cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7924/r4154jq8h
title: Namelists and scripts from: Vertical Dependence of Horizontal Scaling Behavior of Orographic Wind and Moisture Fields in Atmospheric Models

description: Previous work showed that atmospheric model simulations exhibit different scaling behavior of vertically-averaged horizontal wind (u,v) and moisture (q) in the mesoscales for convective (spectral slopes β ~ -5/3) and nonconvective (β ~ -11/5) conditions. Here, the focus is on the transient behavior of horizontal scaling in the vertical during the evolution of extreme orographic precipitation storms in middle- (Appalachians, < 2,500 m) and high-mountains (Andes).  The results show that β exhibits a strong diurnal cycle switching between convective and nonconvective behavior following the space-time evolution of atmospheric stability in the lower troposphere (below 700 hPa) depending on latitude, topography, landform and the synoptic environment.  Anomalous flattening of the wind and moisture spectra (i.e. spectral saturation, | β |< 5/3) at high wavenumbers and up to 200 hPa is tied to convective activity, where and when strong vertical motions develop, corresponding to an abrupt directional switch from horizontal energy transfer to vertical energy transfer including latent heating release and parameterized microphysical processes. In the small mesoscales (< 50 km), β ~ -5/3 at all times up to 200 hPa with nighttime steepening (β ~ -11/5) below the orographic envelope where cold air pools form at low elevations and vertical motion weakens in the Appalachians. In the Andes, the scaling behavior exhibits a stronger diurnal cycle at low levels (below 700 hPa) with significant shoaling between tropical and high latitudes. Blocking and strong modification of regional circulations results in nighttime anisotropy at mid-levels on the altitudinal profile along the North-South topographic divide.
DOI: 10.7924/r4r49m981
title: Data from: Primary blast wave protection in combat helmet design: a historical comparison between present data and World War I

description: Since World War I, helmets have been used to protect the head in warfare, designed primarily for protection against artillery shrapnel.  More recently, helmet requirements have included ballistic and blunt trauma protection, but neurotrauma from primary blast has never been a key concern in helmet design. Only in recent years has the threat of direct blast wave impingement on the head - separate from penetrating trauma - been appreciated. This study compares the blast protective effect of historical (World War I) and current combat helmets, against each other and the'no helmet' or bare head, for realistic shock wave impingement on the helmet crown.  Helmets included WWI variants from the UK/US (Brodie), France (Adrian), Germany (Stahlhelm), and a current US combat variant (Advanced Combat Helmet). Helmets were mounted on a dummy head and neck and aligned along the crown of the head with a cylindrical shock tube to simulate an overhead blast. Primary blast waves of different magnitudes were generated based on estimated blast conditions from historical shells. Peak reflected overpressure at the open end of the blast tube was compared to peak overpressure measured at several head locations. All helmets provided significant pressure attenuation compared to the no helmet case. The modern variant did not provide more pressure attenuation than the historical helmets, and some historical helmets performed better at certain measurement locations. The study demonstrates that both historical and current helmets have some primary blast protective capabilities, and that simple design features may improve these capabilities for future helmet systems.
DOI: 10.7924/r49z94h1s
title: UltraDuke Version 1

description: DukeUltrasound is an ultrasound dataset collected at Duke University with a Verasonics c52v probe. It contains delay-and-sum (DAS) beamformed data  as well as data post-processed with Siemens Dynamic TCE for speckle reduction, contrast enhancement and improvement in conspicuity of anatomical structures.
DOI: 10.7924/r4bv7g09k
title: Data from: Breast cancer in Tanzanian, black American, and white American women: An assessment of prognostic and predictive features, including tumor infiltrating lymphocytes

description: Breast cancer is a major cause of morbidity and mortality for women in Sub-Saharan Africa and for black American women. There is evidence that the pathologic characteristics of breast cancers in both African women and black American women may differ from their counterparts of European ancestry. However, despite the great burden of disease, data on pathologic features of breast carcinoma in Sub-Saharan Africa is limited and often contradictory. This lack of information makes it difficult to prioritize resource use in efforts to improve breast cancer outcomes in the region.
 
