cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7924/g8x34vdz
title: Design and preliminary analysis of a vaginal inserter for speculum-free cervical cancer screening

description: Abstract: Cervical cancer screening usually requires use of a speculum to provide a clear view of the cervix. The speculum is one potential barrier to screening due to fear of pain, discomfort and embarrassment. The aim of this paper is to present and demonstrate the feasibility of a tampon-sized inserter and the POCkeT Colposcope, a miniature pen sized-colposcope, for comfortable, speculum-free and potentially self-colposcopy.

Study Design: We explored different designs using 3D CAD software and performed mechanical testing simulations on each. Designs were rapid prototyped and tested using a custom vaginal phantom across a range of vaginal pressures and uterine tilts to select an optimal design. Two final designs were tested with fifteen volunteers to assess cervix visualization, comfort and usability compared to the speculum and the optimal design, the curved-tip inserter, was selected for testing in volunteers.

Results: We present a vaginal inserter as an alternative to the standard speculum for use with the POCkeT Colposcope. The device has a slim tubular body with a funnel-like curved tip measuring approximately 2.5 cm in diameter. The inserter has a channel through which a 2MP mini USB camera with LED illumination fits to enable image capture. Mechanical finite element testing simulations with an applied pressure of 15 cm H2O indicated a high factor of safety (90.9) for the inserter. Testing of the device with a custom vaginal phantom, across a range of supine vaginal pressures and uterine tilts (retroverted, anteverted and sideverted), demonstrated image capture with a visual area comparable to the speculum for a normal/axial positioned uteri and significantly better than the speculum for anteverted and sideverted uteri (p<0.00001). Volunteer studies with self-insertion and physician-assisted cervix image capture showed adequate cervix visualization for 83% of patients. In addition, questionnaire responses from volunteers indicated a 92.3% overall preference for the inserter over the speculum and all indicated that the inserter was more comfortable than the speculum. The inserter provides a platform for self-cervical cancer screening and also enables acetic acid/Lugol's iodine application and insertion of swabs for Pap smear sample collection. 

Conclusion: This study demonstrates the feasibility of an inserter and miniature-imaging device for comfortable cervical image capture of women with potential for synergistic HPV and Pap smear sample collection.
DOI: 10.7924/g8b56gnq
title: 16s rRNA microarray analysis of murine blood and brain tissue

description: Microbial DNA was isolated from brain tissue and whole blood of healthy mice and assessed by 16S rRNA gene phylogenetic microarray (PhyloChip G3). We present evidence of bacteria found in both blood and brain tissue. Moreover, a significant separation was observed between sample types based on presence/absence and abundance metrics of the detected operational taxonomic units.
DOI: 10.7924/r42n52w51
title: Microcat, current meter and ADCP data from the eastern mid-Atlantic ridge mooring array as part of OSNAP (Overturning in the Subpolar North Atlantic Program)

description: The University of Miami's OSNAP (Overturning in the subpolar North Atlantic Program) is an NSF funded project that is part of the international OSNAP array put in place to measure the full depth, basin-wide overturning circulation and associated transport of heat and freshwater (www.o-snap.org).  The UM array consists of a series of vertical sub-surface moorings deployed along the eastern slope of the Reykjanes Ridge and across the Iceland Basin near 58°N. This dataset contains data from the first two year-long deployments (2014 to 2016) of the Deep Western Boundary Current Array in the Iceland Basin.  Eight moorings were deployed on cruise KN221-03 (2014), were serviced on cruise PE400 (2015), and again on DY054 (2016).  The data sets are time series of pressure, temperature, salinity and currents and have been fully processed, calibrated and quality controlled.  Data are saved in netCDF format, with individual files for each instrument time series.  The structure and naming conventions of the netCDF file follows the OceanSITES data format described here: http://www.oceansites.org/docs/oceansites_data_format_reference_manual.pdf
DOI: 10.7924/g81n7z29
title: Foul tip impact attenuation of baseball catcher masks using head impact metrics

description: Currently, no scientific consensus exists on the relative safety of catcher mask styles and materials.  Due to differences in mass and material properties, the style and material of a catcher mask influences the impact metrics observed during simulated foul ball impacts.  The catcher surrogate was a Hybrid III head and neck equipped with a six degree of freedom sensor package to obtain linear accelerations and angular rates.  Four mask styles were impacted using an air cannon for six 30 m/s and six 35 m/s impacts to the nasion.  To quantify impact severity, the metrics peak linear acceleration, peak angular acceleration, Head Injury Criterion, Head Impact Power, and Gadd Severity Index were used.  An Analysis of Covariance and a Tukey's HSD Test were conducted to compare the least squares mean between masks for each head injury metric.  For each injury metric a P-Value less than 0.05 was found indicating a significant difference in mask performance.  Tukey's HSD test found for each metric, the traditional style titanium mask fell in the lowest performance category while the hockey style mask was in the highest performance category.  Limitations of this study prevented a direct correlation from mask testing performance to mild traumatic brain injury.

