Acute harm from heavy drinking episodes is an increasing focus of public health policy, but capturing timely data on acute harms in the population is challenging. This study aimed to evaluate the precision of readily available administrative emergency department (ED) data in public health surveillance of acute alcohol harms.We selected a random sample of 1000 ED presentations assigned an ED diagnosis code for alcohol harms  in the New South Wales, Australia, automatic syndromic surveillance system. The sample was selected from 68 public hospitals during 2014. Nursing triage free‐text fields were independently reviewed to confirm alcohol consumption and classify each presentation into either an ‘acute’ or ‘chronic’ harm. Positive predictive value (PPV) for acute harm was calculated, and predictors of acute harm presentations were estimated using logistic regression.pm and 5.59 am . PPV among 12 to 24‐year‐olds was 82%.The PPV of the alcohol syndrome for acute alcohol harm was 53.5%. Independent predictors of acute harm were ambulance arrival , younger age , not being admitted  and arriving between 10 The alcohol syndrome provides moderate precision as an indicator of acute alcohol harms presenting to the ED. Precision for monitoring acute harm in the population is improved by filtering the syndrome by the strongest independent predictors of acute alcohol harm presentations.  It is estimated that alcohol misuse cost the Australian society $14.4 billion in 2010, of which almost $1.7 billion was to the health system Capturing timely, accurate and useful ongoing data on people presenting to the ED with alcohol‐related harms are required to monitor changes over time, guide planning and evaluation of policy and support health service delivery. However, in Australia, this remains a challenge, as it is not mandatory to screen for or collect data on alcohol‐related ED presentations Continuous syndromic surveillance in EDs in New South Wales (NSW), Australia, was established in 2003 and is used to rapidly identify increases in public health harms, including those due to infectious diseases, injury and alcohol and other drugs The alcohol syndrome is one of nine broad syndrome categories. It was developed for public health surveillance of alcohol harms at the population level and to describe alcohol harms occurring during major events or mass gatherings, such as New Year's Eve Applications of administrative ED data are limited, as it is not collected or designed to answer specific research or policy‐relevant questions. The diagnosis codes available in ED information systems are influenced by the software system used and do not necessarily reflect the intent of those codes from formal health classifications. Also, ED information systems are not designed to record alcohol as a contributing factor in the ED presentation. For instance, diagnostic codes in the alcohol syndrome only capture around 24% of all alcohol‐related ED presentations because many alcohol‐related ED presentations are coded as other problems, such as injury, or they leave before treatment and diagnosis could occur In the absence of otherwise readily—and routinely—available data, the alcohol syndrome in the NSW ED surveillance system provides an opportunity to monitor trends in ED presentations for alcohol harms at the population level, across both time and place in near‐real time The United States Centers for Disease Control and Prevention identifies positive predictive value as an important attribute of a surveillance system This study used data from the NSW ED surveillance system This surveillance system uses syndromes, which are automatically grouped ED presentations based on the diagnosis classification allocated from the mandatory provisional ED diagnosis field assigned by the treating clinician at patient discharge or admission to a hospital ward. Diagnosis terms selected by the clinician are mapped to a code by the hospital information system. The codes used include any of the Australian clinical implementations of the International Classification of Diseases (ICD) 9th revision, ICD‐10th revision (ICD‐10‐AM) or the Systematized Nomenclature of Medicine—Clinical Terminology (SNOMED CT) The population for this study was defined as all presentations to 68 NSW EDs recorded in the surveillance system in 2014 that were grouped into the alcohol syndrome  version 9.4 for Windows.Information provided for each ED presentation included patient demographics , diagnostic information (diagnosis code and description), service delivery characteristics  and two de‐identified free‐text fields recorded by triage nurses which describe the presenting problem and nursing assessment.Confirmation of alcohol consumption (GW)Manual review of the triage nursing text was conducted for the following purposes:generic terms, including ‘alcohol’ and known abbreviations (e.g. ‘ETOH’ or ‘booze’);type of alcohol, including colloquial language (e.g. beer and wine);consumption terms (e.g. ‘drinking’);intoxication terms (e.g. ‘inebriated’ or ‘drunk’);amount terms (e.g. ‘pint’ or ‘cask’); andlocation of consumption (e.g. pub or club) An ‘alcohol’ flag was applied to each record that referred to:Classification of each record into ‘type of alcohol harm’ (dependent variable) The flag was not applied to a record if the patient denied alcohol consumption.Identification of co‐morbid factors (independent variables) (GW)Classification was conducted by three independent reviewers: an ED physician, an addiction medicine specialist and a psychologist. Two free‐text nursing triage assessment fields were reviewed to classify each record into one of four alcohol harm types: acute alcohol intoxication, chronic alcohol misuse, acute alcohol intoxication in a person with a chronic alcohol misuse problem and undetermined  and the Glasgow Coma Scale (GCS) score were recorded.All statistical analyses were performed using SAS. The dependent variable for the logistic regression analysis was coded as a dichotomous variable, with 1 being equal to ‘acute alcohol intoxication’ presentations (known as ‘acute’ throughout) and 0 being equal to the combined group of chronic alcohol misuse, acute alcohol intoxication in a person with a chronic alcohol misuse problem and undetermined (known as ‘chronic’ throughout). This grouping was intended to ensure that the dependent variable of interest captured acute alcohol intoxication harms only (as a proxy for binge drinking), as distinct from the population that may have an underlying chronic alcohol problem. This is because: (i) the population with an underlying chronic alcohol problem require different, more intensive interventions than the population who present with harms related to binge drinking P‐value cut‐off point of 0.25 were included in the initial multivariate logistic regression model. Covariates remained in the model as a confounder if their exclusion resulted in a change in any other parameter estimate by 15% or more Descriptive statistics were used to compare acute with chronic alcohol harm ED presentations. Univariate logistic regression was conducted to determine statistically significant differences between the groups and to quantify these differences. Backward stepwise selection was used to determine the variables to be included in the final multivariate logistic regression model. Factors with a univariate logistic regression Wald test Ethical approval was granted by the NSW Population and Health Services Research Ethics Committee (HREC/15/CIPHS/13).am and 9.59 pm (55%). A majority of presentations arrived by ambulance (68%), were triaged as non‐urgent (87%) and were not admitted (78%). The mean GCS score was 13.6 (range: 3.0–15.0). However, it was only recorded in 37% of the coded alcohol presentations.Of all the coded alcohol ED presentations, over one‐quarter were aged 12–24 years (27%), including 7% aged 12–17 years. The majority were men (64%), resided in major cities (76%) and in the three most disadvantaged socio‐economic quintiles  either did not refer to alcohol consumption in the triage notes, or the triage fields indicated that the patient denied consuming alcohol.Alcohol consumption was confirmed in 86% of the alcohol‐coded presentations. The remaining alcohol‐coded presentations , and many arrived by ambulance (78%). Yet, most were classified in non‐urgent triage categories (88%) and were not admitted (86%). Injuries were common (24%), with over half of these being non‐violent injuries, such as falls (14%).A large majority of coded alcohol presentations in people aged 12–24 years were for acute harms  text‐based discharge diagnosis options for clinicians; (ii) mapping of these text‐based discharge diagnosis options to coded diagnoses; and (iii) different coded classifications systems. In addition, the lack of standard questions on alcohol consumption in the ED and the variation in content and quality of triage notes limit reporting on alcohol consumption behaviour and subsequent outcomes.The coded alcohol syndrome represents approximately 0.6% of all ED presentations in NSW. It is known to underestimate the burden of alcohol on ED presentations Younger age was independently associated with acute harm presentations when compared with chronic harm presentations. This supports the plethora of literature that documents the association between younger age and harms associated with heavy episodic drinking Emergency departments provide an opportunistic scenario for capturing alcohol‐related injuries. However, systematically identifying alcohol as a contributing factor to injury‐related ED presentations in NSW is not possible Our findings justify consideration of the development of an improved method to accurately identify acute alcohol intoxication harms presenting to the ED using the routine surveillance system. Two potential methods to achieve this goal are described in the succeeding texts.The first method involves the use of a surrogate measure of acute harms by applying independent predictors of acute harm presentations to the broad alcohol syndrome. This method is based on the already established practice used to estimate alcohol‐related injuries, as discussed in the preceding texts An alternative approach is to create an acute alcohol sub‐syndrome of the current broad alcohol syndrome. This would entail grouping all acute alcohol intoxication classification codes assigned by the treating physician in the back‐end of the surveillance system and excluding codes related to chronic alcohol problems. Creating a more specific sub‐syndrome risks reducing the accuracy of the grouping due to known variability in coding practices within EDs There is increasing interest in using administrative datasets for public health research and policy evaluation, given that they can be timely, readily available and relatively inexpensive. The focus of recent policy and legislative changes has been to reduce binge drinking and related harms Table S1. Classification codes included in the alcohol syndrome.Table S2. Alcohol harm‐type definitions.Table S3. ED diagnosis, by the classification from the manual review of the triage notes.Supporting info itemClick here for additional data file.


