dataesr/scientific-paragraphs-categorization huggingface dataset:
ª 2015 The Authors Molecular Systems Biology 11: 789 | 2015 Markus K Muellner et al Targeting a breast cancer cell state Molecular Systems Biology using a top 10 hybrid method with a collision-induced dissociation (CID) MS 2 event followed by a high-energy C-trap dissociation (HCD) MS 2 event for each selected precursor ion. Acquired RAW data were analyzed by the Proteome Discoverer 1. 4. 0. 288 platform integrating MASCOT, phosphoRS, and target decoy PSM validator software modules. Database search was performed against the human SwissProt database (sp_human_v2013. 1) with the following parameters: fixed modification of carbamidomethylation (C); variable modification of oxidation (M) and phosphorylation (S, T and Y); two miscleavage sites; search tolerance of 10 ppm on precursor; and 0. 6 or 0.
A successfully implemented SWOT satellite will provide a science mission with significant applications potential. It will provide data products to facilitate the use of the satellite observations by a wide variety of users  (operational, commercial, civic, governmental). It will also open up a new avenue for scientific research and at the same time create a new operational sector, particularly in hydrology where space observations are developing. NASA and CNES share the goal of involving Early Adopters of products in the process of SWOT data development in order to leverage hydrology and oceanography applications. We are currently experiencing the Anthropocene age of surface water where it is redistributed and artificially managed to the extent that there is no pristine river basin left today in populated regions.
The primary attribute of SWOT data will be the ability to produce high-resolution, nearly instantaneous "snapshots" of sea surface height (SSH), the primary variable, along with information about winds and waves with similar resolution in two 50 km-wide swaths. However, the challenge lies in the combination of this high spatial resolution with lower temporal resolution. With the 21-day exact repeat orbit needed to cover nearly the entire Earth, it will not be possible to observe the temporal development of the small-scale features that will be seen in instantaneous SSH fields. Through composite analysis and numerical models, SWOT will enable oceanographers to describe some of the mesoscale and more importantly submesoscale processes that cannot be resolved by conventional altimeter satellites.
Workshops, Tutorials, Conferences The SAWG will continue to host user workshops to target potential data users for applications in hydrography and oceanography. In workshops convened with water resources managers and others responsible for and interested in assessing freshwater transport and disposition, mission scientists can support the review and assessment of how SWOT and AirSWOT science results may improve on information, products and collaborations for use in decision-making. Collaborations between science team members and Early Adopters will also focus on the development of tools that may be used to inform decision makers on: • River, lake and reservoir levels, • Flood assessments and potential mitigation measures and water storage, • Climatic and ecological impacts on water resources, • Water demands for agriculture and agricultural impacts from changes in water resources, • Sustainable use of water, and • Many other application areas and societal benefits.
, 2013). Among these, the Nile, Niger, Mekong, Indus, Irrawaddy, GBM (Ganges, Brahmaputra and Meghna), Salween and Zambesi are examples that host some of the world's largest population centers. The differences in ground network coverage, monitoring protocols to data recording and sharing, and lack of resources raise the challenge for coordinated surface water modeling in rivers in these basins. One application that currently suffers most from a lack of basinwide coordination of river modeling is flood forecasting in downstream flood-prone regions. Forecasting of transboundary flooding in nations downstream of these basins remains notoriously difficult using conventional modeling approaches that rely on extensive in-situ data. It is expected that SWOT's ability to provide spatially distributed information of surface water bodies (rivers and lakes) will significantly enhance modeling systems for flood forecasting, data assimilation, drought management and even hydropower generation.
Given the clear impacts of SWOT's potential value for applications in the developing world, international cooperation and regional modeling and assessment of the value of currently available altimetry data in transboundary basins is key. Several investigations are under way which indicate how best to integrate SWOT measurements to further enhance applications. For example,  Yoon and Beighley (2014)  have explored how SWOT measurements could aid in flood routing of a system of reservoirs in the developing world where there is virtually no ground data. Hossain et al. (2014a Hossain et al. ( , 2014b) )  have explored the use of nadir altimetry for extending the range of operational flood forecasting for the Bangladesh Government. More recent studies, such as  Maswood and Hossain (2015)  demonstrate how the dual availability of river width and height can reduce the error of river level simulations in hydrodynamic models up to 300% for downstream nations.
