dataesr/scientific-paragraphs-categorization huggingface dataset:
Microchannel master molds Microchannel devices were designed using computer-aided design software (AutoCAD; Autodesk, San Rafael, CA). Channel architectures were based on previously described designs  (41, 42). Devices feature three rectangular seeding ports, each marked with 15 µm diameter pillars evenly spaced at 25 µm intervals and with opposite rows of channels aligned towards the device exterior. Entrances to channels are 100 µm long funnels that taper from an initial width of 18 µm to a final channel width of 12 µm. Chromium-plated quartz photomasks were generated based on these designs by the Minnesota Nano Center (MNC) facilities. Device molds were fabricated on 4" silicon wafers using epoxy-based SU-8 2005 negative photoresist (MicroChem Corp. , Wesborough, MA) and soft photolithography.
Time-lapse imaging of cells in microchannels Time-lapse images were acquired on either a Nikon TiE or Nikon Ti2 epifluorescence microscope under control of NIS Elements software (Nikon Instruments Inc. , Melville, NY). Each system is outfitted with a humidified environment containing 5% CO 2 and stable temperature control at 37°C, provided by a stagetop incubator (OkoLab Llc. , Ottaviano, Italy), a ProScan III motorized stage (Prior Scientific Inc. , Rockland, MA), a white light transmitted LED (CoolLED Ltd. , Andover, UK), LED fluorescence illumination (Spectra X; Lumencor, Beaverton, OR), and DAPI/FITC/TxRed filter set (Chroma, Cat#89014). The TiE system is equipped with a Zyla 4. 2 sCMOS camera (Andor Technologies Ltd. , Belfast, UK) and the Ti2 stand is equipped with a Zyla 5. 5 sCMOS camera (Andor).
Confocal z-stacks of cells in channels Confocal z-stacks were acquired on an LSM7 LIVE swept-field confocal microscope (Carl Zeiss Microscopy, LLC; Jena, Germany) using a 40x/0. 95 NA plan-apofluor objective and Optovar set to 1x magnification. The 488 nm and 405 nm lasers and BP 520-555 and BP 415-480 filters enabled simultaneous acquisition of the blue and green channels. Images were digitized using a 512 pixel 11 bit linear detector. Zen imaging software (Zeiss) provided system control during imaging.
Semi-automated tracking of individual cell nuclei Nucleus position and shape were obtained from the DAPI channel of image sequences using custom semi-automated image segmentation and tracking Matlab scripts (MathWorks) as previously described for tracking fluorescently labeled cells migrating in ex vivo brain slice cultures  (24). Image sequences were cropped to include a single cell that was not in contact with another cell, as ascertained from phase contrast images. Skipped frames (e. g. due to contact with another cell or object in the channel) were omitted during analysis. Centroid coordinates were used to calculate MSD using the overlap method  (40)  and analyzed in the same way as 1D CMS data. Individual cells in some conditions were analyzed using a PRW model  (13). PRW model fits were performed in the same way as fits to the diffusion-convection model.
Statistical analysis Experimental data represent accumulated measurements from N ≥ 2 biological replicates for each condition. Numbers of individual simulations are given in the figure legends. All statistical analysis of experimental or simulated data was performed using the Matlab Statistics Toolbox (MathWorks). We used the non-parametric Kruskal-Wallis test, since the data did not typically follow a normal distribution. When a comparison included more than two groups, we corrected multiple pairwise comparisons using a Dunn-Sidăk post hoc test. Statistical significance for a particular comparison was reached when p < 0. 01.
Acknowledgements Thanks to members of the  Odde and Piel laboratories  for helpful discussions, and thanks to Prof. Margaret Titus  for comments on the manuscript. The authors thank  Dr. Rafaele Attia  and  Mark Fisher  for their assistance with device design, as well as  Geneva Doak ,  Jose Valdez ,  Dr. Daniel Lu , and  Prof. David Wood  for their assistance with photolithography and microfabrication. The authors thank  Dr. Ana-Maria Lennon-Duménil  for use of her laboratory space, and the  Bioimaging Cell and Tissue Core Facility of the Institut Curie (PICT-IBiSA ) for use of microscopes during pilot data collection. Simulations were run in part on high-performance computing resources at the  Minnesota Supercomputing Institute. Portions of this work were conducted in the  Minnesota Nano Center , which is supported by the  National Science Foundation  through the  National Nano Coordinated Infrastructure Network (NNCI)  under Award Number  ECCS-1542202.