Data are arranged according to mask type, and files are available in both .COL and .txt format.
DOI: 10.7924/g8bg2kwp
title: Data and scripts from: Point-to-set lengths, local structure, and glassiness

description: The data files in this collection are associated with the paper "Point-to-set lengths, local structure, and glassiness", S. Yaida, P. Charbonneau, L. Berthier, and G. Tarjus, Phys. Rev. E, 2016. They include .dat, .eps and .m files with associated raw data and generating scripts to allow for replication of the figures.

The growing sluggishness of glass-forming liquids is thought to be accompanied by growing structural order. The nature of such order, however, remains hotly debated. A decade ago, point-to-set (PTS) correlation lengths were proposed as measures of amorphous order in glass formers, but recent results raise doubts as to their generality. Here, we extend the definition of PTS correlations in order to agnostically capture any type of growing order in liquids, be it local or amorphous. This advance enables the formulation of a clear distinction between slowing down due to conventional critical ordering from that due to glassiness and provides a unified framework to assess the relative importance of specific local order and generic amorphous order in glass formation.
DOI: 10.7924/r4pz54w7h
title: Data and scripts from: Copy number variation is associated with gene expression change in archaea

description: Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantitation experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known IS elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments.
DOI: 10.7924/g8g44n63
title: Cryo-sectioned mice for investigating HS-131 uptake

description: Data related to submitted manuscript “A far-red Hsp90 inhibitor reveals mechanism underlying external Hsp90 trafficking”. Brightfield and fluorescence images of an experimental mouse (721 images each) and control mouse (620 images each).
DOI: 10.7924/g8kw5cx3
title: Data and scripts from: Universal non-Debye scaling in the density of states of amorphous solids

description: The data files in this collection are associated with the paper "Universal Non-Debye Scaling in the Density of States of Amorphous Solids", A. Poncet, P. Charbonneau, E. I. Corwin, G. Parisi, and F. Zamponi, PRL, 2016. They include .dat, .pdf, .gnu, .eps and .gle files with associated raw data and generating scripts to allow for replication of the figures.

At the jamming transition, amorphous packings are known to display anomalous vibrational modes with a density of states (DOS) that remains constant at low frequency. The scaling of the DOS at higher packing fractions remains, however, unclear. One might expect to find simple Debye scaling, but recent results from effective medium theory and the exact solution of mean-field models both predict an anomalous, non-Debye scaling. Being mean-field solutions, however, these solutions are only strictly valid in the limit of infinite spatial dimension, and it is unclear what value they have for finite-dimensional systems. Here, we study packings of soft spheres in dimensions 3 through 7 and find, away from jamming, a universal non-Debye scaling of the DOS that is consistent with the mean-field predictions. We also consider how the soft mode participation ratio converges to the mean-field prediction as dimension increases.
DOI: 10.7924/g86q1v5c
title: Data and scripts from: Nontrivial critical fixed point for replica-symmetry-breaking transitions

description: The transformation of the free-energy landscape from smooth to hierarchical is one of the richest features of mean-field disordered systems. A well-studied example is the de Almeida–Thouless transition for spin glasses in a magnetic field, and a similar phenomenon--the Gardner transition--has recently been predicted for structural glasses. The existence of these replica-symmetry-breaking phase transitions has, however, long been questioned below their upper critical dimension, d(u)=6. Here, we obtain evidence for the existence of these transitions in d<d(u) using a two-loop calculation. Because the critical fixed point is found in the strong-coupling regime, we corroborate the result by resumming the perturbative series with inputs from a three-loop calculation and an analysis of its large-order behavior. Our study offers a resolution of the long-lasting controversy surrounding phase transitions in finite-dimensional disordered systems.

PLEASE NOTE: As of 06-06-2017, the data and scripts for Figure 2a, 2b, and 2c have been superseded subsequent to initial data publication. Revised data and scripts are noted as such, and represent the most current version of the data that should be used to replicate the findings presented within the Physical Review Letters article (118, 215701)
DOI: 10.7924/r4sj1f98c
title: QIBA Ultrasound Shear Wave Speed Digital Phantoms