We examined consecutive cases of breast cancer in Tanzanian women (n=83), black American women (n=120), and white American women (n=120).  Each case was assessed for tumor type, grade, mitotic count, ER and HER2 status, and tumor infiltrating lymphocyte involvement.  
The Tanzanian subjects were younger and had higher stage tumors than the subjects in either American group. Breast cancers in the Tanzanian and black American groups were more likely to be high grade (p=0.008), to have a high mitotic rate (p<0.0001), and to be ER-negative (p<0.001) than the tumors in the white American group. Higher levels of tumor infiltrating lymphocyte involvement were seen among Tanzanian and black American subjects compared to white American subjects (p=0.0001). Among all subjects, tumor infiltrating lymphocyte levels were higher in tumors with a high mitotic rate. Among Tanzanian and black American subjects, tumor infiltrating lymphocyte levels were higher in ER-negative tumors.
 
These findings have implications for treatment priorities for breast cancer in Tanzania and other Sub-Saharan African countries.
DOI: 10.7924/r4cv4gx0h
title: Data from: Deep learning for coastal resource conservation: automating detection of shellfish reefs

description: It is increasingly important to understand the extent and health of coastal natural resources in the face of anthropogenic and climate-driven changes. Coastal ecosystems are difficult to efficiently monitor due to the inability of existing remotely-sensed data to capture complex spatial habitat patterns. To help managers and researchers avoid inefficient traditional mapping efforts, we developed a deep learning tool (OysterNet) that uses unoccupied aircraft systems (UAS) imagery to automatically detect and delineate oyster reefs, an ecosystem that has proven problematic to monitor remotely. OysterNet is a convolutional neural network (CNN) that assesses intertidal oyster reef extent, yielding a difference in total area between manual and automated delineations of just 8%, attributable in part to OysterNet’s ability to detect oysters overlooked during manual demarcation. Further training of OysterNet could enable assessments of oyster reef heights and densities, and incorporation of more coastal habitat types. Future iterations will be applied to high-resolution satellite data for effective management at larger scales.
DOI: 10.7924/r4df6q75s
title: Verasonics Processing Test Data

description: Ultrasound elasticity imaging has been developed over the last decade to estimate tissue stiffness. Shear wave elasticity imaging (SWEI) quantifies tissue stiffness by measuring the speed of propagating shear waves following acoustic radiation force excitation. We have released open-source sequencing and data processing protocols of SWEI using a Verasonics system for use by the research community and industry developers.  The associated code repository can be found here: https://github.com/RSNA-QIBA-US-SWS/VerasonicsPhantomSequences  The associated manuscript can be found here: https://doi.org/10.1109/TUFFC.2016.2614944
DOI: 10.7924/r4g44p43t
title: Data from: Indirectly measured ambient electric fields for lightning initiation in fast breakdown regions

description: We report a new approach to measure indirectly the ambient thunderstorm electric fields in fast positive breakdown regions.  For a given geometry of the discharged fast breakdown region, we show that there is a minimum ambient electric field required to produce a given charge moment change.  We apply this approach to the fast breakdown measurements for two events reported by (Rison, 2016) and find that the average ambient electric field in the discharged region is at least 1.0-1.5 \times 10^5 V/m at the 9.5 km initiation altitude of these events.  This electric field is close to the runaway electron avalanche electric field and to the critical field for positive streamer propagation.  These measurements  provide a meaningful starting point for more detailed analyses or simulations of what occurs inside the fast breakdown process that is responsible for the initiation of at least some lightning discharges.
DOI: 10.7924/r4hx1b43s
title: Data from: RoboCOP: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy

description: RoboCOP (Robotic Chromatin Occupancy Profile) is a state space model that incorporates chromatin accessibility data and nucleotide sequence to predict nucleosome positions and transcription factor binding sites. In this paper, we generated the binding profile of the yeast genome using MNase-seq data. We find that the binding profile changes when yeast cells are treated with cadmium for 60 mins. We compare the two binding profiles by running RoboCOP separately with the two MNase-seq data sets: one before cadmium treatment and one after 60 minutes of cadmium treatment. From RoboCOP output, we notice significant changes in the binding profile around the most up-regulated and down-regulated genes. We obtain the set of genes with most changes from the RNA-seq data for the same two time points as the MNase-seq data sets.

