dataesr/scientific-paragraphs-categorization huggingface dataset:
Vision scientists are increasingly relying on the pointlight technique as a way to investigate the perception of human motion. Unfortunately, the lack of standardized stimulus sets has so far limited the use of this technique for studying social interaction. Here, we describe a new tool to study the interaction between two agents starting from point-light displays: the Communicative Interaction Database -5AFC format (CID-5). The CID-5 consists of 14 communicative and seven noncommunicative individual actions performed by two agents. Stimuli were constructed by combining motion capture techniques and 3-D animation software to provide precise control over the computer-generated actions. For each action stimulus, we provide coordinate files and movie files depicting the action as seen from four different perspectives.
Recent works have begun to explore perception of social interaction from biological motion in infants  (Galazka, Roché, Nystrom, & Falck-Ytter, 2014)  and pathological populations such as patients with autism spectrum disorder  (Centelles, Assaiante, Etchegoyhen, Bouvard, & Schmitz, 2013; von der Luhe et al. , submitted)  and schizophrenia  (Okruszek et al. , 2015). The exact characteristics and the neural substrate supporting interpersonal action coding, however, remain unclear. Although the point-light technique offers many advantages to researchers investigating perception of biological motion, the complexity of constructing stimuli depicting interacting pointlight agents has so far limited the use of this technique in studying social interactions. Indeed, while several databases exist for the study of individual actions from point-light displays  (Vanrie & Verfaillie, 2004; Ma, Paterson, & Pollick, 2006; Shipley & Brumberg, 2005) , only few stimulus sets are available for the study of the actions of interacting agents  (Manera et al.
, 2010; Zaini et al. , 2013). Zaini and colleagues  (Zaini, White, Fawcett, & Newman, 2013)  recently published a database of pointlight communicative hand gestures and non-communicative pantomimed hand actions. To the best of our knowledge, however, the only database to present two interacting agents, rather than just one, is the Communicative Interaction Database (CID;  Manera, Schouten, Becchio, Bara, & Verfaillie, 2010). The CID database contains 20 full-body communicative action sequences performed by two female and two male actors. Following  Dekeyser, Verfaillie, and Vanrie (2002) , stimuli were constructed by combining motion capture techniques and 3-D animation software to provide precise control over the computer-generated actions and allow the actions of the two agents to be independently manipulated.
In the present work, we describe the Communicative Interaction Database-5AFC format (CID-5), a new and updated version of the CID which addressed some limitations of the original CID (see Discussion section). The CID-5 consists of 14 communicative interactions selected from the CID the best recognized stimuli based on the normative data  (Manera et al. , 2010)  and seven non-communicative individual actions performed by two agents, not included in the CID. For each action stimulus, we provide coordinate files and movie files depicting the action as seen from four different perspectives. Furthermore, for each action stimulus, we provide five action alternatives, including the correct action description, two communicative and two non-communicative individual alternatives to be employed in forced-choice response paradigms.
In the following paragraphs we first describe the method used to construct the action stimuli and generate the response alternatives included in the 5AFC task, then we provide a detailed description of CID-5 database, including all the materials available for download. Finally, we provide normative data collected to assess the recognizability of the stimuli using the 5AFC format, and compare these results with those collected with an open-ended response format by  Manera et al. (2010).
Data processing After the capture session, the 2-D data from all the position units were processed offline to calculate the 3-D coordinates of the markers. The data from the markers were imported in Character Studio  (Autodesk, 1998) , a software package that was created for use with 3D Studio MAX  (Autodesk, 1997). This allowed us to animate a biped for each actor, consisting of a transparent skeleton and 13 bright dots attached to the center of the major joints (shoulders, elbows, wrists, hips, knees, and ankles) and the head. Next, 3-D coordinates for each of the 13 dots for all the frames constituting each actor's action were extracted, and some manual smoothing was performed to avoid any remaining Bjumpy^dot movements. To create the actual movie files, the smoothed data were imported into 3D Studio as moving bright spheres, and all the frames of the action were rendered as.