As ribonucleic acid (RNA) nanotechnology has advanced, it has been applied widely in RNA‐based therapeutics. Among the range of approaches, enzymatically synthesized RNA structures for inducing RNA interference in cancer cells have potential for silencing genes in a target‐specific manner. On the other hand, the efficiency of gene silencing needs to be improved to utilize the RNA‐based system for RNAi therapeutics. This paper introduces a new approach for efficient generation of siRNA from bubbled RNA‐based cargo (BRC). The presence of bubbles in between to avoid nonfunctional short dsRNAs allows the RNA‐based cargoes to contain multiple Dicer‐cleavage sites to release the functional siRNAs when introduced to cells. BRCs can be synthesized easily in a one‐pot process and be purified by simple centrifugation. Furthermore, efficient target gene silencing by the bubbled structure is confirmed both in vitro and in vivo. Therefore, this bubbled RNA cargo system can be utilized for target‐specific RNAi therapeutics with high efficiency in the generation of functional siRNAs in the target cells. Ribonucleic acid (RNA) has attracted considerable attention for its potential applications in nanomedicine for the treatment of cancer or infectious disease as well as for immunization.Rolling circle transcription (RCT)‐based enzymatic self‐assembly,Among the abovementioned RNA structures, the efficiency of Dicer cleavage plays a critical role in inducing RNA interference by RNA‐based materials. Although the Dicer‐mediated generation of siRNA from a RNAi microsponge was ≈21% in a previous study,FigureTo synthesize BRCs, two types of closed circular DNAs were prepared, as reported previously.One of the advantages of the synthetic approach of RCT‐induced self‐assembly is that the sizes and sequence‐dependent biological functions of the resulting materials can be manipulated easily. As observed in previous research,2+) plays an important role in packing the RNA strands due to its negative charge.Optical and electron microscopes, transmission electron microscopy‐based energy dispersive X‐ray scattering (TEM‐based EDX), and dynamic light scattering (DLS) were used to characterize the BRCs in a range of aspects. Scanning electron microscopy (SEM) of the BRCs revealed their spherical structures with highly porous surface Figure C. To exaz‐axial resolution, was used to analyze the longitudinal dimension of the BRCs , and nanoparticle tracking analysis (NTA) . The low PDI also indicates that the RNA structures are synthesized uniformly . Furthermore, Brownian motion of each nanoparticle was also tracked by NTA , which has a good s Figure F. Cross‐s Figure G and theFigureBefore evaluating its therapeutic efficacy, the in vitro siRNA generation was assessed by treating the BRCs with the Dicer enzyme. The Dicer enzyme is part of the RNase III family, and it cleaves dsRNA to short dsRNA fragments with lengths of 20–25 bp with a two‐base overhang on the 3′ end.To examine the cellular uptake of the BRCs covered with the transfection reagent, the BRCs were first labeled fluorescently with cyanine5 (cy5). During the RCT process, cy5‐labeled uridine triphosphate (cy5‐UTP) was added to the label, resulting in RNA molecules labeled with cy5. The fluorescently labeled BRCs were then analyzed by cytometry Figure C. The inCytometry analysis Figure D and fluFigureTo examine the in vivo RNAi ability of BRCs, noninvasive real‐time fluorescence imaging was performed from the subcutaneous implantation of nude mouse models of GFP‐expressing HeLa after the single intratumoral administration of GFP‐targeting BRCs (0.8 fmole of BRCs per mouse) Figure3A,B. TIn summary, bubbled RNA‐based cargoes were synthesized by an enzymatic approach with a preprogrammed sequence for the specific cleavage sites for Dicer to process. The overall size of the nanoparticles was controlled rationally by adjusting the ratio of template DNAs to the T7 RNA polymerase in the RCT reaction. The BRCs were synthesized by a one‐pot process, which avoided the labor‐intensive synthetic process, as is the case for many synthetic processes of other types of nanoparticles. Moreover, the resulting nanoparticles have a narrow size distribution, and the efficient Dicer‐mediated release of siRNAs from the BRCs was confirmed in vitro. The gene‐specific knockdown was also confirmed in vivo by an analysis of the gene silencing activity of GFP‐targeting BRCs, compared to the nontargeting BRCs. Overall, this study showed that the BRCs can be synthesized and purified easily, and this system can be utilized for target‐specific RNAi therapeutics with high efficiency in the generation of functional siRNAs in the target cells.The methods detailing the BRC synthesis, characterization, Dicer‐mediated siRNA generation, and in vitro and in vivo gene knockdown analysis are included in the Supporting Information.SupplementaryClick here for additional data file.SupplementaryClick here for additional data file.


AI) technique is an established biotechnology for bovine reproduction, the results of AI (conception rates) have a tendency to decline gradually. To our annoyance, moreover, AI‐subfertile bulls have been occasionally found in the AI centers. To resolve these serious problems, it is necessary to control the sperm quality more strictly by the examinations of sperm molecules.Although artificial insemination (AI‐subfertility and also showed our unpublished supplemental data on the bull AI‐subfertility associated proteins.We reviewed a number of recent articles regarding potentials of bovine sperm proteins as the biomarkers for bull AI‐subfertility is caused by the deficiency or dysfunctions of various molecules including regulatory proteins of ATP synthesis, acrosomal proteins, nuclear proteins, capacitation‐related proteins and seminal plasma proteins.Bull AI centers.In order to control the bovine sperm quality more strictly by the molecular examinations, it is necessary to select suitable sperm protein biomarkers for the male reproductive problems which happen in the  Males with one of these dysfunctions suffer from obstructive azoospermia, non‐obstructive azoospermia, oligozoospermia, varicocele, asthenospermia, absent vas deferens, pyospermia, retrograde ejaculation, erectile dysfunction, or other diseases.Meanwhile, the infertile or subfertile males in cattle rarely undergo these treatments, are not selected as sires for animal production, and are finally culled.In cattle, high‐grade ejaculates  usually are used for the production of cryopreserved spermatozoa. In brief, the ejaculates are diluted with the extender and slowly cooled to 4‐5°C. Next, they are further diluted with the cold extender containing glycerol, pulled into the straws, rapidly frozen in the gas that evaporates from the liquid nitrogen, and then stocked in the liquid nitrogen. Dozens‐to‐several hundreds of semen straws are produced from one ejaculate. Before use for AI, several testing straws are rapidly thawed in warm water and frozen‐thawed spermatozoa are used for the motility assessment to examine the sperm's tolerance to cryopreservation (freezability). The straws with the same lot number as the testing straws that passed this final examination are preserved in the liquid nitrogen until use for AI. When a cow becomes in an optimum condition of the estrus cycle for AI, one of the cryopreserved straws is thawed and subsequently frozen‐thawed spermatozoa are injected into the uterine body of the cow. Thus, only the cryopreserved spermatozoa with excellent genetic traits and good motility are actually used for AI in cattle. However, the conception rates in bovine AI programs have been gradually declining in Japan and other countries for the last 20 years.2In order to screen for the protein biomarkers of male AI fertility, detergent‐extracted proteins of bovine spermatozoa were compared by proteomic analysis between bulls with different AI fertility rates. A study showed the proteome profiles of spermatozoa from high‐AI‐fertile (3569 kinds of proteins) and low‐AI‐fertile (3799 kinds of proteins) bulls (Holstein) and reported that 51 and 74 sperm proteins were included more largely in the spermatozoa from the bulls with higher and lower AI fertility rates, respectively.In another proteomic analysis, adenylate kinase isoenzyme 1 (AK1) and phosphatidylethanolamine‐binding protein 1 (PEBP1) were detected abundantly in the spermatozoa from the bulls (Holstein) with higher AI fertility rates.+ transporting mitochondrial F1 complex β subunit, apoptosis‐stimulating of p53 protein 2, α‐2‐HS‐glycoprotein, and phospholipid hydroperoxide glutathione peroxide) and three proteins  were more largely included in the spermatozoa from the bulls  with higher and lower AI fertility rates, respectively.The third report showed that five proteins  are localized mainly in the acrosomal principal segment and equatorial subsegment.In the head of bull (Japanese Black cattle) mature spermatozoa, the tyrosine‐phosphorylated proteins usually were distributed in the acrosomal principal segment and the equatorial subsegment  by multiple staining and found that most of the spermatozoa possessed a normal acrosome and showed the normal distribution pattern of IZUMO1  in almost all of the samples.4Mammalian spermatozoa have a mission of transporting the paternal haploid genome to the oocytes. For the purpose of protecting the sperm genome from damage before fertilization, sperm chromatins are hypercondensed. This hypercondensation is made in the process of spermiogenesis, during which haploid spermatids are elongated and transformed to the spermatozoa in the seminiferous tubules. In the nuclei, most of the core histones are substituted transiently by the transition proteins and finally by the protamines.4.1Sperm nuclei contain at least two forms of protamines that are different among species. Protamine 1 is universally detectable in the mammalian spermatozoa, while protamine 2 is present in certain placental mammals, including primates and rodents.5i, protein phosphorylation, and membrane hyperpolarization during both the early and the late stages in order to induce the entry of the external Ca2+ and release of the internal Ca2+ from the store.2+‐triggered events of hyperactivation and acrosome reaction in the capacitation process.Immediately after ejaculation, mammalian spermatozoa cannot penetrate into the oocytes. They become capable of fertilizing oocytes during their stay in the site‐specific environment that is produced by the female reproductive tract.2+‐activated adenylyl cyclase , protein kinase A (PKA), protein phosphatases, and protein tyrosine kinases.According to a previous article on a certain breed of beef bull (Red Angus cattle),5.12+, compared with the transmembrane types of the adenylyl cyclase, “ADCY1‐9.” This isoform is synthesized most abundantly in mouse testes as either the 189 kDa full‐length form or the 48 kDa truncated form from the same Adcy10 gene by alternative splicing. Although both forms contain two cyclase domains that catalyze the conversion from ATP to cAMP, the specific activity of the truncated form is 20‐fold higher than that of the full‐length form. Moreover, manipulation of this gene showed that this enzyme is indispensable in the progress of the capacitation process and subsequent successful fertilization. For bulls (Japanese Black cattle), the authors showed that ADCY10 was distributed in the neck and flagellar principal piece of the ejaculated spermatozoa and that both messenger RNAs (mRNAs) that coded the full‐length and truncated forms were expressed in the testes by the alternative splicing of exon 11.ADCY10, with the aberrance in the second cyclase domain by retaining the intronic nucleotides  that connect to the initial part of exon 10, and that the incidence rates of this splicing error were largely varied among individual bulls by between 0% and 54.5%. The authors are concerned that such splicing errors in mRNA coding in the important capacitation‐regulatory protein might cause bull AI subfertility.A soluble type of adenylyl cyclase, “ADCY10,”5.2+/K+‐ATPase and its inhibitor, “ouabain.”