IntroductionThe recent novel coronavirus disease 2019 (COVID-19) pandemic has brought the world to a standstill. This outbreak not only affected healthcare systems but the resultant economic losses were also enormous. COVID-19 has demanded that the health care systems globally evolve, develop new strategies, identify new models of functioning, and at times, fall back on the old conservative methods of orthopedic care to decrease the risk of disease transmission. Although, the majority of hospitals are refraining from performing elective surgeries, emergent and urgent procedures cannot be delayed. Various strategies have been developed at the institute level to reduce the risk of infection transmission among the theatre team from an unsuspected patient (asymptomatic and presymptomatic) during the perioperative period.Material and methodsThe present study is a part of an ongoing project which is being conducted in a tertiary level hospital after obtaining research review board approval. All patients admitted either for vertebral fracture or spinal cord compression from February 2020 to May 2020 were included. The present study included 13 patients  with an average age of 35.4 years The oldest patient was of 63 years which is considered a risk factor for developing severe COVID-19 infection. ResultsEight patients (61.5%) presented with spinal cord injury (SCI) due to vertebral fracture with fall from height (87.5%) as the most common etiology. Among the traumatic SCI patients, six (75%) were managed surgically with posterior decompression and instrumented fusion with pedicle screws while two patients (25%) were managed conservatively. There were four patients (30.8%) of tuberculosis of the spine of whom two (50%) were managed with posterior decompression, debridement, and stabilization with pedicle screws, samples for culture, biopsy, and cartridge-based nucleic acid amplification test (CBNAAT) were collected during the procedure; for the remaining two patients (50%), a trans-pedicular biopsy was performed to confirm the diagnosis for initiation of anti-tubercular therapy. Prolapsed intervertebral disc causing cauda equina syndrome was the reason for emergency surgery in one patient (7.7%). COVID-19 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription-polymerase chain reaction (RT-PCR) test was performed in four patients (30.8%), in whom the most common symptom was fever (two patients (50%)). These patients were residents of high prevalence area for COVID-19 infection. Sore throat (25%), fatigue (25%), and low oxygen saturation (25%) were present in one patient which prompted us to get the COVID-19 test. All patients were reported negative for COVID-19.ConclusionThe structural organization and the management protocol we describe allowed us to reduce infection risk and ultimately hospital stay, thereby maximizing the already stretched available medical resources. These precautions helped us to reduce transmission and exposure to COVID-19 in health care workers (HCW) and patients in our institute. The aim of this article is that our early experience can be of value to the medical communities that will soon be in a similar situation. The recent novel coronavirus disease 2019 (COVID-19) pandemic has brought the world to a standstill. This outbreak not only affected the healthcare systems but the resultant economic losses were enormous. COVID-19 has demanded that the health care systems globally evolve, develop new strategies, identify new models of functioning, and at times, fall back on the old conservative methods of orthopedic care to decrease the risk of disease transmission.The usual incubation period of the disease is 5-14 days but with reported outliers up to 24 days .Infection among health care workers (HCWs) is further straining the already overburdened workforce due to a sudden spike in the caseload. Although, the majority of hospitals are refraining from performing elective surgeries, emergent and urgent procedures cannot be delayed. Various strategies have been developed at the institute level to reduce the risk of infection transmission among the theatre team from an unsuspected patient (asymptomatic and presymptomatic) during the perioperative period ,3.India has rapidly surged its capacity of reverse transcription-polymerase chain reaction (RT-PCR) testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) but with its 1.3 billion population and a rapidly increasing infection rate, a selective testing approach was adopted initially. The policy regarding testing in India formulated by the Indian council of medical research (ICMR) has been revised with evolving evidence regarding the spread of infection . Since testing could not be performed in all patients in need of surgical intervention due to time or resource constrain, nor an initial negative test can surely rule out infection, a “consider all positive” approach was adopted by the authors' institute to manage patients requiring emergent or urgent care including the available recommendations regarding reducing the risk of exposure to the surgical team during the perioperative period,We developed a “caution at each step” model in an effort to minimize the risk of exposure to the theatre team from an unsuspected patient. In this study, we elaborate on this model in detail along with our experience of its use in emergency spine surgery cases.The patients participating are also part of an ongoing prospective study on spine injuries at the authors' institute for which institutional ethics committee approval has been obtained. All patients admitted either for vertebral fracture or spinal cord compression from February 2020 to May 2020 were included. The spine conditions included were spinal cord injury (SCI), epidural abscess, epidural hematoma, close reduction of cervical facet dislocation, cauda equine syndrome, surgical spine tumor with spinal cord compression Table . No COVIMethodsThe detailed description of the steps which we took is mentioned below and briefly in Table Precautions at admissionAt presentation, history was recorded and clinical examination performed. The temperature and oxygen saturation at room air recorded for every patient. All patients were screened with a series of questions related to COVID-19 symptoms  as well as TOCC information  . InformaIn the case of history or examination suggestive of COVID 19, the patient was isolated and tested. However, none of the emergency surgeries was delayed while awaiting test results. The sample was sent and surgery was conducted by donning full prescribed personal protective equipment (PPE).Preoperative precautionsPreoperatively, patients and attendants explained about the precautions and measures  recommended by hospital authorities because of COVID-19 pandemic. The patients were provided with a surgical mask throughout the perioperative period. The patient was transferred to an operation theatre only on-call from the operation theatre to avoid overcrowding. The individual operating rooms have separate air-handling units with high-efficiency particulate air (HEPA) filters.Precautions in the operation theatreIntraoperatively, the anesthesia team consisted of a consultant, senior resident, junior resident, and an anesthesia technician. All preparation for general anesthesia was performed by the anesthesia team before shifting the patient to the operation table, during intubation either the consultant or the senior resident intubated the patient donning the prescribed PPE which consisted of Association for the Advancement of Medical Instrumentation (AAMI) level III gown, hood, N95 mask, face shield, boot covers, and gloves. The junior resident or the anesthesia technician was available to assist during the procedure . During Wound closure was done over the drain with staplers and the occlusive dressing was applied.During extubation, theatre personnel was limited to the anesthesia team and the patient was allowed to recover in the operating room to minimize the shifting to the recovery room. In case there was any other emergency case waiting for surgery the patient was shifted to the recovery room .For the cases performed under local anesthesia like a transpedicular biopsy, the team inside the operating room was limited to surgeon, scrub nurse, and radiology technician to operate a C-arm image intensifier. After the procedure, the patient directly shifted to the ward.As per institutional policy, following the procedure. the surfaces of all equipment in the operating room  were thoroughly wiped down after each case. The surgeon and the surgical team changed scrubs after each case. Respirators (N95) were not discarded after each use unless soiled. A new respirator is required each day. As per institutional policy, the N95 masks were reused up to five times unless visibly soiled.Precautions in the recovery roomIn the recovery room, patients were separated from each other by a minimum distance of two meters (six-feet). Personnel taking care of the patient wore an N-95 mask as the patient is under the effect of general anesthesia, might not have control over cough and sneeze. However, the patient’s stay in the recovery area was minimized while maintaining perioperative safety. Patients were made to wear a triple-layer surgical mask in the postoperative period. Over-crowding and non-essential personnel traffic were restricted.Post-operative care protocolsPostoperative rounds were done by the senior resident and informed to the chief surgeon telephonically. The surgical wound was inspected by the resident wearing an N95 mask on the third postoperative day and the drain, if any, was removed. The patient was usually discharged on the same day if the wound was healthy after teaching physiotherapy and other precautions to the patient and attendant to minimize the hospital-stay. For procedures that were performed under local anesthesia, the patients were discharged the next morning. Suture removal was advised to be done at a local hospital. Institute telemedicine number and the resident’s contact number was provided to the patient to consult in case of any surgery-related problem and to schedule follow up.The present study included 13 patients  with an average age of 35.4 years (range- 42-63 years).Eight patients (61.5%) presented with SCI due to vertebral fracture with fall from height (87.5%) as the most common etiology. Road traffic accidents accounted for only one patient as the cause of SCI. Among the traumatic SCI patients, six (75%) were managed surgically with posterior decompression and instrumented fusion with pedicle screws while two patients (25%) were managed conservatively. There were four patients (30.8%) of tuberculosis of the spine of whom two (50%) were managed with posterior decompression, debridement, and stabilization with pedicle screws, samples for culture, biopsy, and CBNAAT were collected during the procedure; for the remaining two patients (50%), the trans-pedicular biopsy was performed to confirm the diagnosis for initiation of anti-tubercular therapy. Prolapsed intervertebral disc causing cauda equina syndrome was the reason for emergency surgery in one patient (7.7%). COVID-19 (SARS-CoV-2 RT-PCR) test was done in four patients (30.8%), in whom the most common symptom was fever (two patients (50%)) and all these patients were residents of high prevalence area for COVID-19 infection. Sore throat (25%), fatigue (25%), and low oxygen saturation (25%) were present in one patient each patient which prompted us to get the COVID-19 test. All patients were reported negative for COVID-19. Among the traumatic SCI patients, four were operated within 48 hours of injury as they were referred from other centers after primary care. All patients were managed within 24 hours of admission. The average hospital stay was 2.7 days (range four to five days) . Inside operation theatre it is important to limit the number of staff allowed as SARS-CoV-2 is mainly transmitted via aerosolized droplets, so by decreasing the air turbulence and the number of air