Physical activity levels typically decline during cancer treatment and often do not return to prediagnosis or minimum recommended levels. Interventions to promote physical activity are needed. Support through the use of digital health tools may be helpful in this situation.The goal of the research was to evaluate the feasibility, usability, and acceptability of an interactive Web portal developed to support patients with cancer to increase daily physical activity levels.A Web portal for supportive cancer care which was developed to act as a patient-clinician information and coaching tool focused on integrating wearable device data and remote symptom reporting. Patients currently receiving or who had completed intensive anticancer therapy were recruited to 3 cohorts. All cohorts were given access to the Web portal and an activity monitor over a 10-week period. Cohort 2 received additional summative messaging, and cohort 3 received personalized coaching messaging. Qualitative semistructured interviews were completed following the intervention. The primary outcome was feasibility of the use of the portal assessed as both the number of log-ins to the portal to record symptoms and the completion of post-program questionnaires.Of the 49 people were recruited, 40 completed the intervention. Engagement increased with more health professional contact and was highest in cohort 3. The intervention was found to be acceptable by participants.The portal was feasible for use by people with a history of cancer. Further research is needed to determine optimal coaching methods. Physical activity levels typically decline during cancer treatments such as chemotherapy or radiation therapy and often fail to return to prediagnosis or minimum recommended levels . PatientIn order to promote physical activity, health professionals, particularly exercise professionals, may suggest the use of commercially available physical activity trackers to their patients. However, data monitoring by health professionals for a large number of patients who use such trackers can be difficult because individual patient data is not readily available as it sits with the patient.Digital health interventions such as the use of Web portals have been shown to be beneficial by supporting engagement in health and wellness activities in individuals with chronic diseases, including people with a history of cancer. A Web portal is generally seen as a secure website that brings information from various sources together in a uniform way -7. Web pPatients who use Web portals may have greater engagement in their treatment, increased treatment satisfaction, and better communication with their health professional care team. This includes a method to record and track patient-reported outcome (PRO) measures -9,13. ThThe use of an integrated clinician-patient Web portal, with a mechanism for automated real-time data transfer, may provide the ability to track physical activity and patient-reported symptoms such as fatigue and provide an opportunity to positively impact behavior change through messaging. The use of messaging, including personalized coaching messaging, has emerged as a promising approach to promoting positive behavior change ,11. HoweThe aim of the study was to assess the feasibility of using a Web portal with activity monitoring and personalized messaging for people diagnosed with and treated for cancer.This was a prospective, longitudinal cohort study to determine user feasibility of a Web portal in cancer patients. The study protocol has been published previously .An interactive Web portal was developed that included integration of real-time wearable activity device data, collection of PROs and symptom information, the provision of educational material, and individualized coaching messaging to support behavior change by encouraging patient engagement in physical activity. The Web portal enabled remote monitoring of physical activity for use by both clinician and patient, along with symptom and health-related quality of life (HRQoL) tracking capabilities. The Web portal also allowed for educational emails, summary messaging, and individual personalized messages to be sent to participants.The Misfit Shine activity monitor was used in this study. The Shine was chosen due to its long battery life. Participants enrolled in the study could also opt to bring their own device from the Misfit, Garmin, or Fitbit product ranges.The inclusion criteria were (1) diagnosed with any cancer, at any stage of treatment receiving or had received anticancer therapy within the last 12 months, (2) aged 18 years or older, (3) Eastern Cooperative Oncology Group performance status 0 to 2, (4) had internet or mobile phone access, (5) willing to complete the intervention and follow-up in English, and (6) provided written informed consent. Participants were excluded if they were unable or had limited ability to speak English or had any condition that would compromise their ability to understand the participant information or give informed consent.Potentially eligible patients registered with the cancer center were invited to participate by a member of their health care team between March and June 2017. Following eligibility check and consent, participants were enrolled serially into one of three cohorts without randomization. Cohort 1 was provided Web portal access and given a wearable activity tracker (Misfit Shine) for 10 weeks. Cohort 2 was provided Web portal access, an activity tracker, and an additional weekly automated summary message via the Web portal detailing average symptom and physical activity scores over the past week, along with specific educational material such as information on cancer-related fatigue and nutrition. Cohort 3 received the same content as Cohort 2 plus personalized behavioral change messaging from an accredited exercise physiologist (MM). Messages were sent weekly through the Web portal to the participants’ email. Each participant received a 20- to 30-minute face-to-face onboarding and setup session.The primary outcome was the feasibility of the program. The intervention was deemed feasible if a compliance rate of more than 70% was observed. Compliance comprised two measures:Log-ins: a patient was defined as compliant if they had more than 2 log-ins to record symptoms over the 10-week study periodQuestionnaires: a patient was defined as compliant if they completed the follow-up questionnaire at week 10.For the Web portal to be deemed feasible, more than 70% of the participants needed to comply with both criteria.The secondary objectives of the study were to describe the number of individuals who were eligible, took up the program, and completed the program; compute the rate of goal attainment as set by the exercise physiologist in week 2; and measure participant satisfaction, acceptability with the intervention, self-efficacy related to change in lifestyle factors, and changes in PROs including symptom and HRQoL scores. For cohorts 2 and 3, median daily step count was recorded and weekly email engagement measured.At the initial face-to-face session, baseline PROs were completed on the Web portal, with follow-up questionnaires administered remotely. Three validated PRO measures were used: symptom tracking scale—Edmonton Symptom Assessment Scale (ESAS) , HRQoL tU test was used to compare the number of symptoms between categorical variables.Baseline demographics are summarized as number and percentage for categorical variables and mean and standard deviation or median and interquartile range (IQR) for continuous variables depending on the distribution. The number of compliant participants within each cohort is summarized as number and percentage. The number and percentage of patients who attained their step goal was summarized weekly and by cohort, along with the median number of weeks taken to attain goals. Daily step count was summarized at weeks 1 and 10 for each cohort as mean and standard deviation or median and IQR. The mean difference and 95% confidence interval for physical activity between weeks 1 and 10 is provided. HRQoL scores are summarized as median and IQR or mean and standard deviation at the initial and week 10 visit for each cohort group. The mean difference between time points is displayed alongside the 95% confidence interval. The number and percentage of opened emails is summarized for cohorts 2 and 3 by each week of the study, and the number of personalized messages opened by cohort 3 is summarized as number and percentage. The number of symptoms reported was used to investigate the association between baseline characteristics and engagement with the Web portal. A Mann-Whitney Participants were invited to complete a semistructured qualitative interview after completing the study in order to provide feedback regarding their perception of the acceptability of the intervention and experience in using the Web portal. Interviews were conducted by an experienced qualitative researcher (AJ) via telephone and audio recordings. Interviews were transcribed verbatim and analyzed thematically  using a Permission to conduct this study was granted by the Royal Prince Alfred Hospital Human Research and Ethics Committee (X16-0051). All participants provided written informed consent.A total of 59 patients were invited to participate, and 83% of those (49/59) were recruited to the study. The first 17 participants were entered into cohort 1 in month 1, the second 17 into cohort 2 in month 2, and final 15 into cohort 3 in month 3. Recruitment numbers for each cohort were lower than planned (n=20) due to delay in the Web portal development, and 80% (39/49) of participants had data included in the analysis. There were no data predictive of patients lost to follow-up. Participants were mostly female  with a history of breast cancer , the median age was 54 years, and 24% (12/49) were receiving concurrent chemotherapy. Median time since last intensive anticancer therapy was 3.5 (IQR 0-12.5) months. The majority  had at least one comorbidity. Most participants  had not used an activity monitor previously, and the majority  were supplied with an activity monitor by the study investigators. Patient demographics are summarized in The number of log-ins and completed questionnaires are shown in Twelve themes were identified from the data, with 4 themes directly applicable to the feasibility and acceptability of the intervention. Participants in the study generally reported a high level of acceptability for the intervention.It was really, really positive and it was really helpful in terms of making a progressive recovery.Participant 4, cohort 2I think from both mental and physical point of view it was really worthwhile for me. Participant 1, cohort 3The mean number of log-ins to report symptoms increased in each of the cohorts depending on the level of interaction. Cohort 1 had a mean of 11 log-ins (range 0-52), cohort 2 had a mean of 17 log-ins (range 0-104) and cohort 3 had a mean of 50 log-ins (range 3-121). The number of patients who attained their daily step count goal are summarized for each week of the study in Daily step count has been summarized at week 1 and week 10 for each cohort in The activity tracker given to participants (Misfit Shine) was generally well received, with participants stating they liked it and found it acceptable to use.Yes. I absolutely love the thing that you wear on your arm. I'm just elated. I think it’s really motivating and I really enjoyed having that.Participant 3, cohort 1Absolutely, absolutely I loved it. It was really good to see exactly what it took to get to my goal each day and I love it. To the point I’m going to get another one and it’s going to be a part of my life to have a fitness tracker now.Participant 3, cohort 3Some participants reported concerns about the accuracy of the device, in particular sleep tracking.So, I don’t think the [sleep] data is accurate, so I didn’t bother.Participant 3, cohort 2Changes in PRO questionnaire results from the initial intake (week 1) to end of program (week 10) are summarized below for each of the 3 cohort groups.The ESAS was used to report pre-post symptom changes such as fatigue and pain and is reported in Change in patient-reported self-efficacy was reported using the CBI-B. A lower CBI-B score reflects improved self-efficacy. At a 95% confidence interval, cohort 1 had a change in score of –0.33 (–15.2 to 14.6), cohort 2 had a change of –6.78 (–21.9 to 8.3), and cohort 3 had a change of –2.18 (–11.9 to 7.6).Change in patient-reported HRQoL was reported using the FACT-G and reported in The most accessed educational topic was sleep (week 6) with 95% (16/17) and 93% (13/14) of participants in cohorts 2 and 3 opening the email, respectively, followed by nutrition (week 3) with 80% (14/17) and 93% (14/15) in cohorts 2 and 3, respectively, opening the email see . A majorParticipants in cohorts 1 and 2 received no direct health professional contact following onboarding. Cohort 3 received weekly personalized coaching messaging for which time data were collected. Weekly, the mean time spent by the health professional to interact with each participant was 11 minutes.Cohorts 2 and 3 had access to a curated selection of Web portal educational information including written and video content. The participants perceived the portal educational content to be acceptable.I thought it was really good, the information was presented in a glaring manner.Participant 4, cohort 2Some respondents reported they would have preferred tailoring of content to their stage of cancer treatment and care.Some of the stuff I might have been interested in two and a half years ago, but it’s not so relevant to me now.Participant 5, cohort 3Qualitative interview data for those participants in cohort 3 who received personalized messaging revealed it was acceptable and provided additional motivation to help them use the Web portal and attain goal.And it actually made me happy. It gave me a sense of achievement, especially when the [exercise physiologist] would send the message saying, “Wow, you've matched your goals. Well done.” I felt a lot of pride in myself.Participant 1, cohort 3...it made me just push myself and even on days when I didn't want to walk I thought no my steps were down and I should get out there and go for a walk and so on.Participant 3, cohort 3Reflecting on the lack of interaction, some participants in cohorts 1 and 2 remarked they would have liked more contact with their health professional throughout the study....but if someone motivated me to say, “Would you like to come in and have a look at that app again and I'll show you what it does. And let's see how you're going with it,” then that might have...I might have engaged with it a bit more...or at all.Participant 3, cohort 1Overall, the participant satisfaction with the intervention was high, with 83% (33/40) of respondents extremely satisfied or moderately satisfied with the intervention. Satisfaction with the activity tracker (Misfit Shine) was high, with 77% (31/40) of respondents extremely or moderately satisfied with using the device. In addition, 73% (29/40) of respondents found the Web portal extremely or moderately easy to use.The results of this study demonstrate the feasibility of using a remote digital health intervention to track and promote physical activity levels and function and that personalized coaching messaging appears to increase participant engagement. The Web portal was found to be acceptable by the majority of participants, and satisfaction with its use was high across all cohorts. Participants accessing the Web portal varied widely in engagement, but overall participants in cohorts 2 and 3 interacted more with the Web portal compared to cohort 1.The attrition rate was lowest in cohort 3, which had personalized contact, and highest in cohort 1, which had no personalized contact. This suggests simply giving patients access to a tool such as the Web portal was not sufficient to keep patients engaged for more than a short time. Regular interaction between patients and health professionals such as that provided by personalized messaging may lead to increases in participant accountability and may be a key method to improving engagement. Personalized messages are seen to be most effective when tailored to each patient rather than generalized to broader audiences ,11,19.The impact of messaging on engagement of participants was clear from the qualitative responses, where they were stated to be motivational and helpful. Further focus on the frequency, length, and content of personalized messaging will be an important development area for the future.This research also builds on previous studies, such as those conducted by Huh et al  and RoseOur study showed that real-time monitoring of symptoms and treatment-related side effects can be reported through remote systems and the use of these systems is acceptable, which is consistent with previous research -23. FurtPRO completion rate for cohorts 1 and 2 was lower than for cohort 3. Only two automated attempts to encourage participants to provide follow-up PRO data were made to each cohort during the study. Further individualized contact may be needed to collect such data when using remote models of care.The usefulness of educational material is likely to be dependent on participants’ stages of disease, cancer treatment, and trajectory. Tailoring of educational content in this Web portal was insufficient to account for individual needs and stages of treatment, recovery, and health literacy. This finding is supported by previous reviews in various populations that indicate digital health interventions need to focus on increasing personal relevance of content -27. FurtThe inclusion of qualitative interviews provided important insights into participant perspectives of the intervention. These data have been helpful in conceptualizing changes to the Web portal, the intervention, and future research studies. Codesigned health systems have been shown to increase functionality, specificity, and uptake .Reduced physical activity levels during cancer treatment can lead to increased symptom burden and, consequently, reduced quality of life. There is no single solution to facilitate positive behavior change across a population of people with cancer in active treatment; however, the innovative use of technology may benefit a proportion of the population.More participants in cohorts 2 and 3 were receiving chemotherapy during the study period, and cohort 1 participants had been off treatment longer than the others. Since these differences were not accounted for in the data provided, it is unknown what impact they had on the findings.The study also had small group sizes and heterogeneous cancer diagnoses of the participants. Broad inclusion criteria were appropriate for this feasibility study to increase generalizability to the larger population of cancer survivors. However, future studies may need to consider the specific requirements of different cancer diagnoses and stages of disease in order to provide appropriately tailored interventions effectively.All participants had access to a mobile phone, which may define them as different from the general cancer population and could result in overestimation of the feasibility and acceptability of the program. However, only 6% of screened participants were excluded due to lack of a mobile phone, suggesting that the study group was representative of the general cancer population in regard to the use of mobile phones.The utility of Web portals for clinicians and clinician-patient relationships is an important benefit of such systems. This study did not include data review or interactions with medical specialists and was limited to interactions with an exercise physiologist.Development of an automated alert algorithm focused on a combination of PRO measures, symptom tracking, and activity monitor data could improve functionality of the Web portal. For example, if pain above a set value for a set number of days were reported, this would trigger a clinical message to the patient’s care team for investigation. Alerts and flagging mechanisms triggering clinician intervention for patients with cancer to report their symptoms have been shown to be effective in several studies; however, none of these studies included integration of wearable activity monitor data -32.The Web portal was not fully integrated into care pathways and the hospital electronic medical record (EMR) as this integration was cost- and time-prohibitive when developing this study. Integration of data into the EMR is a potential area of future development for this Web portal. EMR integration provides opportunity for multiple members of the patient’s care team to provide remote monitoring and support. Integration of remote tracking data into the EMR also increases clinical metrics available to clinicians to inform decision making and referral practices. For example, a patient reporting cancer-related fatigue corresponding with low physical activity levels could be appropriately referred to a local exercise oncology professional for individualized exercise counseling and prescription.Further studies may also consider the inclusion of health economic data. Health professionals are typically time poor, and although this study indicated that weekly time spent for each participant receiving coaching was minimal, future research should report this in greater detail as well as the travel time saved by patients.Our findings from this prospective cohort study indicate it is a feasible digital health tool for people with a history of cancer. Tailored messaging is needed to maximize engagement in this population. It is anticipated that the results of this pilot will inform the design of an adequately powered randomized controlled trial assessing the efficacy of this intervention.