+/K+‐ATPase activity with ouabain promotes an increase of the intracellular Ca2+ (by the suppression of the Na+/Ca2+ exchanger activity), PKA activation, and tyrosine phosphorylation, leading to capacitation. Moreover, the interaction between Na+/K+‐ATPase and ouabain might activate the extracellular signal‐regulated kinases 1/2, phospholipase C, protein kinase C and protein tyrosine kinase signaling cascades, leading to capacitation. This ion transporter, Na+/K+‐ATPase,+/K+‐ATPase might cause precocious capacitation in the spermatozoa with normal motility and morphology. Moreover, there were individual variations in the Na+/K+‐ATPase activity of the frozen spermatozoa among beef bulls.+/K+‐ATPase is potentially a biomarker for bull AI subfertility, owing to the abnormal process of sperm capacitation and the consequent failure of fertilization.A model has been proposed for the induction of bull sperm capacitation by the interaction between Na6At ejaculation, the cauda epididymal spermatozoa are mixed with the secretory fluids from the accessary genital glands, including the seminal vesicles, prostate, urethral glands and bulbourethral glands. In the semen that is collected for cryopreservation, the spermatozoa are swimming in the seminal plasma, which contains a variety of proteins that is secreted from the epididymides and accessary genital glands and that can minimize cryoinjury effects on the sperm viability and motility and acrosome integrity.6.12+‐binding protein) of the seminal plasma originates from the epithelial cells of the seminal vesicle and ampulla.One study discovered the presence of four kinds of fertility‐associated proteins in bull (Holstein) seminal plasma.7For the purpose of finding out those AI subfertile bulls exactly in a short time, it is necessary to evaluate not merely the general characteristics  but also the molecular characteristics of the protein biomarkers in freshly ejaculated and cryopreserved spermatozoa. Actually, the authors and their colleagues have been investigating the general characteristics and distribution patterns of acrosomal tyrosine‐phosphorylated proteins (a protein biomarker for bull AI subfertility) in freshly ejaculated and cryopreserved spermatozoa from most of the sire candidates in the bovine AI center of Hyogo Prefecture, Japan.Conflict of interest: The authors declare no conflict of interest. Human studies: This article does not contain any study with human participants that was performed by any of the authors. Animal studies: All the institutional and national guidelines for the care and use of animals were followed.


AAPM) is a nonprofit professional society whose primary purposes are to advance the science, education, and professional practice of medical physics. The AAPM has more than 8,000 members and is the principal organization of medical physicists in the United States.The American Association of Physicists in Medicine (AAPM will periodically define new practice guidelines for medical physics practice to help advance the science of medical physics and to improve the quality of service to patients throughout the United States. Existing medical physics practice guidelines will be reviewed for revision or renewal, as appropriate, on their fifth anniversary or sooner.The AAPM, has undergone a thorough consensus process in which it has been subjected to extensive review, and requires the approval of the Professional Council. The medical physics practice guidelines recognize that the safe and effective use of diagnostic and therapeutic radiology requires specific training, skills, and techniques, as described in each document. Reproduction or modification of the published practice guidelines and technical standards by those entities not providing these services is not authorized.Each medical physics practice guideline represents a policy statement by the The following terms are used in the AAPM practice guidelines:Must and Must Not: Used to indicate that adherence to the recommendation is considered necessary to conform to this practice guideline.Should and Should Not: Used to indicate a prudent practice to which exceptions may occasionally be made in appropriate circumstances.AAPM Professional Council 3‐31‐2017 and Executive Committee 4‐4‐2017.Approved by  As SRS‐SBRT services are rapidly adopted into the community practice setting, this Guideline has been developed to provide appropriate minimum standards for such services.1.AThis MPPG's scope includes medical physics support for the entire treatment process including acceptance testing, commissioning, technical process development, treatment planning and delivery, and quality assurance related to linac‐based SRS, SRT, and SBRT, hereafter referred to as SRS‐SBRT. For ring‐mounted helical tomotherapy linac delivery systems, this document applies to SBRT only.1.BThis MPPG describes the minimum level of medical physics support the American Association of Physicists in Medicine (AAPM) and the Radiosurgery Society (RSS) deem prudent for the aforementioned scope. This document does not constitute a policy and procedure or standard operating procedure for a specific clinic — that is the professional responsibility of the clinic's Qualified Medical Physicist1.CEnd‐to‐end (E2E) testing — a methodology used to test whether the flow of an application is performing as designed from start to finish. The purpose of carrying out E2E tests in radiation oncology is to identify system dependencies, to ensure that the intended information is correctly passed between various system components, to verify that clinical team members understand their tasks, and to assess overall treatment process accuracy. All aspects of the treatment process should be considered, including immobilization, simulation, respiratory‐related motion management, treatment planning, and treatment delivery using a clinically relevant image guidance method. Each step in the E2E testing should be performed by the staff member who will perform the step when the program is clinically implemented.Medical dosimetrist — a person other than a radiation oncologist or medical physicist who participates in, performs, and/or assists in the procedures required to develop a radiotherapy treatment plan with related treatment delivery parameters, working under the supervision of a radiation oncologist and qualified medical physicist (QMP).Quality Assurance (QA) — as defined in the AAPM Task Group 100 report:Qualified Medical Physicist (QMP) — as defined by AAPM Professional Policy 1.Quality Control (QC) — as defined in the AAPM Task Group 100 report:Stereotactic Radiosurgery (SRS) — as defined in the American College of Radiology–the American Society for Radiation Oncology (ACR‐ASTRO) Practice Parameter for the Performance of Stereotactic Radiosurgery:Stereotactic Body Radiation Therapy (SBRT) — as defined in the ACR‐ASTRO Practice Parameter for the Performance of Stereotactic Body Radiation Therapy2Each member of the SRS‐SBRT team must be appropriately trained, and each team member's responsibilities in the SRS‐SBRT process must be clearly defined to ensure a consistently safe and accurate treatment delivery. , accuracy of targeting through end‐to‐end (E2E) testing, and quality and precision of the image guidance system.Implement and manage a QA program to ensure proper ongoing performance of the treatment delivery unit, immobilization and simulation devices, image guidance system, and treatment planning system.Work with other team members to develop standard operating procedures (SOPs) for major steps through the entire treatment process.Establish a comprehensive safety checklist to act as a guide for the entire treatment process, and determine appropriate methods for the clinic's quality assurance committee to monitor the SRS‐SBRT program.Facilitate and manage the clinic's participation in an incident learning system to ensure a transparent, structured evaluation of all “near miss” and actual deviations in the planning and treatment delivery process.Perform or supervise the dosimetric treatment planning process, providing supervision levels as appropriate to each task .Review the final treatment plan for accuracy and deliverability, consulting with the radiation oncologist to ensure that both professionals are confident of the acceptability of the chosen treatment plan.Validate the chosen treatment delivery parameters via an independent dose calculation. When deemed appropriate, a phantom measurement or treatment delivery “dry run” may also be performed.For the first treatment session, a QMP with relevant SRS‐SBRT training must provide personal supervision of the entire session.2.C2.C.1The radiation oncologist should be certified in Radiation Oncology or Therapeutic Radiology by the American Board of Radiology and have completed specific training in SRS‐SBRT as stated in the ACR‐ASTRO Practice Parameter for SRS2.C.2As stated in the ACR‐ASTRO Practice Parameter for SRS2.D2.D.1A dosimetrist providing SRS‐SBRT treatment planning services should be certified by the Medical Dosimetry Certification Board, have specific training in SRS‐SBRT planning prior to performing patient‐specific procedures, and be supervised by a radiation oncologist and QMP. The QMP with responsibility for the SRS‐SBRT program is responsible for determining the competency of each dosimetrist to provide SRS‐SBRT treatment planning services. Note: A medical physicist with appropriate training in SRS‐SBRT planning may perform the activities listed under Section 2.D.2Participate in simulation sessions as needed to be aware of and provide suggestions related to selection of patient immobilization and likely beam paths, motion effects on target coverage, and other dosimetric considerations.Under the radiation oncologist's and QMP's supervision, delineate normal tissue volumes, assess the target volume for contiguity and proximity to dose‐limiting normal tissues, review findings with the radiation oncologist, and generate treatment plan(s) in accordance with the patient‐specific dosimetric objectives. The QMP supervises the technical aspects of the treatment planning process and consults with the radiation oncologist regarding any additional considerations such as prior treatment, motion management, and implanted medical devices.Upon approval of a treatment plan by the radiation oncologist, document the chosen treatment technique and if necessary, export all relevant delivery parameters to the electronic treatment management and image guidance system(s). Coordinate with the QMP to ensure that appropriate plan review and quality assurance are completed prior to initiation of treatment.Ensure that all aspects of the chosen treatment technique are clearly conveyed to the therapist team. For unusual or complex aspects of a patient's treatment technique, communicate directly with the therapists to ensure that they are aware.2.E2.E.1All radiation therapists should hold an active certification in radiation therapy by the American Registry of Radiologic Technologists, maintain licensure as required by the state, and have specific training in the clinic's SRS‐SBRT procedures prior to performing such SRS‐SBRT procedures.2.E.2For each simulation session, prepare immobilization devices, position patient, and acquire images for treatment planning in accordance with the clinic's SRS‐SBRT procedure and the patient‐specific instructions. Document treatment setup parameters after the radiation oncologist has approved the positioning, images, and target localization.If the QMP has delegated