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Clinical Implications of Biomarkers in Precision Medicine


The year 2003 marked the completion of the Human Genome Project, which initiated an increased focus on genomics within the health care system [1]. Later in the year 2011, four major research institutes: American Academy of Science, National Academy of Engineering, National Institute of Health and the National Science Foundation, proposed a multidisciplinary research plan on precision medicine [2]. In January 2015, President Obama announced that the United States would initiate its research plan on Precision Medicine, with the goal to cure or prevent cancer, diabetes and other diseases [2,3]. Precision medicine would be achieved through the collection of medical records of individuals who are ill. The data collected will help provide an understanding of disease biology, pathogenesis and precision-health care towards specific populations and individuals [3]. The following review focuses on the role of biomarkers through current treatments and the future of precision medicine.
Biomarkers are identified as being a “Cellular, biochemical or alteration that is measurable in biological media such as human tissues, cells or fluids” [4]. Biomarkers are used to identify a normal physiological process within the body where they can note the presence of disease through any changes within the body. Biomarkers can also be used to determine the pharmacodynamics of a drug towards a specific disease. In the clinical setting, biomarkers aid in predicting, diagnosing, and identifying the cause of the disease or the outcome of treatment. Biomarkers often aid in the diagnosis and management of various conditions such as cardiovascular disease, immunological disorders, genetic disorders and cancer [4]. Biomarkers can help to detect the earliest events in the natural history of a disease, where an individual can take action to prevent the occurrence or progression of the disease. Biomarkers can also prevent misclassification of the disease or exposure, which is essential when identifying the proper treatment for an individual. There are two major classifications of biomarkers, those being biomarkers of exposure and the other being of disease. Biomarkers of exposure are used to identify risk prediction, which are characteristics that predict a health outcome. While biomarker of a disease can be used in various applications such as screening, diagnosis, and monitoring [4].
The concept of Precision Medicine has increased drastically after the establishments such as the Human Genome Project. With the use of precision medicine we will have the ability to identify subtypes of a disease within a genome improved the ability to prevent and treat numerous diseases [5]. Establishments such as the Human Genome Project might have contributed to the increased research on precision medicine, but the term precision medicine is not a new concept, for it had occurred in the early 1900s. In the early 1900s, the identification of blood types and transfusion outcomes had been established. They had noted that blood could not be transferred from one individual to another incoherently but instead, patients had to be matched based on blood type to reduce any complications [6]. According to the NIH, precision medicine can be identified as preventive and treatment methods that account personal factors that may affect a patient such as genes, and lifestyle [6]. Precision medicine looks at medicine in a more detailed approach by understanding the genetic and genomic factors within the patient [2]. Some of these factors identified include the genetic, biomarker, phenotypic or psychosocial characteristics, usually compared to a healthy individual to identify any changes occurring [7]. The identification of specific factors in the body will help predict the process of the disease, establishing individualized prevention, diagnosis, and treatment methods [2]. This will result in a decrease of side effects, and an increase in the application of the most effective treatment based on the patient’s biological makeup.
The idea that people may react differently towards a specific treatment is not something new, the way our body reacts to something is based on our genetics, determining how our body may respond towards disease. Modern medicine often utilizes the one-size-fits-most approach, where if many patients were to go to a would probability be prescribed the same dosage as anyone else, without taking into account family history, age, sex, weight, and medical history [6]. Precision medicine brings uniqueness towards an individual’s treatment plan by taking account the genes, surrounding, and lifestyle of the patient. The following factors will help validate that the patient is receiving the most suitable treatment by taking into consideration the effects, mechanisms, and factors the body may have towards a disease [2]. In precision medicine to determine the right treatment, the application of genomics, proteomics and other technologies to analyze and identify the biomarkers of large sample groups and specific disease is crucial to develop a precise and individualized treatment. Precision medicine will result in the decrease of side effects and medical expenses while optimizing therapeutic effect [2]. A majority of complications associated with diseases can be easily prevented while caught in the early stages. This is due to the fact that we have the scientific and technological resources to monitor diseases molecularly and are able to determine when small changes in such diseases occur. This allows health care practitioners – specifically physicians and pathologists – to find the means to deviate away from the complications that may occur by introducing innovations contributing to molecular diagnosis [8].