The CID-5 Database The database consists of a. rar archive that contains 21 folders, one folder for each of the actions listed in Table  1. Each action folder contains coordinate files and movie files depicting the action as seen from four different perspectives. Furthermore, the archive contains a text file with a list of the action alternatives provided for every action stimulus. The database can be retrieved from the supplementary materials of this article, or from the website of the Biology of Social Behavior Laboratory, University of Turin (http://bsb-lab. org/research/). Table  1  Description and features of the action stimuli included in the CID-5. Please note that according to the taxonomy of speech acts  (Searle, 1969 (Searle, , 1979)) , all the communicative (com) actions included in the CID-5 are classified as directive, meaning that the act of the communicator is intended to cause the responder to perform a certain action.
Actions A brief description of each action stimulus is reported in Table  1. For each stimulus, we report the stimulus classification (communicative vs. individual), a brief description of the actions of agent A and agent B, the stimulus duration (number of frames and milliseconds), the actors' gender, and the presence of (invisible) objects in the original scene. Furthermore, for the communicative stimuli, we also report the type of act  (Searle, 1969 (Searle, , 1979) )  and the social motivation, representing why an agent performs a specific communicative gesture (e. g. , sharing, requesting, asking for information;  Tomasello, Carpenter, & Liszkowski, 2007) , together with the original stimulus name in the CID database.
Participants One hundred and thirteen students from the Faculty of Psychology at the University of Turin (Italy) volunteered to take part in this study, and received course credits for their participation. Eighteen participants were excluded from data analysis due to missing responses, leaving the final sample to 95 participants (ten of them male and 85 female; mean age= 22. 9 years, SD= 5. 6, age range= 19-58). All the participants were naive as to the purpose of the study and had no previous experience with point-light displays.
Comparison between the CID and the CID-5 databases The main differences in the materials included in the CID database and the CID-5 database are summarized in Table  3. In order to investigate differences in action identification between the forced-choice paradigm employed in the CID-5 database and the open-ended response format employed in the CID database (where participants were asked to generate a description of each action stimulus, see  Manera et al. , 2010) , action identification accuracy for each action stimulus was submitted to separate chi-square tests, with Group (CID vs. CID-5) as the between-subjects factor. A Bonferroni correction was applied to adjust for multiple comparisons (α =. 05/21, =. 0023). The results revealed no significant difference between the open response format and the forced-choice format for 19 out of 21 action stimuli (χ 2 ranging from.
Discussion In the present paper we describe the CID-5, a database of 21 full-body point-light stimuli depicting two agents engaged in communicative interactions (N=14) or performing noncommunicative individual actions (N=7) as seen from different viewpoints. For each stimulus, we provided five plausible response alternatives (only one being correct), and we collected normative data on 95 naive participants to assess stimulus recognizability. Results confirm that stimuli included in the CID-5 are highly recognizable, thus suggesting that information contained in these point-light displays is sufficient to distinguish com municative i nt eractions from noncommunicative individual actions, and to recognize the specific communicative or individual actions performed by the agents. We are convinced that our stimulus set may represent a useful tool for researchers working on communication and social cognition, since an important factor in the advancement of those studies is the availability of suitable stimulus material.
In particular, the CID-5 has several advantages compared to the existing databases of communicative actions, such as the CID  (Manera et al. , 2010). First of all, the CID-5 contains communicative interactions and non-communicative individual actions directly comparable in terms of the method used for stimulus construction, stimulus format (size, distance between the actors, available viewpoints), and action duration. The presence of individual control stimuli is crucial to test whether human observers are able to discriminate between communicative and non-communicative action stimuli, i. e. , to test whether they are sensitive to interaction dynamics  (Manera et al. , 2011a; b; 2013). Furthermore, the presence of well-matched control stimuli represents a key advantage for studies aiming to investigate the neural correlates of social interaction  (Centelles et al.
An additional advantage of the forced-choice questions is that they decrease the number of missing responses, as the participant can be prompted to select one of the alternatives. Furthermore, the forced-choice can facilitate response scoring, a process that can sometimes be challenging with the open-response format, especially when employing visually degraded stimuli (such as point-light animations) representing complex human actions. Third, we reported normative data collected on a large sample of participants (N=95), specifying not only the percentage of correct responses for each action stimulus, but also the percentage of participants that selected each of the incorrect response alternatives. These data may be used as a guideline by researchers interested in creating easier or more challenging versions of the task.
