The gasoline internal combustion engine has more than 100 years of intense development behind it. But now three researchers from the Massachusetts Institute of Technology (MIT) have modified it in a way that elevates efficiency by a remarkable 25%, an advance that could greatly mitigate greenhouse gas emissions and offers compelling advantages over hybrids and diesels. “This has real potential,” says David Cole, chairman of the Center for Automotive Research, a nonprofit organization of the University of Michigan.The design logic is simple. One can alter an engine to create greater compression of the fuel/air mixture within each cylinder, raising thermodynamic efficiency. One can also add a turbocharger, which force-feeds more fuel/air mixture into the cylinders. This makes it possible to get more power out of an engine, or to downsize an engine without losing power, making it still more efficient.The problem: boosting compression also boosts temperature, and too much heat can ignite the fuel/air mixture prematurely, causing potentially damaging engine “knock.” But Daniel Cohn and Leslie Bromberg of MIT’s Plasma Science and Fusion Center, and John Heywood of MIT’s Sloan Automotive Lab figured out that a little squirt of ethanol into the cylinder from a separate tank could cool it in the same way that rubbing alcohol cools the skin—by vaporizing, then absorbing excess heat. The researchers have formed a company, Ethanol Boosting Systems (EBS), and have drawn several prominent figures on board, including Neil Ressler, former chief technology officer of Ford Motor Company.Calculations of Knock Suppression in Highly Turbocharged Gasoline/Ethanol Engines Using Direct Ethanol Injection, a 2006 MIT report, bench engine tests by Ford show that the knock limit can be vastly alleviated, and unpublished results indicate that a 25% increase in efficiency should therefore be attainable. That would reduce carbon dioxide emissions by about 20%, says Cohn. The engine’s alcohol consumption would be minimal, because the extra cooling is unnecessary under light loads, such as steady driving at low to moderate speeds.According to Although not quite as efficient as the best full hybrid systems, the EBS is far simpler, because it needs no electric motor, extra batteries, or complex software. Cohn says those factors would shave $2,000–4,500 off the cost relative to a full hybrid. The EBS and full hybrid systems would have similar emissions profiles.x) than the diesel engine, and less particulate matter. Many U.S. cities have nonattainment zones for NOx, which contributes to ground-level ozone and can damage lung tissue and vegetation.An EBS engine would also be a couple of thousand dollars cheaper than a diesel engine. The two engines would produce roughly the same amount of greenhouse gas emissions, but the EBS would otherwise be cleaner, emitting fewer nitrogen oxides (NOCar and Driver, editor-in-chief and engineer Csaba Csere praises the EBS technology and says that if some seemingly manageable problems are solved—for example, maintaining fuel economy under real-world conditions of elevated temperatures and substandard fuel—EBS engines could be powering cars early in the next decade.In a column in the July 2007 issue of


CellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allowing for the exchange and archival of models in a computer readable form is a key strategic goal in bioinformatics, because of the associated improvements in scientific record accuracy, the faster iterative process of scientific development, and the ability to combine models into large integrative models.ab initio to correctly process models can be an onerous task. For this reason, there is a clear and pressing need for an application programming interface (API), and a good implementation of that API, upon which tools can base their support for CellML.However, for CellML models to be useful, tools which can process them correctly are needed. Due to some of the more complex features present in CellML models, such as imports, developing code We developed an API which allows the information in CellML models to be retrieved and/or modified. We also developed a series of optional extension APIs, for tasks such as simplifying the handling of connections between variables, dealing with physical units, validating models, and translating models into different procedural languages.We have also provided a Free/Open Source implementation of this application programming interface, optimised to achieve good performance.Tools have been developed using the API which are mature enough for widespread use. The API has the potential to accelerate the development of additional tools capable of processing CellML, and ultimately lead to an increased level of sharing of mathematical model descriptions. Systems of differential algebraic equations (DAEs)  are one F is a function, t is the independent variable, x is the vector of state variables, and x' is the vector of derivatives of the state variables.where DAE systems are often broken up into individual equations, each of which hold true. Systems of DAEs are used to model a wide variety of biological processes, across a diversity of scales. For example, at one extreme there are models describing the action of ion channels , and at Historically, models of DAEs have been exchanged and archived by publishing equations, constant values, initial conditions, specific protocols, and other associated information in a scientific paper. Someone wanting to independently compute results from the published model then needs to convert that model back into a computer program. This process is both time-consuming and error prone. Reviewers are unlikely to check that the published model accurately corresponds to numerical results presented in the paper.Likewise, it becomes prohibitively expensive to do integrative biology , as builCellML  is an XMHowever, for the scientific advantages of using formats such as CellML and SBML for mathematical model exchange to be fully realised, it is important that software used by modellers is able to read and write models in these formats. It is also important that the scientific community has the ability to easily develop software which relies on the existing databases of models in these formats.Using an Application Programming Interface (API) simplifies the task of processing an XML language, thus APIs are important to the exchange of information.Supporting CellML correctly can be a difficult task, due to some of the more complex features in the CellML language. It is therefore important that software developers do not need to re-invent the same functionality every time they develop a new tool. We thus present both an API for working with CellML models, and an efficient implementation of that API.SBML  is anothThe CellML API is a platform and programming language independent description of interfaces, with attributes and operations on the interfaces. These attributes and operations are used to retrieve information about the model, or alternatively to manipulate the model in memory.The overall architecture of the API consists of a core API, along with a series of extension APIs  from the CellMLElement interface. This interface provides functionality which is useful on all elements. For example, it provides the ability to insert or remove any of the child elements of the element concerned, and to set temporary user data annotations, identified by a unique key, against the elements. These annotations do not form part of the in-memory DOM representation, and so do not, for example, appear in the generated XML when the model is serialised.The interfaces for CellML elements which have a mandatory name attribute all inherit from the NamedCellMLElement interface. This interface provides a name attribute (which can be fetched or set), and inherits from the CellMLElement interface. For example, CellMLComponent inherits from NamedCellMLElement, because the CellML specifications require that all component elements have a name attribute.For each type of child CellML element allowed by the CellML specification, the interface for the parent element has a read-only attribute for retrieving all the CellMLElements of that type. The returned set implements an interface specific to the type of element expected. For example, component elements can contain variable elements, so the CellMLComponent interface has an attribute called variables, of type CellMLVariableSet.These specific types of set follow an inheritance hierarchy parallel to those of the element objects in the set. Each set interface has a corresponding iterator interface, which allows each object to be fetched in sequence. Because the iterator interface is specific to the object being fetched, the required interface is returned, avoiding the need to call QueryInterface (see the section on the object model and memory management for information on QueryInterface). However, it is also possible to use the less specific (ancestors in the interface inheritance hierarchy) set interfaces to retrieve a less specific (ancestor) iterator object .Iterators derived from NamedCellMLElementIterator also provide interfaces for fetching elements by name. All descendant iterator interfaces provide more specific fetch by name operations.Set interfaces also provide facilities for modifying the relevant sets by inserting CellML elements. Because order is not important to the meaning of the model, the iteration and insertion facilities provide no control over the actual order of the elements in the model.CellML makes heavy use of the namespace facilities in XML . CellML In addition, CellML models commonly contain metadata  encoded Our implementation of the CellML API also provides an interface allowing access to and modification of the RDF triples  found inCellML 1.1 provides for components and physical units to be imported into models from other models . An impoThe result of supporting CellML 1.1 is that processing one mathematical model can require that more than one CellML file be examined. To deal with this issue, the API introduces the following two concepts: an imported model is said to be instantiated once it has been loaded. When all imports required for a mathematical model have been loaded (including models which are imported by an imported model), the model is said to be fully instantiated.The API has an operation for selectively instantiating particular imports, as well as an operation for fully instantiating the model. For imports that are instantiated, the model element is also accessible, as well as the components they import.We have included three separate attributes for sets of components in the model, with three corresponding sets of units:• local component set - contains only the components in the particular CellML file (excluding imported components);• model set - contains all components which are in the local set, and also the import component elements  in the same file; and• full set - contains all components in the model, across all files making up the model. Where the model containing a component is uninstantiated, the import component element is provided by iterators. When a model is instantiated, the components in the imported model are returned by the iterators, and in addition, these models are examined to identify further imported models to search for components, as appropriate.The three corresponding sets of units follow the exact same semantics as the sets of components, except over units rather than components.The interfaces defined in the API all use the inheritance capabilities of OMG IDL to derive from a base interface, called IObject. IObject is modelled after the similarly named interface in the XPCOM object model. The IObject interface is used to provide interfaces for basic common facilities relating to the object underlying the interface, such as maintaining the reference count (as discussed later), and providing a unique identifier for each object. This unique identifier is useful for determining if two interface references describe the same object, and for building data structures which require that objects can be compared. API implementations use reference counting  to deterIt is worth noting that while IObject provides facilities for reference counting, many programming languages perform automatic garbage collection. When using a direct bridge to these languages, the wrapper code will automatically call add_ref and release_ref on behalf of the user, and so the need for explicit memory