The software published via GitHub as of 01/24/2020 is also available as a Zip file (RoboCOP-master_github.zip) with this data package.
DOI: 10.7924/r4kw5cx8q
title: Data from: Distal conformational locks guide reaction pathways for enhanced metallocene mechanochemistry

description: When incorporated into polymeric materials, mechanophores can be used to produce strain-dependent covalent chemical responses, including stress-strengthening, stress-sensing and network remodeling. In general, it is desirable for mechanophores to be highly inert in the absence of force but highly reactive under applied tension. Metallocenes possess remarkable combinations of force-free stability and force-coupled reactivity, but the mechanistic basis of this reactivity remains largely unexplored. Here, we use single molecule force spectroscopy to probe the mechanical reactivity of a series of ferrocenophanes and elucidate the mechanistic factors that dictate their mechanochemical activity. The force-coupled rate of cyclopentadiene (Cp) dissociation among various ferrocene derivatives varies by several orders of magnitude at ~1 nN, and the differences in reactivity are not correlated with ring strain in the reactants, but the extent of rotational realignment of the two Cp ligands. Mechanophores with pulling points that are conformationally restricted by distal attachments to an eclipsing orientation are most labile, whereas conformationally unrestricted ligands reorient under force to effectively superpose "catch bond" like contributions onto the overall mechanically assisted dissociation reaction. The ability to program the mechanism of ferrocene dissociation to proceed through ligand "peeling", as opposed to the more conventional "shearing" mechanism of the parent ferrocene, leads to enhanced macroscopic, multi-responsive behavior including mechanochromism and force-induced crosslinking in ferrocenophane-containing polymers.
DOI: 10.7924/r4gm8633x
title: Forests in floodplains and wetlands
DOI: 10.7924/r4t72cv5v
title: Data from: Evaluation of the mycobiome of ballast water  and implications for fungal pathogen distribution

description:  Global marine transport via sea vessels has the potential to alter the geographic range of marine microorganisms. One mechanism by which fungal species could be dispersed within the marine habitat is through the release of ballast water, water used to stabilize ships during transport. Recent culture-independent studies have investigated the bacterial portion of the microbiome of ballast water but no studies have examined the mycobiome in detail. In addition, no study has focused on the potential of ballast water to contain and spread fungal pathogens. Therefore, sixty ballast and harbor samples from four major ports and five ocean samples were examined using culture-independent techniques to: 1) determine if ballast water contained fungal pathogens that could impact human society and coastal marine wildlife, and 2) determine the potential risk to which fungal taxa within ballast water could reside within coastal ecosystems. Results support that ballast water contained fungal taxa that are relevant human and marine fish pathogens. Fungal genera were identified that contain known coral and coastal plant pathogen species , however species level identification for this potential pathogens could not be conclusively resolved .  Community and phylogenetic analyses suggest that ballast water and harbor mycobiomes contain similar species suggesting that environmental filtering will not inhibit the spread of fungal taxa in ballast water into harbor ecosystems. This study draws attention to the potential risks of transporting and releasing ballast water into foreign harbors and suggests further study is needed to mitigate the potential spread of these fungal pathogen.
DOI: 10.7924/r49s1r065
title: Data from: Enhanced polymer mechanical degradation through mechanochemically unveiled lactonization