particles decreases the disease transmission; it will help in implementing the social distancing concept while also decreasing the demand for PPE ,11,16-18To decrease the risk of transmission from airborne droplets it is mandatory to use PPE. The surgical team must wear PPE which includes AAMI III gowns, gloves, face masks, and N95 with face shield/goggles to minimize the risk of transmission and cross-infection ,11,12. AoC exposure for 60 minutes as an accepted method for decontaminating the N-95 masks. Further, it is documented that the COVID-19 virus does not survive on inanimate surfaces beyond a period of five days [At our institute, N-95 masks are reused unless they are visibly soiled. Each HCW is given a set of five N-95 masks that are numbered from 1 to 5 and HCWs are supposed to write their name and number over it. After the duty shift, HCWs are supposed to put it in sealable plastic cover and next day use the next mask. The masks are deposited at the designated place from where the infection control nurse (ICN) collects them for drying under the sun on two consecutive days for at least nine hours/day. The masks are issued to the same user only after the fifth day of submission. Each mask is used maximum for five times. Subsequently, the mask is disposed of appropriately. Single-use of the N-95 mask is recommended if it is contaminated with blood, respiratory or nasal secretions, or other bodily fluids from patients. It should be discarded following close contact with or exit from, the care area of any patient co-infected with an infectious disease requiring contact precautions, and if it is damaged or clogged. The rationale behind this is dry heat 70ive days ,21. As per the advisory issued by the Ministry of health and family welfare on re-processing and re-use of eye-protection (goggles), the goggles are to be reused; after each use, the goggles are cleaned with soap and water and then immersed in freshly prepared 1% sodium hypochlorite for ten minutes. This is followed by cleaning with water and then allowed to air dry completely and then store in clean cover. The goggles are to be discarded if broken or rendered optically non-clear on repeated usage. The recommended maximum reuse is for up to six times . These mOur surgical team was on HCQ prophylaxis as recommended by the ICMR in a dose of 400 mg twice a day on day one and 400 mg once a week for seven days . HCQ hasIt is not recommended for prophylaxis in children under 15 years of age and during pregnancy and lactation . The aerosols generating procedures in orthopedic surgery include the use of electrocautery, high-speed burr, ultrasonic devices, and power tools like an oscillating saw, drills, reamers, and pulse lavage . While iThe postoperative length of stay in the hospital should be minimized. The post-operative care  can be managed at the patient’s home or the nearest hospital. The patient is instructed to perform self-directed physical therapy at home and transfer to inpatient rehabilitation should be minimized which can significantly reduce the length of hospital stay ,17,19,25Post-discharge visits to the hospital have been minimized with the majority of the follow-up by the surgical team through telemedicine or remote consultations (e.g. telephone or video consultation). The hospital visits were limited to those who are having issues/complications such as wound healing problems, suspected fracture, stiffness, and non-compliance to physiotherapy ,7,11-13.There are chances of a “second wave” which were seen in SARS and Spanish flu which may lead to a sudden increase in COVID-19 cases . We needThe above structural organization and management protocol helped us to provide efficient care to emergency spine conditions, without undue stretching the resources of a tertiary care center which is also catering to a large number of COVID-19 patients. An attempt is made to reduce infection transmission to health care workers without compromising the patient's safety.We recognize that the small patient number is a limitation of this study and follow up is short. We have not assessed the problem faced by a home-based rehabilitation program and is a subject of further researchIn these unusual times of the COVID-19 pandemic, the healthcare institutions must adopt the emerging pieces of evidence on the safety of HCW’s into the existing hospital policies. Usual theatre practices need to be modified to reduce the risk of virus transmission during surgical procedures to the operation theatre team. The protocol we described has enabled our surgical team to work efficiently and safely without compromising on patient care.


There is debate about the extent to which COVID-19 affects ethnic groups differently. We explored if there was variation in hospital mortality in patients with COVID. Mortality rates in 1,276 inpatients in Bradford with test results for COVID-19 were analysed by ethnic group. The age-adjusted risk of dying from COVID-19 was slightly lower in South Asian compared to White British patients. . This could be because of increased exposure, affecting incidence, underlying comorbidities and other factors affecting severity of disease and mortality following infection. There are few reliable data on community prevalence of infection. However, hospital electronic records contain information on ethnicity, test results and mortality. We aimed to explore variations in hospital mortality for people testing positive by ethnic group.There is a concern that COVID-19 may be disproportionately affecting people from ethnic minoritiesth March to 27th April 2020 in a large teaching hospital in Bradford, a city with a diverse population of which 24.9% are of South Asian (20.4% Pakistani) origin2. We compared the mortality rate of those with a positive and negative COVID-19 test result in hospital and explored whether this differential varied by gender, and ethnicity. These de-identified data are available from Harvard Dataverse3.Information on age, sex, ethnicity, COVID-19 test result and death were collected on all hospital patients who were tested for COVID-19 between 18In order to take into account possible confounding due to factors related to age and the likelihood of hospitalisation or of being tested, we estimated the ratio of the risk of death in those tested positive relative to the risk in those also hospitalised, but who tested negative with the same gender or belonging to the same ethnic group, adjusted for age using multivariable regression. Mortality rates of White British and South Asian patients were compared using a chi-square test. All analyses were conducted using STATA/SE software .The recent Health Service (Control of Patient Information) Regulations 2002 notices requires NHS Trusts and others to process confidential patient information without consent for COVID-19 public health, surveillance and research purposes, thus no ethical approval or consent for publication was required.In total, 812 patients tested negative (63.6%) and 464 positive (36.4%). The overall mortality rate in those testing positive for COVID-19 was 23.5% see. This waThe mortality rate in those testing positive for COVID-19 was higher in White British patients (25.4%) than those of South Asian origin (18.1%) but this was not statistically significant . Mortality among non-COVID-19 cases was 10.0% and 8.2% in White British and South Asian patients, respectively.South Asian origin patients were significantly younger than White British patients (mean 49 vs 66 years), reflecting the local demographics. The age-adjusted RR of dying after a positive versus a negative result was 1.98 for women, 2.11 for men, 2.10 for White British and 1.72 for South Asian. The age-adjusted relative increased risk of dying from COVID-19 compared to test negative was lower, though not statistically significantly so, in South Asian compared to White British .Data from the last month of the outbreak in a large District general hospital in Bradford show that COVID-19 increases risk of death for infected individuals compared to hospital patients with similar symptoms with no COVID-19 infection. They also suggest that this increased risk is not greater in people of South Asian (mainly Pakistani) ethnicity.These data are only for hospitalised patients, and do not account for patients who subsequently died after the date of analysis. It also sheds no light on variations by ethnicity in exposure to, risk of coronavirus infection or the severity of COVID-19 illness in the community.https://doi.org/10.7910/DVN/l6ORLP3.Harvard Dataverse: Replication Data for COVID-19 in-patient hospital mortality by ethnicity.‘Covid19EthinicityData’ contains de-identified patient-level data analysed in this study.Creative Commons Zero ‘No rights reserved’ data waiver (CC0 1.0 Public domain dedication).Data are available under the terms of the Many thanks for a well researched and timely piece of analysis from a large teaching hospital with a large population from BAME communities (N.B. South Asian and Pakistani in origin). The dataset can be downloaded from the Harvard Dataverse and includes all the participants listed in the paper to allow for replication of results. I agree with the conclusions and would only ask for the abstract to reflect this - perhaps "The age-adjusted risk of dying from COVID-19 was not significant but slightly lower in South Asian compared to White British patients. ." Otherwise an excellent paper that will add to the evidence base and perhaps this publication will facilitate further consortia combing datasets coming together to improve the evidence base further.Is the work clearly and accurately presented and does it cite the current literature?YesIf applicable, is the statistical analysis and its interpretation appropriate?YesAre all the source data underlying the results available to ensure full reproducibility?YesIs the study design appropriate and is the work technically sound?YesAre the conclusions drawn adequately supported by the results?PartlyAre sufficient details of methods and analysis provided to allow replication by others?YesReviewer Expertise:Public health and epidemiology.I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. This is an interesting and clearly presented study which used hospital data from a large Teaching Hospital in Bradford to explore variations in hospital mortality for people testing positive for SARS-CoV-2 by ethnic group. De-identified data was sourced from the Harvard Dataverse. Mortality for those with positive and negative test results in hospital were explored using a multivariate regression analysis for any variation in outcome by gender and ethnicity, adjusting for a number of confounding factors. The methodological approach seems an appropriate analysis for this study. Amongst other study findings, the study found that mortality for COVID-19 for patients of South Asian (mainly Pakistani) ethnicity was lower  than White British ethnicity. It is important to clarify throughout that tests were performed on symptomatic patients  i.e. there were testing criteria. Where described in the report, the comparison group for this project should be stated as ‘hospital patients (with similar symptoms to positive) tested negative’ or similar. In the study conclusions, further cautious language could be used, for instance there could be a brief discussion regarding the power of the study to detect differences in mortality by sex and ethnicity.Is the work clearly and accurately presented and does it cite the current literature?YesIf applicable, is the statistical analysis and its interpretation appropriate?YesAre all the source data underlying the results available to ensure full reproducibility?YesIs the study design appropriate and is the work technically sound?YesAre the conclusions drawn adequately supported by the results?YesAre sufficient details of methods and analysis provided to allow replication by others?YesReviewer Expertise:Infectious Disease Epidemiology.I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.