Current Treatments
When applying systems biology within precision it is not just limited to an explanation of disease progress, but it also helps determine screening, diagnosis, monitoring, prognosis, and selection of therapy towards a specific disease based on the genetic make-up of an individual — current applications of the precision medicine range in various specialties including mutation-specific therapies, personalizing early detection strategies and disease prevention [7]. Mutation-specific therapies are to create and identify personalized treatments specific to an individual’s genetic make-up. An example of a current application of a mutation-specific therapy would be amongst those with cystic fibrosis who have the CFTR gene mutation. The CFTR gene has a gate-like structure which manages the influx and efflux of salts within the cell but if a mutation is present the opening and closing of the gate slows down which causes a buildup of mucus within the lung. In precision medicine, if the biomarker CFTR has a gene mutation, the drug ivacaftor could be applied to bring the influx and efflux of salts back to its normalized speed, preventing the buildup of mucus [9]. However, note, only those who have the specific biomarker will benefit from the following drug. Another application of biomarkers in precision medicine would be the application of circulating biomarkers within those who are high-risk cancer patients. These biomarkers can help calculate patient risk, tumor mass and prediction of treatment outcomes in real time. This is achieved through the use of assays such as reverse transcriptase quantitative PCR, which identifies tumor-derived biomarkers in blood and other fluid. An example of this application would be gathering tumor cells in bone marrow from those with neuroblastoma, which can be used to identify biomarkers for prognosis and disease progression [8]. Table 1 of the appendix is a list of ­­­­current precision medicine applications towards various cancers, epilepsy and HIV.
Future of Precision Medicine
With the rising interest in biomarkers, a lot of research on precision and biomarkers are arriving into foreign territory allowing increasing the horizon on the many possible applications of biomarkers within precision medicine for many different specialties. Possible applications in the future may include the increased application of digital biomarkers, patient derived cellular avatars, intensive personalized health monitoring and biomarkers usage amongst high risk cancer patients. Currently, some medications focus on altering the genetic pathways in cancers, in the future the application of targeted immunotherapies for cancer will exist. The targeted immunotherapies will consist of antibodies that work against tumor or immune checkpoint pathways rather than alternating the genetic path of cancer [7]. This can be achieved through the use of autologous T cells engineered to target specific antigens. The method of biomarkers will aid in the identification of which antibody pairs with what antigen. Once established, the use of targeted immunotherapies will be wildly applied in oncology [7]. With the drastic increase in precision medicine, there’s no doubt that one day in the near future precision medicine could be applied in the clinical setting to diagnosis and determine the most effective treatment. However, some challenges may come across the process from research to clinical. Future and current doctors will need to learn more about omics, data integration, and bio information, to apply the concept of precision medicine to their work [10]. Precision medicine is a term often coined by those in biomedical research and oncology. There is currently a lack of awareness when it comes to precision medicine, by teaching current and future medical professionals and researchers about precision medicine the sooner we would be able to integrate the concept into the clinical setting.
Challenges of Precision Medicine
One challenge of successfully implementing and supplying precision medicine is finding more effective biomarkers within the body that are associated with specific diseases and their detection. Finding more effective biomarkers would help improve treatment regimes, especially for diseases that lack genetic susceptibility and are harder to identify such as Alzheimer’s disease and concussions. However, being provided with the resources in order to do this may prevent such an advancement. This is due to the fact that in order to achieve these means, an adequate amount of funding is required needed for research, and most funding is used towards marketing new drugs rather than creating new diagnostic tests. There is also controversy towards mammography, which is used to test for prostate-specific antigens – which may hinder the idea of finding biomarkers regardless of how sensitive and specific they are [7]. Another challenger associated with precision medicine is regarding how to transfer and present data – either derived from omic data or from environmental and lifestyle factors – that would be able to conclude clinical outcomes and drug responses. Omics data in itself has the complication of being difficult to derive well established biomarkers from despite it being fairly accurate. For example, biomarkers that are omic-based of cancer are not as strong, which can affect the predictive value of other groups with the similar type of cancer[11]. Lastly, the application of precision medicine and omics must be incorporated into the curriculum of future and current medical professionals since the topic is usually only mentioned in research and oncology.