description: The mechanical degradation of polymers is typically limited to a single chain scission per triggering chain stretching event, and the loss of stress transfer that results from the scission limits the extent of degradation that can be achieved. Here, we report a mechanically triggered, delayed scission strategy that allows many eventual scission events to be initiated within a single polymer chain. The strategy is demonstrated via a mechanophore with a [4.2.0]bicyclooctene (BCOE) core that leverages a mechanochemical, orbital symmetry-forbidden 4-electron disrotatory ring-opening reaction to set up a subsequent, force-free and thermodynamically favorable lactonization. Ultrasonication of a 120 kDa BCOE copolymer triggers the desired mechanical remodeling of the polymer backbone, and the resulting lactonization leads to a gradual decrease in molecular weight over the course of 9 days to a final value of 4.4 kDa, more than an order of magnitude smaller than control polymers in which the ring-opened BCOE is protected from lactonizing. The force-coupled activity of the ring-opening reaction is probed by single molecule force spectroscopy and through the use of internal standards in sonication, and the forces required for activation are far smaller than is typically required for the mechanical chain scission of conventional covalent polymers.
DOI: 10.7924/r4s46nm6p
title: Data from: Low-severity fire as a mechanism of organic matter protection in global peatlands: thermal alteration slows decomposition

description: Worldwide, regularly-recurring wildfires shape many peatland ecosystems to the extent that fire-adapted species often dominate plant communities, suggesting that wildfire is an integral part of peatland ecology rather than an anomaly. The most destructive blazes are smoldering fires that are usually initiated in periods of drought and can combust entire peatland carbon stores. However, peatland wildfires more typically occur as low-severity surface-burns that arise in the dormant season when vegetation is desiccated, and soil moisture is high. In such low-severity fires, surface layers experience flash heating, but there is little loss of underlying peat to combustion. This study examines the potential importance of such processes in several peatlands that span a gradient from hemiboreal to tropical ecozones and experience a wide range of fire return intervals. We show that low-severity fires can increase the pool of stable soil carbon by thermally altering the chemistry of soil organic matter (SOM), thereby reducing rates of microbial respiration. Using XPS and FTIR, we demonstrate that low-severity fires significantly increase the degree of carbon-condensation and aromatization of SOM functional groups, particularly on the surface of peat aggregates. Laboratory incubations show lower CO2 emissions from peat subjected to low-severity fire, and predict lower cumulative CO2 emissions from burned peat after one to three years. Also, low-severity fires reduce the temperature sensitivity (Q10) of peat, indicating that these fires can inhibit microbial access to SOM. The increased stability of thermally-altered SOM may allow a greater proportion of organic matter to survive vertical migration into saturated and anaerobic zones of peatlands where environmental conditions physiochemically protect carbon stores from decomposition for thousands of years. Thus, across latitudes, low-severity fire is an overlooked factor influencing carbon cycling in peatlands, which is relevant to global carbon budgets as climate-change alters fire regimes worldwide.
DOI: 10.7924/r4n877f1k
title: Data from: High-elevation monsoon precipitation processes in the Central Andes of Peru

description: Measurements at the high-elevation Lamar Observatory in the Mantaro Valley (MV) in the Central Andes of Peru demonstrate a diurnal cycle of precipitation characterized by convective rainfall during the afternoon and nighttime stratiform rainfall with embedded convection. Data from three wet seasons 2016-2018 reveal long-duration (6-12 hours) shallow precipitating systems (LDPS) that produced about 17% of monsoon rainfall in 2016 and 2018 associated with El Niño and La Niña respectively. The LPDS fraction of monsoon rainfall doubles to 35% with weekly recurrence in 2017 under El Niño Costero (coastal) conditions. Backward trajectory analysis shows that precipitable water sustaining > 80% of seasonal precipitation and LPDS originates in the western Amazon foothills and it is transported to higher elevation in 1-2 days. LDPS occur under favorable moisture conditions dictated by the South America Low Level Jet (SALLJ) and Cold Air Incursions (CAIs). High inter-annual variability of precipitation processes occurs with increased moisture supply in the mid troposphere due to higher frequency of CAIs during the 2017 El Niño Costero, with low-level advection from the eastern Andes foothills tied to SALLJ strength and enhanced moisture convergence ahead of CAI fronts. These findings highlight the role of eastern Andes in organizing the low-level moisture supply to high-elevation precipitation systems. Analysis of ground-based vis-à-vis the Global Precipitation Measurement (GPM) mission satellite-based radar observations points to significant challenges to precipitation detection and estimation measurement from space as the GPM clutter-free height (~2 km) exceeds the depth of precipitation systems in the MV (50% overall).
DOI: 10.7924/r4z31t79k
title: Data and code from: Waveforms optimized to produce closed-state Na+ inactivation eliminate onset response in nerve conduction block