certain daily QC tasks, perform the relevant QC tests under the QMP's supervision following the procedure established by the QMP.For each treatment session, prepare the treatment room for the SRS‐SBRT procedure in accordance with the clinic's procedure and the patient‐specific instructions, position the patient and localize the treatment isocenter, and operate the treatment unit after the radiation oncologist and QMP have approved the clinical and technical aspects of the treatment delivery.3Because of the high dose per fraction and the critical importance of targeting accuracy, SRS‐SBRT services require a strong commitment by the radiation oncology program and the facility to provide the appropriate resources. Both the clinical team and the institution's administration must understand their roles and commitments in this regard prior to implementing SRS‐SBRT services. In this context, “resources” refers to appropriate staffing and coverage, appropriate equipment to support the treatment process, appropriate instruments for QC, clear operating procedures with delineation of duties and appropriate time intervals for all staff to safely perform their work, and a safety culture rooted in transparency and process analysis.An institution should not offer SRS‐SBRT services unless it can provide the following resources and supports the following programmatic imperatives.3.AAdequate medical physicist staffing to ensure that a QMP with appropriate SRS‐SBRT training is available to review QC results and consult with the clinical team on patient‐specific aspects of treatment planning and delivery and to provide personal supervision for the first treatment session of every SRS‐SBRT treatment course and as necessary for portions of all subsequent treatment fractions.Adequate radiation oncologist staffing to ensure that a radiation oncologist with appropriate SRS‐SBRT training is available for direct or personal supervision (as described in the department's SOPs) of the simulation, treatment planning, and treatment delivery of every SRS‐SBRT treatment course.Adequate staffing to ensure that a dosimetrist or medical physicist with appropriate SRS‐SBRT training can devote the time necessary to develop a treatment plan with comprehensive review of all technical aspects such as prior treatment, respiratory motion of target and adjacent organs, multimodality image registration, and potential limitations in treatment delivery.Adequate therapist staffing to ensure that at least two certified radiation therapists are present for every treatment session, with at least one therapist who is appropriately trained in the SRS‐SBRT treatment technique being used.3.BRedundant radiation detectors suitable for small fields.Reference‐grade electrometer suitable for low‐signal readings.Appropriate E2E phantoms for the scope of SRS‐SBRT services offered, available for use on site in a timely manner (not to exceed 72 hr).QC device to perform a radiation isocentricity beam alignment verification.3.CAppropriate devices for patient setup and immobilization.Appropriate devices for proper motion management.Computerized treatment verification system.Digital access to MRI and positron emission tomography (PET) image data.Capability to characterize and quantify internal anatomical changes with respiratory motion .Multimodality image fusion capability.Capability to calculate, display, and evaluate composite dose for patients who have received prior radiation therapy.Linac‐based treatment delivery system with appropriate mechanical accuracy, field‐aperture size, and resolution for small‐target conformality, and image‐guidance devices for target localization and verification including motion management technology relevant to the scope of SRS‐SBRT services to be offered.3.DCommitment to support the delineation of duties, procedure‐specific QA, and staff authority required for safe delivery of SRS‐SBRT services, as defined in SOPs developed by the institution's QMP and medical director of radiation oncology consistent with the institution's credentialing process.Commitment to facilitate and pay for independent peer review of the SRS‐SBRT program and on‐site proctoring of the first SRS‐SBRT treatment(s) if the clinical team does not have relevant prior experience with the SRS‐SBRT service being implemented at the center.Commitment to support ongoing training for members of the SRS‐SBRT team as deemed necessary by the medical director and QMP. Such training may be necessitated by staff turnover, changes in staff roles, or low SRS‐SBRT procedure volume resulting in infrequent staff experience.Robust preventive maintenance and field service support arrangements for the key simulation, planning, and treatment delivery systems.44.AThe QMP must be involved with the process of facility design, equipment selection and specifications, and provide direct supervision during the acceptance testing process.4.BTo determine the scope of SRS‐SBRT commissioning, the QMP must understand the scope of procedures/services to be offered. Commissioning encompasses the overall process of validating the planning and delivery system for the services to be offered, and developing appropriate QC and technical procedures to support these services. The scope of commissioning must therefore be commensurate with the scope of clinical services to be offered.4.B.1Commissioning of a linac‐based treatment delivery system is performed after acceptance testing. Commissioning tests should be developed by the institution's medical physics team to explore in detail every aspect of the system with the goal of developing a comprehensive baseline characterization of the performance of the system, identifying any limitations relative to clinical use, and developing procedures for QA and clinical use.Treatment delivery machineImmobilization devicesAncillary systems for imagingTreatment planning systemsEach SRS‐SBRT system is highly specialized with fixed cones and/or multileaf collimators (MLCs). Specific validation should be considered based on manufacturer recommendations and the determined scope of the practice. Commissioning of such systems includes, but is not limited to, a safety and geometric accuracy evaluation of the treatment and imaging components, comprehensive small‐field data measurement with appropriate stereotactic detectors and careful equipment setup, evaluation of treatment planning system capabilities including multimodality image processing and calculation accuracy for small fields, and the development of a comprehensive QA program for each of the following critical components:Small‐field dosimetry as used in SRS‐SBRT is challenging due to many factors including source size, detector size, and response.Upon completion of beam data measurements, key data points (such as percent depth dose at 10 cm depth and output factors for field sizes ≤2.0 cm) should be compared to other machines of identical design, whether in the same institution or from other centers, to guard against gross errors which could arise from inappropriate detector selection or misaligned equipment setup.Immobilization equipment should be evaluated for its effectiveness in targeting accuracy and precision , and should be evaluated for its beam attenuation and surface dose characteristics.TM, or MLC fields if in scope), calculation accuracy for couch attenuation and effect on surface dose,Commissioning of the treatment planning system's dose model should include all aspects described in AAPM Medical Physics Practice Guideline 5,If the planned scope of clinical services includes treatments affected by respiratory motion, the entire treatment chain  should be assessed with E2E testing using a dynamic phantom setup with clinically relevant motion parameters . The tests should include assessment of spatial targeting accuracy and measurement of delivered target dose.All new SRS‐SBRT programs should have independent validation of the beam model and machine calibration prior to initiation of the clinical service. This can be accomplished through E2E phantom tests from the Imaging and Radiation Oncology Core,The scope of commissioning work and key results should be summarized in a written commissioning report. The report should clearly identify known limitations in the delivery chain, limits for clinical implementation , and baseline data to support the equipment QC program. If the full commissioning report is not completed prior to initiation of the clinical service, an Executive Summary describing the known limitations and limits for clinical implementation must be prepared and shared with the clinical team prior to initiation of the clinical service.4.B.2Clinical implementation of a stereotactic program requires agreement within the clinical team on the scope and clinical goals of the program. Development and validation of the technical process to be followed for delivering a clinical SRS‐SBRT service may be regarded as process commissioning, and should be completed prior to the first patient treatment. The SOPs for each anatomical site to be treated should be developed in collaboration with the clinical team. That team includes the radiation oncologist, the QMP, the medical dosimetrist, the radiation therapist, and often the radiation oncology nurse. There are several references available including AAPM task group reports,Specific clinical implementation guidance is found in Section VII of the AAPM TG 101 report.Site‐specific SOPs should address the components essential to the patient review, simulation, planning, treatment, and follow‐up (see the Appendix for a sample SOP document). Patient safety should be the primary consideration when developing any SOP.SafetyThe roles and responsibilities of each member of the clinical team should be clearly described in the SOP document. See section Mechanical tolerances will be established during commissioning and should be well documented. Additional tolerances for clinical operation should be considered for each SRS‐SBRT service, and should be clearly defined in the SOP document.The SOP should establish certain process expectations for safe implementation such as appropriate time intervals from simulation to treatment with critical points along the path allowing for reconsideration or rescheduling.Every team member has the right and responsibility to halt a case and/or a particular procedure based on safety imperatives.Patient selectionPatient selection criteria should initially be determined using data available from clinical protocols or published guidelines. Maximum target size should be documented along with standard prescription dose and fractionation schemes. Where possible, a multidisciplinary review or a peer review of proposed cases should be completed prior to simulation. If the patient is enrolled in a clinical trial, the rules and guidelines of the clinical trial must be followed.SimulationReproducible immobilization techniques should be developed for each treatment site.The reference imaging study to be used for treatment planning should cover the target and all relevant organs at risk. A typical scan length should extend at least 10 cm beyond the treatment field borders. For non‐coplanar treatment techniques, the scan length may need to be further extended to adequately model the beam paths and resultant scatter doseFor SBRT applications, tomographic slice thickness of 1–3 mm should be used. For SRS applications, slice thickness should not exceed 1.25 mm and scan field of view should be optimized for maximum in‐plane spatial resolution while including all necessary anatomy and immobilization hardware in the field of view.Respiratory motion management should be considered in thoracic and abdominal sites. At least one of the five categories of motion management as described in the AAPM Task Group 76 reportTreatment planningThe treatment planning