management is avoided. For example, the Java bridge makes use of the finalisation facilities in Java, combined with the memory management facilities provided by the Java Native Interface, so that Java users do not need to explicitly modify reference counts.In addition to the reference counting scheme, the IObject interface also provides a QueryInterface operation. This operation is used to ask an object if it supports a particular interface, and if it does, to provide an interface representation. As discussed earlier, the API is often accessed through wrapper code, and so users of the API should always perform QueryInterface operations on API interfaces, rather than directly using the language-specific casting mechanisms.ab initio, or loaded from a file). Modifications can be made to the model in memory. The original file will only be updated if the application uses the API to serialise the CellML model back to XML, and then writes that XML to disk, replacing the original file. Likewise, if the same model is loaded twice, there will be two separate, and independent instances of the model in memory. Modifying one instance will not automatically change the other instance. Where a model is imported, a separate instance of the imported model exists for each import element, and for each instance of the importing model. However, all elements, sets, and iterators in the core CellML API are 'live', in the sense that making any change to an in-memory instance of a model through the API will immediately affect responses from the API, even if the element, set or iterator was retrieved prior to when the change was made. For example, if an iterator is created, and has iterated through all units elements but one in a model, and that remaining units element is deleted, and next element is retrieved from the iterator, it will return a null value, signifying that there are no remaining units elements to iterate.Objects which are created by API implementations exist purely in memory . Our implementation makes consistent use of exception safety techniques , such asThe language independent IDL based interfaces do not provide a solution to the 'bootstrap' problem of how an interface is initially obtained, for example, the interface for creating a new model. The solution to this problem is language dependent. In each language, we provide functionality to retrieve a pointer to a bootstrap interface. For example, in C++, this is obtained by a method defined in a header. The bootstrap interface is defined in IDL, and therefore standardised across all language bindings. Each extension API has a separate bootstrap interface.Our implementation of the API is not designed to allow for two writes  to occur concurrently, or for a read to occur concurrently with a write, on the same model. Applications accessing the same model on multiple threads need to either protect all access to the API with a mutex, or more efficiently, use a read-write lock to ensure that there is no activity concurrent with a write.In addition to the core API, we have also produced APIs to provide services which are beyond the scope of the core API.The core API does not depend upon the extensions, and so individual API implementations can choose not to support all extension APIs. However, all extensions depend upon the core API, and some extensions also depend on other extensions  API provides the ability to allocate and release a set of annotations, without needing to worry about interfering with other annotations being placed by independent calls to the same code, or about needing to individually remove all annotations left on objects.The IDL specification for the AnnoTools API can be found in the file interfaces/AnnoTools.idl, in the CellML API source tree.AnnoTools implementations generate a unique prefix for each AnnotationSet, and allow the user to set annotations with that prefix. They keep an internal list of all annotations which were added, and clear all annotations in the AnnotationSet when the AnnotationSet is destroyed.The AnnoTools API also includes facilities for more easily setting and retrieving string, integer, and floating point annotations.The CellML Variable Association Service (CeVAS) API facilitates the treatment of interconnected CellML variables as the same mathematical variable . These variables may come from different components, some of which may be imported from different models.The IDL specification for the CeVAS API can be found in the file interfaces/CeVAS.idl, in the CellML API source tree.CellML 1.0 and 1.1 require that variables which are connected to variables in other components have a public or private interface value of 'in' or 'out'. Whether the public or private interface applies depends on the encapsulation relationship between the components. In CellML, all 'in' interfaces must be connected to an 'out' interface, encapsulation is always acyclic, and valid CellML models have a finite number of variable elements. This means that, in a complete and valid model, there is always a variable in each connected network of variables that has no 'in' interfaces. This variable is called the source variable, and is used by CeVAS as a representative of all variables connected (directly or indirectly) to it.The interface allows users to supply a CellML Model interface, and pre-compute which variables are connected. All variables connected to a particular variable can be iterated, and the source variable can be retrieved.n components and m connections is in O), where α is the inverse Ackerman function. Note that the inverse Ackerman function grows very slowly; for example, α = 1, while α = 3.This is implemented using an efficient disjoint sets algorithm, which allows for inverse Ackerman amortised time merges of sets . InitialThe CellML Units Simplification and Expansion Service (CUSES) API provides facilities for processing physical units in a CellML model.The IDL specification for the CUSES API can be found in the file interfaces/CUSES.idl, in the CellML API source tree.g.m2.s-1. In addition, the modeller can define their own derived units , or a new base unit. However, when processing models, it is important to know what the relationship between connected variables is, so the appropriate conversions can be performed, if necessary. For example, when a variable in metres is connected to a variable in millimetres, tools are expected to insert an implicit conversion factor, so the same variable is compatible across the two components. CUSES allows tools to implement this more simply.CellML has a set of built-in units. These units are defined in terms of the SI  base uniAll units are firstly expanded to be expressions in terms of the base units. SI Prefixes are converted to multipliers. All units are converted to a canonical form, consisting of the product of powers of base units, each base unit occurring at most once, possibly with a single multiplier and/or offset. The base units, and their corresponding exponents, are exposed to users of the API in an enumerable list of base unit instances. Facilities are provided to enquire whether two units are dimensionally equivalent. This is useful for determining if a connection is valid. The necessary offset and multiplier needed to perform a conversion can also be retrieved.The Validation Against CellML Specification Service (VACSS) API accepts files which are putatively CellML files, and identifies whether or not the CellML is valid, and where the file is not valid, it attempts to build a list of the problems.The IDL specification for the VACSS API can be found in the file interfaces/VACSS.idl, in the CellML API source tree.Errors that can be detected fall into two types:• representational - errors relating to the encoding of CellML in XML, such as essential elements or attributes which are missing, or illegal extraneous elements; and• semantic - higher-level errors, where the basic elements of the CellML are in the correct form, but there are inconsistencies, such as references to names which are required to exist but do not, or violations of any of the numerous rules specified in the CellML Specification. Semantic warnings, such as about potential units problems in mathematical equations, due to dimensional inconsistency, are also made available.One task which is common to many applications is to convert the fragments of MathML embedded in CellML documents into fragments of text in some other linear text-based representation, such as programming language source code.i.e. reference to a variable by identifier). It then makes use of AnnoTools to retrieve an annotation (which the user can set) containing the symbol to be used for that variable in the output. The IDL specification for the MaLaES API can be found in the file interfaces/MaLaES.idl, in the CellML API source tree.The MathML Language Expression Service (MaLaES) API provides functionality to assist with this task. MaLaES makes use of CeVAS in order to identify the source variable corresponding to each MathML ci element  to be converted into the units of the source variable, and also for the result of an expression to be converted. In order to allow for conversion into many different languages to occur, MaLaES uses a specification in a custom format called MAL (MathML to Language). The MAL description describes the mapping between MathML elements and their forms in the output text-based representation , as well as describing the precedence of each operation, what strings are used to begin and end groupings of low precedence operators inside a higher precedence operator, and the format of conversions. The MAL is precompiled into an efficient in-memory representation, which can then be used to generate output.Another common task is to convert an entire CellML model into code in a procedural programming language, capable of solving the model. The CellML Code Generation Service (CCGS) API simplifies this task.The IDL specification for the CCGS API can be found in the file interfaces/CCGS.idl, in the CellML API source tree.The CCGS is specialised for the common case where there is a single independent variable  and the index of the DAE system is at most one ,1. UsersOn this CodeGenerator interface, it is possible to specify a wide range of different attributes about the language to be generated. This means that code can be generated for a wide range of procedural programming languages .Because CCGS relies upon MaLaES to translate individual mathematical expressions into the correct text-based form, the user also needs to supply a MAL description for the language of interest.x, with an initial value of 0, and then an equation such as x and t, the independent variable, is also treated as a computation target for consistency). Note that when a variable is used in several components, but the variables are connected together , there will only be one computation target for all the variable elements.CCGS uses the terminology 'computation target' (represented by a ComputationTarget interface pointer) to represent anything which is required to be computed to evaluate the equations in a CellML model . There is not a one-to-one relationship between variables in the CellML model and computation targets. For example, there may be a variable called CCGS gives every computation target a degree . All computation targets which have a corresponding computation target of higher degree are treated as being state variables, while computation targets with a lower degree computation target are treated as being rates. Computation targets which have both a higher and lower degree computation target are in the unique position of being both a rate and a state variable. CCGS generates code for this case by making use of the standard technique for transforming an ordinary differential equation (ODE) system with higher derivatives into an equivalent ODE system with no higher than first order derivatives .n otherwise unknown constants from n equations . This is done in our implementation using a heuristic algorithm which guarantees that the smallest possible systems are found when the largest indivisible system needed to be solved has at most three equations with three unknowns, and has given good results in our testing.Initially, CellML variables which are in fact constant in value are identified and marked as such. Variables which are computable using only constants are in turn classified as constants (with this process repeating until no further constants can be identified). It is possible that a system of simultaneous