Applied Science at NASA The NASA Earth Science Directorate Applied Sciences Program (ASP) funds projects that enable innovative uses of NASA Earth science data with respect to policy, business, and management decisions. ASP is supporting missions, including the SWOT concept, that were identified in the Earth Science Decadal Survey  (NRC, 2007). Applications teams are tasked with implementing Decadal Survey and NASA climate-centric architecture goals related to applications. Activities include working with partners to identify and organize potential applications communities, and to develop and promoting a process to optimize the reach of existing applications efforts to enhance the applications value of the missions. Another goal is to promote project-level awareness of mission planning decisions that may increase or decrease the utility of data products to diverse user and potential user communities (NASA, 2011).
SWOT Applications at CNES The French Investment Program (FIP) is the primary driver for the CNES SWOT Applications directives and approach. Innovative and economic aspects of the SWOT mission are highly relevant for the support of the mission by the FIP. Fundamental considerations for the program recognize the high climatic and environmental stakes we face as a global community in the decades to come: How can we improve our models to answer critical questions about current and future trends? What observational accuracies will be required? For the SWOT oceanography user community, existing elements can be built upon from the framework of conventional altimetry to reach new users with applications in the highresolution data that SWOT will provide. This will lead to improvement of existing applications and new perspectives especially for coastal areas As SWOT will be the first global survey of Earth's surface water, the hydrology community will see dramatic advancements in access to information and avenues for decision support.
Still, much remains to be accomplished. The pillars of this approach will include: • Outreach -stemming from the AVISO registered users' database gathering more than 6,000 people, as a tool for operational users to receive information about product parameters and availability. AVISO resources such as RSS feeds, newsletters, IOS/Android apps will be used to reach end-users, • Existing operational agencies; Mercator Ocean, MyOcean, • Support of downstream services development. The goals of the CNES along with the FIP are to: • Develop space applications for the water sector, • Develop services and technologies based on available data products, • Build on existing outreach resources, engage and inform stakeholders of SWOT capabilities, • Define a business model that includes cost reduction for value added products (required by FIP), • Standardize products and processing to meet user requirements.
Flood Forecasting So far, nadir altimetry applications for flood forecasting or river modeling have been reasonably successful and have provided good justification for the potential value of SWOT data in similar applications. A nadir altimetry (Jason-2) satellite-based flood forecasting system  (Hossain et al. , 2014)  that has been implemented in Bangladesh, accurately detected the monsoonal flood wave swelling from the north in the upstream Indian region of the Brahmaputra basin and tributaries during the 2014 flood season. Heavy rains engorged the Brahmaputra, Jamuna, and Teesta rivers in India and Bangladesh. Rushing waters disintegrated several flood control embankments. According to the Daily Star Newspaper of Bangladesh, over 3,500 families had already been displaced and many acres of crop fields were damaged (see servirglobal.
Insurance and Commerce Given the challenges associated with assessing flood hazards and risks for regions with limited in situ measurements, the SWOT mission will provide the insurance industry with a unique opportunity. Although, SWOT is not intended to sample instantaneous flooding conditions, the measurements provided from repeat overpasses will enable users to estimate local hydraulic controls. Relative to existing elevations from the Shuttle Radar Topography Mission (SRTM), the SWOT mission will provide both a range in water surface elevations (i. e. , repeat visits), as well as improved accuracy. SWOT-based river elevations will be used to estimate reference river elevations for improved localized hazard estimates. Although the SWOT mission is intended to advance our understanding of river hydrodynamics, the resulting data products represent a significant increase in complexity relative to SRTM.
The SWOT early adopter program will enable potential users to fully understand expected SWOT measurements, accuracies, uncertainties and data formats and develop applications to utilize the data prior to mission launch. Thus, users will be able to benefit from SWOT as soon as data products become available The commercial sector is driven by the need to define and address profitable markets for data products that can be provided by remote sensing systems. An assessment of market opportunities for altimetry products for use by commercial organizations will need to focus on areas that offer a demand for data products that is large enough to support a profitable business. Data product development and analysis capabilities need to provide information products that are not readily available by other technologies.
Marine Operations and Fisheries Marine operators such as marine transporters, commercial fishing vessels, oil companies with offshore production facilities, and recreational boaters, to name a few, will be able to use data from SWOT. The high-resolution information about ocean circulation and the finer scale resolution (10 to 200 km over the ocean) could be highly beneficial to optimizing their operations in both coastal and open ocean environments. Fisheries operations may also benefit from long term, regional observations of ocean conditions that may be provided from these data by observing and measuring physical properties of the ocean that influence fish habitats and migration. Altimetry data products, particularly the higher resolution SWOT products, can be combined with other sensor data (ocean color, wind measurements, ocean temperature, salinity) to provide critical information for support of good fisheries management practices, optimizing operations, safety at sea and more.
escape ASPERA-3 a b s t r a c t The Mars Express (MEX) Ion Mass Analyser (IMA) found that the detection rate of the ring-like distribution of protons in the solar wind outside of the bow shock to be quite different between Mars orbital summer (around perihelion) and orbital winter (around aphelion) for four Martian years, while the north-south asymmetry is much smaller than the perihelion-aphelion difference. Further analyses using eight years of MEX/IMA solar wind data between 2005 and 2012 has revealed that the detection frequency of the pick-up ions originating from newly ionized exospheric hydrogen with certain flux strongly correlates with the Sun-Mars distance, which changes approximately every two years. Variation due to the solar cycle phase is not distinguishable partly because this effect is masked by the seasonal variation under the MEX capability of plasma measurements.
, 2006) , and showed that the estimated exospheric temperature changed more drastically than the expected change from the EUV variation (see also  Chaufray et al. , 2009; Clarke et al. , 2014). Bertucci et al. (2013)  analyzed MGS magnetic field data during one year (from September 1997 to September 1998) and showed that proton cyclotron waves upstream of the bow shock (indication of generation of exospheric-origin cold protons) are observed most frequently during perihelion. However, no direct ion observations have been reported on the solar EUV dependency of the amount of ionized exospheric neutrals in the solar wind. Mars Express has over 10 years of observations at Mars, including ion mass analyzer (IMA) observations of the solar wind outside the bow shock. In this region, IMA is capable of observing the pick-up ions of exospheric origin  (Dubinin et al.
The low mass-resolution mode is best for detecting the low mass ions like H þ and He þ , while in the high mass-resolution mode, the solar wind protons are often completely deflected to outside the sensor area. Therefore, one may not mix IMA data taken during different mass-resolution modes for statistical studies. Note that light ions which are deflected outside the sensor area are reflected back from the outer wall of IMA, reaching the sensor in the central area of the MCP, and generating counts in the incorrect mass channels. MCPs that are used in many medium-energy (around 1 keV) ion sensors including IMA often degrade after long exposure to intense ion beams such as those from the solar wind and radiation belt (e. g. ,  Yamauchi et al. , 2013). However, the efficiency of MEX/ IMA has not degraded during more than 10 years of operation since the accumulated total count over 10 years was much lower than the specification for the IMA/MCP (In fact, the MCP bias voltage did not require adjusting in order to maintain sensitivity).
Therefore, all data collected during 2005-2012 (more than 10000 inbound or outbound traversals across the bow shock) may be treated equally. ASPERA-3 electrons are measured with Electron Spectrometer (ELS). With angular acceptance width of 4°, ELS covers an energy range from 0. 5 eV to 20 keV and is capable of helping identification of bow shock and foreshock, and hence confirming IMA observations of pick-up ions. Both IMA and ELS are top-hat instruments with 360°azimuthal field of view, divided into 16 sectors (0-15), each 22. 5°wide. Note that some reports that have used IMA data refer to different sector numbering (1-16), whereas this paper uses numbering of 0-15 (the same as  Yamauchi et al. , 2006 Yamauchi et al. , , 2011)). For details of the IMA and ELS instruments, see  Barabash et al.
1a ) does not give a hint of curvature in the spectrogram and therefore it is difficult to judge if these ions are pick-up ions, reflected solar wind, foreshock ions, or even the solar wind O 6 þ  (Yamauchi et al. , 2011, in press; Nilsson et al. , in press). The change in the intensity during these three consecutive traversals is apparently not due to the change in the IMF orientation. Thus, although MEX is not optimized for studying the pickup ions (explained in the following paragraph), IMA is capable of judging the appearance and disappearance of the pick-up ions even within a day. The restrictions in using the IMA data in detecting the pick-up ions are: (a) IMA often misses pick-up ions due to its limited fieldof-view (FOV); (b) protons can cleanly be detected only when their energy is above a certain value (above about 1-2 keV depending on the observation mode); (c) temporal resolution is as slow as 192 s (yet MEX/IMA spends sufficient time in the vicinity of the bow shock to obtain adequate spatial resolution as reported in previous studies  (Yamauchi et al.
, 2008 (Yamauchi et al. , , 2011 (Yamauchi et al. , , and 2012 )), and (d) the Mars Express payload does not contain a magnetometer (which is necessary to identify the anticipated direction and energy of the ions which gyrate around the local magnetic field direction). As a result, one cannot judge whether the absence of the ring distribution (signature of pick-up ions or reflected ions) is due to a physical process (they are really absent) or an artificial process (partial blockage of the FOV, too low an energy to be efficiently detected, frequent change in the IMF, or a non-optimal orientation of the magnetic field). Yet, in spite of the above restrictions, the quantity and quality of our dataset (same efficiency for 10 years) allows us to take a statistical approach in obtaining the variation in the occurrence frequency, although the values of probability are only approximate ones, for observing the pick-up ions.
2b  (lowest mass resolution mode that gives the highest counts for the same flux of the pick-up ions). Unfortunately, IMA was not  continuously operated under the lowest mass-separation mode, e. g. , with sometimes long data gaps. Therefore, the dataset from the medium mass resolution (pacc¼ 4) mode is primarily analyzed for both the automated method and manual method. In addition, the dataset from the lowest mass resolution (pacc ¼7) mode is also analyzed for the automated method to show the difference between these two modes. The medium mass-resolution (pacc¼ 4) mode is most frequently used during the entire mission. Yet, there are still data gaps (too little statistics, i. e. , less than 20 traversals per 2 months) in  2005, 2006, 2007, and 2011. In our previous studies using the manual method  (Yamauchi et al.
Results Fig. 2  shows the probability of observing the ring-like ion distribution (the pick-up ion occupies a ring that is centered at the solar wind velocity in velocity space) by using the automated method applied to dataset from (a) medium mass resolution (pacc ¼4) mode and (b) lowest mass resolution (pacc ¼7) mode. % Y MSO 2 + Z MSO 2 [R M ] pacc=7 pacc=4 X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] X MSO [R M ] Y MSO 2 + Z MSO 2 [R M ] Y MSO 2 + Z MSO 2 [R M ] Fig. 2. Probability of observing the ion distribution that is consistent with pick-up ions using the automated method  (Hara et al. , 2011 (Hara et al. , , 2013)) , that is applied to dataset from (a) medium mass resolution (pacc ¼ 4) mode, and (b) lowest mass resolution (pacc ¼ 7) mode.
Cylindrical coordinates are used, i. e. , vertical axis is distance from the Sun-Mars axis, and the data includes both hemispheres. Probability is calculated over four months during orbital summer ( 7 2 months from perihelion of Mars) and orbital winter ( 7 2 months from aphelion of Mars). Orbital summer and winter defined in this way (by the Sun-Mars distance) correspond closely to summer and winter in the southern hemisphere (the hemisphere with many magnetic anomalies), respectively. The data are arranged by the Mars season, i. e. , aphelion and perihelion, and presented using the Mars Solar Orbital (MSO) cylindrical coordinate system (i. e. , vertical axis of Fig. 2  represents the distance from the Sun-Mars line). As mentioned in the previous section, the lowest mass resolution mode detects the pick-up ions much easier than the medium mass resolution mode, but the number of data is insufficient for statistical studies.
1c , are displayed with orange bars. Some ring-like ion distributions are difficult to distinguish from reflected ions or foreshock ions like Fig. 1a , or are found only at one 192-s scan, and these difficult cases are marked as gray bars (difficult). We examined all data several times until the eye-identification converged to within a 5% difference between two examinations of the data. As is shown in Fig. 4a , there are data gaps particularly during a large part of 2006 (observation mode was not appropriate for detecting pick-up ions). In spite of this limitation, Fig. 4a  clearly shows the nearly two-year variation that synchronizes with the Sun-Mars distance indicated in Fig. 2. The obvious question then is how well does this change track changes in the EUV flux at Mars. Y MSO 2 + Z MSO 2 [R M ] pacc=4 X MSO [R M ] Fig.
Summary and discussion The eight-year data of MEX/IMA during 2005-2012 revealed that the occurrence rate of the pick-up ions varies with Sun-Mars distance, i. e. , sharply increases during the Martian orbital summer (around Mars perihelion). The variation thus appears to be mainly driven by the Sun-Mars distance rather than the season of the (southern) hemisphere that possesses large magnetic anomalies. This variation is dominant over the variation at a longer time scale that corresponds to the solar cycle, although MEX/IMA is not capable of judging whether or not the solar cycle effect is seen in the pick-up ion production. Furthermore, the same level of EUV flux, e. g. , between the orbital summer of the solar minimum (March-June 2009) and orbital winter of solar maximum (early 2012), results in different probabilities of detection of the pickup ions.
It should be noted that solid statistics using MEX data are not optimum for conducting plasma measurements of the type required for this study, particularly for the pick up ion distributions. Therefore, Figs. 2 3 4 give only the variation level of the dominant variation (seasonal effect) but not the absolute percentage of the occurrence rate or variation level of minor variations such as the solar cycle effect. The solid statistics will have to wait until the MAVEN spacecraft is able to obtain sufficient data to produce proper statistics. Yet, we can state some quantitative outcomes from Fig. 4a. First, in our manual method, the count threshold for clear cases (this is nearly proportional to the energy flux) is about 20 counts per 100 ms observation (cf. the noise level is 2 counts). Therefore, the ion distributions that are classified as "no pick-up ions" have at least one order of magnitude less energy flux (and hence ion density) than the "clear cases".
(Woods et al. , 1998) , and (c) daily sunspot number at the Earth as a proxy for the solar cycle. There are about 7500 solar wind (either inbound or outbound though the bow shock) traversals during 2005-2012 with the medium mass-resolution mode. Note that the total number of hours under a specific mass-resolution mode of IMA varies from time to time, and MEX is sometimes completely downstream of the bow shock for about one month. Therefore, taking monthly averages is not appropriate. However, data becomes rather smooth if two-month time intervals are integrated. Yet, some two-months periods have too few statistics  (in 2005, 2006, 2007, and 2011) , and two-month periods with less than 25 traversals are not shown. For the EUV flux estimation at Mars, the separation angle between the Earth and Mars is accounted for by time-shifting daily averaged measurements of the TIMES/SEE instrument  (Wood et al.
4a , there are few isolated detections of pick-up ions during orbital winter, e. g. ,  during 2008, 2010, and 2012. Quick changes in the intensity of the pick-up ions can occur within one orbit (7 h) as observed in the IMA data presented in the time series in Fig. 1. We are unable to study the reason for such appearances because of the lack of a magnetometer on MEX and limited FOV of IMA. This problem should be solved with full plasma measurements, such as that provided by the MAVEN spacecraft.