Limitations and future research directions Despite the important advantages of the CID-5 compared to the existing databases of communicative actions, some limitations should be noted. First of all, the CID-5 contains a limited number of non-communicative individual stimuli (N=7). This may represent a problem for studies needing to employ a larger number of stimuli (e. g. , neuroimaging studies). However, it should be noted that in the CID-5 we also provided listings of the 3-D coordinates of the point lights for each stimulus and for each actor. This allows researchers to create different non-communicative individual stimuli by combining different actions performed by agent B (the respondent in the communicative interactions). Another limitation lies in the paradigm employed for the collection of normative data assessing stimulus recognizability.
, 2006; Jiang et al. , 2007; Secco et al. , 2013a). Pi concentration measurements revealed that 3 days of -Pi led to a threefold reduction in root Pi concentration, while 21 days -Pi resulted in a 6 fold decrease in root Pi concentration compared to plants continuously grown under Pi sufficient conditions (Figure  1C ). Resupplying Pi for 1 day was sufficient to increase the root Pi concentration >4 fold compared to plants grown under Pi deficient conditions, and within 3 days of Pi resupply the root Pi concentration was similar to that of plants continuously grown under Pi sufficient conditions. To investigate the transcriptional responses to Pi starvation and resupply, RNA sequencing (RNA-seq) was performed on root samples from all time points, using three biological replicates per condition (Figure  1 -source data 1, available at Dryad,  Secco et al.
, 2015). Hierarchical clustering of the steady state transcript abundance of the 5570 genes identified as significantly differentially expressed (Cuffdiff, FDR < 0. 05) in at least one of the time points revealed a gradual increase in the number and fold change of differentially expressed genes upon -Pi, associated with the length of the Pi deprivation (Figure  1D, E ; Figure  1 -source data 1, available at Dryad,  Secco et al. , 2015). Of note, several phosphate starvation-induced (PSI) marker genes, including the SPX genes, MGD2 and PTs, were already induced and showed high steady state transcript abundance after only 3 days of Pi deprivation (Figure  1 -source data 1, available at Dryad,  Secco et al. , 2015). Surprisingly, 52 days of Pi deprivation was associated with a decrease in the number and extent of significantly differentially abundant transcripts, including most of the PSI marker genes, potentially due to the concurrent occurrence of panicle development and grain filling.
01) in at least 7 of the 9 samples in each of the conditions were considered for further analysis,   (Secco et al. , 2015). DOI: 10. 7554/eLife. 09343. 003 The following figure supplement is available for figure  1 : resulting in the identification of 175 high confidence root PSI DMRs (Figure  2 -source data 1, available at Dryad,  Secco et al. , 2015). Among these 175 PSI DMRs, 84% were hypermethylated in response to Pi starvation (147 hypermethylated, 28 hypomethylated regions, Figure  2A ). As observed for  transcript abundance, 3 and 7 days of Pi deprivation resulted in fewer changes in DNA methylation levels, which increased with the duration of the Pi starvation. Indeed, hierarchical clustering of the 45 root samples based on their CNN methylation levels in the 175 PSI DMRs revealed two main clusters, with cluster 1 containing all +Pi samples as well as the 3 and 7 days -Pi samples, and cluster 2 comprising all longterm -Pi time points (≥21 days) in addition to the Pi re-supplied samples (Figure  2 -figure supplement 1).
In addition, RNA-seq analysis failed to reveal any significantly differentially expressed TEs (Cuffdiff, FDR < 0. 05) that overlapped with PSI DMRs, between Pi sufficient and deficient conditions (7 and 21 days), with more than 80% of them not being expressed (Figure  2 -source data 2, available at Dryad,  Secco et al. , 2015). Next, each of the 175 PSI DMRs were assigned to the nearest gene, resulting in the association of 126 unique genes with PSI DMRs (Figure  2 -source data 1, available at Dryad,  Secco et al. , 2015). Gene transcript abundance analyses revealed that 66 of these DMR-associated genes (52%) were differentially expressed by >2 fold (FDR < 0. 05) in response to 21 days -Pi (Figure  2D ). The steady state transcript abundance of 35% of the 126 genes was >4 fold higher following 21 days Pi starvation.