Significance: Currently, tissue biopsies are sectioned into 3- to Aim: We aim to show that, by transmission microscopy of optically cleared tissue punches, the tissue architecture can be determined without the need for fluorescent staining.Approach: Transmission microscopy is used by combining bright field microscopy with dark field and epifluorescent microscopy to compare samples that have also been analyzed by fluorescent confocal microscopy.Results: With increasing distance to the focal plane, the higher-frequency part of the spatial frequency spectrum of transmitted light is attenuated increasingly. This property is exploited for tissue segmentation, detecting whether tissue is present at a certain position in the focal plane image. Using this approach, we show that a 3D rendering of the internal cavity or tubules structure of punch biopsies, which are up to 1-mm thick, can be acquired in Conclusions: Images of the overall tissue architecture can be obtained from transmission microcopy; they are similar to those from the confocal microscopy benchmark without requiring fluorescent staining. Tissue clearing is still needed. The total scan time of the present method is significantly shorter at a fraction of the device costs. This development is fueled by the increase in –,More recently, non-destructive 3D imaging of clinical samples has been proposed as a potentially valuable diagnostic tool to image intact biopsiesHere, we report on a system with the unique capability of visualizing the global tissue architecture  in bright field (BF) and dark field (DF), as well as implementing fluorescent detection of cells of interest, which is demonstrated using punches of intact clinical prostate samples.22.1Archival formalin-fixed, paraffin-embedded (FFPE) prostate specimens from patients who had undergone radical prostatectomy for prostate cancer at the Erasmus Medical Center between 2012 and 2017 were included. Specimens were fixed in neutral-buffered formalin, transversely cut into 4-mm slices, and embedded in their entirety for histopathologic evaluation. Regions of interest were selected for 3D imaging using H&E-stained tissue sections and included benign hyperplasia, a benign transition zone, and Gleason 4 ill-formed growth pattern with intraductal carcinoma, which is often correlated with aggressive disease. The use of tissue samples for scientific purposes was approved by the institutional Medical Research Ethics Committee  and was in accordance with the “Code for Proper Secondary Use of Human Tissue in The Netherlands” as developed by the Dutch Federation of Medical Scientific Societies .2.2,Punches of 2.3,This study uses a modified research version of the oCelloscope device.The instrument is equipped with a microscope objective of Prior to the sample scanning, reference images are acquired for flat field correction for all channels to correct for non-uniformities in illumination for BF and DF and excitation light for FL. In addition, these calibration images eliminate non-uniform camera responses. For fluorescence calibration, we use a fluorescent microscope slide .Fluorescently labeled and optically cleared samples were placed in a custom-made cartridgeFor each sample, z-stacks comprising 200 focal planes of two sequentially imaged channels  are obtained to cover the total height of the sample . During 2.4For BF imaging, the scattering of light, due to the mismatch of refraction indices at interfaces between different substances in a tissue, introduces spatial variations in light intensities within the focal plane observed by the scanner. The point-spread function (PSF) describes the response at the image sensor of the imaging system to a point source anywhere in the scanned 3D area. Due to the PSF, points located outside the focal plane will have a contribution to the acquired image. For an increasing distance to the focal plane, the higher-frequency part of the spatial frequency spectrum is attenuated increasingly. This property is exploited for tissue segmentation, detecting if tissue is present at a certain position in the focal plane image. By observing the amount of spatial high-frequent energy present in the spatial local neighborhood of the position in the image, cell tissue is assumed to be present when this energy exceeds a threshold level and tissue is assumed to be absent  when the energy is below the threshold level. By doing this for multiple image positions within multiple focal planes, a complete 3D tissue segmentation of the scanned 3D volume is created. This tissue segmentation has the interesting property that cavities  of sufficient size  and covered with a #1 cover glass  to avoid direct contact of the microscope objective and immersion water with the BABB. Imaging was performed with an upright Leica SP5 confocal microscope  equipped with a long (1.95 mm) working distance 33.1–Typical tissue biopsies and FFPE punches are 5 to 10 mm in length and have a diameter of ut 4 min . In BF mTo assess the validity of the approach, we first compared experimental imaging parameters and resulting 3D images of two clinical prostate tissue punches to confocal microscopy containing either a benign transition zone  or Gleascroscope  and 4. AQuantitative assessment of structural similarity between images is typically done by analyzing metrics such as the structural similarity (SSIM) index3.2As the previous section has shown, a relevant advantage of transmission microscopy is that the information about tubules can be obtained without staining the samples, whereas in confocal microscopy this depends on fluorescent staining. The BF information shows variations in tissue architecture based on scattering properties and is used to create a 3D map of the biopsy morphology, including internal cavities and tubules . In the The data show that it is possible to reconstruct a 3D image of the biopsy, having morphological information based on BF [4–,,–,In the literature, several methods have been described for the analysis of intact biopsies in 3D, including the use of confocal microscopy,,Overall, the analysis of intact biopsies by optical means in 3D may be used to gain further insights in tumor growth patterns over medical imaging as optical imaging offers a 3 orders of magnitude higher resolution (5We have shown that combining transmission microscopy (BF and DF) with an epifluorescence system enables fast (5 min) 3D biopsy visualization. Through the detection of the spatial high-frequency energy from BF images, the internal cavity or tubules structure can be detected without requiring fluorescent staining. We have shown that images of the overall tissue architecture that are similar to those from the confocal microscopy benchmark can be obtained. Tissue clearing is still needed. Furthermore, the total scan time of the present method is significantly shorter at a fraction of the costs. If a faster tissue clearing method would become available, this may open the way to fast 3D assessment of intact prostate biopsies and tissue punches. Finally, we have shown that DF imaging offers additional contrast to BF imaging.Click here for additional data file.Click here for additional data file.Click here for additional data file.Click here for additional data file.Click here for additional data file.


Optical remote sensing images can be used to monitor slope deformation in mountain regions. Abundant optical sensors onboard various platforms were designed to provide increasingly high spatial–temporal resolution images at low cost; however, finding the best image pairs to derive slope deformation remains difficult. By selecting a location in the east Tibetan Plateau, this work used the co-registration of optically sensed images and correlation (COSI-Corr) method to analyze 402 Sentinel-2 images from August 2015 to February 2020, to quantify temporal patterns of uncertainty in deriving slope deformation. By excluding 66% of the Sentinel-2 images that were contaminated by unfavorable weather, uncertainties were found to fluctuate annually, with the least uncertainty achieved in image pairs of similar dates in different years. Six image pairs with the least uncertainties were selected to derive ground displacement for a moving slope in the study area. Cross-checks among these image pairs showed consistent results, with uncertainties less than 1/10 pixels in length. The findings from this work could help in the selection of the best image pairs to derive reliable slope displacement from large numbers of optical images. Slope deformations are important precursors for imminent landslide hazards, which pose serious threats to mountain communities around the world ,2,3. WitOptical remote sensing has been increasingly used to monitor slope deformations ,6,7,8. IThere are several factors that can influence the performance of the image correlation methods . Errors Quantifying uncertainties in image pairs is crucial for deriving reliable displacements . LacroixThis work used the Sentinel-2 images to uncover temporal patterns of uncertainty to derive deformations. Launched by the European Space Agency, the Sentienl-2 mission has two solar-orbiting satellites, 2A and 2B . The SenBy using all available Sentinel-2 images in the east Tibetan Plateau, the objectives of this work were (1) to quantify temporal patterns of uncertainties in deriving slope displacement and (2) to test the full capacity of all available Sentinel-2 images, to derive ground deformation information from optical images.The study area was located on the eastern Tibetan Plateau along the Jinsha River . The rivTo carry out the image correlation analysis, a stable zone was selected to derive possible image misregistration. The stable zone  method was used to derive ground displacement from the Sentinel-2 images . The metUncertainties of the COSI-Corr method were measured using the standard deviations of displacements in a stable zone  from November 2015 to November 2018, and moved (>5 m of displacement) from November 2018 to November 2019 . TherefoFor each cluster pair, standard deviations of ground displacement were derived from the stable zone. Image pairs with the least standard deviations in the stable zone were regarded as the most reliable results. Among these best image pairs, the top few that shared the same target image were selected to cross-validate the derived displacements. To derive slope deformation, the mean E/W and N/S displacements from the stable zone were used to correct the image shifts, for pixels with SNR values larger than 0.9. Aspects to constrain displacement were also used to filter out displacement with contradictory directions .A clear image from 13 November 2015 was used to compose image pairs with the other clear images, to derive a time series of standard deviations of E/W and N/S displacements in the stable zone. To further investigate the temporal patterns of uncertainties, six base images from January and February 2017 were used to derive standard deviations in the stable zone, using all of the clear images taken from 2018 to 2020. Another five base images taken in July and August 2017 were used to derive ground displacement from 2018 to 2020. Standard deviations of E/W and N/S displacement in the stable zone are shown in A previous study showed that the slope was stable  from November 2015 to November 2018, and moved from November 2018 . In theoThree results from 24 August 2019 with the least standard deviations are shown in To further check the derived slope deformation, the derived displacements from January 2020 in e and AugPrevious works show that uncertainties in deriving slope deformation from optical images could result from DEM errors during image orthorectification, different viewing angles of the sensors and illumination differences of the landscape during image acquisitions . Yang etUsing more image pairs may not lead to better results in slope deformation detection . On the Sentinel-2 is a European Space Agency’s mission to monitor earth surface dynamics, which has two twine satellites in orbit, and can revisit anywhere on earth between 56° south and 84° north every 5 days at the equator . In thisStandard deviations of displacement in the stable zone are widely regarded as a reliable measure of uncertainty ,10,11, wIn this work, all available Sentinel-2 images on 7 February 2020 in a mountain region in the east Tibetan Plateau were used. We found the Sentinel-2 images had a very short revisiting time of two/three days in this study area, but unfavorable weather conditions contaminated 65.7% of all observations. Using the remaining clear Sentinel-2 images, an image correlation method was applied to assess the temporal patterns of uncertainty in deriving slope deformation. We found, for a given base image, displacement uncertainties fluctuated annually, and the smallest uncertainty can be achieved by using target images taken on similar dates. As more optical images are becoming available to the public at low costs, selecting the best ones from a large number of optical images to derive slope displacements is becoming more difficult. This uncovered temporal pattern of uncertainty can facilitate the selection of optimal images to derive reliable ground displacements.