Background: The Head and Neck Cancer Working Group of Swiss Group for Clinical Cancer Research (SAKK) has investigated the level of consensus (LOC) and discrepancy in everyday practice of diagnosis and treatment in head and neck cancer.Materials and Methods: An online survey was iteratively generated with 10 Swiss university and teaching hospitals. LOC below 50% was defined as no agreement, while higher LOC were arbitrarily categorized as low (51–74%), moderate (75–84%), and high (≥85%).Results: Any LOC was achieved in 62% of topics (n = 60). High, moderate, and low LOC were found in 18, 20, and 23%, respectively. Regarding Head and Neck Surgery, Radiation Oncology, Medical Oncology, and biomarkers, LOC was achieved in 50, 57, 83, and 43%, respectively.Conclusions: Consensus on clinical topics is rather low for surgeons and radiation oncologists. The questions discussed might highlight discrepancies, stimulate standardization of practice, and prioritize topics for future clinical research. This is the second part of the article “A Review of Controversial Issues in the Management of Head and Neck Cancer: A Swiss Multidisciplinary and Multi-Institutional Patterns of Care Study,” providing the results for the items concerning radiation oncology discipline, each followed by a short discussion if deemed relevant.The details of the methodology is presented in the first part of this series.Omitting the elective treatment of the contralateral neck is safe in well-lateralized primaries of the tonsil: moderate LOC (80%).➢ For a cT2 carcinoma of the tonsil, the uninvolved contralateral neck is omitted if the tumor is well lateralized and with <10 mm of the superficial mucosa of soft palate and/or base of tongue in 8/10 centers. The remaining two centers always perform bilateral treatment.Although no prospective randomized trial was performed to exclusively answer this question, there is mounting evidence to support the safety of ipsilateral treatment of well-lateralized OPSCC. As endorsed by the American College of Radiologists, treatment can be limited to the ipsilateral side in tonsil primaries with a N0-1 nodal stage when the primary exhibits <1 cm invasion into the soft palate or base of tongue –4 and inCompartmentalization of the tumor bed and the levels of the nodal basin for post-operative radiotherapy in terms of dose and volume: no consensus.➢ In 3/10 centers, the post-operative primary tumor bed is not included in the target volumes, if the indication for adjuvant radiotherapy arises only due to nodal factors after neck dissection. The remaining 7 centers do not separate the tumor bed and the dissected nodal levels.Similarly, regarding the elective/low risk volumes in the post-operative setting, in 5/10 centers the whole post-operative neck is considered as an inseparable target compartment. In the other half of the centers, the levels are thought of separable compartments, and, in eligible cases based on the nodal distribution pattern reported by the pathology, radiotherapy to a portion/level of the post-operative neck is omitted.The selection of radiotherapy target volumes is strongly influenced by tradition. More than a decade ago, the landmark EORTC 22931 and RTOG 9501 trials defined the major and minor risk factors for the indications of post-operative CRT and radiotherapy, respectively. However, the question of the necessity of such an “all or nothing” approach concerning different parts of the target volume(s) remains unanswered. Surely, one of the arguments for irradiating the primary tumor bed in case of multiple nodes with or without ECE has been the general loco-regional recurrence risk and difficulties to irradiate the primary tumor recurrences after previous nodal irradiation, especially in the past due to technical limitations. Nevertheless, from a purely medical and not a technical perspective, it is not clear, why the post-operative primary tumor bed should be irradiated due to multiple nodal positivity and/or ECE, whereas the same patient and tumor bed would not receive any radiation if the neck would have been pN0-1. Similarly, there is no data indicating perineural extension as a risk factor for nodal recurrence.Concerning the post-operative nodal target volume, half of the radiation oncologists still treat the entire surgical bed covering both the primary tumor bed and the operated neck (at least the involved side). On the other hand concerning the post-operative primary tumor target volume, most oncologists still treat the entire surgical bed at least within a low risk volume irrespective of risk factors specifically related to the primary tumor or the neck . NeverthAdaptation of the dose or target volumes  after induction chemotherapy is not preferred: moderate LOC (80%).➢ After an induction chemotherapy, 8/10 centers would not adapt the dose or target volume  regardless of a partial or complete response. In one center clinical target volume (CTV) would be adapted based on tumor shrinkage. In another center, both dose and volume would be de-escalated based on response.For radiotherapy planning after induction chemotherapy radiotherapy, Salama et al.  recommenDefinition of treatment volumes for the treatment of CUP: no consensus.➢ No consensus was reached concerning the treatment volumes in CUP situation. Treatment volumes of a CUP always contain bilateral neck and potential mucosal sites (4/10); only the involved side(s) of the neck (3/10); and involved side(s) plus corresponding mucosal sites only in case of human papillomavirus (HPV) or Epstein-Barr Virus (EBV) positivity (2/10). One center always treats the mucosal sites but only with the involved side(s) of the neck.The literature about the optimal management of CUP is conflicting. There is no convincing data supporting the elective irradiation of the contralateral uninvolved neck in the modern series –19, wherUse of an isotropic margin and respecting the anatomical barriers is the preferred method to generate high-risk CTVs around the gross tumor volume (GTV): low LOC (60%).➢ When contouring the high risk CTV around the primary tumor, 3/10 centers use the predefined anatomical subsites defined by Eisbruch et al. . One cenThe survey was completed before the recent publication of the international consensus guidelines for the delineation of the primary tumor CTV by Grégoire et al. , in whicA restricted use of intermediate-risk dose only in the levels with ECE is preferred: high LOC (90%).➢ In case of pathologically-confirmed ECE, only the involved levels are treated with an intermediate dose of 60–66 Gy in 9/10 centers. The rest of the neck is treated with an elective/low-risk dose. In one center, all involved levels are treated with 64 Gy irrespective of ECE, and the uninvolved levels are treated with a lower dose, since systematical anatomical marking of the lymph node levels on the surgical specimen is not performed sufficiently.Traditionally, some head and neck cancer oncologists were concerned about the intraoperative spillage of the tumor cells, in case of ECE and/or positive resection margins. However, even in the twin landmark RTOG (9501)  and EORTUse of tailored planning target volumes (PTV) for different anatomical subsites: no consensus.➢ In some anatomical subsites , 4/10 centers use additional geometric margins concept to compensate for possible organ movement. In one of these centers, an anisotropic margin for larynx and soft palate primaries are used. For the remaining 6 centers, such an internal target volume concept is not used based on subsite. On the other hand, the policy of these centers is to re-plan and adapt the margins according to movement based on daily imaging, if considered necessary.The conventional fields in the 2D radiotherapy era encompassed the target volumes with enough margins to compensate for movement. As an example, the larynx is known to move up to 20–25 mm craniocaudally , 33. DesDefinition of high- and low-risk volumes for laryngeal primaries: no consensus.➢ Laryngeal primaries are treated by including the whole larynx in the high-risk volume in 2/10 centers. Five centers prefer to treat the primary tumor with a predefined margin. In the rest of the centers, the larynx (in one center the involved hemilarynx) is considered as a compartment which shall be treated with an elective dose. The primary tumor is treated to a high dose with a predefined margin.The 3D volume definition for laryngeal primaries was just a translation of traditional 2D fields to the 3D era. This resulted in the continuation of treating the whole larynx within the high-risk volume receiving the highest dose, even for early stage tumors without infiltration to cartilaginous structures, contralateral extension, etc. This concept is still being used in some centers. At the other end of the spectrum, hemilarynx , 38, eveThe use of simultaneous integrated boost (SIB) is the preferred boost technique: moderate LOC (80%).➢ Centers were asked to provide information about the boost techniques and dose/fractionation regimens for target volumes . SimultaIMRT with inverse planning allows SIB to multiple target volumes during the course of radiotherapy by means of a dose painting approach. The beams used to deliver the planned dose to the high-risk volume are exploited for the dose application to the encircling low-risk volume(s). In contrast to the traditional sequential shrinking field/volume approach, SIB enables the generation of single-phase plans with the possibility of a more flexible plan optimization process. This allows an advantage over SEQ in terms of better control of dose around the high risk PTV and reducing the unwanted high dose areas within. Although there are countless retrospective and prospective studies, in which patients were treated with SIB, no prospective randomized trial compared both technical modalities until recently. Lertbutsayanukul et al.  conducteHypofractionation for the treatment of early stage glottic larynx cancer: no consensus.➢ For early stage glottic larynx cancer, 4/10 centers perform hypofractionated radiotherapy (≥2.25 Gy per fraction).p < 0.01) and lower voice handicap index scores in almost all follow-up visits performed in regular short intervals until 18th month (p < 0.01). In contrast, a recently published phase I trial with extremely hypofractionated radiotherapy using robotic SBRT yielded inferior local control and not necessarily less toxicity compared to the literature (There is mounting evidence supporting the shortened treatment time in the treatment of stage I-II glottic larynx cancer for increased tumor control . Reportsterature . This waAltered fractionation is preferred in case of radiotherapy without concomitant systemic agents: moderate LOC (70%).➢ Altered fractionation is used in 7/10 centers. In the corresponding question, altered fractionation was defined as any treatment not fitting to the following arbitrary description in the questionnaire: single fraction/day throughout the whole treatment course with a fraction size between 1.8 and 2.2 Gy for the high-risk volume. The distribution among the altered fractionation regimens were as following: acceleration (six fractions per week or concomitant boost) in 6 centers, hyperfractionation in 3 centers (two centers use both strategies). Three centers combine systemic agents with hyperfractionation and/or acceleration.Compared to normofractionated radiotherapy, the survival and loco-regional control benefit of altered fractionation is proven, particularly in the form of hyperfractionation in the definitive radiotherapy setting without concomitant systemic treatment . HoweverThere are numerous combinations of systemic agents and altered fractionation schedules for the treatment of HNSCC . In summThere is no standard in terms of dose prescription and plan normalization: no consensus.➢ 95% = 95% of the prescribed dose).During the radiotherapy planning process, 5/9 centers use the median dose to PTV for dose prescription. Of those, only 2 centers normalize the plan according to a minimum dose coverage criterion , but without a strict restriction of the use other dose-volume prescription values. In practice, there is a large variety in internal clinic protocols and clinical trial protocols. As an example, in the modern EORTC trials for HNSCC , it is requested to prescribe the dose on D50%, and obtain a dose coverage of at least 95% of the prescribed dose to the 95% of the PTV, whereas normalization to D95% instead of D50% is demanded in the RTOG protocols . It is likely, that no consensus will exist in the near future. Nevertheless, it is important to be aware of these differences to correctly implement the dose, fractionation, and incorporate new techniques used in clinical trials into routine practice.The authors of the ICRU 83 report  only sugRefer tofor LOC for each post-treatment response evaluation modality for the neck.