In conclusion, biomarkers play a crucial role in precision medicine, without the use of biomarkers we would not be able to characterize genomic, biochemical and behavioral changes occurring in response to treatments, disease or interventions. There are various forms of precision medicine currently available ranging from omics, wireless monitoring devices and DNA sequencing which can be clinically used with monitoring, diagnosis, prognosis, screening, and selection of therapy. We are not just limited to the precision medicine techniques currently available, we have barely touched the tip of the iceberg in the world of precision medicine, and the pipeline for new biomarkers just started flowing. However, there will be some challenges in the near future for not many medical professionals know about the possible applications biomarkers may have in the medical field. Therefore, intensive teaching will have to be done to inform medical professionals about concepts such as omics and DNA sequencing. Precision medicine would yield more accurate outcome predictability for relevant health care practitioners, such as scientists and other medical staff, both advocate and support the implementation of policies towards cost efficiency for users. These changes in precision medicine are envisioned towards improved outcomes along with health care certainty and management within all health care systems which would overall lean towards long-term sustainability solutions. Additionally, this supports the argument related to the pharmaceutical industry as it counters cost effective.
In the following paper, literature was obtained using PubMed, Open Access Journals, ScienceDirect and CINAHL. The terms used while searching for the following literature included personalized medicine, precision medicine, and biomarkers.

A future direction for the precision medicine of the future should include more proper and adequate education and dissemination of information about biomarkers. This can be beneficial and solve the following challenges: the lack of information about the inadequacy of some diagnostic testing techniques and biomarkers, and lack of funding. For example, by educating the right medical professionals about such inadequacies, there may be more direction created towards the need of implementing new techniques for identifying for effective biomarkers for certain diseases. Also, by forwarding such education and information to stakeholders that are relevant to the field, funding towards new diagnostic testing can be done.
[1] Pritchard, D. E., Moeckel, F., Villa, M. S., Housman, L. T., McCarty, C. A.,

Factors Affecting Total Bacteria Count on Liquid Milk Dairy Farms

Table of Contents
Milking plant hygiene:
Teat hygiene pre-milking:
Post-milking teat disinfection and hygiene effects on mastitis incidence
Milk cooling
Environment and seasonality effects on bacteria counts
Milk total bacterial count (TBC) is an indication of on-farm hygiene practices and microbial quality of raw milk. TBC bacteria include staphylococcal aureus, streptococcal aureus, coliforms, enterobacteriaceae and E.coli. In 2015, the milk quota was abolished, due to this abolition it gave farmers the opportunity to expand their herds. Subsequently, an increased herd means raw milk will be stored on farms for longer periods of time (O’Connell et al., 2016). Milk supplied in Lee Strand Co-operative is separated as liquid milk and manufacturing milk. TBC results are kept on file and any supplier with results over the threshold will be manufacturer processed the following month. Liquid milk produce requires strict standards as it is a ready-to-eat product with severe consequences if viable bacteria numbers are present (Sugrue., 2018). Microbial growth increases the longer it is stored on farm. There are many EU regulations in place to ensure the safe production of milk that is safe for human consumption. Ireland have a threshold of 100,000 cfu/ml for TBC (EC regulation no. 852-853/2004). Cfu/ml are colony forming units per ml which is a measure of bacteria numbers. Milk exceeding this threshold cannot be accepted by liquid milk processors. Milk not accepted by the processors mean the milk must be discarded. Discarded milk is a massive loss to the farmer’s profit, making good farming practises their most valuable asset. Farmer’s with low TBC counts carry out hygienic farm practices. Farmers’ will be provided with a milk quality bonus for supplying good quality milk. TBC above standards is high risk contamination and can cause serious consequences to the food chain. The majority of liquid milk processors implement an initiative to maintain standards such as deductions if thresholds are disobeyed. TBC is influenced by many on-farm factors. TBC and on farm practices have stayed relevant over the years with hygiene practices still contributing to total bacteria counts. The aim of this literature review is to identify ways to improve total bacterial counts on farms and to research if different hygiene programmes have different impacts on plate counts. It will also be researched what environments have an impact on total bacteria count. Udder hygiene (Galton et al., 1983), teat preparation (Gleeson et al., 2009), milking plant hygiene (Neijenhuis et al., 2001) and winter housing are all foundations of lowering the risk of bacterial contamination.