Background: Exclusive breastfeeding (EBF) during the first six months of life is critical for child’s linear growth. While there is strong evidence in favor of EBF, the evidence with regards to other interventions for linear growth is unclear. We evaluated intervention domains of micronutrients, food supplements, deworming, maternal education, water sanitation and hygiene (WASH), and kangaroo care, for their comparative effectiveness on linear growth.Methods: For this review, we searched for randomized clinical trials (RCTs) of the interventions provided to infants aged 0-6 months and/or their breastfeeding mothers in low- and middle-income countries reporting on length-for-age z-score (LAZ), stunting, length, and head circumference. We searched for reports published until September 17th, 2019 and hand-searched bibliographies of existing reviews. For LAZ and stunting, we used network meta-analysis (NMA) to compare the effects of all interventions except for kangaroo care, where we used pairwise meta-analysis to compare its effects versus standard-of-care. For length and head circumference, we qualitatively summarized our findings.Results: We found 29 RCTs (40 papers) involving 35,119 mother and infant pairs reporting on the effects of aforementioned interventions on linear growth outcomes. Our NMA on LAZ found that compared to standard-of-care, multiple micronutrients administered to infants (MMN-C) improved LAZ , whereas supplementing breastfeeding mothers with MMN did not . No interventions including MMN-C  reduced risk for stunting compared to standard-of-care. Kangaroo care, on the other hand, improved head circumference  and length  compared to standard-of-care.  Conclusion: Our study found important improvements for kangaroo care, but we did not find sufficient evidence for other interventions.Registration: PROSPEROCRD42018110450; registered on 17 October 2018. However, many children still fail to reach their linear growth potential, particularly those living in low- and middle-income countries (LMICs)3. Linear growth in early childhood is a marker of healthy development that is closely linked with neurodevelopment4. The first six months of age (birth to 6 months) is a critical life stage for early child development, and exclusive breastfeeding during this life stage plays an important role in impacting the growth velocity of children. There is a strong evidence to support the benefits of exclusive breastfeeding during this life stage which includes protection against gastrointestinal infection, growth faltering, infant death syndrome etc.7. Exclusively breastfed children aged between zero to six months are known to have better growth rates and immune system. As such, mechanisms and resources to facilitate appropriate self-care in addition to psycho-social support for breastfeeding mothers is necessary to improve both health outcomes of mothers and babies. For instance, poor maternal nutrition could lead to lactation issues creating barriers for mothers to exclusively breastfeed3. Inadequate care, poor hygiene, and control of diseases for infants and mothers may also inadvertently limit the growth of infants who are adequately breastfed9.In past decades, important progress achieved in maternal, newborn, and child health (MNCH) have led to substantial reductions in maternal and child mortality ratesThe current evidence for other interventions, such as micronutrients, food supplements, deworming, maternal education, and kangaroo care (i.e. early skin-to-skin care) interventions is unclear for the exclusive breastfeeding life stage. Although there are numerous published reviews aimed to assess the effectiveness of these interventions that can be provided during exclusive breastfeeding period , their sThis article uses a comprehensive literature review for multiple intervention domains of micronutrient, food supplements, deworming, maternal education, water sanitation and hygiene (WASH), and kangaroo care to summarize their effects on linear growth for LMIC-based infants in the exclusive breastfeeding period. For our quantitative summary, we have used network meta-analysis for all interventions except for kangaroo care to summarize their effects on LAZ and stunting outcomes; kangaroo care was assessed using pairwise meta-analysis. As the data was too sparse to facilitate meta-analysis, we qualitatively summarized the evidence base for outcomes length and head circumference.10. The protocol for this study was registered in PROSPERO (CRD42018110450).Our analysis and report was designed and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) extension to network meta-analysis11, inclusive of the umbrella review by Bhutta and colleagues7, for an overview of the literature. Specifically, we hand-searched the bibliography of Bhuttaet al.7 for relevant systematic reviews, global health guidelines, and LMIC-based trials. We also performed additional searches in PubMed and the Cochrane Database of Systematic Reviews for more recent trials and other reviews published after 2013. The list of published reviews relevant to this study is provided inOur search strategy was developed after first reviewing the papers published in the Lancet 2013 Maternal and Child Nutrition seriesExtended data, Supplementary Tables 1–3)12. To increase the sensitivity of our search, we complemented our database searches with relevant trials identified from bibliographies of prior reviews.26. For all intervention domains, except for kangaroo care, we excluded studies that did not report the effects of their respective interventions for at least two months. For kangaroo care, there was no restriction for time of follow-up given short duration nature of this intervention. We excluded non-English language studies.For our systematic literature search, we scanned the following databases from inception to August 28, 2019: the Cochrane Central Register of Controlled Trials, Embase, and MEDLINE  independently reviewed all abstracts and proceedings identified in the literature searches. The same team independently conducted relevant full-text reviews of relevant papers. If any discrepancies occurred between the studies selected by the same reviewers, a third investigator (KT) provided arbitration.Using a standardized data sheet in Microsoft Excel, four investigators  independently extracted data for study characteristics, interventions used, subject characteristics at baseline, and outcomes from the final list of selected eligible studies. Any discrepancies observed during data extraction were resolved through discussion between the investigators until consensus was reached.When sufficient data was available for quantitative assessment, a network meta-analysis or pairwise meta-analysis approach was applied. For all domains of interventions except for kangaroo care, we performed a network meta-analysis for LAZ and stunting. There was a limited number of studies that reported on length and head circumference, so we qualitatively synthesized findings from these trials as an alternative to quantitative analysis. We did not consider kangaroo care as part of the network meta-analysis since these trials involved a shorter intervention duration and follow-up (median follow-up of 2 weeks). R2WinBUGS v14 package28. Bayesian models were performed according to the National Institute for Health and Care Excellence (NICE) in their Technical Support Document 2 (TSD2)29. Estimates of comparative effectiveness were measured using mean differences in LAZ with the associated 95% credible intervals (95% CrI). In all models, we used an empirically informative heterogeneity prior distribution, as suggested by Rhodeset al. 201630 for LAZ and Turneret al. 201531 for stunting. This was done to stabilize the estimation of heterogeneity in the face of low number of trials per comparison in the network. Our model selection was informed by using the deviance information criterion and the deviance-leverage plots that could help identify outlier(s) in terms of model fit, in accordance with the NICE TSD2 recommendations29.We performed a network meta-analysis within the Bayesian framework in R using theet al.32 We performed a sensitivity analysis by excluding cluster randomized clinical trials in our network meta-analysis. For our pairwise meta-analysis on kangaroo care, we performed a random-effects model using theMetafor R package (in R2WinBUGS v14)33. For our network meta-analysis, the estimates of effectiveness were measured using mean differences or relative risk with accompanying 95% credible intervals (CrIs). The estimates of effectiveness were measured using mean differences with accompanying 95% confidence intervals (CIs) for our pairwise meta-analysis on kangaroo care. As no kangaroo care trials involved cluster randomization, our pairwise meta-analysis did not need to adjust for the clustering effect.For our primary network meta-analysis, we included both cluster and non-cluster randomized clinical trials . To adjust for clustering effects of the cluster trials, we assumed a conservative intra-cluster correlation coefficient (ICC) of 0.05, and we inflated variances accordingly for continuous outcomes and adjusted the sample sizes and the number of cases for dichotomous outcomes, as recommended by Uhlmann34. The risk of bias assessment within and across studies are provided in theExtended data (Supplementary Table 8)12. Each full text article was evaluated for reporting quality according to the Cochrane Risk of Bias ToolExtended data, Supplementary Table 5)12 is provided in the online appendix.We identified 20,224 abstracts from our database searches and hand searching of reference lists from published reviews . Of thesExtended data, Supplementary Table 6)12 are provided in the online appendix. Of the 29 included trials, ten were cluster randomized trials . The majority of trials were conducted in Southeastern Asian (n = 14) and African (n = 10) countries, and involved individual randomization  and were open-label trials (n = 9). Several trials (n = 24) focused on a single domain of interventions, with micronutrient (n = 11) and food supplements (n = 9) being the most common intervention domains investigated. There were four trials that investigated interventions from two different intervention domains39, but the scope of these trials was still limited to nutritional (micronutrient and food) supplementations. There was one trial reporting on deworming study39 and another on WASH intervention40, and there were five trials on kangaroo care. There were 24 trials that investigated other intervention domains , the median duration of interventions was 24 weeks . The kangaroo care trials entailed short follow-ups, with intervention durations that varied between one to two weeks.The trial characteristics of the included studies 12. The median age of mothers at enrollment was 25.4 years (ranging from 21.8 to 29.8 years). For infants, the majority of trials enrolled participants from birth (after follow-up of the mother) or within the first month of life, except one trial41 that investigated the effects of food supplements for an early weaning off breastfeeding enrolled subjects at 4 months of age (up to 7 months of age). The proportion of boys included in these trials was 51.3% on average, ranging from 36.6%40 to 73%42.The subject baseline characteristics