equations may need to be solved in order to determine y using an equation like y = f , CCGS will use the assignment pattern to directly assign into the symbol for y. In other cases, the equation might be in the form f  = g, in which case the univariate solve pattern is used to compute y. Finally, for systems of equations, the multivariate solve pattern is used.After identifying the order in which equations or systems need to be solved, code is generated for them. This is done using one of three different patterns supplied to CCGS by the application. Where CCGS needs to compute a computation target Any computation targets which are not constants, states, nor are rates, are classified as being 'algebraic computation targets'. In the same fashion as is done for constants, CCGS works out a directed acyclic graph for the order in which systems or equations are used to work out the rate and algebraic computation targets, using the constants, states, and the independent variables. However, these computations are split into two code fragments. The first code fragment contains all computations necessary to compute the rates from the states, constants, and independent variables, while the second code fragment computes any remaining algebraic computation targets not computed in the first code fragment. This separation allows for more efficient processing of models, because at many time steps, the integrator may not want to report back any results, and so there is no need to evaluate computation targets that are not required to compute the next time step.CCGS has the capability to automatically assign indices into four different arrays:• constants array - stores the values of any computation targets which do not depend on the independent variable, or upon any of the rate or state computation targets;• states array - used to store the values of each state computation target;• rates - used to store the values of the rate of change corresponding to each state computation target; and,• algebraic array - used for all remaining variables.The CodeGenerator object allows the first index to be assigned in each array to be set . Thirdly, the fragment for the remaining variables. The final code fragment contains any functions which needed to be generated (using a pattern supplied to the CCGS) in order to evaluate the code. These functions can then be called from the univariate and multivariate solver patterns, and also in MAL specifications, such as those for evaluating definite integrals.As a CCGS implementation processes models, it will also check for and report back on certain error conditions, such as models which have extraneous equations (reported as being overconstrained), or models which have too few equations to compute all computation targets (i.e. underconstrained models). As CCGS only supports DAEs of index one or lower, it will, for example, report that the model is incorrectly constrained if the model is a valid index two DAE.Defining a new programming language for use with MaLaES requires setting up a MAL description of the language, and configuring this through the API. However, it is convenient to be able to exchange this information with other users, in order to allow for the definition of arbitrary languages by the user. The CellML Language Export Definition Service (CeLEDS) allows for the MAL description of a language to be embedded in an XML file. In addition, it provides a generalised dictionary service, to allow information required to generate output for different languages to be provided to the consumer of the CeLEDS service. The IDL specification for the CeLEDS API can be found in the file interfaces/CeLEDS.idl, in the CellML API source tree.The CeLEDSExporter service builds upon that offered by CeLEDS to support full code generation (based upon CCGS). Instead of programmatically setting attributes on the CodeGenerator interface, all information is specified in a standardised XML format, along with the MAL description. In addition, CeLEDS contains information on the super-structure of the program, including unchanging fragments of code which are required to allow the program to run (such as any supplementary function definitions).This means that all the information required to generate code for a language is encapsulated in a single XML file, which can be read in at run-time. Users can easily modify these definitions in order to customise aspects of code generation, and to create new definitions for conversions to other languages.Due to this standardisation of how conversions are specified, we have created a small repository of CeLEDS/CeLEDSExporter compatible conversion definitions, including definitions for C, MATLAB, and Python. This repository can be found in the CeLEDS/languages subdirectory of the CellML API source code. We have also created a definition for FORTRAN77, although it requires further testing before being considered ready for widespread use.The CellML Integration Service (CIS) API provides an interface for performing simulations of models, and receiving asynchronous notifications as results become available.The IDL specification for the CIS API can be found in the file interfaces/CIS.idl, in the CellML API source tree.CellML Model interface pointers are given to CIS, which then creates a CellMLCompiledModel object. The application then specifies the algorithm to be used, and the parameters of the simulation . The application may also choose to override an initial value without recompiling the model.The IntegrationProgressObserver interface can be implemented by the application, and given to the CellMLIntegrationRun interface prior to starting the simulation. This interface receives information about the values of constants which were computed, as well as the results from each time-step, and an indication of whether the integration has succeeded or failed (with an error message in the latter case).Our implementation of the CellML API internally makes use of CCGS to generate C code. The C code is then compiled using a compiler. For example, in one of our applications based on the CellML API, we bundle a stripped down version of the C compiler from the Free/Open Source GNU Compiler Collection  (gcc) wiad hoc testing on a range of other platforms. The API implementation currently passes all of the above tests.We have also developed an extensive test-suite for validating API implementations. For the core API (including DOM and MathML DOM), and some extension APIs, a program included with the test-suite makes use of every attribute and operation in the API, and checks that invariants which are expected to be true, if the implementation behaves correctly, are in fact true. In addition, the test-suite also includes a series of small programs, as well as a series of inputs to those programs, and expected outputs. For example, the program CellML2C is a small, command-line driven test program, that takes a CellML model as input, and uses the CCGS extension API to generate C code from it. The test-suite calls CellML2C with 17 different models (each of which are crafted to contain peculiarities to test different features). Our API implementation is automatically tested against this test-suite after every commit, on Linux, Mac OS X, and Windows XP, with http://sourceforge.net/projects/sbml/files/test-suite/2.0.0%20alpha/.In the future, we plan to add tests which can confirm that the numerical results provided by implementations of the CellML Integration Service are correct, in a similar vein to the SBML test-suite The CellML API is, to our knowledge, the first publicly available API that supports the processing of CellML models. However, there are other similar projects designed to process mathematical models in different encodings.LibSBML is, in many ways, analogous to the CellML API, except that it processes SBML models. As CellML provides a higher level of domain independence than SBML, it is expected that tools used across many different domains of expertise will need to exchange CellML models. In addition, some tools, such as generic modelling environments, may need to import and export both SBML and CellML models, in which case, both a CellML API implementation, and libSBML can be used together in the same program. Aside from the difference in language support, there are some additional major differences between the CellML API and libSBML.The CellML API emphasises the technical separation of the interface definition  and implementations of the interface. With the CellML API, adding a new language binding involves developing code to automatically produce a wrapper from the IDL description, rather than using SWIG  .In addition, there are plans to make CCGS support dedicated DAE solvers such as IDA , which cAnother important future improvement is the addition of more language bindings. The choice of language bindings will depend on the input we receive from the community, but could, for instance, include Python, Ruby, and Haskell.Other important improvements for future consideration include improving the documentation of the API, providing better support for working with metadata, and providing utilities for easier symbolic manipulation of mathematics.The CellML API and its implementation are available, and are ready for widespread adoption by the community. Developers of tools which process mathematical models are strongly encouraged to support CellML, so that users of the tool can participate in model sharing, with all the associated benefits to the scientific community. The CellML API and its implementation provide facilities which should make this task substantially easier.• Project name: The CellML API. Version 1.6 was the latest release at the time of writing.http://www.cellml.org/tools/api/• Project home page: • Operating systems: The API implementation can be built on any POSIX like system, including Linux, Mac OS X, and Cygwin. It can also be built using Microsoft Visual C++ 2008. It has been tested on Linux , AIX, Windows (XP and Vista) and Mac OS X.• Programming language: The API is in IDL (language independent), and the implementation in C++, callable through bridges from C++, Java, JavaScript, and from other languages through CORBA.• Other requirements: The build requires the omniidl tool, which is part of omniORB , as well• License: The CellML API and implementation can be redistributed under any one of: the GNU GPL version 2 or later, the GNU LGPL version 2.1 or later, or the Mozilla Public License version 1.1. This allows the API and implementation to be used in a wide range of public and private research and applied settings.• Any restrictions to use by non-academics: There are no restrictions on usage of the API. Redistribution requires compliance with one of the licenses above, as well as the licenses of any dependencies being used .The source code and change history is available on SourceForge. Documentation on how to build the API on various platforms is included in the 'docs' directory of the source tree. In addition, the documentation extracted from the IDL files using the Doxygen tool are available in HTML form. Links to these resources can be found on the project home page.AnnoTools: The Annotation Tools; API: Application Programming Interface; CCGS: The CellML Code Generation Service; CeLEDS: The CellML Language Export Definition Service; CellML: An XML-based language for describing mathematical models; CeVAS: The CellML Variable Annotation Service; CIS: The CellML Integration Service; CORBA: Common Object Request Broker Architecture; CUSES: The CellML Units Simplification and Expansion Service; DAE: Differential Algebraic Equation; DOM: Document Object Model; IDL: Interface Definition Language; MAL: MathML to Language; MaLaES: The MathML Language Expression Service; ODE: Ordinary differential equation; RDF: Resource Description Format; URI: Uniform Resource Indicator; VACSS: The Validation Against CellML Specification Service; XML: The Extensible Markup Language; XPCOM: Cross-platform Common Object Model.AKM developed most of the API and its implementation and wrote the first draft of the manuscript. MH contributed to the development of an earlier API, and provided guidance on the development of the API discussed here. JM contributed to the development of the API and implementation. AR developed the CeLEDS and CeLEDSExporter modules. AG contributed documentation for the API. PN, RB, AG, and JC contributed advice on the development of the API and its implementation. All authors provided input into this manuscript.