Discussion: The dairy sector accounts for over 50% of the agricultural industry in Ireland, making the production of high quality milk vital especially for liquid milk producers. After the abolition of the milk quota, Ireland’s dairy milk production increased by 40% (Creed, 2017). With the expansion of herds, it is important farmers still place a good emphasis on the quality of their milk. There is a close link between farm practices and bacterial count (Elmoslemany et al., 2010).
There are many factors that affect the growth of microbes in raw milk:
Dairy hygiene programmes include hygiene of teats pre milking, hygiene of the cow’s udder, hygiene of the milking plant, and milk cooling systems and storage and winter housing periods.
Milking plant hygiene: An operational hygiene routine should be in place to disinfect the milking plant. Bacteria, if left in milk lines can multiply. This can comprise of washing the milking plant before milking or after or both. The cleanliness of milking machines has a direct association with increasing the contact between bacteria and teat ends. Bacteria numbers can be transmitted via the cluster from cow to cow and quarter to quarter. Making teat preparation an important factor pre-milking. If all teats are cleaned adequately, bacterial transmitting will be reduced. Propeller motions of the milking machine vacuum system can aid in the direct transmission of bacteria from the outside of the teat into the teat end (Bramley et al., 1992). Is there a relationship between TBC and SCC? Milk suppliers in Lee Strand who have a high SCC result also tend to have an increased TBC result (Sugrue., 2018). Lopes., (2012) concluded that with increasing bacteria shredding on the teat end, the greater the occurrence of a bacterial infection. The occurrence of a bacterial infection invariably increased SCC. If good hygiene practices are in place, TBC will be reduced, therefore reducing the risk of infections which will in turn, reduce SCC. Good teat conditions are important to reduce risk of bacterial contaminations as they are the first line of defence. Muscles on the outside of the teat contract during milking’s to act as a barrier against bacteria entering the teat gland. Milking machines can damage and change the structure of the teat which reduces its ability to protect the gland against bacteria. “Teat-end callosity” or “hyperkeratosis” result in the thickening of the skin around the teat. Cows with abnormal “teat lengths, teat positions and teat shape” are more prone to developing hyperkeratosis. Hyperkeratosis is developed by extreme vacuum pulsations and liner slipping during milking (Neijenhuis et al., 2001). Hyperkeratosis or teat-end callosity can be prevented by avoiding over-milking the cow or providing an adequate dry period and hygiene routines (Emre and Alacam., 2015). There is a strong correlation between hyperkeratosis and mastitis. Mastitis will occur if bacteria numbers on clusters are high. Gleeson et al., (2004), stated that teats not disinfected after milking had a higher incidence of developing hyperkeratosis which invariably will increase the risk of mastitis and increase bacteria count in milk. Teats can change and develop a hardening on the skin during severe weather conditions. It is important that teats are protected after milking always. An effective way to reduce the incidence of bacterial transmission via the milking machine is to implement a hygiene protocol routine. Circulating hot water and a detergent at correct volume rates through the milking plant lines is the most common cleaning routine. A standard rule of thumb is to have water basins of 14 litres per milking unit to be sufficient enough for cleaning. The most common wash routine includes: Removing any soil on jars, clusters and parlour floor with jetters to remove any heavily soiled areas. Pre rinsing the plant with water at 30oC to remove milk residues, followed by circulating the plant with hot water at 85oC and adding the detergent half way through this stage. To finalise the wash routine, a circulation of cold water through the plant to remove any detergent residues in the milk line which could contaminate milk at the next milking. Some farmers only implement a hot wash routine once a week but research has shown it is the most effective way to reduce bacterial numbers. Modern milking parlours have a built in automatic washing system, which, if implemented correctly can increase labour efficiency (Luciana et al., 2010). Cluster flushing is also a component of new parlours, which eliminates cluster dipping in between cows reducing bacteria numbers that will increase bacteria count.