Firstly, changes in shoot methylation levels were assessed at the 175 PSI DMRs identified in the roots (Figure  2A , Figure  2 -source data 1, available at Dryad,  Secco et al. , 2015) , revealing similar changes in DNA methylation levels in response to Pi starvation in both roots and shoots, though to a lesser extent in the shoots. Secondly, shoot methylomes under Pi-sufficient and deficient conditions were analysed in order to identify shoot PSI DMRs. Due to the lower number of replicates used to identify shoot PSI DMRs (n = 3) compared to the root PSI DMRs (n = 9), a less stringent FDR cut-off of < 0. 05 was selected for further analysis, resulting in the identification of 341 shoot PSI DMRs (FDR < 0. 05) (Figure  2 -source data 3, available at Dryad,  Secco et al. , 2015). Assigning the 341 shoot PSI DMRs to the nearest genes identified 43 distinct genes that were significantly differentially regulated by Pi starvation in the shoots (Figure  2 -figure supplement 5).
Pi starvation induced DMRs are mostly hypermethylated in the CHH context To further examine the potential role of the PSI DMRs, only DMRs that were associated with significant changes in nearby gene transcript abundance following long-term Pi starvation were considered for downstream analysis. Among the 175 root PSI DMRs identified, 100 PSI DMRs were close to genes showing significant changes (FDR < 0. 05) in gene transcription upon long term Pi starvation, corresponding to 66 unique genes (Figure  3A , Figure  2 -source data 1, available at Dryad,  Secco et al. , 2015). Notably, 63 (95%) of these DMR-associated genes were induced by Pi starvation, and included key regulators of Pi homeostasis such as Pi transporters (PT3, PT4, PT9, PT10), SPX genes (SPX1, SPX2, SPX3, SPX5), MGD2, IPS1 and pre-miR827.
Changes in gene transcription occur prior to changes in DNA methylation The detailed time course analysed in this study provides the unique opportunity to decipher the temporal hierarchy between changes in transcription and changes in DNA methylation, which is critical to shed light on the potential causative relationships between the two, and the potential role of the PSI DMRs. The average changes in CNN methylation levels in the PSI DMRs in response to Pi stress were compared to the associated changes in nearby gene steady state transcript abundance (Figure  3B , Figure  3 -figure supplement 1, Figure  2 -source data 1, available at Dryad,  Secco et al. , 2015). After 3 and 7 days of Pi starvation, 18% and 55% of the PSI DMR associated genes, respectively, showed significant changes in transcript abundance (Cuffdiff, FDR < 0.
05), while only 5% and 9% of the 100 PSI DMRs showed significant changes in DNA methylation compared to +Pi samples (t-test, FDR < 0. 05) (Figure  3B , Figure  3 -figure supplement 1, Figure  3 -source data 1, available at Dryad,  Secco et al. , 2015). Long term Pi deprivation (≥21 days -Pi) was sufficient to induce significant changes in both gene transcript abundance and DNA methylation levels, with all PSI DMRs being significantly differentially methylated after 24 days of -Pi compared to +Pi (t-test, FDR < 0. 05). Furthermore, while resupplying Pi starved plants with Pi for 3 days resulted in 87% of the DMR associated genes differentially expressed upon Pi starvation to return to Pi sufficient-like levels, 94% of PSI DMRs still showed significant differences in DNA methylation levels compared to +Pi conditions (t-test, FDR < 0.
However, resupplying Pi for 31 days resulted in 96 of the 175 PSI DMRs showing more than a 2 fold reduction in the differential DNA methylation levels induced by 52 days -Pi, when compared to +Pi, suggesting that the majority of PSI DMRs are returning towards Pi sufficient levels after 31 days of Pi resupply (Figure  4 -figure supplement 1). Indeed, only 14 of the 175 PSI DMRs (11 hypermethylated, 3 hypomethylated) showed significant differences in DNA methylation level (CNN) between 52 days +Pi compared to 52 days resupply (t-test, FDR < 0. 05), while not presenting significant differences between 52 days -Pi vs 52 days resupply (t-test, FDR > 0. 05), suggesting that changes in DNA methylation persist in only a limited subset of these PSI DMRs after 31 days of Pi resupply (Figure  4A , Figure  4 -source data 1, available at Dryad,  Secco et al.
