obtain a mean P(sub CG) value of 500 moles NO (7 kg N) per flash. The results of this analysis also suggest that on average, P(sub IC) may be nearly equal to P(sub CG), which is contrary to the common assumption that intracloud flashes are significantly less productive of NO than are cloud-to-ground flashes. This study also presents vertical profiles of the mass of lightning NO(x), after convection based on 3-D cloud-scale model simulations. The results suggest that following convection, a large percentage of lightning NO(x), remains in the middle and upper troposphere where it originated, while only a small percentage is found near the surface. The results of this work differ from profiles calculated from 2-D cloud-scale model simulations with a simpler lightning parameterization that were peaked near the surface and in the upper troposphere (referred to as a "C-shaped" profile). The new model results (a backward C-shaped profile) suggest that chemical transport models that assume a C-shaped vertical profile of lightning NO(x) mass may place too much mass neat the surface and too little in the middle troposphere

High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation

Leaf senescence is an essential developmental process that impacts dramatically on crop yields and involves altered regulation of thousands of genes and many metabolic and signaling pathways, resulting in major changes in the leaf. The regulation of senescence is complex, and although senescence regulatory genes have been characterized, there is little information on how these function in the global control of the process. We used microarray analysis to obtain a highresolution time-course profile of gene expression during development of a single leaf over a 3-week period to senescence. A complex experimental design approach and a combination of methods were used to extract high-quality replicated data and to identify differentially expressed genes. The multiple time points enable the use of highly informative clustering to reveal distinct time points at which signaling and metabolic pathways change. Analysis of motif enrichment, as well as comparison of transcription factor (TF) families showing altered expression over the time course, identify clear groups of TFs active at different stages of leaf development and senescence. These data enable connection of metabolic processes, signaling pathways, and specific TF activity, which will underpin the development of network models to elucidate the process of senescence

Disruption of cholinergic neurotransmission, within a cognitive challenge paradigm, is indicative of Aβ-related cognitive impairment in preclinical Alzheimer’s disease after a 27-month delay interval

Background Abnormal beta-amyloid (Aβ) is associated with deleterious changes in central cholinergic tone in the very early stages of Alzheimer’s disease (AD), which may be unmasked by a cholinergic antagonist (J Prev Alzheimers Dis 1:1–4, 2017). Previously, we established the scopolamine challenge test (SCT) as a “cognitive stress test” screening measure to identify individuals at risk for AD (Alzheimer’s & Dementia 10(2):262–7, 2014) (Neurobiol. Aging 36(10):2709-15, 2015). Here we aim to demonstrate the potential of the SCT as an indicator of cognitive change and neocortical amyloid aggregation after a 27-month follow-up interval. Methods Older adults (N = 63, aged 55–75 years) with self-reported memory difficulties and first-degree family history of AD completed the SCT and PET amyloid imaging at baseline and were then seen for cognitive testing at 9, 18, and 27 months post-baseline. Repeat PET amyloid imaging was completed at the time of the 27-month exam. Results Significant differences in both cognitive performance and in Aβ neocortical burden were observed between participants who either failed vs. passed the SCT at baseline, after a 27-month follow-up period. Conclusions Cognitive response to the SCT (Alzheimer’s & Dementia 10(2):262–7, 2014) at baseline is related to cognitive change and PET amyloid imaging results, over the course of 27 months, in preclinical AD. The SCT may be a clinically useful screening tool to identify individuals who are more likely to both have positive evidence of amyloidosis on PET imaging and to show measurable cognitive decline over several years