Teat hygiene pre-milking: A good teat hygiene routine pre-milking must be carried out at each milking to reduce the risk of environmental bacterial contamination into milk. Pre-milking hygiene is the most vital routine a farmer can carry out to try and eliminate and reduce bacteria counts. Hygiene of the teats is the last place in which a farmer can try and control or eliminate bacteria entering the milk. Having a low TBC increases profits and provides a high standard of milk. A research carried out by (Gleeson et al., 2009), provided different pre-milking udder wash routines to groupings of 10 animals. These routines included; an iodine wash, a chlorhexidine foam disinfectant, the use of a paper towel to wash and dry the udder, no preparation at all, a chlorine teat foam and disinfectant wipes. Gleeson et al, found that there was a significant reduction in bacteria on the teats when pre-teat preparations were carried out. Gleeson et al, concluded that using a chlorine dip resulted in a 30% reduction in microbes, iodine resulted in an 18% reduction, and disinfectant wipes and chlorohexidine had a 20% reduction in microbes. No preparation of the teat pre-milking had no effect on microbial count. Magnusson et al., observed that the use of a moist towel followed by a paper towel to dry the teat, was the most effective way to reduce microbial numbers pre-milking. Although implementing a pre-teat hygiene programme increases labour time and costs due to disinfectant costs, it greatly reduces the incidence of bacterial contamination and infection which in turn, increases profit margins. Mastitis incidence can be reduced by up to 43% when implementing a pre-milking teat hygiene practice to reduce bacteria numbers occurring (Oliver et al., 1993). These costs can be massive to a farmer with costs occurring for discarded milk and antibiotic treatment of the infected cow. Along with pre-milk teat hygiene, care of the udder is also important. Udder preparation resulted in the lowest plate count of bacteria (Galton et al., 1983). Fore stripping the udder can be done to check for any clots in the milk which indicates a mastitis infection which in turn will increase TBC (Watters et al., 2012). Keeping the udder clean will in turn make pre-milking hygiene practices quicker which reduces labour time. A healthy udder will reduce the incidence of mastitis. Udders should be checked daily for signs of mastitis by fore milking the cow. Any cow with signs of mastitis should be milked separately and into a different holding tank. This cluster used to milk this cow should be flushed to avoid contamination to the next cow. If communal cloths are being used to wash cows pre-milking, any cow with mastitis signs should not be washed with this cloth as infection can be spread to the next cow. Udder health also includes clipping of the hair on the udder to avoid clumps of dirt and faeces collecting on the udder (Dufour., 2010).
Post-milking teat disinfection and hygiene effects on mastitis incidence: The occurrence of mastitis on farms causes an increase in bacteria numbers in milk. Farmers who implement both a pre-milking and post-milking teat disinfection programme have significantly reduced bacteria counts. Post milking teat dipping is a preventative for mastitis (Yu et al., 2017). Post-milking teat dipping reduced bacteria numbers multiplying on the teat. Mastitis is an inevitable situation on most dairy farms resulting in losses and reducing the overall quality of milk. Pathogens within the environment are the main cause of the occurrence of clinical mastitis in dairy herds. Control of environmental pathogens will invariably reduce the cost on antibiotic treatment (Smith and Hogan., 2016). A study was carried out by Wesen and Schultz (1970) to examine the efficacy of post-milking teat dips. They concluded that teats that were dipped with iodine directly after milking had a 53.2% reduction in udder infections than those who were not post-dipped. Wesen and Schultz concluded that a post-dip was the most effective way to prevent new infections occurring, therefore lowering bacteria numbers.
Milk cooling: When milk leaves the udder it is 35oC and needs to be cooled rapidly in order to reduce the growth of microbes (Wildridge et al., 2018). After rapid cooling the milk must be kept at a steady temperature to ensure no further microbial contamination. Milk kept at a storage above 15oC has the ability to rapidly multiply bacteria numbers. (Paludetti et al., 2018). Along with the reduction of bacterial numbers, Murphy et al., (2016) has stated that pre-cooling milk also saves on energy costs of up to 50%. Pre-cooling significantly decreases the temperature of milk before it reaches the bulk tank. Pre-cooling is also very efficient as the water implemented in the pre-cooling stage can be used to wash dairy floors and udders. According to O’Connell et al., (2016), milk that is supplied every day only requires a cooling temperature of 8oC, whereas milk that is held for more than 48 hours requires a cooling temperature of 2-4oC to minimize microbial growth. Plate cooling is an effective way to help reduce the milk temperature rapidly. There are different types of plate cooling systems- single stage and 2 stage plate cooling system. A single stage plate cooler implements a mains or well water and supply. A double stage plate cooler uses mains or well water along with an ice bank to significantly reduce the temperature even further before entering the bulk tank. Typically a single stage plate cooler cools the milk from 35oC to 17oC and a double stage plate cooler cools the milk rapidly from 35oC to 6oC (Paludetti et al., 2018). O’Connel et al., (2016) observed that milk stored at 2oC and 4oC had no increase in bacterial numbers whereas milk stored at 6oC or more was seen to have a substantial bacterial growth rate after 36 hours. Regardless of the quality of milk entering the storage tank, inadequate cooling has a significant impact on microbial growth. Murphy et al., (2016) indicated that cow milk has <1,000 cfu/ml when it leaves the udder, <3000 cfu/ml after leaving the milk lines and if adequate cooling systems are in place, <5,000 cfu/ml in the bulk tank. This is if hygiene programmes are run at each phase of milking. These TBC results will solely be dependent on the first bacteria count leaving the udder. So, if a cow had a bacterial infection, the first TBC leaving the udder would be generally higher, consequently increasing throughout the milking process.