Other funding support was provided by a  3M Science & Technology Fellowship  (to L. S. P. ),  National Science Foundation Graduate Research Fellowship 0039202  and  GROW program  grant (to L. S. P. ), a  STEM Chateaubriand Fellowship  (to L. S. P. ), the  University of Minnesota UROP  (to M. R. S. ),  Association Nationale pour la Recherche  grant  ANR-16-CE13-0009  (to P. V. ),  European Research Council  consolidator grant  311205   PROMICO  (to M. P. ), and  National Institutes of Health  grants  U54 CA210190  and  R01 CA172986  (to D. J. O). P. V. is an INSERM investigator.
4a )  [10]. The samples have then been scanned at ID16A Nano-Imaging beam line (ESRF) with selected X-ray energies of 17. 05 KeV and 33. 6 KeV for the O2 and H2 electrodes, respectively. The detailed protocol for data acquisitions and the procedure for the electrode reconstructions can be found in refs. [10, 57, 58]. The 3D images after reconstruction present a volume as large as 50 µm x 25² µm² x  = 98174 µm 3 with a voxel size of 25 nm (with  3. 1416 : cf. list of symbols) (Fig. 4b ). In complementarity with the X-ray reconstructions, the microstructure of O2 electrode of Cell-B has been also characterized by FIB-SEM tomography (with a FEI Versa 3D microscope) according to the procedure already detailed in  [16, 59]. The FIB-SEM reconstruction exhibits a volume limited to 17 3 =4913 µm 3 with a voxel size of 16.
We present data collected in the framework of the Algerian BAsin Circulation Unmanned Survey (ABACUS) project. The main objective of ABACUS is the monitoring of the basin circulation and of the surface and intermediate water masses' physical and biological properties in a key region of the Mediterranean Sea circulation. Data presented here have been collected through deep glider cruises in the Western Mediterranean Sea during the autumns of 2014, 2015 and 2016; activities at sea are expected to be repeated during the coming years, so that the dataset will be extended. Glider missions were conducted in the Algerian Basin, between the island of Mallorca and the Algerian coast. Across the three glider missions, eight repeated transects were completed which enabled us to investigate the basin-scale circulation and the presence of mesoscale structures, utilising both the adaptive sampling capabilities of the gliders and the higher resolution of the data.
After collection, all data passed a quality control procedure and were then made available through an unrestricted repository host by the SOCIB Data Centre at https://doi. org/10. 25704/b200-3vf5. The actual dataset spans three autumn seasons, providing an important contribution to the data collection in the chronically undersampled Algerian Basin. Temperature and salinity data collected in the first 975 m of the water column allowed us to identify the main water masses and describe their characteristics, improving the understanding of the dynamics of the region. On the timescale of the project, data show a large variability in the surface layer and reduced variability in the intermediate and deep layers. Our measurements have been successfully compared to data previously collected in the area from 1909 to 2011.
, 2017)  and the upcoming Surface Water and Ocean Topography (SWOT) wide-swath radar interferometer  (Fu and Ferrari, 2008) , whereby multi-platform data are expected to help to distinguish noise from small dynamical structures, as a result of cross-calibrations between the different sensors  (Bouffard et al. , 2010; Pascual et al. , 2013). In this study, we present data collected through three SLOCUM G2 (Fig. 1 ) glider missions carried out in the AB during autumn 2014, 2015 and 2016. These cruises were developed along a repeated monitoring line set across the AB and allowed the collection of a huge dataset of physical and biological ocean parameters in the first 975 m of the water column. For each mission, the glider main track was chosen to lie under overflying altimeter satellites tracks, in order to optimise the inter-comparison of the data from the two platforms.