system must have the capability of accurately calculating the predicted dose for the scope of SRS‐SBRT services to be offered.Each treatment site should have a defined list of critical structures to evaluate and stereotactic fractionation based tolerances should be defined based on clinical protocol data or peer‐reviewed literature.Image fusion requirements for target definition should be defined and target margins should be clearly described. Target margins should be based on data from current literature along with knowledge of the limitations of in‐house localization capabilities.Planning strategies and techniques should be described for each treatment site, such as conformal arcs, intensity‐modulated radiation therapy, and volumetric‐modulated arc therapy. These technique definitions should include clinical limitations based on the findings from commissioning. If noncoplanar techniques are included, potential collision should be considered in determining overall beam configuration.In cases of re‐irradiation, the cumulative dose should be evaluated by the treating physician. A description of the method used and the outcome of the evaluation should be documented.The use of an isotropic calculation grid size of 2 mm or finer is recommended. The use of a grid size >3 mm is discouraged.Target dose coverage, dose fall‐off beyond the target, dose conformity metrics, and compliance with critical structure dose objectives An independent dose calculation check must be performed prior to treatment.Treatment deliveryA clearly defined pretreatment QA check should be performed and may depend on the technique usedThe SOP should clearly describe the professional supervision requirements for each SRS‐SBRT treatment type.The SOP should clearly describe the image guidance method to be used, including target anatomy, critical organ avoidance, and localization tolerance. Pretreatment verification of target localization should always be performed; the criteria for intratreatment image guidance should be clearly described.If motion management is used, the SOP should clearly describe the process, tolerances, and professional supervision.Patient follow‐upThe SOP should clearly describe the follow‐up schedule and clinical tests for each treatment site. “There should be follow‐up of all patients treated, and appropriate records should be maintained to determine local control, survival, and normal tissue injury.”ChecklistsEffective checklists support human thinking, allow constructive team member interactions, and facilitate a systematic care delivery by reducing process variability. The AAPM Medical Physics Practice Guideline on development and implementation of safety checklistsTraining should address the need for initial as well as ongoing training and should be supported by a system of documentation and checklists to ensure that all team members are competent to support the clinical service.Training venues Vendor training — When possible, a core team should participate in all available vendor training on relevant hardware and software including off‐site training, onsite training, and case observation. Nonvendor training — Attendance at structured courses and/or “shadowing” procedures at a facility with a mature SRS/SRT/SBRT service should be considered. This should include a review of the SOP for the SRS‐SBRT services to be implemented, including equipment‐specific and patient‐specific QA procedures. If the principal professionals responsible for the SRS‐SBRT service do not have direct prior experience with the services to be offered, the facility must arrange for on‐site review and proctoring of the first clinical procedure by professionals with experience relevant to the new service.Ongoing competency The competency checklist should be reviewed periodically  and updated as the program evolves.Documentation Written standard operating procedures must be developed, and reviewed by all participating staff. All training should be documented. A checklist of relevant competencies should be developed and the checklist completed prior to program implementation.To assess the clinical team's readiness and to validate the SOP, the team should conduct “dry runs” of the entire process, observe and take notes, edit the SOP as needed, and repeat the E2E testing until the process is clear to all participants. The pre‐implementation E2E tests and findings should be described in the commissioning report.Each step in the E2E testing should be performed by the staff member who will perform the step when the program is clinically implemented. E2E process “dry runs” should be performed for each category of SRS‐SBRT service, and when a key aspect of the process is changed.When developing the E2E tests, all aspects of the treatment process should be considered, including immobilization, simulation, respiratory management, treatment planning, and treatment delivery using a clinically relevant image guidance method.55.AA comprehensive QA program for SRS‐SBRT is critical to ensure the correct dose is delivered to the target, given the very small target volumes and rapid dose fall‐off associated with SRS‐SBRT. QA processes and procedures related to SRS‐SBRT should be designed to cover the following aspects of the SRS‐SBRT program: equipment‐specific QA, patient‐specific QA, and procedure‐specific QA. Safety and QA recommendations have been extensively described in several publications.When equipment performance is found to be out of tolerance, the affected module(s) of the delivery system should be promptly adjusted, and the QMP should verify proper performance before clinical SRS‐SBRT services resume. In the event of a significant service interruption, the QMP should coordinate closely with treating physicians to evaluate the impact on patients’ treatment schedules given the importance of completing SRS‐SBRT treatment courses in a short overall time interval .5.BThe AAPM has published task group reports with recommendations for QA related to SRS‐SBRT. TG‐142 describes the linear accelerator QA for both conventional radiation therapy procedures and for SRS‐SBRT procedures.Note: Many tests described in the aforementioned AAPM publications are important for characterizing the system performance regardless of the scope of clinical use; the equipment‐specific QA in Tables 5.C5.C.1Compared with conventionally fractionated radiotherapy, the target volume in SRS and SBRT is much smaller, the dose heterogeneity is higher, and the dose falls off faster in tissue. The term “Patient‐specific QA (PSQA)” for SRS and SBRT, in the context of this Practice Guideline, refers to verifying that the approved treatment plan can be accurately delivered.5.C.2Patient‐specific QA should include verification of patient setup/immobilization, independent check of the approved treatment plan and associated treatment delivery parameters, dose delivery measurements when appropriate, chart rounds and/or peer review, and a dry‐run of the approved treatment plan to check for potential collision. If fixed conical collimators are used, dose delivery measurements are prudent to verify the integrity of treatment, but are not essential as the measured dosimetric characteristics  are directly applied to the dose calculation. When the MLC is applied to modulate the dose, dose delivery measurements should be performed prior to treatment to verify the absolute dose to the reference point .5.C.3The QMP determines the instrumentation appropriate to the SRS‐SBRT technique to be verified. Common instrumentation includes radiochromic film, small‐volume ion chamber (for relatively larger treatment fields), diode detector, portal imaging device calibrated for dose response, detector arrays, and, less commonly, polymer gel dosimetry. The institution must provide appropriate instrumentation to conduct PSQA as deemed necessary by the QMP. The clinical service should not be initiated if appropriate instrumentation is not available for the QMP's use.5.DThe workflows to perform SRS‐SBRT as defined in the SOP documents are consistently followed.Staffing level is appropriate.Staff training and continuous training are available and appropriate.Proper follow‐up actions are taken for any actual and/or potential (“near miss”) treatment incidents.Procedure‐specific QA addresses issues related to operational tasks, such as checking whether:As described in the Clinical Implementation section above, each facility should have SOP documents defining the workflow of each SRS‐SBRT service. These documents should be reviewed and updated regularly, with at least an annual frequency of review.Staffing levels, training, and competency assessments are critical for a successful SRS‐SBRT program. Team members without prior relevant SRS‐SBRT experience should perform a minimum of five procedures working under the supervision of an experienced expert for each SRS‐SBRT service.Ongoing competency assessment is necessary given the rapid evolution of technology and treatment methods for SRS‐SBRT. These activities should be properly documented.5.EThe QA program should be designed by a QMP who has specific training in SRS‐SBRT, and should be reviewed by another QMP with SRS‐SBRT experience. The daily QA procedure can be performed by a physicist or radiation therapist and be reviewed by the QMP prior to any SRS‐SBRT treatment. Other routine QA or patient‐specific QA may be performed by an appropriately trained medical physicist, and reviewed and co‐signed by the QMP.5.FWhen the SRS‐SBRT program is in its initial phase, the QA program should be reviewed bi‐annually as the clinical practice and utilization evolves. The frequency can be reduced to annual reviews once the clinical practice and utilization stabilizes.6For the delivery of SRS‐SBRT services, the two responsible professionals are the radiation oncologist and QMP. All other team members work under the supervision of these professionals — clinical procedures supervised by the radiation oncologist and technical procedures supervised by the QMP. The provision of SRS‐SBRT services should follow a structured approach with clearly defined roles, responsibilities, procedures, and action levels. The clinic's QMP develops SOPs for SRS‐SBRT through an active collaboration with the clinic's medical director.The resources and programmatic components described in Section The scope of commissioning work and key results should be summarized in a written commissioning report. The report should clearly identify known limitations in the delivery chain, limits for clinical implementation , and baseline data to support the equipment QC program. Any relevant limitations must be clearly communicated to the clinical team prior to program implementation.All new SRS‐SBRT programs should have independent validation of the beam model and machine calibration prior to initiation of the clinical service. If the principal professionals responsible for the SRS‐SBRT service do not have direct prior experience with the services to be offered, the facility must arrange for on‐site review and proctoring of the first clinical procedure by professionals with experience relevant to the new service.All members of Medical Physics Practice Guideline 9 completed disclosure statements and pertinent disclosures are shown below. These disclosures were reviewed by the Chair of the AAPM Subcommittee on Practice Guidelines and were determined to be sufficiently managed by disclosure and no other remedial measures were considered necessary.Per Halvorsen: honoraria and travel expenses from ACR Radiation Oncology Practice Accreditation program; Eileen Cirino: none; Indra J. Das: none; Jeffrey A. Garrett: none; Jun Yang: none; Fang‐Fang Yin: none; Lynne A. Fairobent: none.Appendix A: SAMPLE Standard Operating Procedure (SOP) DOCUMENTAppendix B: Example Staffing PolicyClick here for additional data file.


