However, some primary bundles are still only partially reconstructed, or not reconstructed at all. The acoustic radiation (AR) represents a primary sensory pathway that has been largely omitted in many tractography studies because its location and anatomical features make it challenging to reconstruct. In this study, we investigated the effects of acquisition and tractography parameters on the AR reconstruction using publicly available Human Connectome Project data. The aims of this study are: (i) using a subgroup of subjects and a reference AR for each subject, define an optimum set of parameters for AR reconstruction, and (ii) use the optimum parameters set on the full group to build a tractography-based atlas of the AR. Starting from the same data, the use of different acquisition and tractography parameters lead to very different AR reconstructions. Optimal results in terms of topographical accuracy and correspondence to the reference were obtained for probabilistic tractography, high b-values and default tractography parameters: these parameters were used to build an AR probabilistic tractography atlas. A significant left-hemispheric lateralization was found in the AR reconstruction of the 34 subjects.Diffusion MRI tractography allows  Since the introduction of the diffusion MRI tensor model1, one of its major applications has been the localization and description of white matter fibre bundles in the brain3. Most of these well-known bundles correspond to the associative fibre pathways that, coursing the longitudinal plane, connect different cortical regions of the brain. However, these major bundles represent the brain’s “highways” and constitute only a partial sample of all the white matter connections, the full architecture of which is sensitively more complex and unknown.Diffusion-based MRI tractography allows 4. However, some primary bundles are still only partially reconstructed, or not reconstructed at all5. The acoustic radiation (AR) represents an example of such an omission in tractography studies. This bundle constitutes a primary sensory pathway conveying auditory information from the medial geniculate nucleus (MGN) of the thalamus to the auditory cortex on the transverse temporal gyrus of Heschl (HG)7. Because of its anatomical features, the AR goes undetected when using the diffusion tensor model8. In a previous human brain post-mortem dissection study from our group9 we showed that the AR fibres are characterized by a fully transversal course from the mid-line to the cortex, along which they cross some of the major fibre systems of the brain. This topographical feature, with its severe fibre crossing, has largely prevented the investigation of its anatomy in humans in-vivo. At present, most studies investigating the correlation between auditory pathways and auditory deficits employ region of interest (ROI) analyses10; however ROI-based analyses lack anatomical specificity and do not cover the whole extent of the pathway of interest. Tractography studies investigating language comprehension networks haven’t included the AR; however this primary sensory bundle is responsible of inputting the auditory information into the system and it is probably involved in the first steps of language processing11. The successful and reliable in-vivo reconstruction of this bundle using diffusion-based tractography techniques may allow for the exploration of the morphology and topography of these fibres in humans, and for the correlation with anatomical and functional aspects of audition and language.The introduction of more advanced multi-fibre-based diffusion models has helped improving the topographical knowledge of these and other main white matter pathwayspost-mortem Klinger’s dissections can be obtained in-vivo9. However, acquiring such high quality diffusion MRI data can be challenging, in particular with the constrains of typical clinical settings, which are commonly consistent with single shell, lower b-values MRI diffusion acquisition protocols. It is therefore important to understand how single b-value MRI acquisition and tractography analysis choices affect the reconstruction of the AR.The combination of ultra-high b-values and probabilistic tractography showed that results comparable to 13, spatial resolution12, tractography algorithm14, and tractography parameters19 affects the reconstruction of well known white matter tracts. However, as no one-for-all solution exists in diffusion tractography, the optimal parameters depend on the specific bundle under investigation. It remains thus unclear how these parameters affect the tractography reconstruction of the AR.The final result of any MRI-derived tractography reconstruction intimately depends on both the acquisition and the tractography parameters. Different studies have investigated how changing analysis parameters, such as angular resolutionIn this study, we systematically investigated the effects of MRI acquisition and tractography parameters on the diffusion-based tractography reconstruction of the AR using data publicly available from the MGH-USC Human Connectome Project. The main aims of this study are: i) using a subgroup of subjects and a reference AR for each subject, define an optimum set of MRI acquisition and tractography parameters for the reconstruction of the AR by systematically characterizing AR reconstruction effects as function of several parameters , and ii) use the optimum parameter set on the full group of subjects to characterize the AR and build a tractography-based atlas of the AR.b = 1,000; 3,000; 5,000; 10,000 s/mm2), the tractography algorithm (probabilistic versus deterministic), and the tractography parameters (angle threshold and step size) . We found that the choice of parameters notably affected the AR reconstructions. Figures In a subgroup of 5 subjects we first evaluated how tractography reconstructions of the acoustic radiation (AR) were affected by the choice of the MRI shell (s/mm2) and default parameters, the deterministic reconstruction provided almost no AR streamlines in all 5 subjects. On the contrary, the probabilistic methods resulted in a great amount of streamlines reconstructed between the thalamus and the Heschl’s gyrus (HG)  deterministic reconstructions increasingly provided more AR streamlines, and probabilistic reconstructions showed less false positive streamlines on the vertical plane. At the highest b-value , the AR reconstructions of probabilistic and deterministic methods tend to converge to similar anatomical representations .s/mm2, for angle = 20° the overlap coefficient is very close to the reconstruction of the AR at high b-values  were found only for deterministic tractography, for acquisition parameters (p = 0.0127) and angle threshold (p = 0.0327).For each algorithm (probabilistic and deterministic) we used a non-parametric Kruskall-Wallis test to evaluate whether varying b-value, step size, and angle threshold affected the spatial overlap of the tractograms with the reference AR. Significant effects , for which the deterministic algorithm could not reconstruct any or only very few streamlines. Consistently, significant effects in the accuracy of AR reconstruction in comparison to the reference AR were found only for deterministic algorithms, for shell and angle threshold (respectively p = 0.0127 and p = 0.0327). Step size had minor effects on the AR reconstruction .Based on the optimization results, we chose the following parameters to reconstruct the AR from the entire dataset (34 subjects): probabilistic tractography algorithm, b-values = 10,000 CV, the standard deviation divided the mean) as measured for the left (LH) and right (RH) brain hemispheres for the extracted tracts’ volume  and number of streamlines (CV:LH = RH = 0.93). Fractional anisotropy (FA) and apparent fibre density (AFD) mean values were also extracted for each reconstructed AR. FA values were very low for all subjects (<0.3), and showed less group variability , whereas AFD showed considerable variability across the group .The AR was successfully reconstructed in most of the subjects, correctly following macro-anatomical landmarks and showing a low number of false positive reconstructions. Streamlines correctly leave the postero-lateral part of the thalamus and move first in a lateral and then antero-lateral direction, to terminate in HG. We observed no streamlines erroneously following the inferior-superior direction of the external capsule fibres. However, we still observed high variability across subjects: two subjects showed no reconstructed streamlines in the right hemisphere, and in 6 subjects only few streamlines were visible in one hemisphere. This was confirmed by the coefficient of variability (α = 0.01) degree of left lateralization for AFD (p = 4.89E-05), volume (p = 0.0012), and number of streamlines (p = 5.80E-05). FA values show a bilateral distribution in almost all subjects (31/34) (p = 0.014). Overall, only two subjects showed a degree of right lateralization  in each subject. Results of the Wilcoxon signed-rank showed a significant α = 0.0 degree oRho = 0.34, p = 0.043).In order to exclude that the lateralization pattern in AR volume was driven by the volume of the ROIs used in the tractography reconstruction, we measured the Spearman correlation coefficient between the AR volume lateralization index and the HG and thalamus volume lateralization index. Results show no significant correlation for the AR and thalamus volumes  or AR and HG volumes , that was left lateralized (LI > 0.2) in 13/34 subjects, and bilateral in 21/34 subjects. In none of the subjects the AF was right lateralized. However Spearman’s correlation coefficient between AR and AF lateralization indices did not result significant .Given the possible implication of the AR in speech comprehension processing, and the association between language and the left hemisphere, we also investigated the correlation between the AR volume and the volume of the arcuate fasciculus (AF). The AF was virtually dissected in each subject and Wilcoxon signed-rank results showed a significant difference in volume across the two hemispheres . While showing good overlap at the thalamus origin of the bundle, the atlases diverge most near to the cortical termination of the AR in the Heschl’s gyrus.As a last step, we built a probabilistic tractography AR atlas in MNI space using the tractography reconstructions from the 34 subjects  and more DW directions (≥128) increase the accuracy of the AR reconstruction for both probabilistic and deterministic tractography; (ii) only probabilistic tractography can reconstruct the AR at low b-values (≤3000 s/mm2); (iii) the AR reconstruction remains challenging and highly variable across subjects; and (iv) the AR volume was found to be predominantly left lateralized. Additionally, we built a probabilistic tractography-based atlas of the AR reconstructed from 34 healthy subjects which we make open access (https://neurovault.org/).We investigated the effect that different diffusion MRI acquisition and tractography parameters have on the final 3D reconstruction of this bundle. The main findings of the study are: (i) higher b-values , tractography algorithm (probabilistic and deterministic), and tractography parameters (angle threshold and step size) differently affected the sensitivity and specificity of AR tractography results. Previous studies investigated the dependence of tractography outcomes on user-defined parameters22. This has great impact on the AR, being a relatively small pathway, compared to other white