are provided in the online appendix 12 included 18 trials consisting of 27,896 mother-infant dyads randomized to 52 intervention arms. The results of our primary analysis on LAZ that included both cluster and non-cluster randomized clinical trials are illustrated inThe LAZ network 12 included 18 trials that consisted of 27,896 mother-infant dyads randomized to 52 intervention arms. The results of our primary analysis that included both cluster and non-cluster randomized clinical trials are illustrated inExtended data, Supplementary Figure 912. While supplementation of zinc to infants  showed a trend towards reduced risk of stunting, its CrI contained the null effect of 1.00. In fact, no interventions demonstrated any improvements towards reducing the risk of stunting.The stunting network 12 and stunting 12 can be found online along with forest plots 12 and cross-tables 12. In our sensitivity analysis on LAZ, no interventions showed improvements for LAZ when compared to standard-of-care, and similarly for stunting, no interventions showed reduced risks for stunting. This is likely due to very few studies being available for sensitivity analyses; only nine trials were available for LAZ and stunting analyses.Our sensitivity analyses were limited to individually (non-cluster) randomized clinical trials only. The network diagrams for LAZ . All kangaroo care trials were conducted in Southeastern Asian countries , in hospital settings and involved low birthweight neonates. Kangaroo care consisted of skin-to-skin contact between the mothers’ breasts, where infants in the control group were kept under either a warmer or incubator. The effects of kangaroo care on head circumference and length growth velocities are shown inExtended data, Supplementary Figures 12 and 1312, respectively. All studies except for Acharya 201442 showed improvements in head circumference (Mean (SD): 31.5 (1.4) 95%CI -0.5, 0.646; Kangaroo mother care (KMC): 0.75 cm vs conventional method of care (CMC): 0.49 cm p<0.00156;) and length (KMC: 0.99 cm vs CMC 0.70 cm p<0.00156). The pooled estimates of growth velocities for head circumference and length showed improvements for kangaroo care in comparison to the control. Relative to the control, kangaroo care showed an improved mean difference of 0.20 cm/week  for head circumference, and for length, a mean difference of 0.23 cm/week .Five randomized clinical trials investigating the effects of kangaroo care on linear growth of newborns were included in the pairwise meta-analysis74.There is no blinding of participants in the kangaroo care studies, indicating a high performance bias in the studies. However, the impact of the expected degree of bias on the estimated treatment effect is difficult to assess72. Of these trials, three were cluster randomized clinical trials that investigated interventions related to maternal education and breastfeeding promotion: Le Roux57 Vazir72, and PROMISE EBF66 did not find differences in their maternal education and breastfeeding promotion interventions. In this three-arm trial conducted in India, mothers in the Complementary Feeding group  received nutrition education messages on breastfeeding and complementary feeding from community health workers (CHWs), and the mothers in the Complementary Feeding + Play group  received messages on psychosocial stimulation in addition to the same nutritional messages received by the women in the complementary feeding group . The mothers were approached by the trial investigators during pregnancy, and the interventions began when their child was three months old. By the age of six months, this trial found no differences in terms of length between the three groups .There were twelve trials available for our qualitative summary72. Of these nine trials, JiVitA-3 trial75 and Ostadrahimi65 provided supplements to mothers from pregnancy into postpartum, where the other five trials provided supplements to children. PROCOMIDA38 provided food to the entire family. Ostadrahimi65 enrolled pregnant women from the 20th week of gestational age and were provided daily fish oil supplements (120 mg docosahexaenoic acid and 180 mg eicosapentaenoic acid) or placebo up to 1 month into the postpartum, with their child being followed-up up to six months of age. At the 6-month assessment of this trial, there were no differences found in neither length  or head circumference  between the fish oil and placebo groups. Mofid39 found that deworming interventions provided to mothers who tested positive for soil-transmitted helminth infection at baseline had a positive impact on mean length gain  and LAZ  of infants at six months of age.Additionally, nine trials investigated the effect of nutritional interventions  on the incidence of changes in head circumference, or changes in length64. In Feliciano48, three different dosages of Vitamin D supplements  were provided to Chinese infants from birth up to six months of age; at the 6-months assessment, differences in length between the three groups were observed. Another placebo-controlled trial64 conducted in Bangladesh found that daily zinc supplements (5 mg) to children between the age of one month to six months did not change the length or head circumference.Three of the five trials investigated the effectiveness of micronutrient supplements administered directly to childrenet al.41 was a multi-national trial  that randomized four-month old infants to either cereal-based precooked porridge fortified with MMN or the control group consisting of local food. The mean consumption of supplement varied from 133 to 189 kcal/day. There were no differences in length (cm) between the supplemented and control groups in all four countries at six months of age. In Lonnerdalet al.61, one-month old infants of non-breastfeeding mothers were randomized to receive regular formula or formula fortified with bovine osteopontin (65 or 130 mg/L). There were no differences in length or head circumference between children who were randomized to different formula groups. This trial also recruited infants whose mothers had expressed the desire to exclusively breastfeed up to six months of age and used this breastfeeding group as a non-randomized control. The breastfeeding group had a higher mean head circumference but similar length at six months of age.There were two trials that explored the role of food supplements to children. SimondonDespite recent global achievements towards improved MNCH, the existing evidence on exclusive breastfeeding period interventions for linear growth remains unclear. Our study aimed to improve the current evidence base by assessing the comparative effectiveness of interventions across several domains: micronutrients, food supplements, maternal education, WASH, deworming, and kangaroo care. Both network meta-analysis and pairwise meta-analysis techniques were undertaken to appraise and synthesize findings from relevant studies reporting the desired outcomes for infants of age 0–6 months in LMICs (i.e. LAZ and proportion of stunted), and due to limited number of studies, length and head circumference were summarized qualitatively.59. Our analysis of kangaroo care also exhibited important improvements in growth in terms of increased head circumference and length growth velocity. However, kangaroo care interventions were excluded from the network meta-analysis and were analyzed separately via pairwise meta-analysis. This was due to the specific nature of this type of intervention, consisting of skin-to-skin contact between mothers’ breasts during a precise period for a limited duration (of between 1 and 6 weeks). In relation to this point was the observed heterogeneity in the intervention duration between included studies, generally, creating an added challenge when making comparisons across interventions. Deworming and WASH interventions did not show any improvements in both LAZ and stunting. We found that MMN supplementation to infants (i.e. MMN-C) was the only intervention that showed important improvement for linear growth during the exclusive breastfeeding period. However, this finding was limited to only one trial in the study76. Previous reviews have focused only on intervention(s) within a single domain Appendix 2. Details to our statistical analysis.Appendix 3. List of included and excluded studies after full-text review. (Contains Supplementary Tables 4 and 5.)Appendix 4. Details of the evidence base. (Contains Supplementary Tables 6 and 7.)Appendix 5. Bias Assessment. (Contains Supplementary Table 8.)Appendix 6. The intervention networks for LAZ and stunting. Appendix 7. Primary analysis leverage and consistency plots. Appendix 8. Forest plots, cluster and non-cluster trials. Appendix 9. Forest plots for kangaroo care Appendix 10. Cross tables for LAZ and stunting. (Contains Supplementary Tables 9–12.)https://doi.org/10.17605/OSF.IO/T3JZQ12.Open Science Framework: PRISMA checklist for “Interventions to improve linear growth during exclusive breastfeeding life-stage for children aged 0–6 months living in low- and middle-income countries: a systematic review with network and pairwise meta-analyses.”Creative Commons Attribution 4.0 International license (CC-BY 4.0).Data are available under the terms of the The changes made have improved readability and it is clearer that outcomes were assessed at 6 months of age. The issues I raised around timing of the interventions were understandably difficult to tackle because of heterogeneity, however this should be made clear as a limitation in the discussion since it is plausible that effects vary between conception and 6 months of age.Are the rationale for, and objectives of, the Systematic Review clearly stated?YesIs the statistical analysis and its interpretation appropriate?PartlyAre sufficient details of the methods and analysis provided to allow replication by others?YesAre the conclusions drawn adequately supported by the results presented in the review?PartlyReviewer Expertise:Infection and nutrition in infants and children; clinical trials; cohort studies; anthropometry.I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. The authors state that exclusive breastfeeding during the first six months of life is critical for linear growth. Although the evidence is strong to support the benefits of exclusive breastfeeding on linear growth, the evidence for other interventions is not as clear. Numerous published reviews have assessed the effectiveness of micronutrients, food supplements, deworming, maternal education and kangaroo care during the exclusive breastfeeding period but their scope has been limited to single intervention within a single domain. Because the determinants of linear growth for the exclusive breastfeeding period is multi-faceted there is a need to summarize the evidence from multiple domains. The study therefore uses a comprehensive literature review for multiple intervention domains of micronutrients, food supplements, deworming, maternal education, water sanitation and hygiene and kangaroo care with a goal to summarize their effects on linear growth during the first 6 months of life (exclusive breastfeeding period). The main outcomes of interest were LAZ, stunting, changes in linear growth and changes in head circumference. Network meta-analysis was used to analyze data except kangaroo care which was