➢ The participating centers were asked to provide their post-(chemo)radiotherapy response evaluation schedules, which are summarized in 18FDG-PET/CT is indeed cost-effective radiotherapy response evaluation tools and the optimal time interval, the highest level of evidence was generated by the PET/NECK Trial , which dffective  comparedffective .18FDG-PET/CT is reported to have a higher accuracy in the detection of recurrent lesions when compared to CT and MRI radiotherapy. Recent studies demonstrated further increased accuracy with delayed image acquisition around 16 weeks after treatment with NPVs reaching 100%  is not clear, especially if the above-mentioned imaging modalities are already planned.No particular preference exists for palliative radiotherapy regimens: no consensus.➢ Among centers, there was a heterogeneity in palliative radiotherapy regimens. Three centers did not provide any preferred regimen. The most frequently mentioned regimen was the Australian Quad-Shot (4/10). Details are provided in There are various radiotherapy regimens for the palliative treatment of head and neck cancer . In the Hypofractionated stereotactic body radiotherapy (SBRT) is considered in re-irradiation setting with curative intent: low LOC (60%).➢ SBRT is considered for palliative irradiation: low LOC (60%).➢ SBRT is performed in  6/10 centers with an indication for re-irradiation with a curative intent. In 6/10 centers  it is used for palliative treatments. In one center, it is also used to apply the boost dose following the elective course of radiotherapy. In 2/10 centers it is never used.n = 50) demonstrated 6% acute and 6% late grade 3 toxicity rates with 40–44 Gy in five fractions over 2 weeks (n = 291)  . The resn = 291) .IMRT appears to be a feasible alternative as well . Recentlp < 0.01). Both techniques showed similar overall survival in RPA class III, but significantly better survival with IMRT in class II. Comparable overall survival and loco-regional control were reported on RPA class II small tumors (≤ 25 cm3) with SBRT (>35 Gy in ≤ 5 fractions) and IMRT . SBRT was associated with slightly less toxicity than IMRT  or SBRT  boost following 46 Gy in 23 fractions with concomitant cisplatin (The Erasmus MC group published their results of T1–2 OPSCC cases treated with either pulsed-dose brachytherapy (isplatin . ToxicitVarious applications of SBRT in head and neck cancer are reported (its use in glottic larynx cancer is mentioned previously):The findings of our survey indicate a low LOC among head and neck oncologists working in academic and multidisciplinary setting in 10 Swiss institutions. Regarding the results and the discussion concerning the specialties other than radiation oncology, the reader is advised to read the corresponding parts of this article. The highest LOC was achieved among medical oncologists, whereas the lowest was observed among head and neck surgeons. On the other hand, this level of disagreement may also depend on the topics chosen for the survey, and not necessarily the heterogeneity within the disciplines. It is also interesting to witness a low LOC regarding topics, where a high level of evidence actually does exist, and vice versa, such as definition of post-induction chemotherapy or post-operative treatment volumes, diagnostic modalities and time interval used to evaluate treatment response, use of boost techniques and dose/fractionation in early stage glottic laryngeal cancer. This article is expected to serve the head and neck oncologists to be aware of their discrepancies even among academic institutions and to stimulate discussion toward standardization of practice and prioritize topics of future clinical research. We support the concept of and the adherence to standardized guidelines, which should address controversial but relevant topics as well. Importantly, the level of evidence or the lack of thereof should always accompany the guideline recommendations. Last but not least, we would like to emphasize that this article series is not a literature review in the classical sense.All datasets generated for this study are included in the manuscript/supplementary files.GH, MB, OE, PD, and PP: conception and design. OE and PP: collection of data. All co-authors: generation of the initial and final versions of the questions, drafting of the manuscript and approval of the final version.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.


The success of driver graduated licensing systems (GLS) is demonstrated primarily in jurisdictions that licence at young ages with requirements expiring at age 18. In Australia, GLS requirements typically apply for all applicants aged under 25. In 2007, the Queensland licensing system was strengthened, extending the learner and introducing a 100-hour supervised driving requirement, introducing restrictions on passenger carriage at night and high-powered vehicles for provisional drivers, and on phone use for all novice drivers . The objective of the current research was to evaluate whether these changes were associated with reductions in crashes  and killed-and-serious-injury (KSI) crashes involving novice drivers, and respective casualties. Government licensing and police crash records were linked and interrupted time series analysis was used to examine potential shifts in crash trends by rates of licensed drivers per month. Substantial declines were found in novice driver crashes , crash casualties , KSI crashes  and associated casualties . Compared to the total licensed driver population, declines in crashes  and crash casualties  but not KSI outcomes were observed. More narrowly, declines were found for provisional-licensed driver crashes  and KSI crashes  that were approximately 2.6% and 1.2% greater than respective declines for 25-29-year-old open-licensed drivers. Substantial declines also were observed in novice driver single-vehicle, night, passenger and alcohol crashes. Overall, these results demonstrate that GLS can be effective in a later age licensing jurisdiction. However, KSI outcomes were limited. Modelling research is recommended on ways to further strengthen Queensland’s GLS to achieve greater trauma reductions. In the state of Queensland (QLD), Australia, young newly-licensed drivers are over-represented in road trauma statistics, as found globally . For exaInternational evaluations have identified this licensing approach as extremely effective in reducing crashes and injuries –5. HowevWhile QLD had elements of a traditional three-stage GLS in place since 1 July 1999, its GLS requirements and restrictions were strengthened from 1 July 2007 with the specific aim of reducing the number of people killed or seriously injured in crashes involving a novice driver . The changes included a shift from a three- to a four-stage system involving two phases of provisional licence: the first year as “P1” and following two years as “P2”. This allowed additional restrictions in the first year, identified as the period of highest risk for newly-licensed drivers, not only in QLD but elsewhere in Australia and internationally [The main changes to the learner stage were a six-month extension of the minimum period (to 12 months) with a corresponding six-month reduction in the minimum learner age (to 16 years). A requirement for 100 hours of logged supervised practice driving was introduced along with restriction from use of any phone functions (including hands-free) by drivers and from use of loudspeaker functions by passengers. These phone restrictions were also introduced for the P1 stage along with a night passenger restriction: only one passenger aged under 21 years from 11pm to 5am (excluding family). A high-powered vehicle restriction was introduced across the three provisional years (i.e. P1 and P2). These changes applied only to novice drivers aged under 25 years. However, from 1 July 2010, the zero alcohol limit that already applied to under-25 year-old novice drivers prior to the 2007 changes was extended to apply to all new learner and provisional drivers (regardless of age).Other aspects of QLD’s GLS are of note but were not specifically evaluated. The introduction of the 100 hours logbook requirement for learners included a requirement for a minimum of 10 hours at night and also a “3-for-1” scheme. Under this scheme, one hour with a professional driving instructor can count as three hours for the first 10 hours of lessons; therefore there is the potential to reduce the minimum logbook hours to 80 hours. Additional conditions that applied to novice drivers both before and after the GLS changes included a reduced demerit point threshold for traffic offences (4 points compared to 12 points for open-licensed drivers). For all drivers irrespective of licence type, if the threshold is reached the driver has a choice of a three-month licence suspension or a one-year “good driving behaviour” period, during which no more than one demerit point can be accumulated. If breached, a six-month suspension applies. Further, for provisional drivers (only) under a good driving behaviour condition or returning to driving following a licence suspension or disqualification (including as a result of reaching the demerit point threshold), a late night driving restriction applied from 11pm to 5am.A preliminary evaluation of the potential impact on QLD’s revised GLS was conducted in 2009 . The before-after study compared the crashes of novice  drivers to open-licensed 25–35 year-olds over time, controlling for exposure by person months of licensure. Results suggested that the GLS achieved a 4% reduction in crashes, 13% reduction in fatal and serious injury crashes, and 30% reduction in fatal crashes, involving novice drivers. The authors concluded that more years of data were required for a full evaluation, particularly to determine the potential impact of the individual GLS changes. This was in part because during the transition from the old to new GLS special legislative allowances were made for anyone turning 16.5 years of age or applying for their first licence in the first six months following its introduction (to complete only a six-month minimum learner period and 60 hours of supervised driving). This resulted in multiple different GLS pathways at the time of the evaluation.The objective of the current research was to evaluate whether the new GLS in QLD was achieving its goal of reducing the number of people killed or seriously injured through involvement in a novice driver crash. Associated changes in novice crashes  and in novice fatal and serious injury crashes were first examined in order to compare the results to previous international evaluations. These analyses were then repeated to examine changes in the casualty outcomes of these crashes. Further, changes in novice driver single-vehicle, night, passenger and alcohol-involved crashes were analysed.The overall study design was to use interrupted time series analysis to assess any changes in crash outcomes involving a novice  driver comparing the years from commencement of GLS on 1 July 1999 through to the introduction of the new GLS on 1 July 2007 to available data post the new GLS up to 31 December 2015 (dependent on outcome as detailed below under ‘Data sources’). Trends were examined to explore changes in rates of licensed drivers per month, to account for different numbers of licence holders over time, in several ways:Changes in crashes and killed or seriously injured (KSI) crashes involving novice drivers.Changes in crashes and KSI crashes involving novice drivers relative to those of the remainder of the licensed driver population in Queensland.Comparison of changes in crashes and KSI crashes involving provisional-licensed novice drivers only to those involving 25–29 year-old open-licensed drivers only.The second set of analyses was included to act as a control for other potential influences on outcomes over time, such as general improvements to roads and vehicle occupant protection. The third set of analyses included a more narrow age control comparison. This was included to address a concern that the global economic downturn (which occurred around the same time the new GLS was introduced) might have particularly affected younger drivers .Additionally, certain sub-types of novice crashes and KSI crashes were examined, including single-vehicle crashes (i.e. those involving only the novice driver vehicle) as a proxy for at-fault status. To explore the potential contributions of specific aspects of the new GLS, night crashes (11pm to 5am), passenger crashes (any passengers) and alcohol (BAC>0.00) crashes were also explored. There were too few crashes to analyse night passenger crashes specifically, and