matter bundles, that crosses major projection systems  at an almost orthogonal angle. This results in an under-representation of its signal in the diffusion data and consequent small volume fractions in the reconstructed FODs. For low b-values , no, or only a few (<5), streamlines were reconstructed using the deterministic approach. For higher b-values , more streamlines belonging to the AR could be reconstructed. However, their anatomical accuracy remained lower than probabilistic results. Visual inspection of tractograms suggests there may be false positive reconstructions at the level of the thalamus, that are not present in probabilistic counterparts .The major effect in AR reconstruction accuracy is given by the higher b-value, for both probabilistic and deterministic tractography. This is most likely due to the higher angular resolution that can be achieved at higher b-values and allows to better resolve crossing configurations inside the voxelOverall, deterministic results were found to be less robust than probabilistic results relative to the parameters used. We believe this is related to the very nature of the algorithm. At every voxel, the deterministic algorithm follows the direction of the extracted maxima of that FOD lobe. This makes the algorithm extremely sensitive to parameters that affect the estimation of the main peak (acquisition parameters) or the propagation along that direction (tractography parameters). Probabilistic tractography however draws samples from the distribution of directions around the main peak, treating the ODF as if it were a probability mass function. This inherently introduces a higher degree of tolerance, given the diminished dependency on the FOD maxima. Accordingly, significant effects in the Dice coefficient were shown for the b-value and angle threshold only for deterministic reconstructions.b = 10,000 s/mm2 data using the default tractography parameters . Increasing the angle at high b-values only increased the false positive reconstructions and decreased anatomical accuracy, as previously shown15. The effects of increasing the step size were almost negligible  and deterministic tractography results were improved by increasing the angle threshold up to 60°. Conversely, for low b-values and probabilistic tractography, results could be improved when small angle thresholds were used in the reconstruction (20°), obtaining results comparable to high b-values in terms of anatomical accuracy  and the MGN, are subject to extreme anatomical variability across individuals and hemispheres, both in location and size7. The HG is characterized by very different configurations across subjects, and even across hemispheres27: narrower and smaller configurations might make the tractography reconstruction more challenging. Further studies might investigate the relationship between HG anatomical configurations and AR reconstructions.The reconstructions of the AR using the optimal parameters showed a high level of inter-subject variability. For example, the number of reconstructed streamlines ranged from 0 to 631, and the tract volume from 0 to 6834 25. However, FA values were overall very low (min 0.17–max 0.32), even lower than previous studies looking at FA values in the AR8, and lower than what it is usually considered to be the threshold to differentiate grey and white matter (0.2). This is most likely related to the dense fibre crossing of this region. This poses limits on the possible uses of this metric to evaluate this specific white matter bundle, and makes the implementation of more advanced quantitative measures necessary29. In this study we also evaluate the AFD of the AR, as implemented in MRtrix3. Similarly to tract volume, AFD showed high variability across subjects. This measures has been recently introduced30 and used in clinical populations31. However, at this point we cannot put our AFD findings in perspective with the literature because to the best of our knowledge no studies have investigated AFD variability across subjects and white matter bundles.The group variability of metrics derived from the AR was lower for FA values, in agreement with previous studiespost-mortem brains7. The small number of subjects we analysed in this work limits the certainty of the results. More studies investigating this asymmetry in different populations, and using different methods are needed. Even if we did not find a significant correlation in hemispheric lateralization between the arcuate fasciculus and the AR, our findings open interesting avenues for investigating the well-known relationship between the left hemisphere and language processing33.Significant hemispheric difference was found in the AR reconstruction of the 34 subjects, showing a strong left lateralization Table . These r20 showed spatial overlap discrepancies, especially at the termination site on the HG. This difference was more evident when comparing our atlas with the tractography based atlas from Yeh et al. For both atlases the higher overlap is shown in the first part of the bundle, at its stemming from the thalamus. Further studies are needed to understand whether this difference is due to anatomical variability in the AR or to the different methodologies used and their possible limitations. As in all diffusion MRI tractography studies, the results obtained in this study are restricted to the parameters used for MRI acquisition, diffusion modelling and tractography reconstruction. Different acquisition protocols, low level models, tractography parameters, and region of interests, could lead to different findings. In this study, for example, we did not investigate the effects of MRI spatial resolution (kept at 1.5 mm isotropic), which may affect tract reconstruction and diffusion metrics estimation35. However, previous studies showed that varying spatial resolution, up to certain limits (<2.5 mm isotropic), did not affect tractography reconstructions as much as changes in angular resolution36. Also, we did not specifically address whether it was the number of DW directions or the b-value that affected the reconstruction the most. Given that optimal angular resolution might be obtained by a combination of the two, it is possible that the same results are obtainable for lower b-values and more DW directions37. Our findings suggest that anatomical reconstructions of the AR are more accurate when using the high b-values of the HCP data. The acquisition of such high b-values has well known challenges in terms of SNR. These may be at least partially addressed by the technological advances that make possible the use of stronger and faster magnetic field gradients in new generation MRI systems, such as those used by the Human Connectome38. Further experiments are needed to evaluate the degree to which atlases constructed from HCP data may used to drive the reconstructions of tractograms derived from diffusion MRI data acquired with less performing gradients. In this study the accuracy of the tractography reconstructions was evaluated by comparing them to subject’s specific AR references computed in a previous study9 and manually filtered to eliminate false positive artefacts. This allowed us to evaluate the results on an anatomical qualitative and quantitative basis: increased number of streamlines, or increased volume, most often are weakly related to the anatomical accuracy of the reconstruction. However, our reference had clear limitations. Being tractography-based itself, it suffers from the same limitations of the other reconstructions. The manual filtering was aimed at eliminating most false positive of the reconstruction. However, false negatives in the initial reconstruction may bias comparison with the other tractograms. Moreover, these references were reconstructed using probabilistic tractography, which might have favoured probabilistic tractograms in the comparison. Future studies might improve the quality of this comparison, using references obtained with different methods, such as more advanced post-mortem validation techniques39.The comparison between the AR probabilistic atlas constructed in this study and two publicly available AR atlases40. However, those studies used the Dice coefficient to quantify test-retest reproducibility of the same tract over two different scans, thus making the comparison with our study not straightforward. In a previous human brain post-mortem dissection study, we defined three sub-components of the AR bundle: the genu, the stem, and the fan9. Future steps of this study will include applying this knowledge on the reconstructed AR, by isolating the AR stem. Previous studies have shown that performing tractography from the stem improves the final tractography reconstruction, by minimizing the constrained posed by cortical terminations41. We think this might help on different fronts in the tractography reconstruction of the AR: we would avoid seeding from the thalamus, which is well-known to be challenging in tractography15 and we might increase the number of streamlines that successfully reach the cortex on HG, given that the AR stem is lateral to the intermingling fibres of the internal capsule.The Dice scores obtained in the study were overall low, and lower than other reports on different tractsex-vivo dissection study from our group9. The optimized reconstruction parameters for the acoustic radiation and the atlas may be used in future studies interested in identifying and characterizing the acoustic radiation both in health and in disease. The in-vivo reconstruction of this bundle would help understanding its involvement in cognitive deficit related to music and language processing, and in more general hearing disorders. Congenital and early deafness studies have shown differences in grey and white matter regions of the auditory system43, but to the best of our knowledge, no specific study on the AR in deaf subjects has been conducted to date. Furthermore, considering the evolution of brain surgery towards functional tailored resections, successful AR tractography reconstruction can be crucial for surgical planning44, in cases of temporal lobe resection, or even pre-operative assessments for cochlear implantation45.This study presents the first human tractography atlas of the acoustic radiation from a population of 34 young healthy subjects. The atlas was constructed using high quality MRI data from the Human Connectome Project. The acoustic radiation reconstruction was optimized with a systematic evaluation of MRI acquisition and analysis parameters using as reference reconstructions validated from an 9 we investigated the human AR morphology by comparing post-mortem micro-dissections and AR tractography reconstructions using a subset of the same dataset and default Mrtrix tractography parameters. That study raised the question of whether an optimal set of tractography parameters would exist for AR reconstruction and how this would change for different acquisition parameters. In this study a subgroup of 5 subjects is used to investigate the effects of MRI acquisition (b-factor and number of diffusion directions), tractography method (probabilistic or deterministic), and tractography parameters  on AR tractography reconstruction. Optimal parameters are used to reconstruct the AR in all the remaining subjects and build a tractography atlas of the AR.Pre-processed diffusion and structural MRI data of 35 healthy adult subjects  provided by the MGH-USC Human Connectome project were analysed. In a previous study by our group46. The data is constituted by a multi-shell