analyzed using pairwise meta-analysis. The main finding from this analysis was that micronutrient supplementation to infants was the only intervention that showed improvement in linear growth during the exclusive breastfeeding period. This is a valuable study and generally well designed. It can be improved in the following minor areas:Introduction:including linear growth.”The introduction could be tweaked to make it clearer. In the first paragraph it is not clear that linear growth is a clear benefit of exclusive breastfeeding during the first 6 months. For example “…is a critical life stage for early child developmentMethod:Clarify how the LAZ was calculated and if the same data was used to calculate LAZ among all trials.There seems to be an error in reporting the length of the intervention among studies. For example on page 4/17 it reads “we excluded studies that did not report the effects of their respective interventions for at least three months”. However in table 3 under outcomes it states “At least one of the following outcomes ”. Please clarify if this is 2 or 3 months.At the bottom of page 4/17 the last sentence states “if any discrepancies occurred between the studies selected by the same reviewers, a third investigator provided arbitration”. Do you mean discrepancies in the review of the studies?Top of second column page 4/17 - should this be subject characteristics rather than patient characteristics?Table 3 should likely be table 2 and vice versa, since table 3 was written first in the text.It is not clear in the methods when the respective outcomes were measured. Were they all measured before 6 months of life?Also not clear why 2 or 3 months (depending on which one is accurate) was chosen as the minimum length of time for each intervention (except kangaroo care).  Results:Page 5/17 second column second paragraph the word “patients” is used rather than subjects?What does CHW mean on page 9/17?Discussion:Include a comment on whether the duration of the interventions were appropriate to see the desired outcomes.Title:with network and pairwise meta-analysis...”.Substitute with for and in the title: “...a systematic reviewAre the rationale for, and objectives of, the Systematic Review clearly stated?PartlyIs the statistical analysis and its interpretation appropriate?I cannot comment. A qualified statistician is required.Are sufficient details of the methods and analysis provided to allow replication by others?YesAre the conclusions drawn adequately supported by the results presented in the review?YesReviewer Expertise:Nutrition.I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Dear Dr. Courtney-Martin:Thank you for your thorough review of our manuscript. Our responses to your individual recommendations and comments are marked with bullets below.Sincerely,Edward J. MillsThe introduction could be tweaked to make it clearer. In the first paragraph it is not clear that linear growth is a clear benefit of exclusive breastfeeding during the first 6 months. For example “…is a critical life stage for early child development including linear growth.”Thank you for your comment. We have revised the introduction to improve the readability. The goal of this paper was to see if there was any evidence of other interventions, such as micronutrients, food supplements, deworming, maternal education, and kangaroo care that impacted linear growth in children during the exclusive breastfeeding period. We have highlighted the benefits of exclusive breastfeeding in the article [A version of the article has been submitted to Gates Open Research].   Clarify how the LAZ was calculated and if the same data was used to calculate LAZ among all trials. Thank you for the suggestion. We have updated the methods section to include the following:th paragraph]“We used LAZ reported from the individual trials that were calculated using the WHO Child Growth Standards”. Include a comment on whether the duration of the interventions were appropriate to see the desired outcomes. We have indicated under the discussion section of the article that there are observed heterogeneity in the intervention duration among included studies which created a challenge when making comparisons across interventions.  Substitute with for and in the title: “...a systematic review with network and pairwise meta-analysis...”. Thank you for the suggestion. We have changed the title of the article to “Interventions to improve linear growth during exclusive breastfeeding life-stage for children aged 0-6 months living in low- and middle-income countries: a systematic review with network and pairwise meta-analyses”.   This is a very valuable analysis of the effects on stunting of interventions applied to mothers and infants in pregnancy and/or during the first six months of life. The methods used allow some comparisons between interventions to be made and aid interpretation of the limited data across the different type of interventions.Intervention in the target age group 0-6 months is of key importance given that it is a period of very rapid relative growth, exclusive breastfeeding is not practiced to 6 months of age in many low and middle income settings, and stunting seems to occur even when exclusive breastfeeding is reported.My main comments are around lack of analysis or reporting of duration of interventions and the age/timing of when they were applied.In the trials in more than one domain, infant supplementation (LNS etc.) was given after 6 months of age - hence these components do not always fall within the target age range, presumably some of these components were excluded and this could be specifically mentioned under trial characteristics.Timing - it would be helpful to readers to add the periods of pregnancy or during the first six months of life where interventions applied, and when LAZ was assessed as columns to Table 2.In figure 2, were the lower brown nodes  administered to the infants or to the mothers? If mothers, then were they before, during or after pregnancy? For infants, from what age for zinc, MMN and foods? The timing (trimesters and say 0-2m/3-5m) and recipient (mother or infant) could be indicated by shape.'Infant' rather than 'child' would be more appropriate throughout.Within the target period, there are differences in timing and age between the interventions and also potentially differences in plasticity in length or head growth with age. Kangaroo care applied in a selected LBW group at the lowest end of the infant age range when head and length growth is most rapid (and possibly most plastic) and was treated separately, but pre/post-partum and timing within the first 6 months could similarly be a determinant of response. If so, this would be very important for policy. Timing and duration of intervention could be examined as covariates in the network analysis vs SOC, and the estimated effects reported.For kangaroo care, the mean length and head circumference estimates are presented as absolute cm values rather than z scores and are presented as per week increment during a very short period of intervention. For the other interventions, the overall effect is reported despite varying duration. I appreciate the reasons for treating kangaroo care separately. However, it would be much more valuable to readers to report all results as changes per week over n weeks (or x weeks prepartum plus y weeks postpartum). For example, the foods given from age 4 months in some studies (a maximum of 2 months of intervention before assessment at 6 months), or formula milk at 1 month (for how long?) clearly differ in terms of both timing and duration from other interventions.Unless all studies other than kangaroo care reported measured LAZ at 6 months of age or another standardized time point, this would also need to be addressed in analysis, especially if any interventions went on for longer than the first 6 months of life.In the qualitative summary please specifically comment on blinding in the kangaroo care studies since these measurements are operator dependent and knowledge of the randomization at measurement could be a problem.Please replace '...showed a trend towards...' with '...was not statistically significant at the x percent alpha level...'. Zinc and MMN-m mentioned under Network meta-analysis on stunting do not look like borderline results. Overall, these would be more clear if presented as Forrest plots, similar to those under Network meta-analysis on LAZ.Are the rationale for, and objectives of, the Systematic Review clearly stated?YesIs the statistical analysis and its interpretation appropriate?PartlyAre sufficient details of the methods and analysis provided to allow replication by others?YesAre the conclusions drawn adequately supported by the results presented in the review?PartlyReviewer Expertise:Infection and nutrition in infants and children; clinical trials; cohort studies; anthropometry.I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Dear Dr. Berkley:Thank you for your thorough review of our manuscript. Our responses to your recommendations and comments are marked with bullets below.Sincerely,Edward J. MillsIn the trials in more than one domain, infant supplementation (LNS etc.) was given after 6 months of age - hence these components do not always fall within the target age range, presumably some of these components were excluded and this could be specifically mentioned under trial characteristics.Thank you for your comment. For the purpose of our analysis, we included outcomes that were reported within 6 months of age. Supplementary tables 6 and 7 report age of mother/child during enrolment and the intervention duration.  Timing - it would be helpful to readers to add the periods of pregnancy or during the first six months of life where interventions applied, and when LAZ was assessed as columns to Table 2. https://doi.org/10.17605/OSF.IO/T3JZQ. Supplementary Table 7 does report average gestational age at the time of recruitment. We have also updated the table to include average age of child (if applicable) at the time of enrolment. Supplementary Table 6 reports intervention duration of each trial. Information from both Table 6 and 7 can be used to gauge when LAZ was reported. The updated supplementary file can be found here: In figure 2, were the lower brown nodes  administered to the infants or to the mothers? If mothers, then were they before, during or after pregnancy? For infants, from what age for zinc, MMN and foods? The timing (trimesters and say 0-2m/3-5m) and recipient (mother or infant) could be indicated by shape. Interventions provided to mothers have been indicated as “maternal” on the nodes. Thus, the lower brown nodes show interventions that were administered to infants. Supplementary Table 7 indicates the ages of mother and child at enrolment as well as the average gestational age during recruitment. The network diagram was drawn from a treatment network generated from our Bayesian network meta-analysis tool which shows multiple treatment comparison among all the trials. Treatments have not been segregated according to duration for data analysis purposes.   