incomplete passenger age data did not allow analyses focused on passengers within a specific age-range. The trend analyses for novice driver crashes, KSI crashes and these crash sub-types were repeated in relation to the resulting casualties in the crash.The study protocol was approved by the Human Research Ethics Advisory Panel H: Science and Engineering, The University of New South Wales . This study used de-identified, collated, state record data only, not requiring project-specific informed consent from individuals.Data were sourced from routinely collected licensing and police records maintained by the state government road authority, the Department of Transport and Main Roads. The TRAILS licensing database included records of when licences were acquired. Key variables for the current study included birth date, and start and end date (when applicable) of holding each licence  for car drivers. The Queensland Road Crash Database dataset included detailed information on police-recorded crashes. Key variables for the current study included the crash date and crash severity, with varying years of data available dependent on severity type. Data on fatal crashes, from which at least one person died within 30 days, were available to 31 December 2015, whereas data on serious injury crashes, those from which at least one person was admitted to hospital but no-one died, were available to 31 December 2013. Therefore, KSI crash analyses were limited to the end of 2013. Medical treatment crashes, from which at least one person sustained injury requiring medical treatment but no one was killed or seriously injured, and minor Injury crashes, those from which at least one person sustained a minor injury but no one was killed, seriously injured or had a medically treated injury, were available to 31 June 2012. Non-injury (property damage only) crashes, from which no one was injured, were available to 31 December 2010 only. Therefore, as including non-injury crashes would limit the years of data available in the new GLS period substantially, analyses of all crashes excluded the non-injury category (a category known to be under-reported to police regardless ).As elements of the previous GLS were introduced from 1 July 1999, available records commencing from this date were the focus. Records from the TRAILS and Queensland Road Crash Database were linked by Transport and Main Roads for each level of crash severity using independent identifiers . Each crash severity dataset was subsequently linked into a single dataset by the research team based on the Transport and Main Roads unique identifiers.eti is the autoregressive process. The coefficient β2 is a measure of whether the rate “shifted” up or down and β3 is an indication if the trend changed with the introduction of the new GLS.To examine the overall trends in novice crashes over time relative to the start of the new GLS system on 1 July 2007, an interrupted time series analysis was conducted with the log of the ratios of numbers of licensed novice drivers  as an offset and also with all crashes as an offset. An autoregressive error process to account for serial correlation was estimated and this model had the form:Separate models were fit for all novice driver crashes, proportion of novice driver crashes relative to all licensed drivers in QLD, provisionally-licensed driver crashes and 29 year-old open-licensed driver crashes and their respective KSI crashes, as well as for novice driver single-vehicle, night, passenger and alcohol crashes and KSI crashes. Models also were fit for corresponding analyses of crash casualties. Parameters were estimated by maximum likelihood and statistical inference was performed using likelihood-based methods. Tabulated summary statistics for analyses of crash trends for the licensed driver population include the estimate, 95% confidence intervals (CI) and p-values. The estimates “Change in Trend Post New GLS” corresponded to the estimates of monthly and yearly changes in rates, such that these were computed from the model estimate by:All analyses were performed using SAS version 9.4  and R version “Sock it to me”.The overall trends in novice driver crashes and KSI crashes over time are depicted in For crashes involving novice drivers as a proportion of all crashes in QLD , the treFocusing just on provisional-licensed drivers, the trend in crashes per 10,000 provisional licences  followinFor the comparison group, the trend in crashes involving only drivers aged 25–29 years on an open licence per 10,000 respective licences also changed following the new GLS . A decliThe trends in different sub-types of novice driver crashes and KSI crashes over time are depicted in Differences in pre and post trends in novice night crashes  and nighChanges in pre and post trends in novice alcohol crashes  and alcoThe analyses of overall trends in novice crashes, KSI crashes and their sub-types were repeated focusing on the number of casualties involved. Summary statistics are included in In summary, the following trends were found in relation to casualties in crashes involving novice drivers following introduction of the new GLS:A decline in novice crash casualties  at a rate of 1.2% per month or 13.9% per year.A decline in novice crash casualties  relative to the overall licensed driver population in QLD at a rate of 0.2% per month or 2.9% per year.A decline in novice KSI crash casualties at a rate of 0.4% per month or 5.2% per year.No decline in novice KSI crash casualties relative to the overall licensed driver population in QLD.A decline in novice single-vehicle crash casualties at a rate of 1.0% per month or 12.1% per year.A decline in novice single-vehicle KSI crash casualties at a rate of 0.3% per month or 3.8% per year.A decline in novice night crash casualties at a rate of 1.4% per month or 17.1% per year.A decline in novice night KSI crash casualties at a rate of 0.7% per month or 8.5% per year.A decline in novice passenger crash casualties at a rate of 1.2% per month or 14.2% per year.A decline in novice passenger KSI crash casualties at a rate of 0.4% per month or 5.4% per year.A decline in novice alcohol crash casualties at a rate of 1.7% per month or 20.4% per year.A decline in novice alcohol KSI crash casualties at a rate of 0.8% per month or 9.7% per year.Our examination of trends in crashes involving novice drivers in QLD pre and post changes to the state’s GLS identified that the new GLS was associated with declines in novice driver-related crashes and with similar rates of decline in crash casualties. The results suggested that, while crashes and casualties were declining for all drivers over the study period, the new GLS contributed to greater declines among novice drivers. While declines for novice KSI crashes and KSI crash casualties as a proportion of all such crashes in QLD did not pass the p<0.05 threshold, the declines for provisional-licensed drivers were greater than those for 25-29-year-old open licensed drivers; a more narrow age control comparison of independent drivers. Novice driver single-vehicle crashes, KSI crashes and associated casualties, a subset of crashes in which the novice drivers were most likely to be at-fault, also were found to decline.The results of the current analyses, which controlled for exposure in terms of the licensed population (number of licences per month) supported the positive conclusions of the preliminary evaluation based on individual level exposure (person months of licensure) albeit with differing age controls and estimates of crash reductions . Of compBy further examining the novice driver trends by crash types, the results suggested that the night passenger restriction was a key contributor to the reductions, given that night and passenger crashes were found to reduce by almost 16% and 14% respectively each year, and respective KSI crashes by 9% and 5% per year; with equivalent findings for respective reductions in casualties. Moreover, declines of around 20% in novice alcohol-involved crashes and respective casualties and declines of around 10% in novice alcohol-involved KSI crashes and respective casualties were found immediately following introduction of the new GLS, despite no change in the zero alcohol restriction at that time. This suggests there might have been an associated impact of the night passenger restriction on novice alcohol crashes. Recent self-report research in the United States is consistent with this finding: graduated driver licensing systems that were more restrictive generally  were found to be associated with reduced risky alcohol-use behaviours as well as alcohol-related risky driving and passenger behaviours [It is also noteworthy that previous self-report research in Queensland indicated that the 100-hour supervised driving requirement might have resulted in delayed provisional licensure, such that older age (greater maturity) at this time might be implicated in the improvements found . There hDespite the positive findings identified, as noted in the introduction, provisional licence holders nonetheless remain substantially over-represented in QLD crash statistics, suggesting further strengthening of the GLS is warranted. Research on fatal crashes in the United States has demonstrated that substantial gains can be made with stronger graduated driver licensing systems, with 30–55% greater reductions for strong versus weaker systems –17. BaseWhile potential contributions of other features of QLD’s new GLS are difficult to isolate, a recent review found international evaluations provide strong support for a minimum learner period of 12 months and developing support for the relatively high number of 100 supervised driving hours required in QLD . HoweverThis is the first full evaluation of an Australian graduated driver licensing system, which commences from age 17, applies through to at least age 25 and includes a much longer provisional period compared to international systems: confirming that graduated licensing can be effective in late licensing age jurisdictions. The evaluation also confirmed that the declines in crashes and KSI crashes over time were associated with corresponding declines in crash casualties (including the novice drivers as well as other road users involved in their crashes). Analysis strengths of the current evaluation include the use of population level data, the interrupted time series approach, and control for exposure to crashes in terms of the number of licensed drivers by each licence type on a month-by-month basis. While this approach adjusted for potential differences in licensing rates over time, including potential declines in response to strengthening GLS policies , any difA limitation in interpreting these findings relates to the timing of the introduction of the new GLS at a time now considered to mark a global economic downturn . ResearcA further limitation that could not be directly addressed was the potential impact of a short-term divergence in the reporting of injury severities during the evaluation period. In 2006, a new incident recording system was implemented by Queensland Police. During the transition period the injury severity for some casualties was not recorded by police in the usual way and therefore sourced through other means such as medical records. This administrative change may have contributed to a drop in serious injury crashes in 2006–2007, following increases in prior years. As including the 2006–2007 serious injury data was a more conservative approach, we chose to retain these data.In conclusion, we found that the new GLS in QLD was associated with declines in overall novice driver crashes and novice driver fatal and serious injury crashes, with similar rates of declines confirmed for associated crash casualties. While identified declines when analysing all crashes were often substantial, comparative results for fatal and serious injury crashes were moderate and did not meet p<0.05 criterion when examined proportional to the QLD licensed driver population. Results suggest the night passenger restriction was a key contributor to these declines, including declines in both night and passenger crashes, and potentially associated declines in alcohol crashes. However, young novice drivers continue to be substantially over-represented in QLD crash statistics. Further strengthening of the GLS in keeping with international best practice has potential to result in the prevention of considerable more deaths and debilitating injuries. Further research directions include exploring potential confounding influences of the economic downturn for specific age and gender groups and modelling the potential for additional casualty reductions by further strengthening QLD’s GLS.S1 Dataset(CSV)Click here for additional data file.


Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes . Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics. Introgression of Neanderthals and Denisovans left genomic signals in anatomically modern human after Out-of-Africa event. Here, the authors identify a third archaic introgression common to all Asian and Oceanian human populations by applying an approximate Bayesian computation with a Deep Learning framework. The migratory routes used by anatomically modern humans (AMH) after the African diaspora and aspects of the interbreeding between AMH and presently extinct hominins living at the time in Eurasia  are still under debate. Recently, several genetic studies have argued that there was only one main Out of Africa (OOA) event8 that happened less than 100 Kya, with earlier dispersals, which most likely does not contribute much to present-day variation11. Sequencing of ancient Neanderthal and Denisovan fossils supported introgression events into AMH out of Africa;13 however, recent studies also support the presence of gene flow from AMH into Neanderthals15, thus suggesting a complex hominin evolution.All modern humans are genetically related to each other at a time depth of up to 300 thousand years ago (Kya)8. Moreover, the geographic limits of Denisovan introgression are not well established16. Interestingly, Australian Aborigines also harbour high amounts of EEH due to several introgression events12. Although the evidence for Denisovan introgression in Oceanian populations is clear, the amount of introgression varies between 3 and 6% depending on the methodology17. Also, there is disagreement about the number of introgression events necessary to explain patterns of admixture in modern Australian Aborigines11. The second main point is to identify all the cryptic ghost archaic populations that have introgressed with hominins with known genomes . It has been suggested that other archaic hominins could have interbred with Denisovans16. Furthermore, introgression of extinct hominins beyond those of Neanderthals and Denisovans into some AMH populations, both within Africa18, as well as in South Asia6 and Tibetan populations19 has been proposed. Recently it has been also found that there could have existed two different pulses of Denisovan admixture in East Asia20.A complex demographic model considering archaic introgressions out of Africa is needed to properly address two main points. First, the number of introgression events from Neanderthal and Denisova into AMH, which remains controversial, and their impact on the AMH gene pool. A difficult point is to account for the higher amount of Neanderthal introgression in Asia than in Europe21, requires manual expertise22 and/or fitting23. Consequently, all of these different demographic models have not been tested together using the same methodology. Furthermore, it would be interesting to have an estimation of the parameters that define a demographic model given the data. However, this is not available in commonly applied algorithms (i.e. Admixtools23). Within this context, Approximate Bayesian Computation (ABC) is a flexible statistical framework that allows estimating the posterior distribution of a parameter/model through the generation of simulated datasets for cases when there is no close-form of the likelihood of the function24. ABC is widely used in the field of population genetics25. However, identifying the proper transformations of the data to generate informative summary statistics (SS) is model and parameter dependent, and including non-informative redundant SS can jeopardize the performance of the ABC approach22. Jiang et al.26 recently proposed a theoretical improvement of the ABC framework by considering Deep Learning (DL) for generating informative SS from a set of (raw) SS. DL is a type of Artificial Neural Network (ANN) topology based on multiple hidden neural layers, and it has been used for population genetics inference in non-ABC frameworks27. Since ANN performs a nonlinear transformation of the input features towards the output28, DL provides an optimal way of extracting and maximizing the non-redundant information out of the raw SS26. Thus, a DL can be trained using a large number of raw SS as input features to predict the parameters that generated the simulated data, or to classify a simulated data in a set of models, and use this classification prediction or parameter estimation as a new SS (SS-DL).However, comparing the likelihood of competing complex demographic models given the observed data is cumbersome29. This statistic is the core of many frequency based statistics applied in population genetics for distinguishing among competing topological trees and detecting archaic introgression , determining migration rates, time of split and/or differences in the effective population sizes in models of two populations that split and migrate (i.e. Fst29). Moreover, the SFS is not affected by recombination30. SFS has been shown to allow robust demographic estimates31 and the folded SFS has been previously used in classical ABC frameworks for estimating the population size32. However, SFS is high dimensional and it combinatorically increases on the considered number of samples and populations29. Our proposed methodology takes advantage of the nonlinear nature of the DL for compressing the SFS to extract the underlying patterns defined by all the dimensions of the SFS that allow distinguishing among proposed models or obtaining the value of the demographic parameters of interest. This SS-DL is then used in an ABC framework.In the present study, we considered the multidimensional absolute site frequency spectrum (SFS) as raw SS. SFS accounts for the number of single nucleotide polymorphisms (SNPs) present in a particular combination of derived alleles in the sampled populationsWe apply our newly developed method in a large set of whole genome sequences of present and ancient remains to estimate the posterior probability of competing complex demographic models with a focus on introgression events. We find that ABC-DL is powerful for distinguishing between plausible introgression models and propose a third archaic introgression event happened , which is common to all Asia and Oceanian populations.16. Using a common variant calling , we found with D-statistics and F4 ratio test that all Asian populations  have higher amounts of Neanderthal ( > 1%) and Denisovan ancestry ( > 1%) compared to Europeans (Table 33 and Denisovan12) gave different results  and statistically significant (Z score > 3). In contrast, when using Denisovan as outgroup, this estimate diminishes and loses statistical significance (~0% ± 0.15%). We then used simulations considering different demographic models .16 has been considered in all models, and this introgression does not affect directly our core results. From this basic model, several variations have been proposed to better fit the genetic data; here we consider the following. Model B: decrease of European Neanderthal ancestry due to admixture with a modern human, “basal Eurasian”, a ghost population non-introgressed by Neanderthals (Xn)34. Model C: two introgression events from Neanderthals, the first affecting all OOA populations and the second only affecting Asia36. Model D: two introgression events both from Neanderthals and Denisovans, with a Denisovan introgression on Asians before the split of Oceanian populations16. The remaining models have a single introgression of Neanderthals and Denisovans (as in Model A) but with an introgression to Asian and Oceanian populations from an extinct (Xe) hominin population that is a sister group of Neanderthals (Model E), or is a sister group of Denisova , or is an outgroup of both Neanderthals and Denisovans . Given the recently discovered Neanderthal–Denisovan hybrid37, we also considered a scenario in which this extinct hominin is an admixed population between Neanderthals and Denisovans (Model H)37, a similar model of a trichotomy as will be seen below. Furthermore, Model E and Model F can be considered particular cases of Model H when the percentage of Denisovan admixture is 0 or 100%, respectively. In all the models, the basic tree structure remained constant although all the demographic parameters—including the amount of introgression- were estimated.We considered several plausible competing demographic models which describe scenarios that have been proposed by different studies to explain the observed genetic diversity of introgression patterns among current old world AMH populations, Neanderthals and Denisovans see Fig. . The impsim) with posterior probability P(Modelsim = Modelabc | Data) > 50% in all the models. When comparing the eight considered models by ABC-DL with the observed data, the ABC model inference supports model H (P(Model = H|Data) = 0.46), namely the introgression of genes from an archaic Denisovan-Neanderthal admixed extinct population (Xe) into Asian AMH populations, before the split of Oceanian groups, closely followed by Model F (P(Model = F|Data) = 0.38), which models Xe as a sister population of Denisovans. Model H is slightly more likely than Model F (1.2 times more likely), and much more likely than models E (5 times more likely), G (7.6 times) and D (107 times). Models not considering the presence of an extinct archaic ‘ghost’ population introgressing AMH -A, B, C and D- obtained a posterior probability of ~0 . The confusion matrix (Supplementary Table 38), whereas the split between African and OOA populations took place 121 Kya (CI from 78 Kya to 167 Kya); (ii) the Denisovan introgression to Oceanian populations was 1.6% (CI from 0.4% to 2.5%) and took place 43 Kya (CI from 29 Kya to 50 Kya); finally, (iii) the estimated amount of introgression in the AMH ancestor of current Asian populations by the extinct archaic population Xe was 2.6% (CI from 0.7% to 4.6%) at 51 Kya (CI from 45 Kya to 58 Kya). According to our analyses, Xe appeared 304 Kya (CI from 211 Kya to 375 Kya) from an admixture event of Denisovans and Neanderthals that would have occurred only 14 Kya after the divergence of Denisovans and Neanderthals . The estimated divergence between Denisovan and Neanderthals is relatively recent compared to the estimated in16 (381–473 Kya when considering a mutation rate of 0.5e-09 per bp per year or 1.45e-08 per generation assuming 29 years by generation) but higher than in16 (190–236 Kya when considering a mutation rate of 1e-09 per bp per year or 2.9e-08 per generation). Since the number of non-shared variants depends on the time of divergence, the genetic drift at each population and the mutation rate, a possible explanation for the differences in time of divergence could be the mutation rate, which substantially variate among studies. Demographic parameters estimated for Model F are similar in magnitude to the ones estimated in Model H, with credible intervals that overlap the ones obtained for Model H .The ABC-DL analysis supports that all Asian and Oceanian populations, including East Asians, received an introgression from