acquisition  for a total of 552 directions, of which 512 diffusion weighted (DW) and 40 non-DW volumes (b = 0), at a spatial resolution of 1.5 mm isotropic. In order to investigate the effect of acquisition parameters, the four shells were divided and separately analysed in MRtrix323. For each b-value we extracted all the corresponding diffusion volumes, without varying the number of diffusion encoding directions 2. For each shell, bias field correction and global intensity normalisation were performed and an average response function was calculated from the subjects’ specific response functions. Fibre orientation distribution functions (fODF) were then recovered for each subject using constrained spherical deconvolution (CSD) on the basis of the shell-specific average response function. The tensor model was also fit to the data and fractional anisotropy (FA) maps were extracted.Diffusion weighted data was pre-processed as previously describedhttps://fsl.fmrib.ox.ac.uk/fsl, version 5.0). For better co-registration results, the up-sampled FA map (1 × 1 × 1 mm3) was first registered to the T1, and then the inverse transformation was applied to the T1 image. The registered T1 was then segmented in FSL48 to obtain white matter, grey matter, and CSF partial volume estimate (PVE) maps, and subcortical nuclei masks. This information was combined to create a five-tissue-type image to be used for anatomically constrained tractography (ACT)49.The T1 weighted structural MRI of each subject was linearly registered through affine registration to the diffusion space of each subject in FSL  to initiate tractography of the AR  if two HG gyri are present50. In every subject the HG was first identified on the sagittal slice and its borders were marked for every slice from the first medial slice, where HG becomes visible as a protrusion of the STP, to the more lateral slice where it disappears. Once defined on the sagittal slice its shape was followed and refined on the axial slice, carefully following the grey matter near to the transverse sulcus and Heschl’s sulcus. As a last step the coronal plane was checked. Both grey matter and white matter were included in the segmentation, and, if present, the second gyrus was included as well. The same ROI was drawn five times for each subject and each hemisphere and accuracy was then measured by calculating the Dice coefficient between successive drawn ROIs, and mean and standard deviation were calculated (mean and sd) 9 and the number of seeds per voxel (n = 2000) were kept constant 2). Seed points were generated at random by uniform sampling of the seed ROI for both probabilistic and deterministic algorithms23. This number of seeds was chosen to limit false-negative results related to poor sampling  was used to investigate the effects of MRI acquisition and tractography parameters on AR tractography reconstruction. For each one of these subjects, the left and right hemisphere AR was reconstructed using one set of acquisition and analyses parameters as defined in Table 9 after these have been manually inspected and filtered (edited) by the neuro-surgeon (author S.S) that performed the post-mortem dissections  was excluded from the reference generation, since both the automatically reconstructed and the filtered tractograms resulted in too few streamlines to allow for meaningful comparisons . To quantify the anatomical correspondence between the reference tractograms and the reconstructed tractograms a binary mask was created for all voxels intersected by at least one streamline. From these binary masks the volumetric overlap was quantified as the Dice similarity coefficient. The Dice coefficient has been used before in tractography studies to assess reconstruction reproducibilitys/mm2, probabilistic tractography, 0.75 mm step size, 45° angle threshold. One subject was excluded (MGH_1020) because it had an incomplete acquisition (482 volumes instead of 552 b = 10000 s/mm2 volumes).The set of acquisition and tractography parameters that better reconstructed the profile of the AR were then applied to the complete dataset (34 subjects): b-factor = 10000 s/mm2, to avoid FA confounding at high b-values54. Apparent fibre density (AFD) was computed using the afdconnectivity command in Mrtrix3. At high b-values (as used in this study) the integral for a particular FOD ‘lobe’ is considered proportional to the intra-axonal volume of axons associated with that lobe30. Compared to FA which is voxel-based, AFD is tract-specific. Only the lobes of the FOD that are associated to AR streamlines are used to compute the AFD. This makes AFD a more specific measure, less prone to complex fibre configuration biases. Coefficients of variation (CV) were computed for each extracted measure and each subject in both hemispheres. CV is defined as the ratio of the standard deviation σ to the mean of the population. A laterality index (LI) was also computed  on the tract-specific metrics to investigate AR hemispheric asymmetry. The LI ranged from −1  to +1 . In concordance with prior studies, bilateral representation was defined in the −0.2 to +0.2 range55.Hemispheric tract-specific AR measures were then extracted . FA values were extracted from the FA scalar map computed for b = 1000 56. The AF was virtually dissected in Trackvis (www.trackvis.org) by author C.M. starting from the whole brain tractogram. The whole brain tractogram was obtained using the same optimal parameters used for AR reconstruction: b-factor = 10000 s/mm2, probabilistic tractography, 0.75 mm step size, 45° angle threshold. To dissect the AF two ROIs were used: one encompassing the white matter of the superior temporal gyrus and one near the pars opercularis. Only streamlines passing through both ROIs were retained. Tract volume was extracted for each bundle.In order to investigate the relationship between the AR lateralization and language we also reconstructed the arcuate fasciculus (AF), a tract that is associated to language processing and is often found to be left-lateralized57. The up-sampled subject’s FA map (1 × 1 × 1 mm) was first registered to the subject’s T1; the subject’s T1 was then registered to the MNI_152_1 mm space. The inverse warps were then concatenated and applied to the reconstructed streamlines of each participant through the tcknormalize command implemented in MRtrix3. We then computed the tract density image (TDI) of each streamline AR bundle in MNI space and binarized it in MRtrix3. All binary images were then summed together and divided by the number of subjects to build the final AR atlas. The tractography reconstructions were not computed in standard MNI space in an attempt to preserve the individual anatomical information. This could be especially important in the case of the AR because of the great structural variability of the Heschl’s gyrus (HG) across subjects and hemispheres. For this same reason we manually drew the HG segmentations in each individual subject. As a last step, we also measured the Dice spatial overlap between the AR tractography-based atlas and two publicly available atlases of the AR: a post-mortem histological atlas available in FSL6, and a more recent tractography-based atlas available in DSI Studio (dsi-studio.labsolver.org).The AR atlas was constructed using the optimal AR reconstructions from the 34 subjects. We first computed the warping images between the diffusion space of each participants and the standard MNI space through a two step diffeomorphic registration performed in ANTS softwarep < 0.01) data resulted normally distributed. However given the small sample size (N ≤ 34), we decided to use non-parametric statistics throughout the analyses. A Kruskall-Wallis non parametric test was performed to evaluate the effect of varying acquisition and tractography parameters on the Dice coefficient. Alpha level was set to 0, 05 given the small sample size (N = 4). The Wicoxon signed-rank test was used to look for differences in tract-specific metrics across hemispheres. Aplha level was set to 0, 01 in this case. To investigate the correlation between variables we measured the Spearman’s correlation coefficient setting alpha at 0, 01.Statistical analyses were carried out in Python using Pandas and Scilpy frameworks. We tested our data for normality using the Shapiro Wilk test. With the exception of a few variables (AR streamlines count and FA, Supplementary Material


Internationally, inclusion of physical rehabilitation services during early disaster response is relatively new. The aim of the study was to gain an understanding of disaster relief physical rehabilitation in Iran.A qualitative study design was employed and sixteen semi-structured interviews were conducted for data collection. Content analysis was used for data analysis. The participants in this study were purposively selected among people who experienced the Bam (2003) and Varzaghan (2012) earthquakes.Three main themes were explored including: indispensable intervention, barriers to continuous in-tervention and opportunities for intervention. Almost all participants reiterated the importance of effective physical rehabilitation services during disasters. Some participants mentioned significant barriers for delivering such services in the context of Iran. The lack of an effective responsible body, weak disaster-related competencies and under-prioritization by government were among other barriers. On a more positive note, some interviewees talked about national programs that could facilitate service delivery.Providing disaster relief physical rehabilitation has faced many barriers in Iran. However, there are some facilitators in the country that could help provide these services. Finally, the feasibility of post-disaster physical rehabilitation services delivery completely depends on the current national rehabilitation system. Death, disability and injuries are among the human impacts of disasters, which lead to 2-3 times more injuries than deaths.4 In term of injuries, fractures, blunt trauma, head trauma and spinal cord injuries are common in disasters.6 Proper medical response to disasters is critical in saving lives and treating injuries.5 The ultimate goal of medical intervention is the recovery of those injured so that they can attain an optimal level of independence.In total, 41 million Iranians inhabitants were affected by natural disasters between 1994 and 2013. This puts Iran among the top 10 countries with the highest absolute number of affected people over the past 25 years or so.6 It refers to a process that helps individuals with health conditions to reach and maintain optimal independence, and includes measures that restore the current function level for persons with probable disabling.7 Medical response in disasters is usually limited by various challenges such as managerial, human, technical, and financial problems.8 Rehabilitation in disasters, as a part of the whole medical response, encounters more challenges particularly in the early intervention of post-disaster impacts, as it is a new concept in disaster management.10 In 2005, the World Health Organization (WHO) emphasized the importance of rehabilitation during disasters. Accordingly, two groups of individuals benefited from disaster rehabilitation intervention; persons with existing disabilities, and people with severe injuries.7 WHO also point out that in addition to the affected populations, relief workers are also at risk of injury in the aftermath of natural disasters.11Rehabilitation is considered a main healthcare strategy in some literature.12 