description: The delivery of kilohertz frequency alternating current (KHFAC) generates rapid, controlled, and reversible conduction block in motor, sensory, and autonomic nerves, but causes transient activation of action potentials at the onset of the blocking current. We implemented a novel engineering optimization approach to design blocking waveforms that eliminated the onset response by moving voltage-gated Na+ channels (VGSCs) to closed-state inactivation (CSI) without first opening. We used computational models and particle swarm optimization (PSO) to design a charge-balanced 10 kHz biphasic current waveform that produced conduction block without onset firing in peripheral axons at specific locations and with specific diameters. The results indicate that it is possible to achieve onset-free KHFAC nerve block by causing CSI of VGSCs. Our novel approach for designing blocking waveforms and the resulting waveform may have utility in clinical applications of conduction block of peripheral nerve hyperactivity, for example in pain and spasticity.
DOI: 10.7924/r4k072k9s
title: Data from: Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections

description: The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier's wave function delocalization is regulated by the solvation induced localization and the quantum delocalization among the π stacked base pairs at any instant of time. Using a newly developed localized orbital scaling correction (LOSC) density functional theory method, we accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA. This approach can be used to diagnose the extent of delocalization in fluctuating DNA structures. Our studies indicate that the hole state tends to delocalize among 4 guanine-cytosine (GC) base pairs and among 3 adenine-thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. The relatively small delocalization in AT base pairs is caused by the weaker π-π interaction. This extent of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering coherent carrier transport in DNA.
DOI: 10.7924/r4rf5r157
title: Data from: Correlation of IgG autoantibodies against acetylcholine receptors and desmogleins in patients with pemphigus treated with steroid sparing agents or rituximab

description: Introduction: Autoantibodies (autoAbs) against desmoglein-1 (DSG1) and desmoglein-3 (DSG3) have conventionally been studied and well accepted in the pathogenesis of pemphigus vulgaris (PV) and foliaceus (PF).  Recent studies have suggested that non-DSG autoAbs may contribute to the pathogenesis of pemphigus, including autoAbs directed at acetylcholine receptors (AChR) and thyroid peroxidase (TPO). The purpose of this study is to retrospectively analyze PV and PF patient sera to better understand the relationship between anti-AChR and -TPO Abs to disease activity and DSG reactivity between patients treated with prednisone and steroid sparing agents (SSA; n=22) or prednisone and rituximab (n=21).

Methods: Patients were evaluated at 2 time points, T1 and T2, for disease activity using the Pemphigus Disease Area Index (PDAI), and sera were tested for the presence of TPO, DSG1, DSG3, muscarinic (M3) and nicotinic (n) AChR IgG autoAbs, as well as antibodies against Varicella Zoster Virus (VZV) by ELISA.

Results: Disease activity significantly decreased in patients from T1 to T2 (p < .0001). A significant difference was seen in IgG anti-DSG1 (p < .0001) and anti-DSG3 (p=.0049) levels when T1 was compared to T2 in both treatment groups. A significant increase was found between pemphigus patients and normal subjects with nAChR (p < .0001) at T1 but not with m3AChR, TPO or VZV Abs. No significant difference was seen between T1 and T2 values in patients with pemphigus for the non–desmoglein Abs TPO (p = .7559), M3AChR (p = .9003), nAChR (p = .5143) or VZV (p = .2454). These findings demonstrate that although an increase in IgG anti-nAChR autoAbs was found in PV and PF subjects, these Abs did not decrease with treatment. No other non-DSG Abs were increased or significantly changed over time in patients with pemphigus. This suggests that anti -AChR and -TPO Abs may not play a direct role in the pathogenesis of most patients with pemphigus, but does not rule out a role for non-DSG auto antibodies in distinct subsets of pemphigus patient.