an unknown extinct archaic hominin population. However, the exact relationship of this extinct hominin population with the other known archaic populations is not completely disentangled. The two models mostly supported by our ABC-DL model comparison suggest that Xe corresponds to one of the two sister-Denisovan lineages (Model F) or this hominin was closely related to the Neanderthals and Denisovans with a slightly greater similarity to Denisovans than to Neanderthals (Model H). In our analyses, Model H is slightly better supported than Model F. Nevertheless, the Bayes factor between Model H and F is so close to one that the difference in the posterior probability of the two models is hardly worth mentioningry Table . Therefo6 or Tibeto-Burman). The admixed Neanderthal–Denisova archaic ghost population of Model H that introgresses in Asia also explains previous results showing that Asian populations have a higher amount of Neanderthal and Denisovan introgression than Europeans16. Furthermore, both most supported models agree with the conclusion recently reached by Browning et al.20 that proposed two Denisovan-like introgressions in Asian and Oceanian populations using a completely independent methodology. However, Browning et al.20 proposed that Altai Denisovan-like admixed with East Asians whereas the same sister-Denisovan population would have introgressed with Asian and Papuan populations. In our model comparisons we had not considered such model given that East Asian, South and South-East Asia populations showed a similar amount of Denisovan ancestry in our analyses; we considered a shared Denisovan-like ancestry from the same population source as a more parsimonious scenario than the described in20. Similarly, Neanderthal dilution in Europeans is also suggested before40. In our analyses, the only model considering Neanderthal dilution in Europeans (Model B) is not supported compared to models that consider introgression from unknown hominin. This result does not necessarily exclude Basal Eurasian admixture, as we have not considered more complex models considering Neanderthal dilution in Europeans and archaic introgression in Asian and Oceanians, which we disregarded a priori as less parsimonious than the considered ones. Nevertheless, we would like to point out that the less Neanderthal ancestry in European compared to Asians can be partially explained  by the Model F/H due to shared ancestry  between all EEH populations.Independently of this limitation, both F and H models can explain some previously contradictory results. For example, they would explain the dearth of African ancestry in some populations  in Model H compared to previous estimates8. However, taking into account the percentage of Xn introgression in Oceania, the total amount of Denisovan-like introgression is 4.2%, within the range of proposed values in Oceania8. Similarly, it has been suggested that the introgressed EEH populations split off from the Altai and Denisovan samples  quite early16. In principle, this could affect the estimated percentage of Neanderthal introgression out of Africa and the Denisovan introgression in Oceania. Nevertheless, this sample bias cannot explain the relative increase of both Neanderthal and Denisova ancestry in Asian populations compared to Europeans , which seems highly unlikely. Similarly, it has been proposed that the Neanderthal ancestry is diminished over time by differential negative selection acting stronger in Europe. Although it is accepted that Neanderthal ancestry decreases over time in European populations most likely by negative selection45, it is unclear why this process would not be similar in Asian populations46. We also have not inspected a model where a population that is an outgroup of both human and Neanderthal–Denisova lineages has introgressed in Asian populations. A similar population has been hypothesized to have introgressed into Denisovans16, but an introgression from such a population into Asians will not result in the observed Asian excess of Neanderthal and Denisova ancestry compared to Europeans as detected by D-statistics and can be omitted from the analysis.In the same context, there are other demographic models that have not been considered here, since they are not relevant for our conclusions. The exact relationship of Oceanian populations with Eurasian populations is contested. Some studiesIn conclusion, we have implemented a method that couples ABC with DL that allows to use all the data at the same time and properly comparing complex demographic models. Our novel analytical approach based on ABC-DL supports a model of human evolution in which the OOA populations have had introgression not only from Neanderthals and Denisovans, but also from a third, related group, still genetically and archaeologically uncharacterized. However, the whole genome SFS approach that we used in our ABC-DL implementation does not consider additional information—such as the length and nature of the introgressed fragments—that can be important for distinguishing between some of the models. Further development of the ABC-DL framework will be required to include the fragment length of the ancestry of the genomic fragments. Similarly, new analyses and ancient genome sequences will be required to better understand the nature and consequences of this third related group in the genome of modern humans.47, Simons Genome Diversity Project (SGDP)8 and Mondal et al. 20166 (available at European Nucleotide Archive: PRJEB11455 and PRJEB16019) 43 and one Denisova (DENI)12 BAM files from their respective sites. In case the BAM files were not accessible, we mapped the FASTQ files ourselves to create BAM files. All the information on the samples and their respective origin is mentioned in Supplementary Table We used already published and publicly available data from 1000 Genome Project 3rd Phase high coverage data5 thus removing repeated regions . We have also used two Irulas from SGDP data set to map on the chimpanzee genome reference to exclude any biases from the reference genome . We used Admixtools1.423 to calculate D-statistics and F4 ratio test. We developed a pipeline .We have used the mapability mask as suggested previously21. Each simulation comprised simulating 9643 genomic regions, comprising 651 Mb, and one diploid individual per population using the demographic topology of one of the proposed trees , we scaled the mutation rate μr of each region r by the fraction of included fragments (Lc) over the total length of the region (Lr):52, using the script postpr with option mnlogistic for model comparison and the script abc with option loclinear for parameter estimation.In order to statistically test among competing demographic models and estimating the posterior distributions of the parameters of a given model, we developed an ABC-DL approach using as raw summary statistic the SFS . For each population we considered two samples, except in the case of Neanderthal and Denisovan, where we only considered the Altai Neanderthal and Denisovan individuals. Simulations were generated using FastSimcoal253 (see Supplementary Note 2). An innovative aspect of our implementation of DL is the development of SFS-like noise injection. The latest hyper-parameter is motivated by the fact that the DL is trained with data simulated from the proposed models of interest, whereas the real model that generated the observed genomic data is -by definition- more complex and (at best) partially overlaps/generalizes with (some) of the considered models. In this case, it can be expected that a trained DL with data from models different from the real one will produce biased SS-DL with regards to the real data. In our study, we propose overcoming this problem by applying an innovative modified version of the noise injection algorithm4. In the classical injection algorithm, white noise  is dynamically added at each iteration to the elements of the training data set in order to force model generalization. However, properly adding white noise requires independence between the input variables, which is not the case of the considered SS. In order to perform a noise injection-like approach in the case of the SFS statistic, we took advantage that we have two individuals for each population—with the exception of Neanderthal and Denisovan. We split the observed data set in two, one comprising samples that will be used to add “observed data-like” noise to the simulated SFS, and a second one that will be used for the estimation of the posterior distributions using the ABC approach. At each iteration of the DL training algorithm, we define for the j cell of the SFS of simulation i from model s:α is sampled from a uniform distribution in the range  and r corresponds to the observed “real” data. Introducing noise from an independent observed data set offers an additional advantage. By analogy with image detection, we can imagine that the simulated training data corresponds to a sharp high-resolution image of an object from the known simulated model/parameter, whereas the observed r data is at best an image showing one of the model/parameter objects at low resolution on a foggy environment (i.e. the parts of the model generating the data not considered in our models). This difference between the data used for training and the final observed data that we want to classify can introduce biases in the final model classification. By generating new SFS patterns by means of noise injection, increasing robustness in the network classification against model departures can be expected.For the DL topology, we generated a supervised four layer feedforward DL network using Encog3.4https://github.com/oscarlao/ABC_DL to (i) generate FastSimcoal2 input files from the prior distributions of each parameter and read the SFS from the simulation, (ii) implement feedforward DL using the JAVA Encog3.453 and (iii) generate input files for ABC analyses with the R package abc52. Details of the full implementation of the DL and ABC-DL algorithm are provided in the Supplementary Note 2.We implemented a JAVA-based pipeline available at Further information on experimental design is available in the Nature Research Reporting Summary linked to this article.Supplementary InformationPeer Review FileReporting Summary