Moreover, a review of literature points out the challenges in providing effective disaster rehabilitation interventions.13 In addition, WHO released a guidance document in 201610 which proposed to add rehabilitation specialists to the Emergency Medical Teams (EMTs) and outlined the minimum standards for rehabilitation in disasters.Although most of the current literature focuses on the importance of physical rehabilitation during disasters, few studies explain how these services should be provided. According to WHO guideline, the functional recovery of the severely injured is complicated and requires the coordination of multiple professionals and treatment of secondary medical sequences.14 This study therefore aims to outline the barriers to and opportunities of the disaster physical rehabilitation services in Iran.There are very few studies in Iran and other low- and middle-income countries (LMICs) indicating how these services are provided. According to a study done after the Bam earthquake, the medical rehabilitation process was hampered by insufficient or ignored information.We used a qualitative approach through content analysis of semi-structured interviews with the providers and receivers of physical rehabilitation services after the Bam and Varzaghan earthquakes.Data collection and participant selectionPurposive sampling was used for participant selection. The selection process was based on three criteria: physical rehabilitation service delivery in the affected area, the service receiver, and rehabilitation administration. All interviews were conducted between April 19 and June 30, 2015. To ensure comprehensive data collection, service deliverers as well as service receivers were interviewed. All interviews were performed in Persian except for those conducted with people who used physical rehabilitation services after the Varzaghan earthquake. Their interviews were in Turkish. One of the participants was a child and his father responded to the questions. Every interview was recorded and then transcribed verbatim. Initially, all interviews were transcribed in Farsi and then translated into English. The interviews were based on general questions about the participants’ rehabilitation related experiences and observations during the earthquakes. The principle investigator conducted 16 individual in-depth interviews. The interviews lasted between 30 to 60 minutes and were conducted at home (n=3), at the workplace (n=10) as well as at other places including hospitals and rehabilitation clinics (n=3). Interviews were recorded with consent and later transcribed immediately. Participant selection continued until data saturation was reached and the authors realized that new participants would not provide any new data.Because the aim of the study was to investigate different points of the delivery of physical rehabilitation services during natural disasters, the researchers decided to conduct the interviews with participants who had different experiences. In the case of the Bam earthquake, only physical rehabilitation professionals were interviewed. Persons with disabilities and injuries were selected from people living in areas that were affected by the Varzaghan earthquake. Otherwise, physical rehabilitation providers were selected among those who experienced the Bam earthquake because the services provided in Bam were relatively broad and comprehensive.Data analysis15 At the beginning, the texts were read several times and the meaning units that describe a specific experience were highlighted; then, codes were generated through the headings. Then, 48 sub-categories were obtained via codes and were grouped in order to reduce the number, and in the next step, 11 categories were generated and finally, three main themes were created.The inductive approach was used for content analysis. Ethical considerationThe study gained ethics approval from the Ethical Committee of Tehran University of Medical Sciences and the approval letter number is: IR.TUMS.REC.1394.145.TrustworthinessRegarding the credibility of this study, the principal investigator (GHM) has many years of experience in the field of rehabilitation and disaster. He also used trust for data collection and analysis. Also, the research findings have been presented to four experts with experience of field and research work in this area, as a means of expert check, and they were asked to approve the data validation. In this way, participants’ approval has also been used, by means of member check. For dependability, the first step was to conduct interviews in a relaxed environment and all interviews were fully recorded. In fact, an attempt was made to record the voice of the interviewee fully and transparently carefully.Indispensable interventionThe three categories created in the main theme included: The increasing unmet needs for rehabilitation; physical rehabilitation in pre-hospital care; and physical rehabilitation in hospital care. All participants emphasized the importance and effectiveness of physical rehabilitation with regards to their experience and background.The increasing unmet needs for rehabilitationSome persons with disabilities benefited from assistive devices, such as wheelchairs, crutches and walkers, and some were completely dependent on such devices for mobility. Also, some people had orthotics and prosthetics or depended on other equipment to stay alive. Due to their dependence on a device, all of these people were more vulnerable in disasters and emergencies. One of the participants with a leg brace mentioned: “This device is essential for me because without it, my speed and reaction are reduced”.In the event of a disaster, assistive devices might be lost or damaged. Not only did persons with disabilities use assistive devices, but there were also people using such devices for a short time as a result of temporary mobility limitations. “Some braces were repaired by local people, but some other braces needed experienced people who needed to come from Tabriz”.Some of the participants emphasized the importance of other kinds of highly needed accessories. These included air mattresses and diapers, which participants said were critical in the life of persons with severe disabilities. Almost all participants accepted that the distribution of assistive devices was critical in the affected areas. Some participants believed that responsible organizations should keep reserves of such devices so that they can be distributed at the right time. “Rehabilitation and disability related accessories usually did not include relief packages, and this problem results in serious health problems for the permanent users of the accessories”.Some participants talked about their experience of providing relief to people with disabilities during earthquakes and in the immediate aftermath. In such situation, people need specialist support from rehabilitation experts, because other people in the affected areas are not familiar with the specific conditions and needs. People with disabilities are more vulnerable due to cognitive and motor constraints than others and need to be transferred to specialized centers. One of the participants said: “I sent two disabled people to a residential center in Ahhar city. Because we had strong after-shocks one month after the earthquake and disabled people couldn’t stay at home. For this reason they couldn't run outside when the ground started shaking”.Some participants who experienced the Varzaghan earthquake stated that regular referrals to rehabilitation therapy programs were discontinued after the earthquake. One participant was a hemiplegic child who was less than a year old at the time of the Varzaghan earthquake. His father responded to questions. “We didn’t know that he had a problem. No one came here”.He was angry and upset as he felt that if specialists could have diagnosed his child’s problem in time and given him proper consultation, he could have followed his therapy program properly.Physical rehabilitation in pre hospital careSome of the participants witnessed a great number of those injured in the Varzaghan earthquake being brought to hospital by private vehicle. They believed that people with injuries came to the hospital without triage. They also mentioned that health professionals, such as rehabilitation specialists, could play a role in triage and properly immobilize the injured limbs of victims prior to transportation to hospital.Rehabilitation specialists, based on their expertise, can train rescue and relief workers in the preparedness phase and can serve as consultants during early the response phase as well. “In my opinion, it is better for rehabilitation specialists to teach the rescue and first aid trainers the proper ways of transporting injured persons to hospital. Regarding their critical role in rescue and transportation of injured people after disasters, rehabilitation specialists should be trained in order to improve their life-saving skills”.Rehabilitation specialists, because of their great knowledge and expertise, can participate actively in the early assessment and immobilization training given to educators, search and rescue workers and even the general public.Physical rehabilitation in hospital careSome of the participants believed that rehabilitation specialists, such as physiotherapists and occupational therapists, would be of “great help” in the management of the injured persons brought to the hospital with simple health problems. One of the participants said: “We were so busy and could not carefully examine the injured people, and made a mistake in fracture diagnosis. The presence of a physiotherapist can be of great help. He or she can manage patients with simple problems, such as ankle sprain or other conditions which need non-surgical intervention”.Rehabilitation experts were able to counsel the victims in hospitals to continue and complete their treatment and remind them of how long rehabilitation takes. They can tell the injured people what actions should be avoided so that their injuries do not worsen. Many injuries do not require surgery, and rehabilitation specialists can handle these injuries. Also, rehabilitation experts have adequate knowledge and competence in the field of immobilization of fractures and in returning the range of motion in joints. “…For example, we had wrist trauma which needed fixation and immobilization for a week, and then we needed to work on the range of motion in the joint”.According to participants’ experiences, a large proportion of patients were hospitalized with simple injuries, who took a lot of specialized doctors. Due to the low number of medical specialists and the importance of their presence in cases with severe head injuries requiring surgical intervention, simple hospital injuries could be managed by rehabilitation practitioners. “There were too many patients and only a few health personnel. We had to focus on one patient to keep them alive and avoid multi trauma…you had to splint the fracture for the patient but you had no time to talk to them and give them advice. If the rehabilitation team was present, they could have provided consultation for the patient to let them come back to continue the process of treatment. Most of our time was spent on serious patients”.Barriers to continuous interventionThe main theme in disaster physical rehabilitation relief in Iran was generated by three categories: the lack of an effective responsible body; weak disaster-related competencies; and under-prioritization by government. Physical rehabilitation