Whose Data Is It Anyway? Lessons in Data Management and Sharing from Resurrecting and Repurposing Lidar Data for Archaeology Research in Honduras

As a response to Hurricane Mitch and the resulting widespread loss of life and destruction of Honduran infrastructure in 1998, the United States Geological Survey (USGS) conducted the first wide-area airborne lidar topographic mapping project in Central America. The survey was executed by the Bureau of Economic Geology at the University of Texas at Austin (BEG) in 2000, and it was intended to cover 240 square kilometers distributed among 15 flood-prone communities throughout Honduras. The original data processing produced basic digital elevation models at 1.5-meter grid spacing which were used as inputs for hydrological modeling. The USGS published the results in a series of technical reports in 2002. The authors became interested in this dataset in 2013 while searching for geospatial data that would provide additional context and comparative references for an archaeological lidar project conducted in 2012 in the Honduran Mosquitia. After multiple requests to representatives from the USGS and BEG, we found various types of processed data in personal and institutional archives, culminating in the identification of 8-mm magnetic tapes that contained the original point clouds. Point clouds for the 15 communities plus a test area centered on the Maya site of Copán were recovered from the tapes (16 areas totaling 700 km2). These point clouds have been reprocessed by the authors using contemporary software and methods into higher resolution and fidelity products. Within these new products, we have identified and mapped multiple archaeological sites in proximity to modern cities, many of which are not part of the official Honduran site registry. Besides improving our understanding of ancient Honduras, our experiences dealing with issues of data management and access, ethics, and international collaboration have been informative. This paper summarizes our experiences in the hope that they will contribute to the discussion and development of best practices for handling geospatial datasets of archaeological value

Conventional Cervical Exercises Compared with a Mixed-Reality-Based Game in Asymptomatic Subjects: An Exploratory Crossover Pilot Study.

Mixed reality presents itself as a potential technological tool for the management of people with musculoskeletal disorders, without having as many adverse side effects as immersive virtual reality. The objective of this study was to explore the possibilities of a mixed-reality game, performing task-oriented cervical exercises compared to conventional therapeutic exercises in sensorimotor outcome measures in asymptomatic subjects. A randomized crossover pilot study was performed with two intervention groups: a mixed-reality group (MRG) and a conventional exercise group (CEG). The cervical joint position error test (CJPET) and deep cervical flexor endurance test (DCFET) were measured as sensorimotor outcomes. Statistically significant differences were found in the pre–post comparison in the DCFET for both groups (MRG: t = �����3.87, p < 0.01; CEG: t = �����4.01, p < 0.01) and in the extension of the CJPET for the MRG (t = 3.50, p < 0.01). The rest of the measurements showed no significant differences comparing both groups pre- and postintervention (p > 0.05). Mixed reality has apparently the same positive effects as conventional exercises in sensorimotor outcomes in asymptomatic subjects. These results could help in future studies with mixed virtual reality in the management of people with musculoskeletal disorders.post-print882 K

Ancient Maya Regional Settlement and Inter-Site Analysis: The 2013 West-Central Belize LiDAR Survey

During April and May 2013, a total of 1057 km2 of LiDAR was flown by NCALM for a consortium of archaeologists working in West-central Belize, making this the largest surveyed area within the Mayan lowlands. Encompassing the Belize Valley and the Vaca Plateau, West-central Belize is one of the most actively researched parts of the Maya lowlands; however, until this effort, no comprehensive survey connecting all settlement had been conducted. Archaeological projects have investigated at least 18 different sites within this region. Thus, a large body of archaeological research provides both the temporal and spatial parameters for the varied ancient Maya centers that once occupied this area; importantly, these data can be used to help interpret the collected LiDAR data. The goal of the 2013 LiDAR campaign was to gain information on the distribution of ancient Maya settlement and sites on the landscape and, particularly, to determine how the landscape was used between known centers. The data that were acquired through the 2013 LiDAR campaign have significance for interpreting both the composition and limits of ancient Maya political units. This paper presents the initial results of these new data and suggests a developmental model for ancient Maya polities

Linking complex forest fuel structure and fire behaviour at fine scales

Abstract. Improved fire management of savannas and open woodlands requires better understanding of the fundamental connection between fuel heterogeneity, variation in fire behaviour and the influence of fire variation on vegetation feedbacks. In this study, we introduce a novel approach to predicting fire behaviour at the submetre scale, including measurements of forest understorey fuels using ground-based LIDAR (light detection and ranging) coupled with infrared thermography for recording precise fire temperatures. We used ensemble classification and regression trees to examine the relationships between fuel characteristics and fire temperature dynamics. Fire behaviour was best predicted by characterising fuelbed heterogeneity and continuity across multiple plots of similar fire intensity, where impacts from plot-to-plot variation in fuel, fire and weather did not overwhelm the effects of fuels. The individual plot-level results revealed the significance of specific fuel types (e.g. bare soil, pine leaf litter) as well as the spatial configuration of fire. This was the first known study to link the importance of fuelbed continuity and the heterogeneity associated with fuel types to fire behaviour at metre to submetre scales and provides the next step in understanding the complex responses of vegetation to fire behaviour