Funding agreements were developed under the JERICO TNA third call (grant no. 262584) for ABACUS 1, the SOCIB external access for ABACUS 2 and JERICO-NEXT TNA first call (grant no. 654410) for ABACUS 3. Up to 2016, a total of eight repeated transects were completed between the island of Mallorca and the Algerian coast. In 2014 and 2015, after the completion of the defined transects, the glider track was changed in order to sample specific mesoscale structures in the study area (Fig. 2 ). During these cruises ABACUS gliders collected temperature, salinity, turbidity, oxygen and chlorophyll (Chl a) concentration data in the first 975 m of the water column. Each mission had an average duration of about 40 days and was always performed between September and December. In situ data collection was supported by remotely sensed data from different platforms over the Western Mediterranean Sea.
3 ) with limited presence and sampling in the layer of 0-20 m depth. In particular, during the 2014 mission, data collection in the surface (0-20 m depth) was limited at every third ascending profile, resulting in a sampling spatial resolution of 8. 4 km for depths shallower than 20 m. In 2015 we collected a complete cast from surface to bottom at about 5 km resolution, as a result of the increased general resolution of the glider sampling, which was now performed during both upcast and downcast. Finally, in 2016 we tested the glider possibility to sample the entire water column from 0 to 975 m depth at the resolution of 2. 8 km. This was obtained by sampling during both upcast and downcast and by programming the glider to reach the surface after every cast. The experiment was successful, but limited in time due to battery constraints.
seabird. com/combination-sensors/eco-flntu/ family?productCategoryId=54758054352, last access: 23 January 2019), both of them embedded inside the central hull segment of the glider commonly known as the "science bay". Additionally, an oxygen optode to measure absolute oxygen concentration and saturation (%) by AADI (https:// www. aanderaa. com/productsdetail. php?Oxygen-Optodes-2, last access: 23 January 2019) was externally mounted on the aft, and wet, section of the glider. The accuracy of the measurements, their vertical resolution and depth range vary according to the specific instrument and measured variable as reported in Table  1. Temperature, salinity and oxygen data were sampled to full diving depth (0-975 m depth), while the acquisition of the other optical parameters ceased at 300 m depth.
Nonetheless, gradients along space, depth and time can successfully be observed and discussed. Generally, real-time data transmission from the glider can be adaptively configured before and during the mission. For the ABACUS missions, it was set to occur at about every 6 h, in correspondence with every second upcast for most of the glider transects. Real-time data (with a file size ranging be- tween 20 and 90 Kb) were transmitted using Iridium satellite link and contained a subset of all measurements, populated taking one out of every three samples for each parameter. This strategy permitted the retrieval of a first overview of the data collected, as well as the eventual transmission of new sampling and navigation directives to the glider. The full resolution dataset remained stored locally inside the glider until the vehicle was physically brought back to SOCIB facilities once the mission was completed.
Then, data were transferred to the SOCIB Data Centre, where pre-processing, processing and validation were carried out and NetCDF files created. The structure and content of the ABACUS NetCDF file are described in Sect. 3. The pre-mission activities were carried out at the SOCIB glider facility  (Tintoré et al. , 2013)  and included all ballasting, pressure tests, compass validation and adjustment operations needed to assure the glider capability to reach the surface. This capability is achieved by adjusting the overall weight of the vehicle and by distributing part of that weight so that inclination and roll are neutral when the glider sets its mechanical actuators (pump, mass shifter, air bladder and fin) in neutral mode (0 cc, 0 in. , no inflation and 0 rad respectively). This tuning is driven by the hydrographical characteristics of the target waters to be navigated, i.
e. their minimum density, since they condition the execution of the operations mentioned. Within this scope, the climatological maximum value of temperature and the minimum value of salinity for the studied area and period have been analysed. These data were used as extreme hydrographic characteristics of the target waters and allowed us to derive the minimum density (1024. 0683 kg m -3 ) needed to precisely tune the glider for the target waters. This tune-up is required in order to make sure that the vehicle will always be able to break into the surface and to raise its tail above the water to enable clear and robust communications. As regards compass,  Merckelbach et al. (2008)  developed a method to assess the glider compass error in SLOCUM gliders. This approach has been followed for gliders used during the later ABACUS experiments.