No estimates of influenza‐associated mortality exist for India.To evaluate national mortality and viral surveillance data from India for assessing their appropriateness in estimating influenza‐associated mortality using varied analytic approaches.CRS), Medical Certification of Cause of Death (MCCD) and the Sample Registration System (SRS). We compared and scored the different sources of mortality data using specific criteria, including the process of cause of death assignment, sample size, proportion of ill‐defined deaths, representativeness and availability of time series data. Each of these 5 parameters was scored on a scale from 1 to 5. To evaluate how to generate an influenza‐associated mortality estimate for India, we also reviewed 4 methodologic approaches to assess the appropriateness of their assumptions and requirements for these data sets.We reviewed influenza virus surveillance data from a national influenza surveillance network. We also reviewed national mortality data from Civil Registration System (SRS data had the highest score with 20 of 25 possible score, whereas MCCD and CRS scored 16 and 12, respectively. The SRS which used verbal autopsy survey methods was determined to be nationally representative and thus adequate for estimating influenza‐associated mortality. Evaluation of the modelling methods demonstrated that Poisson regression, risk difference and mortality multiplier methods could be applied to the Indian setting.The influenza virus surveillance data included year‐round sample testing for influenza virus and was found to be suitable for influenza mortality estimation modelling. Based on scoring for the 5 mortality data criteria, the Despite significant challenges, it is possible to estimate influenza‐associated mortality in India. Scores were allocated as 1: ≤5000, 2: 5000‐10 000, 3: 10 000‐100 000, 4: 100 000‐1 million or 5: ≥1 million annual deaths reported.Proportion of ill‐defined deaths: Systems which had fewer ill‐defined deaths, that is deaths coded to symptoms, signs, ill‐defined conditions and incompletely recorded deaths were scored higher than those that reported higher proportions of ill‐defined deaths. Scores were allocated as: 1: proportion of ill‐defined deaths >50%, 2: 35%‐49%, 3: 20%‐34%, 4: 10%‐19% and 5: <10%.Coverage : Data sets which covered a larger country‐level population were scored higher than those with less coverage. Scores were allocated as: 1: coverage <30%, 2: coverage 30% to <50%, 3: coverage 50% to < 70%, 4: coverage 70% to < 90% and 5: coverage ≥90%.Availability of time series COD data: To capture the full impact of influenza on mortality, models typically use 1 or more categories of coded mortality data: pneumonia and influenza deaths, respiratory deaths, circulatory deaths or all‐cause deaths.2.3The WHO document “Practical guide for designing and conducting influenza disease burden studies”33.1For the ICMR‐NIV influenza surveillance network, specimens were tested for influenza virus using standard protocols coordinated by NIV, Pune, WHO National Influenza Center for India. The clinical virology laboratories were located across ten cities in 8 states providing geographical and climatic representation of India Figure . Five to3.2After scoring each system Table , the SRSThe overall score for the CRS system was 12 of 25  periods so that the difference in observed mortality between the 2 periods can be assessed to estimate the excess impact. The epidemic cut‐off is arbitrarily decided based on percentage of influenza specimens testing positive (eg 10% or 15%).3.4.4This method requires age‐specific number of ICD‐coded deaths for specific causes such as pneumonia and influenza (P & I) deaths to multiply the proportion of influenza per cent positive for that age group to calculate estimates of influenza‐associated P & I mortality. This can be done for areas with adequate (>70%) coverage of deaths available by month4Through our systematic evaluation of data sources and methods for estimating influenza‐associated mortality in India, we identified that robust influenza virus surveillance data were available from a national influenza surveillance network and could be applied to several different methods. Among the national mortality data sources evaluated, SRS had the highest score and therefore is the most appropriate for inclusion in models for excess influenza‐associated mortality estimation. Except for the Serfling method, which requires very well‐defined influenza virus seasonality, the methods that we reviewed  could all be applied to Indian settings.Earlier reviews of the SRS database also demonstrated it to be the most representative source for mortality in India,State or regional‐level estimation is also important because influenza virus circulation patterns may vary within India. While majority of the country experience influenza virus circulation during the monsoon season, a few northern states with more temperate climates experience peaks in influenza activity during winter months.As weekly virological data from NIV provided influenza virus data by subtypes and coincided with weekly SRS data of sufficient sample size at the national level, the Poisson regression was determined to be the most appropriate method for deriving national influenza‐associated mortality estimates in India. In the future, for subnational mortality data which may become available but may not meet data requirements for regression models, the use of both the multiplier and rate difference methods could be explored for Indian estimations. In recent years, while the multiplier method is increasingly being used in countries without available detailed time series data,There are some limitations to this review of data and approaches for influenza mortality estimation. As this evaluation was based mainly on data review, carrying out the actual estimation could present with additional issues pertaining to application of the estimation methods to Indian data. Also, we were only able to evaluate national influenza surveillance data that were available either publically or by request. Thus, there may be influenza virological data that we did not have access to but which could be added or utilized at a local level. Similarly, we evaluated mortality data sets that were available either publically or by request. Both CRS and MCCD data may have valuable data at the state and local level which could contribute to these efforts at subnational level.5Although there are considerable challenges for estimating influenza‐associated deaths in India, data sources are available that would allow use of modelling methods for this estimation. This evaluation of data sources and analytic methods provides ways to use the data within its limitations to provide information on influenza burden that could inform public health policy. Because of India's size and global importance, modelling methods may be a highly relevant approach to defining public health priorities and strategies. Thus efforts to retain and grow both the virology and mortality data sources in India would help to work towards these goals.The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of All India Institute of Medical Sciences, New Delhi, and US Centers for Disease Control and Prevention, Atlanta.