relief during disaster cannot be separated from the current rehabilitation system in the country.The lack of an effective responsible bodyMost of the participants believed that the cause of the many problems regarding rehabilitation in Iran was the lack of an effective responsible body. According to most participants, this problem has affected the country's rehabilitation system not only in emergency situations but also under normal conditions as it undermines the system’s position and function with regard to other aspects of health. The main weakness is the lack of a defined organization with enough authority at the national level. Almost all participants expressed the aforementioned weakness. Moreover, according to the participants, in spite of several governmental organizations functioning in the field of rehabilitation, rehabilitation leadership is complicated and unclear. “Rehabilitation has no responsibility at national level……We have infrastructure-related problems in rehabilitation. We have no rehabilitation deputy in the Ministry of Health or even a general manager. When there is no section for rehabilitation services in the Ministry of Health, there will be lots of divisions and subdivisions”.The main consequence of this situation is the absence of rehabilitation services in the national health system plan. This absence has consequences in society; rehabilitation service delivery becomes problematic during disasters as well as in more normal situations. Another problem, expressed by the participants, was the low coverage of rehabilitation at national level. Rural areas were greatly affected by the Varzaghan earthquake, and had no rehabilitation facilities before the earthquake. Some participants who were injured during the earthquake could not use the physical rehabilitation services optimally. “I didn’t know what electrotherapy (physiotherapy) was. My doctor didn’t inform me at first about receiving electrotherapy. I went after three months of the earthquake incident…my family couldn’t take me to physiotherapy because of the long distance between our village and Tabriz, and I was required to go there several times".Another participant who was injured as a result of earthquake said: “I could have easily gone for physiotherapy if physiotherapy was near our village and certainly my foot would have been better”.A number of participants talked about the remoteness of the rehabilitation centers. This problem has caused some injured people not to complete their rehabilitation sessions. This problem has caused many injured people not to have access to rehabilitation services. “One of the problems with rehabilitation is the distance between patients and the hospital. There should be a center close to the patients”.Weak disaster-related competenciesEvery specialist needs some skills to work in the disaster field. Rehabilitation specialists are never trained for disasters and emergencies at university. Moreover, most of the specialists believe that rehabilitation isn’t an important issue. “Practical curriculums have been removed from students’ education”.Many of the specialists are reluctant to work in affected areas. Based on responses from the participants, this reluctance is due firstly to a lack of training for disaster affected areas, and secondly a lack of skills for rehabilitating injured people. “But, unfortunately, as no good education and training are provided to our colleagues in universities about the definition of rehabilitation, they don’t come”.Their unwillingness to attend the disaster areas, especially in the early days, is linked to the lack of preparedness. These experts do not therefore have a proper understanding of the real needs in these areas which prevent them from doing their job properly.Under-prioritization by health ministryTraditionally, rehabilitation follows on from medical treatment, so it is not included at prevention level. As expressed by some participants, rehabilitation isn’t needed in the early days of the disasters. The Ministry of Health and Medical Education has no good plan in emergency-related activities regarding rehabilitation. “Priorities of Health Ministry are more surgically oriented in natural disasters”.Because of the low priority, lower resources are allocated to rehabilitation. Currently only medical treatment is free of charge in hospital, and disable people are required to pay for physiotherapy. Some participants stated that government organizations are moving toward healthcare rather than rehabilitation. They believed that rehabilitation was costly and therefore not a priority for governmental organizations. “Red Crescent Society should organize rehabilitation teams for disasters; the society gives low priority to rehabilitation services”.Opportunities for interventionParticipants believed that, in spite of the barriers, there are considerable potential in the national rehabilitation system, including recent developments in rehabilitation, national and international NGOs, volunteers and the private sector and Community and Family Based Rehabilitation.Recent developments in rehabilitationBased on the responses, the rehabilitation sector is well developed in the country, relatively speaking. Every year, a large number are graduated in rehabilitation studies. Rehabilitation in Iran has a relatively long history and there are rehabilitation centers in all provinces that provide specialized services to those in need.“Almost 1000 facilities function at country level. These government-supervised facilities provide both day and residential care for people with disabilities”.According to some participants, these facilities can provide considerable help during emergency evacuation. However, one of the participants doubted these facilities have been prepared well. The participants believed that residential centers have sufficient resources and equipment. They also said that the centers have experts to manage persons with severe disabilities. “… In my opinion, persons with severe disabilities should be transported to residential settings, because families will not be able to care for them in the first days after the earthquake, they may have lost their families …”In the experience of some participants, care of people with severe disabilities in hot weather and under a tent was “very difficult” and “not healthy”. As a result, they believed that the residential facilities were the best places for them.National and international NGOs, volunteers and the private sectorIn addition to governmental organizations, nongovernmental, private and volunteer institutions also provide skilled rehabilitation services to people with injuries and disabilities. “A private sector institution agreed to provide some braces for people with injuries and disabilities after the Bam earthquake” said one participant who provided artificial limbs in Bam.Some participants expressed that, in their experience, benefactors and charities were even ahead of government agencies when it comes to meeting the needs of people with injuries or disabilities. They stated that they had been surprised by benefactors who, for example, had bought mattresses for wounded people and had donated money to a hospital. The participants considered volunteers to be highly capable. If organized properly, such people can help with the development of rehabilitation programs in disaster affected areas alongside nongovernmental organizations.According to some participants, in addition to Iranian charities, a number of international non-governmental organizations were also present in the disaster areas  and were engaged in rehabilitation activities. “There were donations from NGOs from foreign countries such as France”.Some participants referred to the advocacy role of volunteer organizations that could influence decision-makers to ensure policies and programs for providing the services.Community and Family Based RehabilitationParticipants informed us that there are currently various rehabilitation programs in the country. Community- and family-based rehabilitation is one form this kind of program takes.In Iran, the national governmental welfare and rehabilitation organization (Behzisti) is legally responsible for community- and family-based rehabilitation. Community-based rehabilitation (CBR) focuses more on rural regions and family-based rehabilitation (FBR), is relatively new, and relies on family members and close relatives to support people with disabilities. A participant mentioned: according to another participant, FBR has no extension, as CBR has, but it does have the capacity to deploy in order to meet the needs of persons with disabilities during an emergency. CBR teams could contribute to rehabilitation in villages. They can have a good role in identifying the people in need and providing the necessary services. “Facilitators of CBR first came during the earthquake and, because they knew the locations of people with disabilities, especially in villages, they were sent to villages to assess the needs …”, “the facilitators are voluntary local young women”.This study is the first one of its kind in the Eastern Mediterranean Region and highlighted barriers to and facilitators of continuous disaster physical rehabilitation in Iran. The findings are divided in three categories; indispensable intervention, barriers to continuous intervention and opportunities of intervention. Since all the interviews were conducted in Iran, the findings are based on the strengths and weaknesses of the geographical context. However, the rehabilitation situation is quite similar in developing countries.16 Some studies in recent years have directly assessed the effect of physical rehabilitation services on post-disaster impacts. Zhang et al. reported that rehabilitation intervention improved the long-term functioning of Sichuan earthquake survivors with severe injuries.17 Ni et al. showed that rehabilitation intervention alleviated mental disorders, as well as physical dysfunction in fracture victims of the Sichuan earthquake.18 Yongqiang et al. demonstrated that formal physical rehabilitation improved the functional outcomes in a series of spinal-cord-injury victims from the 2005 Sichuan earthquake.19 These all imply that rehabilitation intervention can be useful during medical and surgical treatment. Knowlton and others stated that amputation rehabilitation professionals helped during the preoperative phase in the choice of limb amputation level. 20 Also in line with our findings, Rathore et al. stated that although persons with disabilities, caused by natural disasters, required early and proper transportation from disaster area, injured people were often evacuated and transported to local health facilities by untrained people and first responders without rehabilitation knowledge. The authors believed that rehabilitation should not only be involved in intermediate and long-term care settings but should also be included in immediate disaster response.21 Moreover, all studies support the necessity and importance of physical rehabilitation relief during early disaster response and long-term intervention.The findings explore the necessity for medical rehabilitation relief after a natural disaster such as an earthquake. According to our findings, the benefits of physical rehabilitation teams following a disaster were numerous, from medical help by rehabilitation professionals to meeting the disaster-related needs of persons with disabilities for rehabilitation services. The benefits of the participation of rehabilitation professionals in pre-hospital care are clearly presented in the article. This finding was confirmed by Gosney et al. as they proposed that rehabilitation professionals could function actively in the triage of injured people and play a significant role in pre-operative and post-operative care. 22 In addition, a system approach also is needed to be considered for improving rehabilitation of the disaster victims, as another study in a similar disaster context has also indicated regarding a system approach to injury prevention and its severity. 