Environment and seasonality effects on bacteria counts: With Irish dairy farms predominantly grass based, cattle are housed for the winter period of the year. When housed, cattle are very susceptible to contamination from bacteria if housing hasn’t been cleaned adequately (Oliver et al., 2005). A clean environment is essential for quality milk production and animal welfare (Hauge et al., 2012). Bacteria numbers rapidly increase when faeces is not trafficked through slats (Ward et al., 2002). Trafficking occurs when cattle move freely around the slated shed, pushing faeces down into the slats while doing so. A shed low stocked has less trafficking, therefore increasing faeces build up. Automatic scrapers have become a big part of modern farming. Automatic scrapers are activated by a timer and scrape animal waste down the slats as often as the farmer allows. The implementation of automatic scrapes reduces labour time and Bramm et al., (1997) has stated that automatic scrapers decrease ammonia emissions. Cattle housing is most important in terms of cleanliness. Faeces from cattle contain enterobacteriaceae which can potentially cause a foodborne illness (Hauge et al., 2012). In low tbc herds, 97% of farmers implemented a regular clipping and a pre and post dipping routine (Hauge et al., 2012), and 84% of farmers claimed they scraped out housing 2 times a day. Housing design is also an important factor for cow cleanliness. Kirkland and Steen., (2001), observed that housing with good ventilation had reduced condensation. Condensation results in wet bedding and cattle which influences bacteria growth. It was experimented by Barbari and Ferrari (2014) that mats on cubicles with 3.3kg of straw per cow was the best practice for low TBC results. It is important to note that when implementing a straw bedding routine, a good infrastructure must be in place. If poor ventilation is present in a cubicle shed, condensation will occur. Condensation wetting the straw will provide an environment favourable for bacteria growth which can be transferred onto the cow’s teat. High TBC results came from farms where cows were in cubicles with no mats or bedding. An acceptable level of hygiene and relatively low TBC comes from cows on cubicles with mats. This practice is one most implemented on the majority of Irish farms as it is more labour efficient. Although, implementing a housing with straw bedding is a high input cost and high labour, if carried out correctly, TBC will be significantly lower.
Conclusion: TBC results are a major factor of liquid milk production to produce a high standard quality of milk. With strict regulations outlined in the EU regulation 852-853/2004 it is important farmers adhere to hygiene protocols. As outlined in regulation no. 853/2004 it is mandatory for the liquid milk processors to carry out at least 2 TBC tests a month. Acceptable criterion is that all milk samples are below threshold of 100,000 cfu/ml in order to be accepted (FSAI., 2004). Cattle housing are the first source where bacteria can grow. A clean, hygienic housing implements an easier milking routine. Hauge et al., (2012) concluded that 68% of farmers that had a high TBC resulted admitted to only scraping out houses every 2 days and not implementing a teat hygiene routine. The next source of contamination occurs in the dairy. Applying a teat hygiene programme is important to reduce bacteria numbers entering the milk (Gleeson et al., 2009). It is vital that liquid milk production is of high quality standard as it is a ready-to-eat product (FSAI., 2004). The production of liquid milk requires strict on-farm hygiene protocols that must be carried out. Gleeson et al., (2009), concluded a chlorine or chlorhexidine pre-milking teat dip resulted in the lowest TBC. The initial TBC leaving the udder is the most important, low TBC at the first stage will result in a low TBC throughout if conditions are right (Murphy et al., 2006).
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