An ever‐growing wealth of information on current drugs and their pharmacological effects is available from online databases. As our understanding of systems biology increases, we have the opportunity to predict, model and quantify how drug combinations can be introduced that outperform conventional single‐drug therapies. Here, we explore the feasibility of such systems pharmacology approaches with an analysis of the mevalonate branch of the cholesterol biosynthesis pathway.Using open online resources, we assembled a computational model of the mevalonate pathway and compiled a set of inhibitors directed against targets in this pathway. We used computational optimization to identify combination and dose options that show not only maximal efficacy of inhibition on the cholesterol producing branch but also minimal impact on the geranylation branch, known to mediate the side effects of pharmaceutical treatment.We describe serious impediments to systems pharmacology studies arising from limitations in the data, incomplete coverage and inconsistent reporting. By curating a more complete dataset, we demonstrate the utility of computational optimization for identifying multi‐drug treatments with high efficacy and minimal off‐target effects.We suggest solutions that facilitate systems pharmacology studies, based on the introduction of standards for data capture that increase the power of experimental data. We propose a systems pharmacology workflow for the refinement of data and the generation of future therapeutic hypotheses. APIApplication Programme InterfaceBPSBritish Pharmacological SocietyBRENDABraunschweig Enzyme DatabaseCIDcompound identifierFDAUS Food and Drug AdministrationFDFT1farnesyl‐diphosphate farnesyl transferase 1GtoPdbGuide to Pharmacology DatabaseHMGCRhydroxymethylglutaryl‐coa reductaseHMGCS1hydroxymethylglutaryl‐CoA synthaseHPChigh‐performance computingKEGGKyoto Encyclopedia of Genes and GenomesIUBMBInternational Union of Biochemistry and Molecular BiologyIUPHARInternational Union of Basic and Clinical Pharmacologyn2sname‐to‐structureODEordinary differential equationSBGNSystems Biology Graphical NotationSBGN‐MLSystems Biology Graphical Notation Markup LanguageSBMLSystems Biology Markup Languageet al.,et al.,systems pharmacology  with 253 added in 2015 . Reactome currently holds 2148 human pathways involving 10 684 proteins and isoforms (http://reactome.org/stats.html)  model of the pathway, which we parameterize as far as possible from the literature. We identify relevant pharmacological agents that act on this pathway and parameterize them as far as possible from the literature and online databases. We then use computational optimization techniques to identify the drug combinations that are most effective at suppressing the outputs of the pathway that lead to cholesterol production and that minimize off‐target effects. In completing our analysis, we identify many of the problems that prevent this type of work being undertaken routinely, and we suggest solutions that would enable systems pharmacology to make a regular contribution to therapy development.Here, we describe a systems pharmacology study of the et al.,et al.,et al.,et al.,et al.,et al.,et al.,et al.,et al.,et al.,acetyl‐CoA to squalene and that forks to produce geranylgeranyl‐diphosphate. As a precursor to cholesterol, we would expect squalene synthesis to track cholesterol synthesis and so we use this as a proxy. The branch of the pathway that produces geranylgeranyl‐diphosphate has been shown to mediate both the innate immune response  and the SBGN‐ED add‐on to VANTED   using the Braunschweig Enzyme Database (BRENDA)  sourced from a reference that could be accessed and therefore verified. For many enzymes, this yielded a range of values for each parameter, and where this was the case, we used the mean of the values obtained.We identified the kinetic parameters that quantify each reaction unambiguously (Ki) was reported; and (iii) the assay conditions were reported. Crucially, all data were checked against the primary literature references. Where this yielded a range of inhibition constants for nominally identical compounds, the most potent Ki values were used.Inhibitor compounds not already indexed in GtoPdb were identified for each reaction from ChEMBL and BRENDA, databases that we took to be representative of the community of target databases. We included a compound in our set if it met three criteria: (i) the enzyme used in the assay was wild‐type from one of the three main mammalian model species: human, mouse or rat; (ii) an experimentally determined reaction‐specific inhibition constant . Comparison of unique structural identifiers allowed us to identify duplicates within the ChEMBL, BRENDA and literature‐derived dataset, and to establish whether the chemical structure reported in a given reference matched the marketed drug or research compound structures.We verified the correct chemical structures of the inhibitors by cross‐referencing the original references against the online chemical databases PubChem  in parallel with a population size of 200 and a function tolerance of 10−6. Matlab was chosen as the modelling platform for its flexibility, stability and comprehensive libraries. The genetic algorithm started with one instance of a set of drug concentrations where each drug was assigned a concentration equal to its Ki. A 199 further instances of sets of drug concentrations were automatically generated from this instance by adding Gaussian noise to the concentration of each drug . These 200 instances comprised the first generation of candidate interventions. All instances of sets of concentrations were evaluated for their efficacy at suppressing squalene synthesis whilst maintaining geranylgeranyl diphosphate production. Two hundred new instances were created as a second generation of candidate interventions from the two most effective instances of the first generation and with the addition of Gaussian noise. The 200 new instances were then themselves evaluated with the two most effective instances used to generate a further 200 new instances, the third generation. This process was repeated until we arrived at instances from which no improvement in efficacy could be found for 20 consecutive generations, at which point we interpreted the best performing instance identified thus far as optimal.This was implemented using the Genetic Algorithm function available on Matlab ]. A second parameter had been transcribed  where the literature source contradicted itself, specifying Km = 10 μM in the abstract and Km = 10 mM in the manuscript. Because computational hypothesis generation is highly sensitive to the values of the parameters, ambiguous or inaccurate reporting can have a significant impact on any predictions made.The parameters required for the resulting ODE model are shown in Table et al.,Substrates were reported in varying levels of structural detail. Common names were used that could refer to multiple explicit forms of a chemical structure. However, variations in the chirality and chemical structure can significantly affect substrate affinity. The relative enzyme concentrations had been inferred previously (Watterson Supporting Information Table i), are listed in Table L‐659,699 for hydroxymethylglutaryl‐CoA synthase (HMGCS1) and 3‐hydroxy‐3‐methyl‐6‐phosphohexanoic acid for phosphomevalonate kinase] in order to maximize coverage of the pathway. Two enzyme paralogues (isopentenyl diphosphate Δ‐isomerases 1 and 2) had no reported inhibitors with available Ki values, representing a region of the pathway that cannot currently be modulated in our modelling process. This can be contrasted with the enzymes HMGCR and farnesyl diphosphate synthase, each of which had an extensive list of inhibitors. Inhibition constants could be obtained for 8 of the 10 enzymes in the pathway. Where reported, these values came from studies conducted across a range of pH levels from 6.8 to 7.5 and temperatures from 25°C to 37°C.The inhibitors obtained from GtoPdb, BRENDA and the literature, together with their inhibition constants (KBoth explicit structure and name‐to‐structure (n2s) ambiguities existed around the reporting of inhibitor entities. In some cases, the common or trade name of a compound was used, without specification of the exact chemical structure and stereochemistry. In other cases, we found a different n2s assignment across different database resources or indeed within the same resource. For example, under the HMGCS1 entry of BRENDA, the same inhibitor is listed twice as L‐659,699 and ‐11‐[3‐(hydroxymethyl)‐4‐oxo‐2‐oxytanyl]‐3,5,7‐trimethyl‐2,4‐undecadienenoic acid.et al.,et al.,FDFT1) enzyme, whilst in fact, the paper describes results for the yeast Candida albicans and rats.Several results recorded in ChEMBL were transcribed against the incorrect drug target. Three inhibitors listed against the enzyme HMGCS1 describe results obtained from experiments with HMGCR  platform. However, the HPC demands were modest. Using an eight‐node desktop computer running MATLAB in parallel, we can see that the score  converges rapidly on an effective drug combination. It successfully identified an optimal combination in 46 min and achieved an approximately optimal solution in less than 10 min.http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=104, an example of which is shown in Supporting Information Figure The results of our curation of the pathway and the inhibitors that target it are available in GtoPdb at http://biomodels.org . Promiscuous drugs can be incorporated advantageously into the generation of these hypothetical interventions, provided that their interactions are known and parameterized.Multi‐drug approaches can minimize the pleotropic effects of an intervention. As we demonstrated for statins, where a single drug intervention suppressed the output of a pathway to the same extent as multiple drugs targeting the same pathway, not only was the dose of each of the multiple drugs significantly lower than the dose of the single drug but also the combined dose of all of the multiple drugs was significantly lower than the dose of the single drug. This intrinsically reduces the risk from off‐target or pleotropic effects for each drug.The systems pharmacology approach allows us to predict multi‐drug strategies that may be optimal to treat a disease and can be used as a prioritization triage for future drug development. It can support personalized and stratified medicine, where we adapt the parameter sets of the underlying models of pathway activity to represent an individual  or a subpopulation (for stratified medicine) and we develop interventions that are customized to be optimal for the patient or patient group. A challenge lies in developing optimized therapies so that they preferentially target key tissues. Pathway models and pharmacological interactions can be made tissue specific by generating a new parameter set for each tissue. Hypothesis generation would then use optimization to determine an intervention that impacted upon a key pathway in a key tissue, leaving other pathways unchanged across all tissues and with a minimal impact on the key pathway in non‐targeted tissues.et al.,Entresto, was approved in 2015 and is in Phase III of clinical trials for the treatment of cardiovascular disorders. Establishing drug combinations using a conventional drug development pipeline creates significant challenges as development essentially replicates the single drug development process multiple times. Systems pharmacology is therefore critical to expanding the range of multi‐drug interventions available in a cost‐effective manner. Although it may add extra steps to the preclinical stages of the drug development process, it could have a significant positive impact on the cost‐efficiency associated with each success by reducing the attrition rate in the later stages of the pipeline  has been