'Infant' rather than 'child' would be more appropriate throughout. Thank you for the suggestion. We decided to use the term “child” specifying the age range in order to be more specific. Infants usually indicate young children between the age of 0-1 year (https://www.cdc.gov/ncbddd/childdevelopment/positiveparenting/infants.html)   Within the target period, there are differences in timing and age between the interventions and also potentially differences in plasticity in length or head growth with age. Kangaroo care applied in a selected LBW group at the lowest end of the infant age range when head and length growth is most rapid (and possibly most plastic) and was treated separately, but pre/post-partum and timing within the first 6 months could similarly be a determinant of response. If so, this would be very important for policy. Timing and duration of intervention could be examined as covariates in the network analysis vs SOC, and the estimated effects reported.For kangaroo care, the mean length and head circumference estimates are presented as absolute cm values rather than z scores and are presented as per week increment during a very short period of intervention. For the other interventions, the overall effect is reported despite varying duration. I appreciate the reasons for treating kangaroo care separately. However, it would be much more valuable to readers to report all results as changes per week over n weeks (or x weeks prepartum plus y weeks postpartum). For example, the foods given from age 4 months in some studies (a maximum of 2 months of intervention before assessment at 6 months), or formula milk at 1 month (for how long?) clearly differ in terms of both timing and duration from other interventions.Thank you for this comment. We acknowledge that there is substantial heterogeneity observed in the duration of the interventions and the timing of outcome assessments. To address the heterogeneity in trials, we employed random-effects model for our network meta-analysis. For kangaroo care studies, our outcomes reporting has been limited to growth velocity of head circumference and length (cm per week). Given the heterogeneity in timing and duration of interventions, we calculated pooled estimates of growth velocities.   Unless all studies other than kangaroo care reported measured LAZ at 6 months of age or another standardized time point, this would also need to be addressed in analysis, especially if any interventions went on for longer than the first 6 months of life. The highest duration of intervention in the studies was 24 weeks (i.e. 6 months). Among those studies that reported an intervention duration of 24 weeks, some recruited mothers during pregnancy, while the children were recruited within a few days of birth. For the purpose of analysis, outcomes reported within the first 6 months of life were included.  In the qualitative summary please specifically comment on blinding in the kangaroo care studies since these measurements are operator dependent and knowledge of the randomization at measurement could be a problem. Thank you for pointing this out. We have added one paragraph under kangaroo care, which is as follows:   “There is no blinding of participants in the kangaroo care studies, indicating a high performance bias in the studies. However, the impact of the expected degree of bias on the estimated treatment effect is difficult to assess”. (https://www.bmj.com/content/368/bmj.l6802) [Page 9 under kangaroo care] Please replace '...showed a trend towards...' with '...was not statistically significant at the x percent alpha level...'. Zinc and MMN-m mentioned under Network meta-analysis   on stunting do not look like borderline results. Overall, these would be more clear if presented as Forrest plots, similar to those under Network meta-analysis on LAZ.st paragraph]. Forest plots on stunting have been included in the supplementary file . Available here:https://doi.org/10.17605/OSF.IO/T3JZQ. We do not use terms such as “statistically significant or insignificant” to avoid dichotomization of scientific evidence. Zinc administered to infants was the only intervention that showed some promise on stunting, but its interval contained the null effect of 1. We have removed the effect of local food+MMN-m from the article. [Page 9, 1


Genetic recombination processes, such as reassortment, make it complex or impossible to use standard phylogenetic and phylodynamic methods. This is due to the fact that the shared evolutionary history of individuals has to be represented by a phylogenetic network instead of a tree. We therefore require novel approaches that allow us to coherently model these processes and that allow us to perform inference in the presence of such processes. Here, we introduce an approach to infer reassortment networks of segmented viruses using a Markov chain Monte Carlo approach. Our approach allows us to study different aspects of the reassortment process and allows us to show fitness benefits of reassortment events in seasonal human influenza viruses. Reassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. Here, we introduce a coalescent-based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. This algorithm provides the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full-genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses. Through rapid evolution, human influenza viruses are able to evade host immunity in populations around the globe. In addition to mutation, reassortment of the different physically unlinked segments of influenza genomes provides an important source of viral diversity . If a ce4To characterize reassortment events, tanglegrams, comparison between tree heights , 8, or aWhile the reassortment process has been intensively studied . While many approaches to inferring ARGs exist, some are restricted to tree-based networks , 13, meaHere, we introduce a Markov chain Monte Carlo (MCMC) approach specifically designed to jointly sample reassortment networks and the embedding of segment trees within those networks under the coalescent model, without any additional approximations. This approach allows us to jointly infer the reassortment network, the phylogenetic trees of each segment, the reassortment and coalescent rates, as well as evolutionary rates.SI Appendix, Table S1. Finally, we study how reassortment rates differ on edges with high and low fitness of these reassortment networks.We first show that this approach is able to retrieve reassortment rates, effective population sizes, and reassortment events from simulated data. Secondly, we discuss how a lack of genetic information influences the inference of these parameters. Thirdly, we show how using the coalescent with reassortment can influence the inference of effective population sizes, as well as evolutionary rates. We then apply this approach to quantify reassortment across the five seasonal human influenza subtypes, as listed in In order to test our ability to infer effective population sizes and reassortment rates from genetic sequences, we performed a well-calibrated simulation study . Additionally, these results also hold when using the more complex Hasegawa–Kishino–Yano (HKY) + SI Appendix, Figs. S2 and S3).Network Summary).To test how well true reassortment events are recovered, we computed the probability of observing exactly the same reassortment events as present in the true (simulated) network. We considered two reassortment events to be the same if the subtree of each segment below that node is the same and if the relative direction of each segment at the reassortment event is exactly the same  trees . On the other hand, the The SI Appendix, Table S1. These include the same datasets described in We compared the reassortment rates of the five different seasonal human influenza types listed in Influenza A/H3N2 shows the highest rates of reassortment, while pandemic 1918 (p1918)-like H1N1 and influenza B show the lowest inferred rates of reassortment . H2N2 anDifferences between p1918-like H1N1, H2N2, and H3N2 are particularly interesting since these strains share many common segments. All segments with the exception of HA, NA, and PB1 of influenza A/H3N2 originate from the p1918-like H1N1 strain . It showSuch variations in reassortment rates may be driven by a number of factors. Differences in coinfection rate (which may be linked to the effective population size) lead to different probabilities of viruses being in the same host at the same time and therefore to a difference in the rate at which reassortants appear. In particular, the higher incidence of influenza A/H3N2 and the correspondingly likely higher number of coinfection events compared with other influenza A viruses or influenza B viruses may contribute to the higher observed reassortment rate in that case. Additionally, reassortants in the different seasonal human influenza viruses could have, on average, a different fitness and therefore be more or less likely to be transmitted.Next, we test if there is a fitness effect associated with reassortment events. To do so, we classify every network edge from the posterior distribution of inferred networks as either “fit” or “unfit.” We define a fit edge to be any edge having descendants that still persist at least 2 y into the future, while every other edge in the network is defined to be unfit. Unfit here, however, still means that the viruses are likely fit enough to be transmitted. If reassortment events are beneficial, lineages that are the result of reassortment events should have a higher survival probability and are therefore more likely to persist further into the future.To test if reassortment is beneficial, we calculated the number of reassortment events on fit edges and on unfit edges for all networks in the posterior distribution of the MCMC. We then divided this number by the total length of fit respectively unfit edges. As shown in SI Appendix, Figs. S9 and S10). For p2009-like H1N1, where the overall sampling interval is only 10 y, the evidence for fitness benefits of reassortment events, however, decreases when using 4 and 6 y instead of 2 y.For the other human influenza viruses, fitness benefits of reassortment are less pronounced. For p2009-like H1N1 and H2N2, the sampling time windows (both) or number of samples (H2N2) was however rather small, and the results are likely driven by a lack of data. p1918-like H1N1 on the other hand had relatively few reassortment events, overall driven by a low reassortment rate, and the results are likely driven by a lack of reassortment events. These same general patterns hold when the definition of what is a fit edge is changed to having descendants at least 4 or 6 y into the future . Over shorter time frames, the effect of fitness is less visible since selection has not had enough time to filter out less fit strains. In turn, this means that if we look at datasets sampled over short times , we should estimate reassortment rates consistent with the estimated rates on unfit edges. To test this, we compiled 9 datasets, each with 100 to 200 sequences sampled from 2 seasons between 2000 and 2018. Averaged over all nine datasets, we find the short-term reassortment rate to be approximately 0.2 reassortment events per lineage per year, which is consistent with the reassortment rate estimates for unfit edges .We conducted further analysis to probe the robustness of our result for H3N2, for which densely sampled sequences of long time intervals are available. We analyzed two more influenza A/H3N2 datasets, one sampled