During surgery for spinal deformities, accurate placement of pedicle screws may be guided by intraoperative cone-beam flat-detector CT.The purpose of this study was to identify appropriate paediatric imaging protocols aiming to reduce the radiation dose in line with the ALARA principle.w doses with default and lowered exposure settings. Images from 126 scans were evaluated by two spinal surgeons and scores were compared (Kappa statistics). Effective doses were calculated. The recommended new low-dose 3-D spine protocols were then used in 15 children.Using O-arm® , three paediatric phantoms were employed to measure CTDIw doses 89–93%. The effective dose was 0.5 mSv . The optimised protocols were used clinically without problems.The lowest acceptable exposure as judged by image quality for intraoperative use was 70 kVp/40 mAs, 70 kVp/80 mAs and 80 kVp/40 mAs for the 1-, 5- and 12-year-old-equivalent phantoms respectively . Optimised dose settings reduced CTDIRadiation doses for intraoperative 3-D CT using a cone-beam flat-detector scanner could be reduced at least 89% compared to manufacturer settings and still be used to safely navigate pedicle screws. It is well-documented that radiographic examinations for spinal deformity during childhood increase the lifetime risk of cancer, particularly breast cancer , 2. It fNew technologies have advanced surgery for spinal deformities. The use of pedicle screws requires accurate placement to avoid damage to the spinal cord and the large vessels in front of the spine. To secure the correct placement of pedicle screws, intraoperative imaging is imperative. For many years, fluoroscopy was the only available intraoperative imaging modality. However, in the last two decades, navigation based on preoperative CT has been developed. However, it is not widely used, possibly due to the time-consuming registration process (coupling of the preoperative CT with patient anatomy) of up to 15–20 min per vertebra making it almost impossible to use in spine deformity surgery with instrumentation of 10–15 vertebrae in a single operation. On the other hand, the need for navigation is most pressing in young patients who have both deformed and small pedicles.Intraoperative cone-beam flat-detector X-ray systems have changed spinal surgery and are rapidly being implemented worldwide. These provide both 2-D fluoroscopic and 3-D images, which when coupled to a navigation system add significant value to surgical outcomes . With suAccording to Zhang et al. , the patOur aim was to identify appropriate intraoperative exposure settings for children for a cone-beam flat-detector system, aiming to reduce the radiation dose.The O-arm®  cone-beam flat-detector system was used. The system has an O-ring type gantry and an X-ray tube equivalent to 32 kW, and a X-ray filter of 4 mm Al. The flat-panel has an amorphous silicon-based detector of 30 cm × 40 cm with a 0.194-mm pixel pitch. The system can be configured in 2-D fluoroscopic mode or 3-D mode. In this study, only 3-D mode was used and only the low-definition mode. In the low-definition mode, 192 single images (compared to 392 images in high-definition mode) of slice thickness 0.833 mm were recorded in a 360-degree rotation of the detector and the radiation source with an image matrix of 512 × 512. The time for image acquisition was 13 s with a beam on-time of 3.91 s. The source-to-isocentre distance of the O-arm was 64.7 cm and the source-to-detector distance 116.8 cm. The collimated X-ray beam was 22.18 × 16.62 cm and the 3-D reconstructed volume was 20 cm × 15 cm.Besides the 16 default imaging protocols , the O-Arm allows manual adjustment of kVp and mA. With the manual setting, the kVp can be varied between 50 and 120 with 1-kVp intervals, and the mA can be varied between 10 and 120 in predefined steps.The manufacturer’s advice  for abdominal imaging is to use the default values for small (waist circumference 12–26 cm) or the default values for medium (waist circumference 20–34 cm).The studies were conducted using polymethyl-methacrylate (PMMA) phantoms to estimate patient dose equivalence. Four cylindrical PMMA phantoms were made with diameters of 10 cm, 16 cm, 24 cm and 32 cm  using the ICRP 103 tissue weighting-factors [The dose to the patient was expressed as CTDI-factors . To perfhttp://rsb.info.nih.gov/ij/) was used.Signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were measured. SNR was calculated as S1/σ1, where S1 represents the mean pixel value within a region of interest (ROI) in the PMMA phantom with all PMMA rods inserted at the position of the bone samples and σ1 represents the standard deviation of pixel values within the same ROI. CNR was estimated as |S2−S1|/σ1, where S2 is the mean pixel value in the pure bone sample. For this purpose, ImageJ version 1.32  was evaluated independently by two spinal surgeons, both with more than 10 years of experience in spinal surgery and intraoperative imaging. The image quality was deemed adequate if the outlines of the bones were visible and if it was possible to discern whether the screw penetrated the bone. If the outlines of the bone sample and the screw position could be visualised with certainty, the image quality was deemed as adequate. In all other cases, the image quality was deemed inadequate. Interobserver agreement was measured with Kappa statistic 6 scans w.The scans started with the factory default settings, followed by a series of scans with decreasing mA until the lowest possible tube current of 10 mA was reached. If image quality was still acceptable, additional scans were acquired at 10 mA while reducing kV until an unacceptable image quality was achieved. The scan parameters with the lowest dose to the phantom where the image quality in all four bone samples were accepted were recorded as the suggested optimum low-dose settings for that specific phantom size. Scans were then acquired with all holes filled with solid PMMA rods to measure image noise and dose.After institutional review board approval, the recommended new low-dose 3-D spine protocol was tested in clinical practice in 15 children  with severe deformities in whom it would not have been possible to place pedicle screws without navigation. This would otherwise require conventional preoperative CT with a higher dose. Only the 16-cm and 24-cm protocols were used. The average age was 11.5 years . An average of 9.7 vertebrae were scanned  using an average of 2.5 acquisitions , as shown in Table As expected, SNR and CNR decreased nonlinearly with decreasing radiation dose Fig. . SNR andTable The observers agreed that the lowest acceptable dose for intraoperative imaging was 70 kVp/40 mAs for the 1-year-old-equivalent phantom (10 cm), 70 kVp/80 mAs for the 5-year-old-equivalent phantom (16 cm) and 80 kVp/40 mAs for the 12-year-old-equivalent phantom (24 cm). Figure The interobserver agreement for all scans had a kappa = 0,70 . For thIn all 15 operations using the optimised setting, the spinal surgeon achieved adequate intraoperative imaging with the cone-beam flat-detector scanner followed by navigation using the Stealth system . Figure The phantom model allowed a systematic evaluation of different dose settings from the highest to the lowest possible. It also allowed different bone inserts containing pedicle screws to be evaluated with regard to image quality. This is especially important as the cornerstone of image guidance during pedicle screw insertion is the ability to clearly identify the cortex relative to the pedicle screw. Streak artefacts from metallic implants are a major concern, and any realistic model needs to incorporate this. Our phantom model could only be used to evaluate 90-degree perforations of the cortex due to the small size of the bone samples. However, to compensate for this limitation, for the sample with the perforating screw, the perforation was made as small as possible.100 does not measure the actual absorbed dose by the individual patient but should be considered an index for comparisons. The homogeneous PMMA does not simulate the different tissue types and heterogeneities in vivo. The CTDI100 will underestimate the radiation dose because the 100-mm pencil ion chamber only partly covers the collimated beam width. For X-ray beams wider than 40 mm, a pencil chamber longer than 100 mm is required. The CTDIw will underestimate the ideal CTDIw with approximately 20% at a collimated beam width of 20 mm [The CTDIof 20 mm . Dixon [of 20 mm  has descThe patient dose of the cone-beam system relative to CT has been described by Zhang et al. , who sho2 with slight variation in several recent studies [2 (age 5 years) to 1.0 g/cm2 (age 17 years) with much greater variation [Would a vertebra have been a better bone sample for the phantom part of the study? This would without doubt have better represented the normal anatomy. The cortical thickness of the femoral head is greater than the cortical thickness of the vertebra, and this would have influenced the accuracy of the imaging representation . A more  studies , 21. Lumariation , 19. A sA substantial number of pedicle screws are misplaced when navigation is not used. The rate of pedicle perforation varies between 10% and 40% –24. Our There are currently few alternatives to the system used in our study , 33. OthAbul-Kasim et al.  have alsThe cylindrical-equivalent diameter of a body is defined as the diameter of the cylinder that the body would form if laterally compressed into a cylinder of equal cross-sectional area. This definition should not be confused with the definition of patient-equivalent cylinder based on the patient’s weight and height as suggested by The Danish National Board of Health . The equThe phantoms in our study simulated the lumbar anatomy. The results may therefore not adequately reflect the dose reduction achievable in the thorax. Based on the level of scattered radiation in the thorax compared with the lumbar level, we would anticipate the dose in the thorax to be even lower.The lower-contrast images of the cone-beam scanner are not comparable with a standard CT , but in The parameters of the optimised protocols were to some extent dictated by limitations of the generator. Even at the lowest possible tube current (10 mA), all phantoms at all voltages above 90 kVp showed acceptable image quality. If the mA were lowered further, a lower patient dose might have been achievable since the same dose at a higher kVp would result in a lower absorbed dose to the patient. Dose to the patient may have been reduced further by using a bow-tie filter typically employed in standard CT scanners . A preliWith optimised exposures at 70 kVp/40 mAs for a 1-year-old-equivalent phantom, 70 kVp/80 mAs for a 5-year-old-equivalent phantom and 80 kVp/40 mAs for a 12-year-old-equivalent phantom, radiation doses for intraoperative 3-D imaging with a cone-beam flat-panel detector scanner were reduced at least 89% and could still be used to safely guide the placement of pedicle screws. The effective doses for optimised scans were estimated at approximately 0.5 mSv and were between 91–94,5% lower than the effective dose estimated for the manufacturers' default exposure values.