Generation of high coverage methylomes enabled the identification of 36 PSI DMRs in the panicles of plants grown for 52 days in +Pi and -Pi (FDR < 0. 05). However, no significant differences (t-test, FDR < 0. 05) could be observed in the DNA methylation levels of these 36 regions between panicles of plants grown for 52 days in -Pi compared to those resupplied with Pi for 31 days (Figure  4B , Figure  4 -source data 2, available at Dryad,  Secco et al. , 2015). Yet, using a less stringent FDR cutoff of < 0. 1, two of the 36 PSI DMRs identified in the panicles, including SPX2_DMR2, showed persisting differences in DNA methylation despite 31 days of Pi resupply, suggesting that a limited number of PSI DMRs could potentially be transmitted to newly generated tissue that has never experienced the stress.
We next tested whether PSI DMRs could be transmitted from Pi stressed plants to their progeny, and thus potentially act as a transgenerational stress memory mechanism. To do so, individual seeds from five individual plants continuously grown under Pi sufficient or deficient conditions were harvested, and subsequently germinated and grown for 10 days under Pi sufficient conditions (Figure  1A ), before performing whole genome bisulfite sequencing on the corresponding root genomic DNA (n = 5 for each condition, Supplementary file 1). Analysis of the methylation levels in the progeny of stressed and nonstressed parents in the 175 root PSI DMRs that were identified in the first generation of plants failed to identify any significant differences in DNA methylation levels (t-test, FDR < 0. 05) (Figure  4C, D, E , Figure  4 -figure supplement 2, Figure  4 -source data 3, available at Dryad,  Secco et al.
, 2014). In this study, WT and DCL3a RNAi plants were grown as previously described (Figure  1A ) and subjected to 21 days of Pi sufficient or deficient conditions, before performing RNAseq and whole genome bisulfite sequencing on the root tissues. RNA-seq analysis (n = 3) confirmed that DCL3a was the most abundant DCL3 family member in the roots, with 11 times higher steady state transcript abundance than DCL3b under Pi sufficient conditions (Figure  5 -figure supplement 1A; Figure  5 -source data1, available at Dryad,  Secco et al. , 2015). In the DCL3a RNAi line, the transcript abundance of DCL3a decreased by 4. 6 and 3. 3 fold compared to WT in Pi sufficient or deficient conditions, respectively, while the abundance of DCL3b transcript was unaffected (Figure  5 -figure supplement 1A,B, Figure  5 -source data1, available at Dryad,  Secco et al.
, 2015). In +Pi conditions, the reduced transcription of DCL3a was accompanied by widespread changes in DNA methylation, significantly altering DNA methylation levels in 9379 regions in the genome (6694 hypo-and 2685 hypermethylated regions in DCL3a RNAi line compared to WT; FDR < 0. 05), in addition to 3531 genes displaying a significant change in transcript abundance (Cuffdiff, FDR < 0. 05) compared to WT +Pi (Figure  5A , Figure  5 -figure supplement 1B). Similar results were also observed between WT and DCL3a RNAi plants under Pi deficient conditions, with 8164 DMRs and 1791 differentially expressed genes identified (Figure  5A , Figure  5 -figure supplement 1C, Figure  5 -source data 1, available at Dryad,  Secco et al. , 2015). Analysis of the DMRs induced in DCL3a RNAi plants revealed that the majority of changes in DNA methylation occurred in the CG and CHG contexts, under both Pi sufficient and deficient conditions (Figure  5 -figure  supplement 1D, E, F, G ).
Among the 175 PSI DMRs identified previously (Figure  2A ), only 8 and 5 regions also showed significant differences in DNA methylation between WT and DCL3a plants under Pi sufficient and deficient conditions, respectively, and corresponded to 11 unique PSI DMRs (8 unique associated genes) (Figure  5A ,B,C, D; Figure  5 -source data 2, available at Dryad,  Secco et al. , 2015). These 11 DMRs corresponded to 7 and 4 regions previously identified as hypo-and hypermethylated in response to -Pi in WT, respectively (Figure  2A ). Of the 4 hypermethylated PSI DMRs altered in the DCL3a RNAi plants, only one was associated with significant changes in nearby gene transcript abundance in response to -Pi in WT, while all the hypomethylated PSI DMR associated genes were significantly differentially regulated by -Pi in WT (Figure  5 -source data 2, available at Dryad,  Secco et al.