The methodology should take place at any location away from sources of hard or soft electromagnetic material (e. g. sport ground); thus it was performed in a forest clearing to minimise electromagnetic interference effects. Using a wooden platform, the glider was placed horizontally and a plastic-made compass stand aligned with true north was used, allowing precise and repetitive heading gradients of 15 •. The measurement error was then estimated by calculating the difference between the heading measured by the glider and the heading that was physically imposed using the stand. A maximum error of less than 10 • was observed during the three tests so that compass recalibration was not considered necessary. All these operations were performed on the two SLOCUM glider used during the ABACUS missions (SLDEEP001 for 2014 and 2016; SLDEEP000 for 2015) as part of the premission tests and contributed to the assessment of the quality of the data collected.
The glider tracks were designed to cross the basin from the island of Mallorca (Spain) to about 37 km off the Algerian coast (Fig. 2 ). The timing of the missions was accurately planned in order to provide synoptic in situ data with respect to the satellite SARAL/ALtiKa and Sentinel-3A passages, being also comparable among the different ABACUS missions  (Aulicino et al. , 2018). In 2014, during the ABACUS 1 mission, three glider transects were completed along the neighbouring SARAL/AltiKa ground tracks 229 and 773 from 15 September to 19 December 2014. The satellite overpassed the glider on 17 September and 26 November 2014 (track 773) and on 12 December 2014 (satellite track 229). During the ABA-CUS 2 mission, which was carried out from 18 November to 11 December 2015, the glider was overflown by the SARAL/AltiKa satellite on 23 October, along the ground track 229 with the glider halfway along the transect.
During the ABACUS 1 mission, the glider was programmed to sample only during downcasts with a final along-track resolution of almost 4 km once the oblique profiles are projected into the vertical. As a result of the first data analysis, the sampling plan for the following missions was modified. During ABACUS 2 (2015) and ABACUS 3 (2016) cruises, both downcasts' and upcasts' data were collected, thus obtaining an improved spatial along-track resolution of about 2 km, while diving angle and speed remained unchanged. Apart from increasing horizontal sampling resolution, this new strategy also has an effect on data quality, enabling the application of the thermal lag correction developed by  Garau et al. (2011) , which requires consecutive up and down profiles of temperature and salinity.
Data quality control After each mission, data were transferred from the internal glider memory to the SOCIB Data Centre, where data processing was carried out and production of delayed time NetCDF files at different elaboration levels (i. e. level 0, level 1, level 2) occurred  (Troupin et al. , 2016; Cusi et al. , 2013)  before web dissemination of the data. Each NetCDF file comprises the main cruise information, data and a short abstract. Level 0 contains the raw data collected by the glider without any elaboration or correction and organised in vectors. Level 1 includes data regularised, corrected and/or derived from raw glider data. Each variable is stored as sequences of measurements along the glider trajectory, with interpolated position coordinates to match the times of measurement by the sensor, and with unit conver-sions and filters applied.
Each variable is described and commented on individually. The level 2 dataset includes the regularly sampled vertical profiles generated from depth binning of (level 1) glider data that have already processed. The profiles are obtained by interpolation of level 1 data to produce regular homogeneous and instantaneous profiles from each up-or downcast, using the mean time and position of the corresponding cast for the profile location and time. In this level, each variable is stored in a matrix. Depth increases with the number of rows, with each row corresponding to 1 m depth, while time, and consequently the number of profiles, changes along the columns. Delayed mode data processing for level 1 and 2 included thermal lag correction, filtering and 1 m bin vertical averaging  (Troupin et al. , 2016).
In particular, in level 1 and 2, filters are mainly focused on the processing of pressure data through a low pass filter and on the interpolation of missing values. Nevertheless, some unexpected high oxygen concentration and high salinity values, as well as abrupt temperature value changes, were still present in the surface layer after this standard quality control protocol. The presence of these unexpected values at the shallower turning depth of the glider supports the hypothesis of a possible effect of glider navigation phase change on the sampling capability. For this reason, during the 2015 and 2016 missions, the glider was programmed to reach the surface after every profile in order to avoid this issue, improve the data collection in the very surface layer (depth < 20 m) and provide a more suitable dataset for the comparison with satellite data.