Negative for NG2 and CNPase, these radixin+/Olig2+ cells are distinct from typical oligodendrocyte progenitors. The expanded Olig2+ population responds rapidly to EGF and proliferates after only 24 hours along the entire RMS, suggesting local activation by EGF throughout the RMS rather than migration from the SVZ. In addition, the radixin+/Olig2+ progenitors assemble in chains in vivo and migrate in chains in explant cultures, suggesting that they possess migratory properties within the RMS. In summary, these results provide insight into the adaptive capacity of the RMS and point to an additional stem cell source for future brain repair strategies.The presence of neural stem cells in the adult brain is currently widely accepted and efforts are made to harness the regenerative potential of these cells. The dentate gyrus of the hippocampal formation, and the subventricular zone (SVZ) of the anterior lateral ventricles, are considered the main loci of adult neurogenesis. The rostral migratory stream (RMS) is the structure funneling SVZ progenitor cells through the forebrain to their final destination in the olfactory bulb. Moreover, extensive proliferation occurs in the RMS. Some evidence suggest the presence of stem cells in the RMS, but these cells are few and possibly of limited differentiation potential. We have recently demonstrated the specific expression of the cytoskeleton linker protein radixin in neuroblasts in the RMS and in oligodendrocyte progenitors throughout the brain. These cell populations are greatly altered after intracerebroventricular infusion of epidermal growth factor (EGF). In the current study we investigate the effect of EGF infusion on the rat RMS. We describe a specific increase of radixin Neurogenesis persists in two distinct niches in the adult brain; the dentate gyrus of the hippocampal formation and the subventricular zone (SVZ) of the forebrain All animal work was conducted according to European and Swedish animal welfare regulations and approved by the Gothenburg committee of the Swedish Animal Welfare Agency (application no. 145/10 and 32/11).Male Wistar rats, 7–8 weeks old, with an average weight of 221±14 grams were used in the study. All surgeries were performed under ketamine  and xylazine  anesthesia, and all efforts were made to minimize suffering. The animals were divided into six groups receiving either vehicle  or EGF (360 ng/day), for 1, 7, or 14 days. The surgeries were performed as described in Lindberg et al http://www.ncbi.nlm.nih.gov/tools/primer-blast/) and Primer express software (Applied Biosystems) and synthesized by Eurofins MWG Operon . Primer sequences were designed with a melting temperature of 60°C spanning an intron site when possible and the efficiency of all primers was tested using a dilution curve. Sequences used: AAAGCCCAGGCCCAATGCGC  and ACAAGTCCTTGTGCTTCCGCAGAC , TGTGATGGACTCCGGAGACGGG , TGTAGCCACGCTCGGTCAGGAT , AACCCATCACCATCTTCCAGGAGCG , ACATACTCAGCACCAGCATCACCCC , CCTACCACAGCGTGTTTTGGA (Radixin forward), TCCCCCTGTGTTCTTCATGC (Radixin reverse). For both primers we used an initial cycle of 15 min at 95°C, followed by repeated cycles of 94, 55, and 72°C . A final continuous fluorescence reading at descending temperatures (melting curve) starting at 95°C was acquired to ensure proper primer functionality and to exclude primer-dimer formation. Fold-changes were calculated using Cq and the ΔΔCq method normalizing against two reference genes (GAPDH and β-actin) according to Vandesompele et al. Quantitative polymerase chain reaction was performed on micro-dissected lateral ventricle wall and olfactory bulb tissue bilaterally and processed according to Lindberg et al The sections were washed in Tris-buffered saline (TBS). For all immunostainings where rabbit α-radixin or mouse α-radixin were used, the washing step was followed by antigen retrieval in 0.01 M sodium citrate pH6 at 97° for 20 minutes. Sections used for BrdU immunofluorescence were treated with 2 M HCl for 30 minutes at room temperature or 37°C followed by neutralization in 0.1 M borate buffer. All sections were blocked for 1 h in TBS with 3% donkey serum and 0.1% Triton-X (0.2% for radixin antibodies) at room temperature, prior to primary antibody incubation. Primary antibody incubation  and a 63× objective. Each fluorochrome was recorded individually in sequential scan mode to avoid channel mixing. Images were acquired from the RMS  in z-stacks of 2 µm increments. For radixin/DCX and radixin/Olig2 quantifications, cell nuclei were selected at random in the RMS, using ToPro3 and selected cells analyzed for either single or double immunoreactivity. BrdU/radixin and BrdU/Olig2 colabeling was analyzed by selecting at least 250 BrdU positive cells per animal for colocalization of immunosignals. Sox22 and 1% CO2 for 72 h. At the end of the experiment the explants were fixed in 4% PFA for 20 minutes. Immunocytochemistry was performed in the chamber slides. Following three 15-minute washes in PBS unspecific antibody binding was blocked by incubation with 3% donkey serum and 0.2% Triton-X in PBS for three hours at room temperature. Explants were then incubated with primary antibodies  and mixed 1∶3 with Matrigel (BD Bioscience). 15 µl of the Matrigel-tissue mixture was dispensed in 8-well chamber slides (BD Bioscience), followed by 10 minutes polymerization at 37°C. Explants were grown in Neurobasal A medium, supplemented with B27 and Glutamax, PenStrep (All from Invitrogen). The explants cultures were kept at 37°C in 5% Odies see  for 72 ht-test was employed. The Mann-Whitney U-test was used for the comparison of radixin/BrdU ratios. All statistical calculations and graphical visualizations were performed in GraphPad Prism 5 (GraphPad Software). All error bars represent standard error of the mean (SEM). Cell numbers and animal weights are presented as mean±SE. Differences of p<0.05 were considered statistically significant (*).In all comparisons, except radixin/BrdU cell ratios, the 2-tailed Student's To assess structural changes in the RMS induced by EGF infusion we quantified the area and cell density at two locations along the RMS; one proximal to the SVZ (bregma +2.50 mm) and a distal location closer to the olfactory bulb (bregma +3.00 mm). In the proximal RMS we observed a reduced cell density along with an increase in RMS cross-sectional area after 7 days of EGF infusion . The bouDCX mRNA expression in the SVZ . The radixin animals . Howevernegative . Occasio and RMS .Previous reports indicate that EGFR activation can shift cell commitment towards the generation of oligodendrocyte-like progenitors Astrocytes, which form the glial sheaths between chains of migrating cells in the RMS were analyzed by immunofluorescence against GFAP. Under EGF stimulation, GFAP expressing cells appeared less regular in shape with thicker processes, indicating a more reactive phenotype .+ cells coexpressing radixin were found  that correspond to neuroblasts and a high expressing population (Sox2high) representing neural stem cells high and Sox2-negative cells were observed within the radixin+/Olig2+ population   .+ cells expressing radixin, we studied the contribution of radixin and Olig2-expressing cells to the proliferative pool. We infused EGF for 1 or 7 days and administered three injections of BrdU during the last 24 hours before perfusion. The percentage of Olig2+ cells in the BrdU+ population increased substantially after 7 days of EGF infusion . The majority of migrating cells expressed radixin and a small portion was radixin+/Olig2+  cells was measured in the entire RMS after just 24 hours of EGF infusion. The radixin+/Olig2+ cells in the control RMS were sparse, while EGF-induced radixin+/Olig2+ cells were numerous, occasionally formed migratory chains and showed activation in the form of pERM expression. Cells of the same phenotype displayed migratory properties and chain formation in explant cultures.In the current study we describe EGF-induced changes in radixin expressing cell populations in the RMS. The EGF stimulated RMS was less dense and displayed reduced DCX expression, while the number of radixin+ cells in the distal RMS after 1 day of EGF infusion speaks in favor of recruitment of local RMS cells, rather than migration of newly generated cells from the SVZ, which would require more time. BrdU labeling showed an increase in the portion of Olig2+ cells among the newly born cells at this location, which in turn indicates a local increase in proliferation within the distal RMS. The reduction in neuroblasts observed after 7 days was further enhanced after 14 days, while the increase detected in the radixin+/Olig2+ population plateaued after 7 days of EGF infusion. These data suggests that the generation of Olig2 expressing cells is a separate event from the decline in DCX expressing cells and not a direct fate shift.The RMS is highly proliferative, which is mostly attributed to rapidly dividing progenitors; however, the presence of slowly dividing stem cells has also been reported + cells can be reverted to neuronal fate determination after EGFR ligand withdrawal Progenitor cells in the RMS react to EGF with increased production of Olig2 cells expressing Sox2, similar to their SVZ counterparts + neuroblasts. Radixin-positive cells co-expressing Olig2 were found throughout the brain. However, in these cells radixin appeared to be unphosphorylated. Under EGF stimulation, the pERM+ neuroblasts