description: Ultrasound shear wave elastography is emerging as an important imaging modality for evaluating tissue material properties. In its practice, some systematic biases have been associated with ultrasound frequencies, focal depths and configuration, and transducer types (linear versus curvilinear), along with displacement estimation and shear wave speed estimation algorithms. Added to that, soft tissues are not purely elastic, so shear waves will travel at different speeds depending on their spectral content, which can be modulated by the acoustic radiation force (ARF) excitation focusing, duration, and the frequency-dependent stiffness of the tissue. To understand how these different acquisition and material property parameters may affect the measurements of shear wave velocity, the simulations of the propagation of shear waves generated by ARF excitations in viscoelastic media are a very important tool. This paper serves to provide an in-depth description of how these simulations are performed. The general scheme is broken into three components: 1) simulation of the 3-D ARF push beam; 2) applying that force distribution to a finite-element model; and 3) extraction of the motion data for post-processing. All three components will be described in detail and combined to create a simulation platform that is powerful for developing and testing algorithms for academic and industrial researchers involved in making quantitative shearwave-based measurements of tissue material properties.
DOI: 10.7924/r4qz26535
title: Conductivity-Temperature-Depth (CTD) data as part of the OSNAP (Overturning in the Subpolar North Atlantic Program), from 2014 on the R/V Knorr (KN221-03)

description: The Overturning of the Subpolar North Atlantic Program (OSNAP) is an effort to determine the strength of the meridional overturning circulation and associated heat and freshwater fluxes in the subpolar North Atlantic. It is a collaborative program with scientists from the U.S., U.K., Netherlands, Germany, France, Canada, and China. Together, a series of hydrographic surveys and mooring deployments have been completed across the boundaries of the Labrador Sea, Irminger Sea, Iceland Basin, and eastern subpolar North Atlantic. 

This submission contains CTD data from the Labrador Sea and Irminger Seas near southern Greenland from the KN221-03 research cruise in 2014. The primary purpose of this dataset is to aid in the calibration of moored instrumentation in the region associated with the OSNAP program. Each CTD file contains pressure-averaged data for one CTD station following the World Ocean Circulation Experiment (WOCE) format and quality specifications for CTD data. CTD sensors have been scaled with pre-cruise calibrations from their respective manufacturers. All CTD salinity measurements have been post-calibrated using bottle salinity measurements.

Additional information may be obtained by contacting Leah Trafford McRaven at ltrafford@whoi.edu
DOI: 10.7924/r48c9vs2c
title: Data from: Lightning initiation processes imaged with very high frequency broadband interferometry

description: Recent measurements of narrow bipolar lightning events (NBEs) by very high frequency (VHF) radio interferometer have resolved the dynamic development of this special lightning process with submicrosecond time resolution, and showed that the fast positive breakdown (FPB) process is responsible for initiating at least some lightning flashes. In this study, with a newly built and deployed VHF interferometer system, we analyzed 31 lightning flash initiation events during three thunderstorms at short range from the interferometer. These events separate into two distinct classes that can be identified based on the time scale and the occurrence contexts of the first detectable VHF emissions from the flash. One class has features completely consistent with previously reported FPB events, and is associated with continuous VHF emissions of 10-20 µs duration. Downward motion of the FPB region centroid merged continuously into the development of the subsequent upward negative leaders. But the majority of the lightning flashes analyzed began with ultrashort, submicrosecond duration, isolated pulses of VHF emission with no identifiable FPB signatures between these pulses and the leader development. These short VHF pulses begin typically a few hundred microseconds before the upward leader developes, and are located at the same position where the leader eventually begins. We suggest that the FPB process is responsible for initiating some but not all lightning flashes, and the extremely short pulse-like VHF emissions play a role in initiating those flashes without any FPB process.
DOI: 10.7924/r4t72c41h
title: Data from: Resistance to flow on a sloping channel covered by dense vegetation following a dam-break

description: The effect of hydraulic resistance on the downstream evolution of the water surface profile h in a sloping channel covered by a uniform dense rod canopy following the instantaneous collapse of a dam was examined using flume experiments. Near the head of the advancing wave front, where h meets the rods, the conventional picture of a turbulent boundary layer was contrasted to a distributed drag-force representation. The details of the boundary layer around the rod and any interferences between rods was lumped into a drag coefficient Cd. The study demonstrated the following: In the absence of a canopy, the Ritter solution agreed well with the measurements. When the canopy was represented by an equivalent wall friction as common when employing Manning's formula with constant roughness, it was possible to match the measured wave front speed but not the precise shape of the water surface profile. However, upon adopting a distributed drag force with a constant Cd, the agreement between measured and modeled h was quite satisfactory at all positions and times. The measurements and model calculations suggested that the shape of h near the wave front was quasi-linear with longitudinal distance for a constant Cd. The computed constant Cd(≈0.4) was surprisingly much smaller than the Cd(≈1) reported in uniform flow experiments with staggered cylinders for the same element Reynolds number.  This finding suggested that drag reduction mechanisms associated with unsteadiness, non-uniformity, transient waves, and other flow disturbances were more likely to play a role when compared to conventional sheltering effects.
DOI: 10.7924/r4jq0xh5k
title: Data from:  Suspended sediment mineralogy in stormflow of the Southern Piedmont