Nevertheless, an additional quality control procedure was developed and regularly performed at the Parthenope University of Naples on all ABACUS data. In particular, this procedure includes an additional single-point spike control, the interpolation of single missing data along the profiles, the application of a dedicated median filter, a five-point running mean along the depth and, finally, an iterative comparison between adjacent profiles. This tool allowed us to identify and discard bad data and artefacts that were still present after the standard quality control. This final product is indicated as level 3 of the ABACUS dataset. An example of the level 3 elaboration steps is given in Fig. 4. This additional procedure was routinely adopted for the quality control of all ABACUS glider missions for each geophysical parameter.
All dataset elaboration levels from 0 to 2 are available at https://doi. org/10. 25704/b200-3vf5, while level 3 data are freely available upon direct request to the authors. Data samples presented in this paper are obtained from level 3 data. Figure  5  shows the mean temperature and salinity profile calculated for each transect completed during the ABACUS cruises from 2014 to 2016. For each mission, a mean profile was calculated using data of a single Mallorca-Algerian coast (or vice versa) transect. In this figure, the first available mean profile for each mission is shown in blue, the second in black, the third in red and the fourth in green. Standard deviation along depth during each transect was also computed for both temperature and salinity (shaded areas in Fig. 5 ). The ABACUS profiles are characterised by a high level of variability in the surface layer that considerably decreases in the intermediate and deeper layers, in agreement with ex-isting literature in the area  (Manca et al.
Data comparison and transect samples In order to test the reliability of ABACUS dataset, a comparison was performed between glider data and a set of historical oceanographic measurements collected in the study area. In particular, a composite dataset including temperature and salinity data along the water column was created, merg-    Group, 2002) , from the Coriolis CORA-3. 4 Dataset  (Cabanes et al. , 2013)  and from the World Ocean Hydrographic Profiles (WOHP) V1. 0 database, in agreement with Viktor Gouretski). The resulting dataset, consisting of about 2450 profiles, spans from 1909 to 2011 with a regular distribution of the data across the different seasons. After the application of standard quality control procedures, including spike removal and the comparison among nearby profiles, the calculation of potential temperature ( ) was carried out and the -S couples from this dataset and the ABACUS observations were compared.
The main properties of the water masses, as well as their spatial and vertical variability and distribution, can be successfully observed through the analysis of vertical transects. Figures  8  and 9  show the vertical along-track sections of temperature, salinity, oxygen concentration, Chl a concentration and turbidity collected along the most recent transect of the ABACUS project. This north-south transect was completed during ABACUS 3, from 1 to 9 December 2016, along the Sentinel-3 ground track number 713. Temperature and salinity data collected in the surface layer (Fig. 8a, b ) show a clear signature of the AC presence. Lower temperatures and salinities are recorded in the southern part of the transect, highlighting the presence of AW recently entering the Mediterranean Sea. On the other hand, the northern part of the transect is characterised by more saline and warm waters with typical Mediterranean properties.
An example of mesoscale variability analysed through ABACUS 1 glider data can be found in  Cotroneo et al. (2016) , which presents the vertical sections of multiparametric observations collected across a mesoscale eddy. ABACUS glider data from 2014 to 2016 are available to the public in NetCDF format through an unrestricted repository at https://doi. org/10. 25704/b200-3vf5 (Budillon et al. , 2018). A set of NetCDF files for data from level 0 to level 2 is created for each glider deployment. The SOCIB Data Centre hosts the data repository and offers a useful interface for data visualisation and download.
Conclusions The Mediterranean Sea is known to be particularly sensitive to changes in external forcings, thus being one of the most responsive areas to climate change  (Schroeder et al. , 2017; Gualdi et al. , 2013) , and its waters have already shown the presence of significant trends, even in the deepest layers  (Fusco et al. , 2008; Budillon et al. , 2009). In this framework, the ABACUS dataset provides about 2400 complete casts along the water column down to 975 m depth across the Algerian Basin, one of the key areas of the western Mediterranean where monitoring programmes should be improved and intensified. In particular, here we present data collected during a series of glider missions carried out from 2014 to 2016 in the framework of the ABACUS project. This effort allowed the collection of a large dataset of physical (temperature and salinity) and biochemical (oxygen concentration, turbidity and chlorophyll concentration) high-resolution in situ observations.