are lost; although the newly generated population of Olig2+ cells in the RMS now expresses phosphorylated radixin, suggesting a cytoskeletal activation in these cells. In addition, radixin+/Olig2+/pERM+ cells were more tightly organized than radixin+/Olig2+/pERM− cells of the control RMS, and occasionally grouped together into chains. Similar cells were also observed in parts of the striatum of EGF-treated animals adjacent to the SVZ and RMS. Migration of Olig2+ progenitors after EGF stimulation has previously been described in the striatum +/Olig2+/pERM+ cells in the striatum were directed towards the RMS. Moreover, in explant cultures radixin+/Olig2+/pERM+ cells are migratory and can form chain-like structures in vitro. Although we present no direct evidence for a direct connection between radixin and EGF receptor activation, a possible link can be seen in the interaction between the EGFR and the ERM binding phosphoprotein 50 (EBP50), putatively modulating radixin function in vitro. Conversely, increased expression of EBP50 has been shown to downregulate EGFR activity suggesting a negative feedback loop for EGFR by EBP50 Activation of ERM proteins by phosphorylation enables interaction with actin and transmembrane proteins resulting in cytoskeleton rearrangement. During tangential neuroblast migration the cytoskeleton needs continuous reorganization when protruding the leading process of the cell, and retracting the trailing end. In the control RMS, we observed, that radixin is phosphorylated in DCXPrevious studies infusing EGF into the adult brain have largely overlooked the effects in the RMS, except for the reduction in neuroblasts


We retrospectively analyzed 25 years of experiences with the button Bentall procedure in patients with aortic root pathologies. Even though this procedure has become widespread, there are only a few very long term follow-ups available in the clinical literature, especially regarding single surgeon results.Between 1988 and 2013, a total of 147 patients underwent the Bentall procedure by the same surgeon. Among them there were 62 patients with Marfan syndrome. At the time of the surgery the mean age was 46.5 ± 17.6 years. The impact of surgical experience on long-term survival was evaluated using a cumulative sum analysis chart.p = 0.002), acute indication , use of deep hypothermic circulatory arrest , chronic kidney disease  and early complication  as significant risk factors for the late overall death. The survival rate for freedom from early complication was 94.3 ± 2.2 %, 88.0 ± 3.3 %, 82.9 ± 4.7 % and 69.2 ± 8.4 % at 1,5,10 and 20 years. The main pathological findings of the aortic wall were cystic medial degeneration in 75 %, fibrosis in 6 %, atherosclerosis in 13 % and no pathological alteration in 6 % of the samples. The overall survival rate was significantly lower in patients operated in first 15 years compared to patients operated in the last decade (log-rank p = 0.011).The Kaplan-Meier estimated overall survival rates for the 147 patients were 91.8 ± 2.3 %, 84.3 ± 3.1 %, 76.3 ± 4.9 % and 59.5 ± 10.7 % at 1,5,10 and 20 years, respectively. Multivariate Cox regression analysis identified EuroSCORE II over 3 % (OR 4.245, 95 % CI, 1.739–10.364, According to our long-term follow-up the Bentall operation provides an appropriate functional result by resolving the lesions of the ascending aorta. Based on our results, 25–30 operations done is necessary to gain such a level of confidence and experince to aquire better results on long-term survival. In addition, we discussed that there were no co-morbidities affecting on the survival of Marfan patients and prophylactic aortic root replacement ensures a longer survival among patients with Marfan syndrome. Aortic root replacement procedures, which include the modified version of the original Bentall  operatioWe retrospectively analyzed 25 years of experience with Bentall procedure. Between 1988 and 2013, a total of 147 patients who underwent aortic root reconstruction at the Heart and Vascular Center, Semmelweis University. Of these patients, 111 (75 %) were male and 36 were female (25 %). 62 patients were with Marfan syndrome (42 %) among them and the diagnosis of the syndrome was verified in every case with the use of the original and later the revised Ghent criteria [An electronic Aortic Root Reconstruction Registry database has been established which includes demographics, types of indications, comorbidities, procedure specifications and follow-up informations. Medical records and patient’s history were used to identify comorbidities. Patients’ follow-ups included clinical examination, computed tomography scans and transthoracic echocardiography, and they were treated by the same surgeon. During the studied period, Tirone David valve-sparing procedures were performed in 27 patients. These patients were excluded from the study.2. We found that 80 patients had hypertension (54 %), 11 patients had diabetes mellitus (7 %) and 6 had hyperlipidaemia (4 %). 21 patients were suffering from coronary artery disease (14 %) at the time of the operation, 4 from chronic kidney disease (3 %) and 7 patients had cerebrovascular accident (5 %). The cardiovascular functional status was determined according to the New York Heart Association (NYHA). EuroSCORE II was calculated in all patients according to the EuroSCORE II protocol [The mean patient age at the time of the operation was 46.3 ± 17.5 years , 8 (5 %) patients were older than 70 years. We measured body parameters of patients (height and weight), and calculated the Body Mass Index. The mean BMI was 25.6 ± 5.6 kg/mThe operation was performed via median sternotomy, and cardiopulmonary bypass was applied by cannulating the ascending aorta, aortic arch, femoral artery, or axillar artery, and the right atrium. Myocardial protection was provided by anterograde, retrograde, or simultaneously anterograde and retrograde intermittent cold hyperkalemic blood cardioplegia. Deep hypothermic circulatory arrest (DHCA) was used in 28 patients (19 %). The coronary buttons were excised with the aortic wall patch and mobilized to facilitate reimplantation. The proximal anastomosis was implemented with pledgeted interrupted sutures. The distal, grafto-aortic anastomosis was accomplished with continuous sutures and the coronary button anastomoses were also performed with continuous sutures.St. Jude composite graft  was used in 101 patients; Carbomedics composite graft  in 16 patients; Carbomedics Carbo-Seal conduit  in 18 patients; Vascutek Gelweave composite graft  in 5 patients; Hancock bioprosthesis  with Vaskutek straight graft in 5 patients; and Shelhigh bioconduit  in 2 patients. The 7 bioprosthetic valve and graft were compiled together by the surgeon during operation.The concomitant procedures were performed in 39 patients 27 %); included mitral valve surgery in 11, coronary artery bypass grafting (CABG) in 12, hemi- and total arch replacement in 10, pacemaker implantation in 2, and others in 4 patients. Operative data are described in Table 7 %; inclWe selected all-cause mortality as the endpoint. No patient was lost during the follow-up period. Death was detected from death records of the Hungarian National Health Insurance Fund, which provided accurate mortality data for every patient. Follow-up period for the overall survival was measured from the date of the operation to the date of death, or of last contact alive. Follow-up ended on October 2013. 118 patients (80 %) of survivors had completed follow-up. The mean length of the follow-up periods was 84 ± 56 months.t-test, Mann–Whitney U-test and χ2 test. Univariate and multivariate analysis of predictors for mortality were performed using a Cox regression model evaluate the association between independent risk factors and mortality. Survival curves were created using the Kaplan-Meier method and compared with the log-rank test. Multivariate logistic regression analysis was used to identify the risk factors of early complication.All continuous variables were expressed as mean ± SD or median with interquartile ranges, whereas categorical variables were expressed as percentage. The Shapiro-Wilk test was used to check the normality of the data before further analysis. For the analysis of the data we used Student’s p < 0.10 from univariate Cox regression, and further examined our data with multivariate Cox regression analysis. A p-value of <0.05 was considered statistically significant , where Xi = 0 for operation without complication and 1 for the presence of early complication, and p0i denotes the predicted probability of the development of early complication within 30 days after surgery. The graph starts at zero, but is incremented by 1- p0i for formation of early complication and decremented by p0i for uncomplicated operation [The impact of surgical experience on survival was evaluated using a time-adjusted cumulative sum complication chart. The statistical principles were adapted from the comprehensive tutorial by Rogers et al. . Cumulatperation . This grperation . Data wen = 1), diffuse hypoxic brain damage (n = 2), ventricular arrhytmia (n = 1) and excess bleeding in 1 patient. Early complications included postoperative resternotomy for bleeding (n = 9), atrial and ventricular arrhytmias (n = 13), renal failure needing hemodialysis (n = 1), cerebral infarction (n = 2) and pericardial tamponade (n = 1) . Causes of early death were low cardiac