24 This paper has focused on the direct relation between the effects of disasters on persons with disabilities and the situation regarding health resources and rehabilitation facilities. One of the problems is poorly developed infrastructure in affected areas. According to our findings, successful rehabilitation intervention during natural disasters completely depends on the rehabilitation resources of the community. WHO`s official paper acknowledged this finding, stating that “In a setting where resources are limited, the impact of disasters on these groups of people [people with disabilities] can be long-term and far-reaching”. 22 This was obviously realized during earthquakes in Pakistan (2005) and Haiti (2010).26 Early health response teams usually include medical and surgical professionals. Disaster health decision-makers do not think about rehabilitation services. From the present findings, this was probably because of the low rehabilitation knowledge of the decision makers and the popular belief that rehabilitation was not an emergent need. Reinhardt et al. reported that the lack of rehabilitation services delivery during early disaster response was due to “surgical bias” and a low level of rehabilitation knowledge among response team members.13 Disasters are serious issues and as such require rapid response. Effective disaster response, including by the health sector, is reliant on the knowledge and competence of healthcare providers.11 Based on the findings, rehabilitation sector needs to and plan separately for the delivery of services in disaster-affected areas. This finding is exactly in line with an WHO document, which states that rehabilitation for work in affected areas requires a separate plan to that of the emergency medical teams.10 This implies that the delivery of physical rehabilitation services during disaster depends on the existing rehabilitation system in a community which should be strengthened.Another important finding concerns the barriers to rehabilitation services delivery during natural disasters. One of the most important findings of the study is that the delivery of physical rehabilitation services during disasters completely depends on the existing rehabilitation system in a community. In areas with no developed rehabilitation systems, the service delivery will be inadequate in time of disasters and emergencies. This finding was clearly stated by the World Health Organization (WHO) in 2005.Besides the barriers, according to the findings, the country has some characteristics which can potentially facilitate the physical rehabilitation relief program. Relatively good human resources exist in the country. Also, high number rehabilitation facilities deliver professional services across the country. Both governmental and nongovernmental organizations provide services in the country. Comprehensive approaches accepted internationally, are implemented in the national rehabilitation system.22 The findings of this study also indicate that the availability of rehabilitation resources and centers in Iran can facilitate the effective provision of rehabilitation services in disaster-affected areas. Based on the responses of professional participants, there is a very close correlation between the status of a country's rehabilitation system and its ability to provide rehabilitation services in the event of natural disasters. Therefore, it can be said that these facilities and resources in any country can be considered as an opportunity for providing rehabilitation services in areas affected by natural disasters. The study states that international non-governmental organizations may be present in the affected areas of Iran and can provide specialized rehabilitation services in the days immediately following a disaster. After the April 2015 Nepal earthquake, international organizations were present from the very beginning in coordination with the local government and provided a range of rehabilitation services.27 According to the findings of this study, the Community-Based Rehabilitation approach, which is currently being implemented at country level, especially in rural areas, can be of assistance in addressing disability issues in emergencies. Given the fact that the plan has a formal mandate in the country, the previous coordination agencies should make it possible to use the plan in the affected areas. The WHO has also addressed this issue in a book, in which the organization emphasized the role of the community-based rehabilitation approach in disaster management. It suggests that this approach helps people with disabilities to have better preparedness to deal with disasters, and improves disaster management plans.28As mentioned above, the World Health Organization has confirmed that those countries with good resources have a good rehabilitation system.Strengths and limitations of the study29 the author also doesn’t claim that the findings can be generalized to other settings.Despite the fact that this article was the first study in the field of rehabilitation in disasters in Iran, it was able to identify some of the hidden aspects of this area using the experiences of specialists, injured people and people with disabilities, but it had some limitations. One of the limitations of the study was a relatively long time between the experience of some of the participants and the interview time. Because of this, we used non-expert participants who used the services recruited from the people living in the Varzaghan area. Another limitation of the study was that since the study was carried out in the context of Iran, its results cannot be generalized to other countries. However, since qualitative study doesn’t aim to generalize the findings,Despite the necessity and importance of physical rehabilitation intervention during disasters, delivery of such services encounters great problems arising from a weak organizational structure and rehabilitation system in Iran. However, some national and international programs in operation can facilitate the utilization of physical rehabilitation during disasters and emergencies. Physical rehabilitation disaster relief can be included in the national disaster health response if the barriers can be broken down and the opportunities utilized.AcknowledgementsWe thank Iranian Handicap Society and all of the participants for the generous support to the study. This study has done as a part a PhD in disaster management at School of Public Health at the Tehran University of Medical Sciences.


Traumatic brain injury (TBI) and its potential long-term consequences are of major concern for public health. Neurorehabilitation of affected individuals has some specific characteristics in contrast to neurorehabilitation of patients with acquired brain lesions of other aetiology. This review will deal with the clinical consequences of the distinct lesions of TBI. In severe TBI, clinical course often follows a typical initial sequence of coma; followed by disturbed consciousness; later, post-traumatic agitation and amnesia; and finally, recovery of function occurs. In the different phases of neurorehabilitation, physicians should be aware of typical medical complications such as paroxysmal sympathetic hyperactivity, posttraumatic hydrocephalus, and posttraumatic neuroendocrine dysfunctions. Furthermore, we address questions on timing and on existing evidence for different rehabilitation programmes and for holistic neuropsychological rehabilitation approaches. Recent studies ,2 estimaNeurorehabilitation of TBI is a vast, many-sided topic—ranging from early rehabilitation of patients with impaired consciousness to support and to accompany reintegration of patients in their social and professional environments. Reviewing the relevant existing literature addressing the different aspects of rehabilitation of TBI in a balanced way is thus not feasible for a short review article. Therefore, we will focus on in-patient rehabilitation and some specific topics that are clinically relevant in neurorehabilitation of TBI, and point out what distinguishes it from the care of patients suffering from other brain injuries.One might think that neurorehabilitation of any brain injury, independent from its aetiology , should be similar. However, this is not the case, as the mechanisms of brain damage and localisation of the lesions are quite different between the different groups. Ischemic stroke leads to damage of the brain, which is determined by the vasculature, hypertensive haemorrhagic damage may show some locations of predilection, but may be localized almost anywhere in the brain. By contrast, TBI often results in bi-hemispheric contusions and lesions, some of them very localized (hematomata in the parenchyma) or in the subarachnoid, subdural, or epidural space, respectively. Furthermore, typically, widespread injuries of cell bodies and axons occur, the latter often being referred to as diffuse axonal injury (DAI) ,7,8,9,10Standard magnetic resonance imaging (MRI) sequences typically lead to an underestimate of the damage even in the presence of cognitive dysfunction . HoweverOn the one hand, focal lesions can show distinctive clinical presentations as in focal ischemia or haemorrhage. Contusional damage shows a certain predilection to frontotemporal lesions, typically causing impairments of attentional, executive, and memory functions, and potentially even more subtle deficits in social and moral behaviour ,15. On tHowever, the distinction between focal and diffuse lesions is somewhat arbitrary as they are often both present in the same patient, and are probably found in more than the 50% of TBI patients, demonstrated by a MRI study . The cogIn a typical case of severe TBI, the natural history of recovery consists of a period of impaired consciousness, sometimes accompanied by paroxysmal sympathetic hyperactivity (PSH), followed by a period of posttraumatic agitation (PA) and/or confusion with amnesia and, subsequently, by a period of post-confusional recovery of function, characterized by a diversity of cognitive, behavioural, emotional, and sensorimotor disturbances . The medFurthermore, moderate-to-severe TBIs often co-occur with polytraumatic injuries including multi-organ injury, fractures, burns, or amputations. Therefore, the range of comorbid conditions and variations in the brain injury itself leads to a very individual array of physical, cognitive, behavioural, and psychosocial impairments in brain injured patients, which require a rehabilitation team specialized for neurorehabilitation of TBI.Severe TBI can lead to prolonged periods of unconsciousness or coma. After a certain interval, post-traumatic coma—according to Plum and Posner, describing a state of «unarousable unresponsiveness» with eyes continuously closed and no clinical or electroencephalographical response to environmental or intrinsic stimulation —often evVS indicates a state with no signs of conscious behavior, but patients show spontaneous eye opening, evidence of sleep–wake cycles in EEG, and