Fine roots of plants play an important role in terrestrial ecosystems. There is a close association between the anatomical characteristics and physiological and ecological functions of plants, but we still have a very limited knowledge of anatomical traits. For example, (1) we do not know if herbs and grasses have anatomical patterns similar to those of woody plants, and (2) the variation among different woody plants in the same ecosystem is unclear. In the present study, we analysed the anatomical structures of the fine root systems of various groups of vascular plants  from the same ecosystem  to answer the following questions: (1) How does the anatomy of the fine roots change with root order in various plant groups in the same ecosystem? (2) What is the pattern of variation within group? The results show that anatomical traits can be divided into 3 categories: traits that indicate the root capacity to transport resource along the root ; traits that indicate absorptive capacity cortical thickness, ; and traits that are integrated indicators (diameter and the stele to root diameter ratio). The traits indicate the root capacity to transport resource along the root order is generally similar among groups, but absorptive capacity is very different. The shift in function is the main factor influencing the fine root anatomy. Some traits show large variation within groups, but the variations in other traits are small. The traits indicate that the lower-order roots (absorbing roots) in distinct groups are of the first one or two root order in ferns, the first two or three orders in eudicot herbs, the first (only two root orders) or first two orders (more than three root orders) in monocots and the first four or five root orders in woody plants and the other roots are higher-order roots (transport roots). The result will helpful to understand the similarities and differences among groups and the physiological and ecological functions of plant roots. Owing to unique trait patterns , 2, moreThe anatomical structure of fine roots is thought to be closely associated with their function –10. For st-order roots of woody plants mainly perform absorption, while the roots higher than the 4th order greatly reduced this function . InIn august of 2012 5 to 10 individuals of each species were randomly sampled. Then the root was dipped in water. After removal of most soil by running water, lateral roots were dissected. The partial root system was put in a culture dish and carefully cleaned using a little brush while observing through a magnifying glass. Individual roots were dissected by root order and then cleaned with deionized water and immediately fixed in a formalin-acetic acid-alcohol (FAA)  for anatomical analysis.st order, and 20 segments were chosen for all the other orders. All the root segments were stained with safranine-fast green (2%), dehydrated in 70, 85, 95 and 100% alcohol and then embedded in paraffin; then, 8-μm sections were mounted on glass slides [st order roots) or the branching point (for higher-order roots) to the root base [We define a “fine root” as roots less than 5 mm in diameter. The roots were then divided into different branch orders following the procedure described by Pregitzer et al. (2002). For each species, 30 root segments were randomly chosen from different plants for the 1oot base . The sliFor each transverse slice of the roots, a range of anatomical features including root diameter, cortical thickness, stele diameter, xylem cell diameter (this is tracheids for gymnosperms and pteridophytes and vessels for the other groups), xylem cell area, diameter of the cortical cells, and number of cortical cell layers were measured to the nearest 1 μm  using MoThe mean, standard deviation and coefficients of variation of root morphological, histological and chemical characteristics were calculated for each root order by species. Fisher’s LSD test (P = 0.05) was used to test the differences in the root characteristics among the orders for each species when the data pass the checking for normal distribution and rank sum test (P = 0.05) was used when the data did not pass the checking. Simple regression analysis was used to determine the relationships among traits. All statistical analyses were performed using SPSS software .The “Mao'er Mountain Experimental Station” is a subordinate organization to “Maoer Mao'er Mountain teaching area” of Northeast Forestry University. The study was approved by Chang song Li, the director of Maoer Mao'er Mountain teaching area.There were some similarities among groups as diameter, stele diameter, xylem cell diameter and xylem cell area increased with increasing root order in all groups Figs  and 2. Tst order roots were slightly lower than those of the 2nd to 3rd orders, and the difference in stele to diameter ratio was not significant in monocots  was higher than that of the 1st to 3rd orders , and the stele to diameter ratio of the 5th to 7th orders was largest in woody plants (0.52–0.70). The diameter of the 2nd to 7th orders differed significantly between adjacent orders (224 μm to 3516 μm), but the diameter of 1st to 4th was similar. Some roots, such as those of the 5th to 7th orders of woody plants, showed strong within-group variation. The main reason for this phenomenon was that most plants had only or less than 5 root orders; only 12 species had 6th order roots, and 3 species had 7th order roots.There were also some differences among and within groups. There was little difference in the diameter, stele diameter and stele to diameter ratio among orders in monocots . The diad orders . The 3rdst and 2nd order, the 3rd and 4th order tracheids area of ferns was not significantly different from those of the 1st and 2nd order. Second, the variation in xylem cell area in eudicot herbs was higher than that in xylem cell diameter and stele diameter. , traits that indicate absorptive capacity  and traits that are integrated indicators (diameter and stele to diameter ratio).With increasing root order, the fine roots require an increased capacity for axial transport , so the Traits related to the absorption function  were very different among groups. The cortical thickness, number of cortical cell layers and diameter of the cortical cells of higher-order roots decrease markedly in woody plants , 26, 27,Given the negative correlation between the radial and axial transport capacity of roots, there is apparently an increasing need to reduce radial transport and thereby ensure axial transport with increasing root order , 30. ButThe lower-order roots of eudicot herbs, monocots and woody plants as well as ferns  apparentPinus korainsis) in this area is higher than the diameter of the fine roots of angiosperms [The woody plants in this study have relatively small fine root diameters. There may be several factors contributing to this phenomenon. First, the plants in the study were all temperate plants, and temperate plants have significantly smaller root diameter than tropical plants . Recent iosperms  but the Actinostemma tenerum Griff.) had only 1 order. It was a major resource of variation within group. Despite these differences, the highest order always had the largest stele diameter, so the greatest variation was in the middle orders. This may imply that the 1st and highest order were similar among species; the only difference was how many orders exist between the 1st and the highest order. There was an analogous situation in groups. tend to form finer diameters Second, some traits that were influenced by the environment also contribute to the variation. The root diameter of some trees is conserved [Remarkable variation was observed within each group. There were 3 factors contribute to the phenomenon. First, the number of root order were various within groups. For example, in 51 eudicot herbs species, 7.8% had 5 orders; 27.5% had 4 orders; 51.0% had 3 orders; 11.8% had 2 orders; and 1 species ; even tFine roots are generally defined according to diameter  , 50, 51,st to 4th order in cortical thickness in woody plants, which implies that the 1st to 4th order of woody plants can be called “lower-order”. We think there are some reasons that contribute to the phenomenon of “cortex does not decline until the 5th order roots”. First, some species show a very different pattern. Such as Menispermum dauricum, a vine, has thicker cortex in the higher order. Second, the cortex of some species will increase in the 3–4 order (tape A) while the thickest cortex of other species is 1–2 order (type B)  and higher-order roots (transport roots). Such as there were no significant difference among 1 B) Figs  and 7. Ties Figs  and 9. Hrd- to 5th-order traits were higher-order roots (transport roots).The boundary was different when using evidence from different traits. Most traits indicate that the first 2 or 3 root order were lower-order roots (absorbing roots) in eudicot herbs, and the 3st order (only two root orders) or the first two orders (three root orders).Most monocots had only two root orders; some had three root orders. In monocots, the boundary will shift with the number of root orders. The so-called lower-order roots (absorbing roots) will be of the 1st order was lower order (absorbing roots), but some other traits, e.g., stele diameter, cortical thickness and number of cortical cell layers, support the view that the 1st to 2nd orders were lower orders (absorbing roots) in ferns.The boundary was different in ferns when using the evidence from different traits. Some traits, e.g., xylem cell diameter, indicate that the 1st to 5th root order in the traits that indicate the root capacity to transport resources along the root. But there were no significant differences among 1st to 4th root order in the traits that indicate absorptive capacity. Presence of a periderm is a key trait associated with loss of absorption and loss of mycorrhizal colonization. The percentage of presence of a periderm increase with the orders. In most species  this percentage increase sharply to 20% to 67% in the 5th order [th to 5th order root. The first four or five orders were lower-order roots (absorbing roots) and the other roots were higher-order roots (transport roots) in woody plants.The situation was complex when we discuss the boundary in woody plants as there were conflicting observations. There were significant differences among 1Of course, these boundaries were not exact due to differences among species. Such as there was no “absorbing roots” and “transport roots” in Actinostemma tenerum Griff. because having only one root order. Furthermore, there were many differences within species. Such as: the coefficient of variation of stele diameter in the 5th root order of Spiraea chamaedryfolia up to 49%; in the 3rd root order of Betula platyphylla, 39% of roots in the stage of deutoxylem, 51% of roots in the stage of having vascular cambium, 10% of roots in the stage of having cork meristem.st (only two root orders) or first two orders (more than three root orders) in monocots and the first four or five root orders in woody plants and the other roots were higher-order roots (transport roots).The traits that indicate transport ability were always similar among groups, but the traits that indicate absorptive capacity differed greatly. The shift in function was the main factor that influences the anatomy of fine roots. Some traits show large variation within groups, but the variations in other traits were small. The traits indicate lower-order roots (absorbing roots) were the first 1 or 2 root order in ferns, the first 2 or 3 orders in eudicot herbs, the 1S1 Table(XLS)Click here for additional data file.S2 Table(XLS)Click here for additional data file.S3 Table(XLS)Click here for additional data file.S4 Table(XLS)Click here for additional data file.