output syndrome (p = 0.050), dissection , concomitant CABG surgery  and concomitant mitral valve surgery  were the independent risk factors for early complication, which defined as possible life-threathening complication within 30 days of initial hospitalization . There have been 23 late deaths (death after one year), whereof 18 cardiac-related (78 %) and 5 non-cardiac-related (22 %) deaths occured. The most common causes of cardiac-related death were aneurysm rupture of descending aorta, sudden cardiac death, congestive heart failure, CVA and low cardiac output syndrome.p = 0.002), acute indication , DHCA use , chronic kidney disease , and early complication  as significant risk factors for the late overall death  were 91.8 ± 2.3 %, 84.3 ± 3.1 %, 76.3 ± 4.9 % and 59.5 ± 10.7 % at 1,5,10 and 20 years, respectively Fig. . Multivap = 0.004) and acute indication  were the independent risk factors for mortality (Table p = 0.877) compared to the non-Marfan group , and patients without Marfan syndrome (non-Marfan group) Table . Multivaoup Fig. .Table 4Rp = 0.031)  Fig. . However31) Fig. .Fig. 2Kap = 0.197; CMD vs. atherosclerosis log-rank = 0.400; fibrosis vs. atherosclerosis log-rank p = 0.876) Fig. During the operation aortic wall and valve samples were collected and sent for pathological examination. The main pathological findings unearthed were cystic medial degeneration (CMD) in 85 samples (75 %), fibrosis in 7 samples (6 %), atherosclerosis in 15 samples (13 %) and no pathological alteration in 7 samples (6 %). Overall survival rates between the patients with CMD, patients with fibrosis and patients with atherosclerosis were similar (CMD vs. fibrosis log-rank p = 0.011) . The other 105 patients were operated at the next decade (71 %). The overall survival rate was significantly lower in patients operated in first 15 years compared to patients operated in the last decade (log-rank 11) Fig. . The tim11) Fig. . The CUSThe mean survival in our study was 190 ± 10.3 months (IQ range:170–210 months). There are only few papers published about the Bentall procedure which include mean follow-up duration of more than six years Table .Table 6PIn our study, we report that the independent predictors of early complication include NYHA class of III and IV, dissection and concomitant CABG or mitral valve surgery. The poor cardiac condition might often associated with early arrythmias, while aortic dissection is a well-known risk factor of the bleeding events.Numerous studies have shown different independent risk factors for death after Bentall procedure , 9. Advap = 0.877) [There are many debates as to whether Marfan syndrome had an influence in long-term survival after the Bentall procedure. Although several papers have been published , 8, 11, = 0.877) . In our The long-term survival of the cardiac procedures are examined from the perspective of the duration of the operation . In our p = 0.197; CMD vs. atherosclerosis log-rank = 0.400; fibrosis vs. atherosclerosis log-rank p = 0.876)  in 85 samples (75 %), which is also known as the pathological change of the aortic wall in Marfan patients . Further76) Fig. .During the cardiothoracic training surgeons need to gain experience in Bentall procedure. Hence the surgeon launches on a ‘learning curve’, and unfortunately, his/her patients may possibly be at a higher risk . The trap = 0.011)  Fig. .n = 4) and NYHA class of III and IV in Marfan patients (n = 2), could not be carried out in logistic regression analysis due to the low number of events.Our paper has some limitations that are unaviodable in a retrospective study. Observational data do not provide casual evidence. After fifteen years of observation time only 10 % of of patients still at risk which is a limitation. Due to incomplete data collection, several important variables, such as ejection fraction after surgery and pharyngeal temperature, were omitted in the statistical analysis. The histology of the aortic wall could not be included in logistic regression analysis due to the missing 33 samples. In our study only two pseudoaneurysm formations was observed at the graft anastomosis sites , 19, butIn summary, as this study was performed from the data of one surgeon, gives us the opportunity to describe the learning curve of the button Bentall procedure and follow the results through his course of carrier. In our series, 25–30 operations gave the surgeon confidence and experince to aquire better results on long-term survival. In addition, we discussed that there were no co-morbidities affecting on the survival of Marfan patients and prophylactic aortic root replacement ensures a longer survival among patients with Marfan syndrome. Finally, upon the statistical results we discussed histological changes of the aortic wall, which has never been described in long-term button Bentall follow-ups.


Crizotinib is recommended as first-line therapy in ROS1-driven lung adenocarcinoma. However, the optimal first-line therapy for this subgroup of lung cancer is controversial according to the available clinical data.Here, we describe a 57-year-old man who was diagnosed with stage IIIB lung adenocarcinoma and EGFR/KRAS/ALK-negative tumors. The patient received six cycles of pemetrexed plus cisplatin as first-line therapy and then pemetrexed as maintenance treatment, with a progression-free survival (PFS) of 42 months. The patient relapsed and underwent re-biopsy. EZR-ROS1 fusion mutation was detected by next-generation sequencing (NGS). The patient was prescribed crizotinib as second-line therapy and achieved a PFS of 6 months. After disease progression, lorlatinib was administered as third-line therapy, with a favorable response.Prolonged PFS in patients receiving pemetrexed chemotherapy might be related to the EZR-ROS1 fusion mutation. Lorlatinib is an optimal choice in patients showing crizotinib resistance. Prolonging the overall survival (OS) of advanced lung cancer patients remains a challenge. The advent of targeted therapeutic approaches led to the classification of NSCLC into subgroups according to factors such as histology and the molecular makeup of the tumor. C-ros oncogene 1 (ROS1) rearrangements are detected in approximately 1–2% of patients with NSCLC , 4. PrecWe herein report a case of advanced lung adenocarcinoma with EZR-ROS1 rearrangement treated by first-line pemetrexed/cisplatin and then pemetrexed mono-drug for maintenance therapy. After progression, crizotinib was used as second-line treatment, and lorlatinib as third-line treatment. The patient showed an excellent response and achieved long-term progression-free survival (PFS).2) and cisplatin (75 mg/m2), achieving a partial response  every month  and cisplatin (75 mg/m2) at a local hospital. At last, the pemetrexed-based regimen for this patient resulted in a PFS of 42 months.A 57-year-old man with a 20-pack-year smoking history presented to the hospital in March 2013 with a persistent cough for 2 months and a palpable right cervical mass for 4 days. Enhanced computed tomography (CT) showed a 9 × 11 mm nodule in the lower lobe of the left lung and multiple enlarged lymph nodes Fig. . The sernse Fig. . Maintennth Fig. . Assessmnth Fig. . The patv1.1). In April 2017, serum CEA levels were increased, and a lung CT scan showed an enlarged nodule /CT scan revealed a 32 × 17 mm nodule in the left lower lobe with intense uptake of 18F–fluorodeoxyglucose and multiple hypermetabolic lymph nodes Figs.  and 2a. ule Fig. . The PFSule Fig. , which wWritten informed consent was obtained from the patient for the publication of this case report.Crizotinib is approved by the US Food and Drug Administration (FDA) for the first-line treatment of NSCLC patients with ROS1 rearrangements with a median PFS of at least 19.2 months , 11. PemThe molecular mechanism underlying the prolonged PFS in ROS1-driven lung cancer treated with pemetrexed remains unknown. Low thymidylate synthase (TS) expression is positively related to the efficacy of pemetrexed in NSCLC patients and may predict a longer PFS , 16. SevIn the present case, NGS identified EZR-ROS1 as the oncogenic driver mutation, and crizotinib, a multi-targeted TKI, showed robust and clinically meaningful efficacy endpoints in this patient . The advLorlatinib is a third-generation macrocyclic ALK/ROS1 TKI with a novel chemical scaffold that shows potent antineoplastic activity against all known mutations resistant to first- and second-generation inhibitors –27. The CEA is a glycosylphosphatidylinositol-anchored glycoprotein that is normally produced during fetal development, and its production stops before birth . High leIn conclusion, the present ROS1-driven lung cancer case showed a positive response to pemetrexed-based chemotherapy as first-line and maintenance treatment, with a PFS of 42 months. Crizotinib and lorlatinib were used as second- and third-line therapies and both elicited a favorable response. Data from this case suggested that pemetrexed-based regimens may not be inferior to crizotinib as first-line treatment for ROS1-driven lung cancers, and lorlatinib may be an alternative treatment choice in crizotinib-resistant disease. Secondary biopsy after each relapse combined with NGS would help to dynamically monitor the histological and molecular evolution of lung cancer and may benefit the individualized selection of treatment regimens. CEA serum levels may be useful for monitoring relapse in lung adenocarcinoma.