typically do not require mechanical respiration—notably, no well-accepted definition of VS exists . In 2010Clinical examination is still the mainstay of assessment and DOC evaluation. The Coma Recovery Scale-Revised (CRS-R) is often used in this context for assessment. It specifically focuses on and graduates signs of conscious awareness concerning motor and verbal behaviour, and thus allows the detection of changes in the clinical state . RecentlAssessed in a Norwegian population, three months after severe TBI, 2% of patients were in VS or MCS and less than 1% remained in a state of DOC after one year . Both stRecently, data of a population of 110 patients with DOC due to TBI followed up for ten years was presented. More than half of the sample achieved near-maximal recovery by one year post-injury. In contrast, a subgroup of patients with delayed emergence from DOC (defined as command following later than four weeks after TBI) still showed significant functional improvement in the period between 2 and 10 years post-injury . The numMost treatment reports of DOC refer to single cases or small case series and only a few randomized controlled trials were reported, as reviewed comprehensively by Schnakers and Monti . The besA paradoxical effect of zolpidem with a temporary emergence of DOC had been observed in single cases. Subsequently, it has been investigated in two larger placebo-controlled trials ,44. FirsMulti-sensory stimulation programmes might be another promising approach, given their low potential to harm. In a preliminary report of a randomised placebo-controlled trial assessing the effect of familiar auditory sensory training, Pape and colleagues noted significant gains in the Coma-near-coma scale, representing arousal and awareness in patients with DOC . SimilarFurthermore, it seems reasonable to provide care in a specialized institution given the particularities in this population. Besides the aforementioned pharmacological options and multi-sensory stimulation programmes ,47,48, pPSH can already occur in the acute phase of hospitalisation and may also be a problem in neurorehabilitation. PSH is defined as a recurrent and episodic syndrome, which includes hypertension, tachycardia, hyperthermia, diaphoresis, and hyperthermia . IntermiPA is a subtype of delirium and may be a major problem in the management and rehabilitation of TBI. Patients show aggressive behaviour, disinhibition, or emotional lability. According to the literature, in the acute phases of brain injury, 35% to 96% of the cases may present PA. PA can persist during the recovery phase and the agitated behaviour profoundly affects the rehabilitation team. It should be mentioned that the diagnosis of PA is a “diagnosis of exclusion” after all medical  and neurologic causes  have been ruled out . It is gLuauté et al.  performeFinally, a Cochrane Review  showed tTreatment effects should be evaluated on a regular basis. Frequent clinical evaluation by the physicians is recommended. Easily applicable scales such as the Richmond Agitation Sedation Scale (RASS)  can be hPTH is the most common treatable complication during rehabilitation of TBI. The incidence of symptomatic PTH ranges from 0.7% to 29% . DifferePTH can be divided into two types: communicating and non-communicating PTH. In communicating hydrocephalus, the different parts of the ventricular system are interconnected and cerebrospinal fluid (CSF) flows from the ventricular system to the subarachnoid space. Communicating hydrocephalus is the most frequent type seen in TBI with blood products or fibrosis impeding the CSF flow into the bloodstream through the arachnoid granulations. This may also present as what is known as normal pressure hydrocephalus (NPH). In non-communicating or obstructive hydrocephalus, CSF flow is blocked from passing between the ventricles or exiting the ventricular system.Risk factors for PTH include intracranial haemorrhage (particularly intraventricular haemorrhage), subarachnoid haemorrhage (SAH), meningitis, status after decompressive craniectomy, the duration of coma, and advanced age of the patient . PTH may lead to clinical deterioration and poor outcome if untreated. A very early sign of developing PTH may be a stagnancy of improvement during early rehabilitation, discordant with injury severity. PTH may lead to clinical deterioration and poor outcome if untreated. Symptomatic PTH is to be distinguished from posttraumatic ventriculomegaly resulting from secondary atrophy. Symptomatic PTH patients are likely to improve when treated by shunting.Kammersgaard et al., in 2013, prospectively followed 444 patients with severe TBI who required long-during rehabilitation . They foAnother cohort study with retrospective comparative analysis  found thTian and colleagues  reviewedEarly signs and symptoms of non-communicating hydrocephalus include manifestations of increased intracranial pressure such as nausea, vomiting, lethargy, headaches, altered mental status, gait disturbances, and papilledema. As in the idiopathic form, secondary NPH typically presents with the clinical triad of gait ataxia, urinary incontinence, and dementia, with gait impairment the most likely to respond to surgical treatment. The cognitive abnormalities include poor activity initiation, psychomotor slowing, decreased attention, and forgetfulness. Ventriculoperitoneal shunts are used most commonly for posttraumatic NPH. Most patients who receive shunt placement will improve clinically and radiographically, as shown in a literature review . HoweverFinally, during neurorehabilitation of TBI, one may be confronted with neuroendocrine disorders due to pituitary lesions. They are often missed and remain unrecognized. The pituitary gland seems particularly susceptible to acceleration–deceleration injuries due to the vulnerability of its vascular supply through the infundibulum and firm encasement within the sella turcica . HoweverIn the chronic state of TBI, the literature is not uniform, and studies have been reported with prevalence rates of hypopituitarism from negligible to almost 70% . The preClinical signs of hypopituitarism may be discrete, especially in a cohort of severely affected patients, and laboratory testing seems to be unreliable in the acute phase . It is tAdmission rates to neurorehabilitation for survivors of severe TBI differ widely between countries. Data from specialized trauma centres in Texas , Switzerland (12 centres), Norway (4 centres), and Denmark (4–5 centres) show rates of 45%, 44% , 75% , and 84%, respectively ,77,78,79A former review by Greenwald and Rigg  presenteEven more basically, the Canadian INESSS-ONF “Clinical Practice Guideline for the Rehabilitation of Adults with Moderate to Severe TBI”  defines Older TBI patients are often denied access to specialized rehabilitation . HoweverFrom a practical perspective, reasons for exclusion from rehabilitation are premorbid states that either profoundly diminish the ability to participate in rehabilitation or that are associated with a poor long-term prognosis—for example, dependency of care before the TBI as in advanced dementia, or palliative situation due to advanced malignant tumours.There are currently no international guidelines regarding treatment in the early rehabilitation phase for patients with severe TBI. Only a few studies have investigated the effect of integrating rehabilitation into acute TBI care. A Cochrane Review evaluating multi-disciplinary rehabilitation for acquired brain injury in adults of the working age  found thIn another review article , Turner-She emphasized that the rehabilitation of TBI is a complex process with several major challenges for clinical research that tend to confound traditional RCT designs. Three characteristics of rehabilitation studies make it difficult use only the RCTs approach because it cannot be applied to address all the questions that need to be answered in TBI rehabilitation ; these iThey found high evidence and, therefore, a strong recommendation for more intensive rehabilitation programmes in severe TBI, which are associated with faster functional gains. Moderate to high evidence exists for specialised or vocational rehabilitation programmes, whereas moderate evidence exists for programmes that continued outpatient therapy and for early rehabilitation programmes. The concept of very early rehabilitation is supported by more recent studies, for example, by Andelic et al. . They inRehabilitation institutions are frequently located elsewhere than the acute care institutions and lack the possibility of intensive monitoring of patients with early medical complications . Therefore, in these conventional settings, the time lapse between the occurrence of brain injury and admission seems to depend primarily on the severity of brain injury and intercurrent complications .The question of optimal intensity of therapies in neurological rehabilitation is difficult to answer, given the heterogeneity of patients. Yet, several studies found evidence of earlier gains in more intensive therapy in TBI. First, Zhu et al.  comparedIn contrast, a recent study by Hart and colleagues  comparedNevertheless, in our practical experience with patients in the first few weeks after severe TBI, they can show limited ability to participate in longer therapy sessions and in group therapies with significant fatigability. This can be an important limiting factor for higher therapy intensities.On the one hand, more intensive therapy potentially can reduce the LOS. Slade et al. compared two groups with different intensities of multi-disciplinary rehabilitation, with one benefitting from 30% more therapy time than the other . After sOn the other hand, as reported based on observational data ,95, longIn clinical settings, different factors influence the LOS in in-patient rehabilitation: (i) health system-related factors such as, for example, predefined maximum LOS, limited capacity of the rehabilitation facilities, availability of intensive outpatient/community programmes and availability of nursing/care home places, respectively; (ii) patient-related factors such as, for example, individual goals and motivation, the availability of support by families and caregivers, and occupational status and position, respectively.Systematic reviews by the Institute of Medicine  and by BFor instance, Cicerone and colleagues could show that an intensive cognitive rehabilitation program as compared with standard rehabilitation may lead to earlier patient productivity . In addiThis neurorehabilitation team typically consists of a specialized nursing team, physiotherapists, occupational and speech therapists, neuropsychologists, and physicians; optionally, it could include nutrionists, social workers, and recreational/vocation therapists. The team regularly unites to reassess the patient’s state and progress and to discuss and redefine treatment goals. Frequent education of the patient and his family is suggested in order to foster comprehension of and compliance to the treatment plan and possible outcomes. Neurologists and other physicians involved in TBI rehabilitation should be aware of the particularities concerning lesion patterns, clinical presentations, and the typical sequence of recovery in moderate to severe TBI, as well as the above-mentioned frequent complications that may interfere with rehabilitation progress. Considering the heterogeneity of physical, cognitive, behavioural, and psychosocial sequelae after TBI, it is in the experience of the authors, and represented in several guidelines too ,102,103,