between 1980 and 2005 and one sampled from 2005 until the present. For both datasets, we find higher rates of reassortment on fit edges  and found that the patterns we observed in the empirical data completely disappeared. This strongly suggests that the elevated rate of reassortment on fit lineages is not due to the particulars of our model but is instead a real effect.Finally, we sought to rule out the possibility that these patterns are simply a property of our reassortment model. To do this, we simulated networks under the coalescent with reassortment with the reassortment rates and effective population sizes fixed to the mean values estimated from the empirical data and the network tip times fixed to those from the same data. In these simulated networks, each edge has the same fitness. We then recomputed the same fit/unfit reassortment rate statistics from these simulated networks . These operators often have analogs in operators used to explore different phylogenetic trees. Here, we briefly summarize each of these operators, providing the complete details in the supplement.The add/remove operator adds and removes reassortment events. An extension of the subtree prune and regraft move for networks  to jointThe segment diversion operator changes the path segments take at reassortment events.The exchange operator changes the attachment of edges in the network while keeping the network length constant.The subnetwork slide operator changes the height of nodes in the network while allowing to change the topology.The scale operator scales the heights of individual nodes or the whole network without changing the network topology.The Gibbs operator efficiently samples any part of the network that is older than the segment tree roots and is thus not informed by any genetic data.The empty segment preoperator augments the network with edges that do not carry any segments for the duration of a move, to allow larger jumps in network space.We validate the implementation of the coalescent with reassortment network prior as well as all operators in the supplement.To summarize a distribution of networks, we use a similar strategy to the MCC strategy  and reassortment rates from another log normal distribution . An average effective population size of 5 is similar to the estimated effective population sizes of seasonal human influenza viruses C, and an viruses C.https://www.fludb.org) . For the influenza A/H2N2 dataset, we used the same sequences as in ref. https://gisaid.org; acknowledgments table can be found at https://github.com/nicfel/Reassortment-Material/blob/master/Applications/H2N2/oridata/gisaid_acknowledge_table.xls). For all datasets but the influenza A/H2N2 dataset, we used subsampling to produce a final set containing at least 500 samples with an even temporal distribution. We aligned all segments using Muscle 3.8.31 .We then jointly estimated all evolutionary rates, the reassortment networks, and embedding of segments trees, as well as the reassortment rates and effective population sizes. For the influenza A/H2N2 dataset, we additionally estimated the sampling times for all sequences for which only the year in which the sample was taken was known. We assessed convergence using effective sample sizes and potential scale-reduction factors  computedhttps://www.fludb.org), the full extensible markup language (XML) files to run the datasets are available online. For the influenza A/H2N2 sequences that were obtained from GISAID, we removed the sequence characters from the XML files in order to comply with the relevant license regulations, leaving the accession numbers intact, and thus still allowing reproduction of results based on these data. All other data, such as log files of BEAST2 runs, as well as scripts to analyze and plot results, are available at https://github.com/nicfel/Reassortment-Material.For virus types with sequences downloaded from the Influenza Research Database (Supplementary File


Patients who have recently received a hematopoietic cell transplant (HCT) are at higher risk of acute complications in the first weeks after discharge, especially during the COVID-19 pandemic.The aim of this study was to test the use of a telehealth platform for the follow-up of HCT patients during the first two weeks after discharge.In total, 21 patients who received autologous or allogeneic HCT for hematological malignancies were screened from April 30, 2020, to July 15, 2020. The telehealth platform assisted in the daily collection of vital signs as well as physical and psychological symptoms for two weeks after hospital discharge. The required medical devices (oximeter and blood pressure monitor) were given to patients and a dedicated smartphone app was developed to collect this data. The data were reviewed daily through web-based software by a hematologist specializing in HCT.Only 12 of 21 patients were able to join and complete the study. Technological barriers were the most frequent limiting factor in this study. Among the 12 patients who completed the study, adherence to data reporting was high. The patients’ experience of using such a system was considered good. In two cases, the system enabled the early recognition of acute complications.This pilot study showed that telehealth systems can be applied in the early posttransplant setting, with evident advantages for physicians and patients for both medical and psychological aspects. Technological issues still represent a challenge for the applicability of such a system, especially for older adult patients. Easier-to-use technologies could help to expand the use of telehealth systems in this setting in the future. Patients receiving a hematopoietic cell transplant (HCT) have a high risk of developing severe acute toxicities in the early posttransplant period. An increased mortality risk has been observed in HCT patients who go on to develop COVID-19, with an estimated mortality rate between 20%-40% -5. DigitThe aim of this study (SMARTCOVID19 study) is to report the feasibility of a real-time patient monitoring system through the use of a smartphone app and mobile health care devices. The institutional review board of Institut Catalá d'Oncologia - Hospitalet approved the study. Inclusion criteria were the following: those aged >18 years who had received autologous or allogeneic HCT while hospitalized and have a smartphone with an operating system able to run the SMARTCOVID19 app. Those who did not have adequate social support were excluded from the study.Patient education regarding the use of the platform was provided by a hematologist at the time of enrollment, which was 1-2 days before hospital discharge.Vital signs  were collected daily using clinically validated oximeters  and a blood pressure monitor , while temperature was measured using domiciliary thermometers. Patients were educated on how to measure their respiratory frequency. A checklist of clinical symptoms was completed daily . An analog visual scale “thermometer” (0-10) used to detect potential cases of anxiety or depressive disorders was completed by patients daily. Scores of >6 resulted in an automatic referral to a psycho-oncologist through the platform, who would contact the patient and evaluate whether psychological support was needed via videoconference. A chat service was available for nonurgent communications. All data were reported to an online platform through a smartphone app  compatible with Apple (iOS Version 9 or higher) and Android systems (Version 6 or higher). A hematologist with experience with HCTs reviewed all patient data daily. Programmed alarms were set in the event of any of the following situations: fever >38 C, oxygen saturation <92%, tachycardia >125 beats per minute, hypotension , altered mental status, and persistent emesis or diarrhea (lasting more than 48 hours). In case of alarm activation, the hematologist contacted the patient by phone to evaluate the need for an in-person visit and determine the clinical management steps that were considered most appropriate. Outpatient monitoring started from the day of hospital discharge 2 days and continued for 14 days. The study accrual period was April 30, 2020, to July 15, 2020. Data were collected prospectively and all patients signed informed consent forms. Finally, two weeks after the end of the recruitment period, patients were contacted by phone and asked to answer a satisfaction questionnaire.During the study period, 16 of 21 patients who received transplants were successfully recruited into the study (76% feasibility). Reasons for patients not being enrolled were the following: language incompatibility (1 patient), no consent (1 patient), and no compatible smartphone (3 patients). Of the 16 enrolled patients, the median age was 50 years (range 22-70 years), 38% (n=6) were female, and 94% (n=15) had lymphatic diseases. In addition, 38% (n=6) of HCTs were autologous and 62% (n=19) were allogeneic.Of the 16 enrolled patients, 4 were not able to use the app due to an inability to use smartphone apps in general. Of the remaining 12 patients, average adherence to reporting study data  was as follows: 89% for temperature, 90% for oxygen saturation, 70% for respiratory frequency, 85% for cardiac frequency, 89% for blood pressure, 65% for symptoms reporting, and 71% for emotional distress.Automatic alarms were activated only 3 times: twice for the presence of clinical symptoms and once for emotional distress. Only one patient spoke with the psycho-oncologist via videoconference. In total, 4 patients used the chat service to communicate with hospital personnel.Despite the feasibility nature of the study, data collected with the digital system helped the clinician to recognize calcineurin inhibitor–induced arterial hypertension in one patient and acute cutaneous graft-versus-host disease (grade I) in another patient.Only two patients in this cohort were readmitted within 14 days of discharge, both due to grade 4 odynophagia related to herpes simplex virus 1/2 reactivation.The patients’ responses to the survey questions about their experience with the telehealth system are reported in Our prospective study showed that the use of mobile health care devices and smartphone apps for self-reported outcomes is feasible in the post-HCT setting. In a study conducted by Nawas et al , it was A study limitation was the small number of patients that completed the study. However, the study population was considered sufficient for a pilot study. In fact, the results obtained should be used to improve the design of the next study, which will recruit a larger number of patients. In addition, the uptake and use of newer technologies could be influenced by country or hospital resources. Such a system would not be feasible to implement within hospitals or health care systems that cannot afford such expenses. This applicability issue is common to the majority of studies using newer technologies.In conclusion, telehealth monitoring could potentially improve patient follow-up in terms of both physical and psychological outcomes. This is especially true whenever an external cause (such as the COVID-19 pandemic) impedes in-person visits. Technological issues still represent a barrier to the wider application of telehealth monitoring systems in a medical setting and these issues should be considered for future studies.