description: The majority of annual sediment flux is transported during storm events in many watersheds across the world.  Using X-ray diffraction (XRD), we analyzed the mineralogy of grab samples of suspended sediment during different stages of storm hydrographs in the Southern Piedmont.
DOI: 10.7924/r4zc7wm7d
title: Data and scripts from: Morphology of renormalization-group flow for the de Almeida–Thouless–Gardner universality class

description: A replica-symmetry-breaking phase transition is predicted in a host of disordered media. The criticality of the transition has, however, long been questioned below its upper critical dimension, six, due to the absence of a critical fixed point in the renormalization-group flows at one-loop order. A recent two-loop analysis revealed a possible strong-coupling fixed point, but given the uncontrolled nature of perturbative analysis in the strong- coupling regime, debate persists. Here we examine the nature of the transition as a function of spatial dimension and show that the strong-coupling fixed point can go through a Hopf bifurcation, resulting in a critical limit cycle and a concomitant discrete scale invariance. We further investigate a different renormalization scheme and argue that the basin of attraction of the limit cycle at the strong-coupling fixed point may stay finite for all dimensions.
DOI: 10.7924/r4c53jx21
title: [Acts of the Apostles]. (multispectral file stack)

description: Multispectral file stack for [Acts of the Apostles] contains 7 image stacks created during imaging and processing of Greek language manuscript fragment dating from between 600 and 800 A.D. (date estimated from comparison to dated papyri written in similar hands). Text is from Acts of the Apostle. Recto text: Acts 7:26-30; verso text: Acts 4:27-31. Further information about the multispectral imaging (MSI) and processing of this object, can be found in the README file below.

For more information about MSI at Duke University Libraries, please see our program webpage: https://library.duke.edu/about/depts/dccs/msi.

For complete information about this object, please see its catalog record:https://find.library.duke.edu/catalog/DUKE008310974
DOI: 10.7924/r4cc0zp95
title: Data from: In vivo pump-probe and multiphoton fluorescence microscopy of melanoma and pigmented lesions in a mouse model

description: We demonstrate a multimodal approach that combines a pump--probe with confocal reflectance and multiphoton autofluorescence microscopy. Pump--probe microscopy has been proven to be of great value in analyzing thin tissue sections of pigmented lesions, as it produces molecular contrast which is inaccessible by other means. However, the higher optical intensity required to overcome scattering in thick tissue leads to higher-order nonlinearities in the optical response of melanin (e.g., two-photon pump and one-photon probe) that present additional challenges for interpreting the data. We show that analysis of pigment composition in vivo must carefully account for signal terms that are nonlinear with respect to the pump and probe intensities. We find that pump--probe imaging gives useful contrast for pigmented structures over a large range of spatial scales (100 μm to 1 cm), making it a potentially useful tool for tracking the progression of pigmented lesions without the need to introduce exogenous contrast agents.
DOI: 10.7924/r4ff3r13q
title: Data from: Development of an international external quality assurance program for HIV-1 incidence using the Limiting Antigen Avidity assay

description: Laboratory assays for identifying recent HIV-1 infections are widely used for estimating incidence in cross-sectional population-level surveys in global HIV-1 surveillance. Adequate assay and laboratory performance are required to ensure accurate incidence estimates. The NIAID-supported External Quality Assurance Program Oversight Laboratory (EQAPOL) established a proficiency testing program for the most widely-used incidence assay, the HIV-1 Limiting Antigen Avidity EIA (LAg), with US Centers for Disease Control and Prevention (CDC)-approved kits manufactured by Sedia Biosciences Corporation and Maxim Biomedical. The objective of this program is to monitor the performance of participating laboratories. Four rounds of blinded external proficiency (EP) panels were distributed to up to twenty testing sites (7 North American, 5 African, 4 Asian, 2 South American and 2 European).
These panels consisted of ten plasma samples: three blinded well-characterized HIV-1-seropositive samples that were included as replicates and an HIV-negative control. The seropositive samples spanned the dynamic range of the assay and are categorized as either recent or long-term infection. Participating sites performed the assay according to manufacturers’ instructions and completed an online survey to gather information on kit manufacturer, lot of kit used, laboratory procedures and the experience of technicians. On average, fifteen sites participated in each round of testing, with an average of four sites testing with only the Maxim assay, seven testing with only the Sedia assay and five sites utilizing both assays. Overall, the Sedia and Maxim assays yielded similar infection status categorization across the laboratories; however, for most of the nine HIV+ samples tested, there were significant differences in the optical density readouts, ODn (N=8) and OD (N=7), between LAg kit manufacturers (p &lt; 0.05 based on mixed effects models. The EQAPOL LAg program is important for monitoring laboratory performance as well as detecting variations between manufacturers of HIV-1 incidence assays.