Effect of killer immunoglobulin-like receptors in the response to combined treatment in patients with chronic hepatitis C virus infection

Killer immunoglobulin-like receptors (KIRs) are related to the activation and inhibition of NK cells and may play an important role in the innate response against infection with viruses such as hepatitis C virus (HCV). We examined whether the different combinations of KIRs with their HLA class I ligands influenced the response to combined treatment (pegylated alpha interferon and ribavirin) of patients infected by HCV. A total of 186 consecutive patients diagnosed with chronic HCV infection were analyzed. Seventy-seven patients exhibited HCV RNA levels at 6 months posttreatment and were called nonresponders (NR), while 109 cleared viral RNA and were named sustained viral responders (SVR). Patients were typed for HLA-B, HLA-Cw, KIR genes, and HCV genotype. In our study, the frequency of the KIR2DL2 allele was significantly increased in NR (P < 0.001; odds ratio [OR] = 1.95), as was the frequency of the KIR2DL2/KIR2DL2 genotype (P < 0.005; OR = 2.52). In contrast, the frequencies of the KIR2DL3 genotype (P < 0.001) and KIR2DL3/KIR2DL3 genotype (P < 0.05; OR = 0.54) were significantly increased in the SVR. Different combinations of KIR2DL2 and KIR2DL3 alleles with their ligands were analyzed. The frequency of the KIR2DL2/KIR2DL2-HLA-C1C2 genotype was significantly increased in the NR (P < 0.01; OR = 3.15). Additionally, we found a higher frequency of the KIR2DL3/KIR2DL3-HLA-C1C1 genotype in the SVR group (P < 0.05; OR = 0.33). These results were not affected by the HCV genotype. In conclusion, patients who carried the KIR2DL2/KIR2DL2-HLA-C1C2 genotype were less prone to respond to treatment. However, the KIR2DL3/KIR2DL3-HLA-C1C1 genotype clearly correlated with a satisfactory response to treatment, defined by the clearance of HCV RNA

Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment

Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacetylated in peripheral neutrophils. Genome-wide mapping of H4K16ac in terminally differentiated blood cells, along with functional experiments, supported a role for this histone post-translational modification in the regulation of cell differentiation and apoptosis in the hematopoietic system. Furthermore, in neutrophils, H4K16ac was enriched at specific DNA repeats. These DNA regions presented an accessible chromatin conformation and were associated with the cleavage sites that generate the 50 kb DNA fragments during the first stages of programmed cell death. Our results thus suggest that H4K16ac plays a dual role in myeloid cells as it not only regulates differentiation and apoptosis, but it also exhibits a non-canonical structural role in poising chromatin for cleavage at an early stage of neutrophil cell death

Association of Candidate Gene Polymorphisms With Chronic Kidney Disease: Results of a Case-Control Analysis in the Nefrona Cohort

Chronic kidney disease (CKD) is a major risk factor for end-stage renal disease, cardiovascular disease and premature death. Despite classical clinical risk factors for CKD and some genetic risk factors have been identified, the residual risk observed in prediction models is still high. Therefore, new risk factors need to be identified in order to better predict the risk of CKD in the population. Here, we analyzed the genetic association of 79 SNPs of proteins associated with mineral metabolism disturbances with CKD in a cohort that includes 2, 445 CKD cases and 559 controls. Genotyping was performed with matrix assisted laser desorption ionizationtime of flight mass spectrometry. We used logistic regression models considering different genetic inheritance models to assess the association of the SNPs with the prevalence of CKD, adjusting for known risk factors. Eight SNPs (rs1126616, rs35068180, rs2238135, rs1800247, rs385564, rs4236, rs2248359, and rs1564858) were associated with CKD even after adjusting by sex, age and race. A model containing five of these SNPs (rs1126616, rs35068180, rs1800247, rs4236, and rs2248359), diabetes and hypertension showed better performance than models considering only clinical risk factors, significantly increasing the area under the curve of the model without polymorphisms. Furthermore, one of the SNPs (the rs2248359) showed an interaction with hypertension, being the risk genotype affecting only hypertensive patients. We conclude that 5 SNPs related to proteins implicated in mineral metabolism disturbances (Osteopontin, osteocalcin, matrix gla protein, matrix metalloprotease 3 and 24 hydroxylase) are associated to an increased risk of suffering CKD

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected