dataesr/scientific-paragraphs-categorization huggingface dataset:
All statistical analyses were conducted in SPSS version 22  (IBM Corp. , 2013). Statistical tests were two-tailed and the significance level was set at p<0. 05. Descriptive statistics were used to analyze the scope and sustainability of GenerationPMTO practice from the first to the last certified generation in each country. The first step in our analysis was to evaluate levels of fidelity by country across generations. Scores, along with means and standard deviations, are provided in Table  2  for the four certification sessions per candidate, including the mean FIMP score as well as scores for each of the five subcategories. Candidates were required to achieve a mean FIMP total score of 6. 0 or higher on each certification session. Across the three nations, candidates in all generations achieved scores at or above the required minimum.
(see Table  3 ). Although the fidelity scores did not differ significantly between generations (p=0. 298, d=2. 44), a visible trend was noticeable (Figure  1 ) suggesting a temporary drop in fidelity at G2 that sustained across later generations; the findings should therefore be viewed as partial evidence to support our second hypothesis. Our next step was to look at descriptive data by country, year and generation for professionals who completed the training program with certification, and those still practicing GenerationPMTO in their respective communities in 2016. Table  3  summarizes these data. As Table  3  indicates, data were available for six generations in Iceland, eight in Denmark, and four in the Netherlands. The total certification completion rates were 82-84% across the three nations, supporting the third hypothesis that each practitioner training cohort achieve 70% completion.
e. , 2012) and the longest interval between certifications was 4 years. This was different in the Netherlands where G2 was certified one year following G1; G3 and G4 were two years apart, and no new generations have completed training since 2012. According to the relevant national databases, the full transfer approach has led to continued practice in GenerationPMTO (PI Research, 2017 in the Netherlands;  Sigmarsdóttir, Gudmundsdóttir, & Frímannsdóttir, 2016 in Iceland; Socialstyrelsen, 2017 in Denmark). As shown in Table  3 , 78% certified therapists in Iceland were still active following certification in 2016 (Mean=4. 0 years; SD=3; range 1 to 14 years). In Denmark, 73% of certified practitioners were still active (Mean=3. 4; SD=2. 3; range 1-10 years). In the Netherlands, 64% were still active (Mean=7.
Discussion This paper presented findings from a naturalistic experiment in which GenerationPMTO, an evidence-based intervention developed in the USA, was implemented in three European countries: Iceland, Denmark, and the Netherlands. Data evaluated the full transfer approach to implementation in which the program developer/purveyor trains the first generation of practitioners (G1) and subsequent generations are trained by the adopting community (see  Forgatch et al. , 2013). The four hypotheses of this study were supported: (1) acceptable levels of fidelity (i. e. , FIMP scores of 6 or above) were sustained following previous reports that fidelity can be sustained following model transfer from the program purveyor to the adopting community  (Forgatch & DeGarmo, 2011). With regard to Hypothesis 1: Each generation in each nation achieved acceptable levels of fidelity at certification, replicating earlier findings  (Forgatch et al.
It should be noted that although Iceland dipped from the good work range into acceptable for G2, the difference for the total FIMP score was not statistically significant, most likely because of power issues. Several plausible interpretations can be offered for the pattern in which fidelity drops and then recovers. One involves a struggle/work-through phase in which the change process requires an adjustment period before the intervention effect is established, a process that has been observed in prior GenerationPMTO studies (see  Forgatch & DeGarmo, 1999; Stoolmiller, Duncan, Bank, & Patterson, 1993). In the present case, as sites assume responsibility for implementation activities, many challenges must be addressed. Material is translated from English to the local language and cultural adaptations are made to the materials including use of relevant metaphors and images, as recommended  (Domenech Rodríguez et al.
In the Netherlands, certifications took place on an annual or biannual basis during the The full transfer approach may be an antidote for the decay in effect sizes frequently found following the scaling up of implementations  (Weisz et al. , 2014). A study of the Norwegian implementation of GenerationPMTO failed to find such a scale-up penalty  (Tømmeraas & Ogden, 2017). The authors attributed the ongoing positive outcomes in part to the strong leadership within the local GenerationPMTO infrastructure and the support of Norwegian Center for Child Behavioral Development (NUBU), the national implementation research center. Although data in the present study do not directly address effect sizes in child outcomes, findings indicate that community sites using the full transfer approach, even with small resources, can sustain practitioner fidelity across multiple generations of trainings and even when relatively independent of the program developer.
Conclusions This study presents data evaluating the full transfer approach to implementation as carried out by the GenerationPMTO program. Practitioners were trained in the method in three European nations. In each case, the first generation of practitioners was trained by the developer or a program purveyor. Subsequent generations were trained by the adopting implementation site. Although in some cases, there was a significant short-term decline in fidelity, the scores recovered. These data indicate that the program can be turned over to an adopting community across nations and continents, given an effective community infrastructure that supports the program. The infrastructure includes a governing authority that maintains a team of trainers, coaches and reliable fidelity raters who are able to certify and recertify practitioners.
Results indicate that the full transfer implementation of GenerationPMTO can successfully be carried out in sites with varying levels of financial resources, different program structures, and population size. Successful implementation using the full transfer approach had been shown earlier in the resource rich country of Norway and is now shown in countries without the same level of resources and with differing governments. It is important to mention that sites with lower populations seemed to disseminate faster than sites with larger populations; nevertheless a steady increase of GenerationPMTO therapists was found in all three nations. It can be said that the full transfer approach saves funds over the long-run as sites operate independently, without needing to pay for long-term and sometimes costly supervision.
the Preparation Stage, for both community and purveyor teams. The community engages relevant stake holders, establishes a governing authority to be responsible for the project, gathers resources, and negotiates contracts; the purveyor provides information, assesses readiness, and prepares training and training materials specific to the implementation. Stage 2 is Early Adoption during which the two teams work together on matters such as managing logistics, adapting materials, training the G1 professionals, creating a database, and ensuring a smooth referral process. Stage 3 is the Implementation Phase when the purveyors conduct further training and families receive services, all while the community infrastructure develops and grows. In this phase community coaches, trainers and fidelity raters are trained.
GenerationPMTO governing authority inIceland is the Government Agency for Child Protection. Professionals from that department implement the program in Iceland. The department oversees several primary roles: (1) training, coaching and certification of new practitioners; (2) sustaining fidelity among certified practitioners with ongoing coaching and training; (3) conducting annual recertification based on FIMP ratings of video recordings of intervention sessions; (4) maintaining interrater reliability of the FIMP coding team; (5) designing, adapting, and updating professional and parental materials, and (6) maintaining the database and webpage. The relevant GenerationPMTO governing authorities in Denmark and the Netherlands provide services similar to those in Iceland. In Denmark, the government agency Socialstyrelsen under The Ministry of Social Affairs was responsible for the project through 2017, and today VIA University College has the governing authority.
Consequently, the base of the serial manipulator follows the movement of the 6-DOF parallel platform. The inertial navigation sensor is fixed on the upper surface of the platform to measure in real-time the orientation of the platform. The information collected by this sensor is transmitted to the real-time industrial computer through a USB data cable. The industrial computer and the manipulator controller are connected through another ethernet cable, thanks to which, the control instructions can be sent to the manipulator controller and the real-time status can be fed back to the computer. The features description of the ABB manipulator, the 6-DOF platform, and the inertial navigation sensor is summarized in Table  1. The ABB manipulator IRB 1600 is a 6-axis industrial manipulator produced by ABB Company.
Therefore, we combine its translational and rotational motions to simulate the movement of underwater vehicles in VSFOS, as illustrated in Figure  16. The INS (inertial navigation sensor) IG-500A is used to accurately measure the attitude angles of the VSFOS. Based on the MEMS (Microelectromechanical Systems) technology, the INS IG-500A can calculate the precise 3D direction data by 3 gyroscopes, 3 accelerometers, 3 magnetometers, and a thermometer. It is commonly used in automobile, aerospace, and other vessels. In our VSFOS, the INS IG-500A is used to measure the attitude angles of the 6-DOF parallel platform.
The sensor sticking to the upper moving base of the 6-DOF parallel platform can measure the attitude angles of the platform. The collected data will then be sent to the industrial computer through the serial port, after being filtered and analyzed. The attitude measurement information will be parsed out from the processed data. As illustrated in Figure  4 , the letter S refers to the processed data, and the letter T denotes the calculated homogeneous transformation matrix. Once the 6-DOF parallel platform starts moving, the manipulator ought to follow the motion. In order to make each joint of the manipulator moving to the target position smoothly, we need to plan carefully the reference joint trajectory for the mobile manipulator. Finally, the joint angles instructions newly generated will be sent to the controller through the network communication; meanwhile, the real-time status of the manipulator will be fed back to the industrial computer.
Serial Port Communication As shown in Figure  5 , the serial port communication unit is displayed at the bottom of the control software interface. To receive the collected data, we need to choose the proper port and bound rate. Then by clicking the "Open serial port" button, the software will parse the data and display it in the corresponding frame. For example, the "Angle data" frame tells the Euler angle of the platform relative to the base coordinate system as well as its linear velocity and angular acceleration; the "Angle initialization" button is set to define  the initial state of the sensor. The bottom right side of the interface is an Excel control, which can be used to display all the current data, as well as save and export it to an Excel file.  4  5  3      4  5  2    4    1  4  5    2   =    =    =   0  0  2  1  5  6  0  1  1  1  6  1  4.
Communication with the Robotic Manipulator For the ABB manipulator, a simulation and off-line programming software, RobotStudio, are provided by the manufacturer. Programming with RAPID language and downloading it to the manipulator controller are allowed by using the RobotStudio software. Indeed, this might be the simplest method to achieve the communication with the manipulator compared with other manual control methods. However, it is not suitable for the VSFOS, due to the high real-time control demands of the VSFOS. Therefore, getting rid of the traditional control method for the manipulator and breaking the communication blockade of this industrial manipulator are demanded. During our research and development of VSFOS, three methods have been tested to communicate with the manipulator controller, which are "read/write files", "socket communication", and "develop software using PC SDK"; detailed descriptions of these methods are presented in the following paragraph.
4. 1. Read/Write Files. Read/write files make use of files to transmit information between the industrial computer and the manipulator controller. At the computer side, a ". doc" file is edited with control instructions inside. Meanwhile, at the controller side, a RAPID program is edited to receive and parse control instructions. Similarly, the current status of the manipulator can be written in another file and then fed back to the industrial computer. To realize the "sending" function, we take advantage of RobotStudio software, thanks to which, the industrial computer can get the "write access" of the manipulator controller. Detailed description of this communication architecture is illustrated in Figure  7. The control variables of the manipulator, such as the "jointtarget" variables (joint angle) and the "robtarget" variables (position of TCP), are written in those files and then transmitted from the computer to the controller.
Socket Communication. This method ensures the communication function based on the client/server mode. The RobotStudio software installed on the industrial computer works as a client, and the manipulator controller connects to the industrial computer with an ethernet cable acting as a server. When the program starts, the client will first request for the "write access" from the server and then send motion instructions to the server periodically after obtaining the "write access". On the server's side, the controller will get these instructions to control the manipulator; meanwhile, real-time status of the manipulator will be fed back to the client; the specific process of the socket communication is illustrated in Figure  8. It is necessary to edit programs on both RobotStudio software and the controller if this method is applied to realize the real-time control of the manipulator.
Developing Software Using PC SDK. PC SDK (Software Development Kit ) allows end-users to add their own customized operator interfaces for the IRC5 controller. Hence, users can control the manipulator over a network from a tailored application on a PC. Furthermore, this application can be developed with any programming language in any development environment. In our case, we developed a control software application written in C Sharp language in Visual Studio compiling environment. This software makes use of the API functions provided by the ABB Company to get access to the manipulator controller very easily; the proposed solution is illustrated in Figure  9. The classes used to access to the manipulator controller functionality together make up the controller API, in which there are many functions that can be used to obtain or change the value of the control variables of the manipulator.
Simulation Scenario: Communication and Function Tests. In this simulation test, the control software and the Robot-Studio software are running on the same industrial computer. The RobotStudio software is used to build the manipulator model and create a virtual controller for IRB 1600. The default IP address of the virtual controller is "127. 0. 0. 1", and for distinction, we change its system ID to "manipulator-1". The control software can be connected to the manipulator by searching the on-line controllers. Once the virtual controller is found, the network connection will be established after confirming the IP address and the system ID. As shown in Figure  11 , when the communication bridge between the controller and the control software is built up, the button name will change from "Connect" to "Connected".
At the same time, a prompt box will pop up to inform the user of the connection status. Since the communication is unblocked, motion instructions can be sent to the controller. A particular geometrical path for the end-effector of the manipulator beforehand and the path function is expressed as follows. 𝑥 = 800 + 100 sin (2𝑡 + 5𝜋 6 ) 𝑦 = 100 cos (2𝑡 + 5𝜋 6 ) (200 ≤ 𝑡 < 300) (11) The corresponding trajectory is illustrated in Figure  12. In order to get a better observation of the simulation results, we tracked the actual trajectory of the TCP. This trajectory is able to be displayed on RobotStudio software in real-time, as illustrated in Figure  13. While conducting the simulation test, it can be seen from the RobotStudio software that the manipulator TCP moved along the designed path very accurately and quickly.
In addition, the actual end trajectory is quite similar to the designed one according to Figures  12  and 13. In order to demonstrate the network communication function of the control software, further analysis of the control result is necessary. Since the motion instructions are distributed to   the joint motors with a series of joint angles, it is intuitive to compare the planned joint angles to the actual joint angles. Therefore, we collect the planned joint angles data and the actual joint angles data which are recorded in the simulation test. The joint 2 and joint 3 with quick movement in the test are taken as an example. A time plot of these joint angles is presented in Figure  14 , and the time plot for the tracking error of the joint angles is displayed in Figure  15. From Figures  14  and 15 , it can be seen that the joint angles curves of the planned trajectory and the actual one are almost overlapping and the tracking errors of the joint angles of axis 2 and axis 3 are less than 0.
Conclusion and Future Work This paper mainly introduces a new virtual submerged floating operational system (VSFOS), which makes it faster and much sager to conduct underwater operational simulations. The hardware framework and software structure of VSFOS are introduced in detail. And two critical questions regarding the manipulator kinematics and the communication with the manipulator are highlighted. In the end, two experiments have been conducted to demonstrate the effectiveness of the proposed VSFOS. The developed control software and the RobotStudio modeling software are combined together to test the developed system hardware and software framework. The test results have shown that the end-effector of the manipulator can follow the desired trajectory with developed system framework. An underwater salvage simulation test is then conducted.
Acknowledgments This work is supported in part by the  National Natural Science Foundation of China  (Grant  91748113  and Grant  51579111 ), in part by the  National Key Research and Development Program of China  (Grant  2017YFB1302302 ), in part by the  Shenzhen Science and Technology Plan Project  (Grant  JCYJ201704I311305468 ), and in part by the  Research Fund from Science and Technology on Underwater Vehicle Technology  (Grant  SXJQR2017KFJJ06 ).
We use several lines of evidence to show that these aberration hubs represent important cancer-related factors. First, we show that aberration hubs can distinguish different cancers and can identify relevant proteins in different subtypes of breast cancer using data from The Cancer Genome Atlas (TCGA)  [16]. Next, we apply AbHAC to the International Cancer Genome Consortium (ICGC) Cancer Genomics of the Kidney (CAGEKID) data  [17]  for the clear cell subtype of renal cell carcinoma (ccRCC). We show that AbHAC can identify known activated molecular networks such as VEGF and Src pathways, but additionally uncovers new candidate factors. These include spleen tyrosine kinase (SYK), which we further validate as a key proliferation regulatory factor in renal cancer cells.
Then, for a particular cancer dataset, we calculated for each protein in the network the number of its direct interacting partners with and without abnormal genetic patterns (e. g. the number of interacting partners with genes identified as being significantly mutated) or abnormal expression patterns (differential expression between tumor and normal samples). As we are interested in the subset of proteins that have more abnormal partners than expected by chance, we calculated a p-value for each protein for the observed numbers of normal and abnormal partners using a one-sided Fisher's exact test (Figure  1 ). To correct for multiple testing, considering the complex dependencies in the protein interaction network and the resulting correlations among the p-values, we randomized the protein interaction network by permuting proteins that have similar number of interaction partners (see Methods and Supplementary Figure  1 ).
Aberration hubs are characteristics of tumor types To test whether the aberration hubs are associated with clinical or phenotypic variations, we applied AbHAC to TCGA breast cancer  [16]  and the ICGC clear cell renal cell carcinomas (ccRCC)  [17]  datasets (Supplementary Tables  1 2 3 4 5 6 7 8 ), and investigated the distribution of aberration hubs across these samples. We calculated AbHAC p-values for all proteins in patients with breast or renal cancer (see Methods for details), and performed principal component analysis (PCA) using these p-values. This analysis showed that "aberration hubs" are different between breast cancer and ccRCC, and can be used to clearly separate patients with different cancers (Figure  2a ). To confirm that this observation was not due to differences in the tissue of origin (kidney vs.
Aberration hubs in breast cancer Breast cancer is a heterogeneous disorder with different subtypes, each characterized by distinct molecular alterations and clinical behavior  [19]. The TCGA datasets provide comprehensive molecular landscapes of intrinsic subtypes as defined by PAM50 classifier  [20]. Using these datasets (Supplementary Tables  1 2 3 4 5 6 ), we applied our statistical approach to the data from the PAM50 subtypes of breast cancer to identify proteins that might be relevant for each subtype (see Methods for details). Our analysis identified 74 aberration hubs using different aberration categories in different PAM50 classes (False discovery rate (FDR) < 0. 05; Supplementary Table  9 ). To verify if any of the 74 proteins had previously been associated with breast cancer, we conducted a literature review using MeSHOP  [21]  with "Breast Neoplasms" as the MeSH term to count how often the proteins are reported to be implicated in breast cancer.
We found a total of 1294 reported proteins of which 39 were in our list. This represents 4. 7-fold enrichment of breast cancer-associated proteins among the identified aberration hubs compared to the background of other proteins in the interaction network (p = 6. 9 × 10 -11 , Fisher's exact test; Supplementary Table  9 ), supporting the efficacy of AbHAC to identify relevant molecules in a given cancer dataset. We further questioned if genes encoding any of these aberration hubs are among significantly mutated or abnormally expressed genes in breast cancer according to TCGA datasets. We observed that only one of these 74 molecules (CDKN1B) is significantly mutated in breast cancers, and that 50 of them are not differentially expressed at mRNA level in tumors (all together or at subtype-level) when compared to non-tumor control samples (Supplementary Table  9 ).