Androgen receptor (AR), an important target in the current androgen derivation therapy, plays a critical role in the development and progress of prostate cancer (PCa). Nonsteroidal antiandrogens, such as enzalutamide and bicalutamide, are commonly used in clinic to treat PCa. Though they are very effective at the beginning, drug resistance problem appears after about 18 months. One of the reasons is that these antiandrogens share similar structure skeleton. Therefore, it is urgent to discover novel antiandrogens with different skeletons for resistance problem. Herein, we combined structure- and ligand-based methodologies for virtual screening chemical databases to identify potent AR antagonists. Then the cytotoxic activities of the screened hit samples were evaluated by using LNCaP prostate cancer cells. Virtual screening and biological evaluation assay results suggest that several chemicals with novel pyrazolopyrimidine skeleton can inhibit the proliferation of prostate cancer cells with similar, or even higher, bioactivities to bicalutamide. AR reporter gene assay experiments proved that Compound III showed potential antagonistic effects. In addition, molecular dynamics simulations results proved that Compound III can properly bind to AR and prevent helix 12 (H12) from closing to distort the formation of activation function 2 (AF2) site, resulting in the invalid transcription. Hence, pyrazolopyrimidine was discovered as a novel, potent and promising antiandrogen skeleton deserved to be further studied. According to the latest cancer statistics 2016  superfamily Evans, . The AR The standard treatment of prostate cancer involves androgen derivation therapy in conjunction with small molecule antiandrogens that block AR signaling  simulations and molecular mechanics Generalized Born (GB) surface area (MM-GBSA) calculations were applied to explore the interaction mechanics between pyrazolopyrimidine and ARs including wild type (WT), F876L and H874Y mutant types.In the current study, a combined structure- and ligand-based screening strategy was applied to virtually screen a big commercial chemical database to fish potential AR antagonists. Considering the published AR protein crystal structures are all in the agonistic manner  is unclear, homology modeling was applied to construct its Anti-AR conformation using the same method as previously reported  is an analytical methodology that can be used to interpret the quantitative relationship between molecular structures and corresponding biological activities. Most importantly, after thorough validation, QSAR models can be used to quantitatively predict the activities of new chemicals. In this study, four QSAR models constructed by using multiple linear regression (MLR) method were employed to 1 was previously reported from our group  were experimentally tested from the AR reporter gene assays. The Y in these QSAR models stands for the negative logarithmic unit of the biological activities, pIC50. These four linear equations were list as follows. The corresponding parameters, demonstrating the model performances, were listed in Table The linear MLR model Y1 = 1.188GATS7v − 1.108BEHp7 − 7.281E2u + 1.453HATS4u − 2.647H6m + 28.810R6u+ − 46.815R8u+ + 12.157Y2 = −2.89IC5 + 1.01GATS5e − 3.17DISPp − 12.99HATS3u + 27.13Y3 = 5.601IVDE − 1.70C-009 + 1.11BLTF96 + 3.02Y4 = 3.18 IC1 − 0.46F05[N-F] + 1.47R4u + 0.409 Depressant-80 + 3.85HATS7m − 7.15Y2 describes the fitting ability and R2 greater than 0.75. The predictive abilities were evaluated by means of four external validation parameters , CCC 1-Y4 to calculate the biological activity of each molecule. Subsequently, all these chemicals were ranked by the calculated biological activities, considering simultaneously the results from four models. Only molecules with high potency, predicted bioactivities from four models greater than 7, can be retained for the succeeding process. Finally, 396 compounds were reserved in database 3 for further structural analysis and experiential analysis.After models construction and validation, these four models were used to calculate the in silico for antiandrogenic potency further study. The representative pyrazolopyrimidine analogs and corresponding predicted activities were listed in the Table The 396 different compounds can be divided into 8 groups according to their skeleton structures. But some of them contain poisonous substructures from the point view of drug, some of them are easy to be hydrolyzed, or some of them have too complex structures etc. Finally, we focused on pyrazolopyrimidine skeleton  were listed in Table 50 value of 45.8 μM, is 2-fold less active than bicalutamide. Compound III were demonstrated to be more effective than the first-generation AR antagonist bicalutamide and exhibited a dose dependent manner as shown in Figure In order to determine whether the screened hit compounds can affect the proliferation of prostate cancer cell, we carried out the cell proliferation assay by using the LNCaP cell line. The corresponding structures and biological activities  long terminal repeat promoters, and luciferase gene bound at the downstream of an AR promoter. The concentration of DHT is 10 nM in all AR luciferase assays. As the result, compound IV have no significantly antagonistic activity against AR, while compound III can moderately inhibit the DHT-induced transcriptional activation of AR at the concentration of 10 μM (29.8%) Figure . We assuIn order to investigate how Compound III produces antagonistic effect on androgen receptor, molecular dynamics simulations and MM/GBSA methods were employed to study the interaction between Compound III and AR, including wild type AR, F876L and H874Y mutant types, which are commonly occurred in the AR LBD and often caused enzalutamide resistance problem . The systems of the Compound III/WT AR, Compound III/F876L AR and Compound III/H874Y AR were clustered into 6, 7, and 7 classes and the representative conformation accounted for 44.0, 29.7, and 35.0%, respectively. From the largest number of cluster, the conformation with the lowest RMSD to the cluster centers was selected. These optimized structures were used to analyze the conformation difference between corresponding initial structure and structure after 80 ns MD simulation, shown in Figure To get the optimized structure of each system, we performed a cluster analysis for the last 20 ns trajectories using Kclust algorithm  was used for screening, which includes 1.6 million compounds. All these molecular structures were protonated/deprotonated by generating ionization states with significant population at the specific 7.0 ± 2.0 in Maestro  and prepared by using the Protein Preparation Wizard in Maestro. The treatments on AR structure include deleting the involved solvents, adding the missing hydrogen atoms (missing loops) and residues via Prime module, protonation protein crystal structure to neutral (pH = 7), minimizing side chains using OPLS 2005 force field, and definition receptor grid using a 12 Å box centered on the ligand. All other adjustable settings were set as default. Moreover, we constructed an antagonistic AR (named Anti-AR) model according to the reported homology modeling methodology  model, respectively. This program is generally used to approximate a systematic search of the conformational, oriented and positional space for the docked compound. The involved active site was defined from the coordination of the built-in ligand, using the default settings. The chemicals that could accommodate into the ligand binding domains of 1T65 and Anti-AR formed database 1. Then, the Lipinski's rule of five  on androgen receptor antagonists  were established and used in the present study. The processes to build models Y2, Y3, and Y4 are as follows.Our group has published a predictive QSAR models  were converted into negative logarithmic unit pIC50 and used as dependent variables. The 3D structures of these molecules were imported into SYBYL 6.9 The chemical structures together with corresponding bioactivities taken from literatures .The obtained lowest energy confirmations were submitted to DRAGON 5.5 in silico bioactivities formed database 3.Here in this study, genetic algorithm was employed to select important descriptors highly related to the bioactivities, using the MLR method to build the QSAR models, executed in QSARINS , and the resulted chemicals were downloaded to form a new pyrazolopyrimidine database 4. Subsequently, LigandFit and Libdock modules were used to dock all these pyrazolopyrimidine analogs to the ligand binding domain of 1T65 and Anti-AR protein, and the four QSAR models were employed to predict corresponding bioactivities. At the end, the hit chemicals with excellent performance both in the docking and QSAR model predictions were selected for further experimental validation.Then, according to our experience on medicinal chemistry and combining with the docking and QSAR results, the novel skeleton of pyrazolopyrimidine was eventually proposed for further research. To thoroughly explore the pyrazolopyrimidine analogs, the specific skeleton was used as a substructure to search the ZINC online database  was added to each well. After 4 h incubation, 150 μL of isopropanol was added to dissolve the crystal. Finally, the absorbance was measured at a wavelength 570 nm.The LNCaP cells were cultured in RPMI 1640 medium containing 10% FBS, 100 unit/ml penicillin and 100 unit/ml streptomycin at 37°C in a humidified atmosphere with 5% CO2 atmosphere for 24 h, cells were treated with the chemicals  in the presence of 10 nM DHT for 24 h. Then, cells were harvested with 150 μL of cell passive lysis buffer (Promega). The firefly and renilla luciferase activities were determined with a Dual-Glo Luciferase Assay Kit (Promega). The data were obtained in triplicate and expressed as inhibition rate over the DHT control. Inhibition% = 1−(RLUtest − RLUblank)/(RLUDHT − RLUblank) × 100%. RLU = relative light unit.Luciferase reporter assay based on androgen response elements (ARE) was used to examine chemicals for androgenic activity. COS-7 cells were seeded in a 24 well plate, and cultured in medium , 2 mM glutamine) for 24 h in a 24 well plate. The plasmids of pcDNA3.1-AR, pMMTV-Luc and pRL-SV40 were transfected in COS-7 cells by using transfection reagent Lipofectamine 3000 according to the instructions of manufacturer. After culturing at 37°C in a 5% COhttp://www.rcsb.org/pdb)The crystal structures of WT, H874Y mutant AR (PDB ID 2Q7L) were obtained from the Protein Data Bank  is consisted of electrostatic interaction energy (ΔEele), van der Waals interaction energy (ΔEvdw), polar solvation free energy (ΔGp) and nonpolar solvation free energy (ΔGnp). Dielectric constants of 1.0 and 80.0 were set for solute and solvent respectively. The polar part of desolvation (ΔGGB) was computed with the modified GB model developed by Onufriev et al. (referred to as igb = 2 in Amber)  was determined based on the solvent accessible surface area (SASA) computed by the LCPO algorithm:  was not considered due to high computational cost and low prediction accuracy  methodology (Massova and Kollman, in vitro evaluation of hit compounds, TS did the molecular docking, molecular dynamics simulations, and they wrote the paper. All authors analyzed the results and approved the final version of the manuscript.XW and JL conceived and coordinated the study. LW did the structure-based virtual screening, screening of pyrazolopyrimidine analogs, The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.