investigated as a potential drug target that lies downstream of HMGCR, the target for statins, in the cholesterol biosynthesis pathway  1548972 and 446155, with the 3R, 5S enantiomer (CID 446155) being significantly more pharmacologically active than the other ‐isomer form. Sigma‐Aldrich currently refers to its marketed version as ‘(RS)‐mevalonic acid’. However, in one study . For a Vmax value to be reusable in subsequent studies, the enzyme concentration must also be reported alongside it. However, we regularly found this not to be the case, making most reported Vmax values unusable.We found cases of incorrect or incomplete kinetic data reported in the primary literature that undermined the ability to model interactions. V50 values instead of Ki values, where Ki and IC50 are related by Ki = IC50/(1 + S/Km) and S is the substrate concentration. For IC50 values to be reusable in future studies, the substrate concentrations must also be reported. Here, again, we found regular omissions that rendered most reported IC50 values unusable.Similarly, inhibitors were frequently parameterized by ICet al.,et al.,Reporting must include clear and thorough descriptions of experimental configurations and unambiguous identification of chemical structures through the use of comprehensive and standard nomenclature. Past experience has shown that effective standards can be developed through open community exercises (e.g. SBML and SBGN). The necessity for appropriate standards has been recognized previously by the chemical biology and pharmacometric communities . The International Union of Pure and Applied Chemistry, the International Union of Biochemistry and Molecular Biology (IUBMB) Joint Commission on Biochemical Nomenclature and the Nomenclature Committee of IUBMB have provided guidelines on biochemical descriptions and enzyme classification. A library of ontologies for the life sciences has also been proposed by the Open Biomedical Ontologies Foundry  facilitate extraction of results for hypothesis generation.Interaction literature seeds databases of biological pathways.Pathway databases containing sufficient information for experimental results to be reproduced accurately. Database APIs facilitate extraction of results for hypothesis generation.Hypothesis generation for single drug and multi‐drug interventions using data obtained through APIs from the pharmacological and pathway databases.Hypothesis testing. Success yields a candidate therapy and provides validation of the database. Failure initiates further exploration of the underlying interactions that in turn refine the databases.Candidate Intervention. Following success, the group of compounds enters an optimization pipeline that reduces them to a minimal set of lead compounds for preclinical testing to establish their efficacy and safety.The following workflow would enable the process to be automated  where IF is the inhibited flux through the endpoint of the pathway and WTF is the wild‐type flux through the endpoint in the absence of inhibitors. Green indicates low inhibition (D = 0). Red indicates high inhibition (D = 1). With eight drugs there are seventy–two possible pairings. These six heat map plots have been selected as being representative of the results. The IC10, IC20, IC30, IC40, IC50, IC50, IC60, IC70, IC80 and IC90 were identified for each drug in isolation. We then combined pairs of drugs at these concentrations and evaluated their effects by calculating the resulting D value. Values of D with both drugs at IC10 are bottom left and with both drugs at IC90 are top right. For Rosuvastatin the IC10‐IC90 concentrations were  nM; for Farnesyl Thiodiphosphate the IC10‐IC90 concentrations were  nM; for Cinnamic acid the IC10‐IC90 concentrations were  nM and for Zaragozic acid A the IC10‐IC50 concentrations were  nM.Click here for additional data file.Figure S2 A representative reaction from the mevalonate arm of the cholesterol biosynthesis pathway, as described on the IUPHAR/BPS GuidetoPharmacology (GtoPdb).Click here for additional data file.Table S1 The publicly available pathway and chemical databases used.Click here for additional data file.Table S2 The inhibitors used in the model of the pathway with structural information. The inhibitors selected were those with the greatest efficacy in humans.Click here for additional data file.Table S3 The ten best performing drug combinations identified using the genetic algorithm as part of hypothesis generation, together with their scores.Click here for additional data file.File S1 Supplementary_Mevalonate_Pathway.sbgn A biologically meaningful, machine readable SBGN file encoding the diagram shown in Figure 1.Click here for additional data file.File S2 Supplementary_Mevalonate_Pathway.sbml A biologically meaningful, machine readable SBML file encoding the mathematical model describing the pathway shown in Figure 1.Click here for additional data file.


Panallergens comprise various protein families of plant as well as animal origin and are responsible for wide IgE cross‐reactivity between related and unrelated allergenic sources. Such cross‐reactivities include reactions between various pollen sources, pollen and plant‐derived foods as well as invertebrate‐derived inhalants and foodstuff. Here, we provide an overview on the most clinically relevant panallergens from plants  and on the prominent animal‐derived panallergen family, tropomyosins. In addition, we explore the role of panallergens in the sensitization process and progress of the allergic disease. Emphasis is given on epidemiological aspects of panallergen sensitization and clinical manifestations. Finally, the issues related to diagnosis and therapy of patients sensitized to panallergens are outlined, and the use of panallergens as predictors for cross‐reactive allergy and as biomarkers for disease severity is discussed. Whilst controversially discussed, panallergen sensitizations have been shown to provide further complexity to the allergic profile of patients www.allergen.org). The involvement of profilins in such essential cellular processes explains their ubiquitous expression and high levels of conservation. This, in turn, can justify the strong serologic cross‐reactivity of the molecules Profilins are 12–16 kDa, actin(–monomer)‐binding proteins, expressed in all eukaryotic cells and certain viruses, with the exception of some protists 2+‐binding proteins comprising a major group of allergenic molecules of this kind. The mostly α‐helical proteins contain the characteristic EF‐hand motifs (helix‐loop‐helix structure), which are responsible for the binding of calcium. Polcalcins have a molecular mass of 9–28 kDa, depending on the number of EF‐hand motifs they hold , and show a monomeric or dimeric structure. They can assume two different conformations; a closed, Ca2+‐free apo‐form and an open, Ca2+‐bound holo form which is more stable and results in stronger interactions with IgE antibodies 2+ levels suggest a contribution in pollen tube outgrowth Polcalcins are a pollen‐restricted portion of widespread Cain vitro, which seems unlikely in vivo, lipid transfer proteins (LTPs) are widely distributed small and basic proteins in higher plants Originally named after their ability to transfer lipid molecules between membranes PR‐10 proteins function in the general defence mechanisms of plants, and their expression is induced by stress and pathogens. They constitute mostly intracellular, intrinsic and highly similar globular proteins with a length of around 160 amino acids. They share a molecular mass of around 17 kDa and are encoded by a diverse multigene family www.fda.gov). The highly heat‐stable tropomyosins comprise the major allergens in crustaceans and mollusks, making them significant food allergens in exposed populations Tropomyosins are α‐helical and, in their native form, dimeric coiled‐coil fibrous structural proteins consisting of two subunits , each with a molecular weight ranging from 34 to 38 kDa. They form co‐polymers with actin and regulate actin–myosin interactions in skeletal muscles and diversify the functions of actin filaments in different intracellular compartments Phleum pratense (timothy grass). Initial sensitizations towards major (Phl p 1 and Phl p 5) and minor  allergens gradually result in the onset of allergic disease, following such disease onset the occurrence of panallergen sensitizations, towards Phl p 12 and 7, increases for a minority of patients in correlation with disease severity. Hence, whilst not being an indicative marker for allergic disease onset, panallergen‐specific IgE responses have the potential as clinical biomarkers for increased severity of disease, although it must be emphasized that only a minority of patients become sensitized Panallergen sensitizations tend to occur as part of a co‐ or poly‐sensitization profile, with panallergen monosensitizations rarely arising Chenopodium album pollen (white goosefoot), sensitization rates of 55% and 46% to profilin and polcalcin, respectively, have been reported Furthermore, such increased rates of panallergen sensitization have been shown to correlate with an increased severity of allergic symptoms . A study carried out by Alverado et al. investigating profilin‐related allergic reactions over both an intense and a mild grass pollen season showed that more severe profilin allergy occurred during the intense season again emphasising the relationship between higher allergen exposures and increased panallergen sensitization rates For only a minority of patients sensitized to panallergens, allergy arises It is of note that these different panallergen families present varying levels of severity with regard to the symptoms induced. Tropomyosin represents the only panallergen family with the potential to induce autoimmune responses Panallergen sensitizations may be indicative of allergic disease severity and key in identifying a specific allergenic source, especially when sensitization rates are high In vitro molecular‐based diagnosis (MBD) uses allergenic proteins, either natural, purified or recombinantly produced, to quantify the amount of allergen‐specific IgE antibodies in the blood circulation Exploration of the hierarchical patterns of cross‐reactive molecules may also provide further insight into panallergen sensitizations and potentially elucidate novel therapeutics based on the concept that some molecules are more cross‐reactive than others. A recent microarray study by Pfiffner et al. investigates the structural basis of cross‐reactivity using an iterative motif detection algorithm In daily clinical practice, it is often observed that individuals allergic to fruits, nuts and vegetables have sensitivities to more than one food, not necessarily belonging to the same family. In addition, many of them are also allergic to pollens and/or seafood. These associations occur when the same IgE antibody is able to recognize similar epitopes in different panallergens and appear to be highly influenced by many variables. This phenomenon explains why some patients develop a severe allergic reaction upon ingesting allergenic foods they have never before encountered In conclusion, panallergens comprise a variety of protein families of plant and animal origin and are responsible for wide IgE cross‐reactivity between different allergenic sources. Panallergen sensitizations are clinical ‘warning signs’ for elevated risk of multiple allergies as well as severe symptoms. Thus, improving the understanding of this immunologic cross‐reactivity is essential for the interpretation of their clinical relevance, the development of improved diagnostic tests and the generation of more efficacious immunotherapy agents. Future studies focusing on the identification and evaluation of cross‐reactive epitopes between different members of panallergenic families might provide the basis for understanding their role in sensitization and allergic reactions.