PPARG2 rs1801282 (C>G); PPARGC1A rs8192678 (C>T); TCF7L2 rs7903146 (C>T); LDLR rs2228671 (C>T); MTHFR rs1801133 (C>T); APOA5 rs662799 (T>C); GCKR rs1260326 (C>T); FTO rs9939609 (T>A); MC4R rs17782313 (T>C) were genotyped in 168 pregnant Caucasian women with or without GDM by High Resolution Melting (HRM) analysis. A significant correlation was observed between TT genotype of TCF7L2 gene and increased risk of GDM (OR 5.4 [95% CI 1.5–19.3]). Moreover, a significant correlation was observed between lipid parameters and genetic variations in additional genes, namely, PPARG2 , APOA5 , MC4R , LDLR , and FTO . Our findings support the association between TCF7L2 rs7903146 variant and an increased GDM risk. Results about the investigated genetic variants provide important information about cardiometabolic risk in GDM and help to plan future prevention studies.Gestational diabetes mellitus (GDM) is the most frequent metabolic disorder in pregnancy. Women with a GDM history are at increased risk of developing diabetes and cardiovascular diseases. Studies have demonstrated a significant correlation between several genes involved in the metabolic pathway of insulin and environmental factors. The aim of this study was to investigate the relationship between clinical parameters in GDM and variants in genes involved with nutrients and metabolism. Several variants Gestational diabetes mellitus (GDM) is defined as “diabetes diagnosed in the second or third trimester of pregnancy that is not clearly overt diabetes” .GDM approximately affects 7% range 2–18%) of all pregnancies –18% of a, and GDM HNF4A, GCK, HNF1A, IPF1, HNF1B, and NEUROD1. Common variants in MODY genes, especially in HNF1A and GCK, have been correlated with GDM and related traits ). Although the rs7903146 in the TCF7L2 was the only variant associated with GDM, a significant relation was also found between APOA5 −1131T>C polymorphism, and MC4R rs17782313 polymorphism with 3rd trimester HDL-C in women with GDM. Then, a significant correlation was observed between PPARG2 rs1801282 and LDLR rs2228671 with 3rd trimester LDL-cholesterol levels. Finally, a significant correlation was observed between FTO rs9939609 and 3rd trimester LDL-cholesterol levels (Supplementary Tables  2-3). Our results show that the associations between SNPs and BMI are not statistically significant (Supplementary Tables  4-5).Only one out of the nine investigated gene variants, namely, rs7903146 in theC carrier in APOA5 and HDL-C ; T carrier in LDLR and LDL-C ; A carrier in FTO and LDL-C , respectively.After adjusting for age and BMI, the significant association was still present between χ2 test p value > 0.05) both in cases and in controls, except for TCF7L2 rs7903146 (C<T) and FTO rs9939609 (T>A) in cases.All the investigated genotype frequencies were within the Hardy–Weinberg equilibrium  and glucagon-like peptide 1 (GLP-1) in intestinal endocrine cells.The TCF7L2 T allele has been associated with an increased risk of T2DM. In fact, Grant et al. [ TCF7L2, including the rs7903146 (C>T), show significant associations with T2DM, and these findings have been replicated by numerous groups, demonstrating the rs7903146 (C>T) SNP as one of the most important T2DM susceptibility variants. Dahlgren et al. [T allele results in overexpression of TCF7L2 in the pancreatic β cell, with a reduced insulin secretion in turn increasing hepatic glucose production. In addition, several studies previously observed a strong association between this variant and GDM in different ethnic groups [C>T) and GDM, previously reported by the literature. In addition, our results demonstrated that this association is not mediated by the presence of variants within other genes involved in food metabolism, among those selected, since no one of the other genes investigated in our study was associated with GDM. Future study will need to investigate the possible role of other genes in this condition.The presence of thet et al.  reportedn et al.  suggestec groups –22. ThusPPARG2, APOA5, MC4R, LDLR, and FTO) and lipid parameters within the GDM women group.Nevertheless, our study evidenced also a significant correlation between common genetic variations in several genes  per C allele [ MC4R and FTO are associated with severe obesity and metabolic impairment in Caucasians [ AA genotype of rs9939609 in FTO was associated with 2.09-fold risk of CVD in men [As to theC allele . Gene vaucasians . In the D in men . TT genotype of LDLR rs2228671 polymorphismand 3rd trimester LDL-cholesterol levels, it is interesting to note that a recent meta-analysis has established rs2228671 as a protective factor of CHD in Europeans [Regarding our results about the significant correlation observed betweenuropeans . APOA5-1131T>C and MC4R rs17782313 with 3rd trimester HDL-C in GDM women. This result evokes the study [mean common carotid IMT-CCIMT) was higher in subjects without diabetes but with previous GDM (pGDM) than in control subjects. In this study when these variables were introduced in a multiple regression analysis, only oxidized LDL (oxLDL) remained significantly associated with CC-IMT. The increased carotid IMT, a marker of preclinical atherosclerosis [All these findings are of great relevance and the presence of these gene variants in our panel could increase the use of genetic information in clinical practice for GDM patients: several data support the potential cardiometabolic risk in later life in patients with previous GDM. In fact, Mai et al.  demonstrhe study  which haclerosis , shows tclerosis . APOA5-1131T>C SNP modulates the effects of macronutrient intake  on BMI and obesity risk in both men and women. In fact, the presence of at least one C allele implicated less weight on a high fat diet than the presence of homozygosity for the T allele. Future studies are needed to evaluate this aspect and to predict increased cardiovascular events risk and diabetes in the mother and offspring [Furthermore, Corella et al.  demonstrffspring .As is known the diagnosis of GDM identifies a population at high risk for T2DM  and metaGDM represents an important opportunity in the era of “Precision Medicine.” Further studies are required to examine whether incorporation of our panel genes into an algorithm including genetic, clinic, and metabolic variables will help further improving the identification of women with GDM at early risk of diabetes and CHD; this would allow a better allocation of resources and the implementation of effective and sustainable strategies of primary prevention. In the last decades, the nutrition science is taking off in the prevention of noncommunicable chronic diseases that account for more than 60% of global deaths annually  and the The present study has some limitations. First, the pooled sample size for the SNPs was relatively small. Future genome-wide studies with larger sample size are still required to identify genes with smaller allele effects and possibly GDM specific risk variants: this to understand the role of these variants of genes involved with nutrients and metabolism, in the aetiology and progression of GDM. Second, our results show the role of lipids only in GDM because in control group they were unavailable: our study suggests that in the future these parameters should be considered at least during 3rd trimester of pregnancy.Third, additional analyses, such as epigenetic studies, will also be required to elucidate the role of the molecular mechanisms to the disease susceptibility. In fact, as is known, the development of noncommunicable chronic diseases is determined not only by genetic variants but also by epigenetic changes as DNA methylation and histone modifications, in response to diet and environmental conditions. It has become clear that adverse epigenetic effects might also influence the foetus during pregnancy and postnatal early life increasing the susceptibility to chronic diseases such as obesity, T2DM, cardiovascular disease, or clinically relevant phenotypic traits.Fourth, we recruited a larger sample of women with GDM compared to the control group. This limit is because the recruitment was conducted primarily at the Diabetes and Metabolism Unit.Therefore, future studies are warranted for better understanding the GDM pathogenesis considering gene-gene and gene-environmental interactions.Supplementary Tables showing genotypes distribution in study subjects and the correlation between SNPs and clinical data (lipid parameters and BMI) of GDM patients.