Correction function for accuracy improvement of the Composite Smeared Finite Element for diffusive transport in biological tissue systems.

Modeling of drug transport within capillaries and tissue remains a challenge, especially in tumors and cancers where the capillary network exhibits extremely irregular geometry. Recently introduced Composite Smeared Finite Element (CSFE) provides a new methodology of modeling complex convective and diffusive transport in the capillary-tissue system. The basic idea in the formulation of CSFE is in dividing the FE into capillary and tissue domain, coupled by 1D connectivity elements at each node. Mass transport in capillaries is smeared into continuous fields of pressure and concentration by introducing the corresponding Darcy and diffusion tensors. Despite theoretically correct foundation, there are still differences in the overall mass transport to (and from) tissue when comparing smeared model and a true 3D model. The differences arise from the fact that the smeared model cannot take into account the detailed non-uniform pressure and concentration distribution in the vicinity of capillaries. We introduced a field of correction function for diffusivity through the capillary walls of smeared models, in order to have the same mass accumulation in tissue as in case of true 3D models. The parameters of the numerically determined correction function are: ratio of thickness and diameter of capillary wall, ratio of diffusion coefficient in capillary wall and surrounding tissue; and volume fraction of capillaries within tissue domain. Partitioning at the capillary wall - blood interface can also be included. It was shown that the correction function is applicable to complex configurations of capillary networks, providing improved accuracy of our robust smeared models in computer simulations of real transport problems, such as in tumors or human organs.

Multiscale smeared finite element model for mass transport in biological tissue: From blood vessels to cells and cellular organelles.

One of the basic and vital processes in living organisms is mass exchange, which occurs on several levels: it goes from blood vessels to cells and organelles within cells. On that path, molecules, as oxygen, metabolic products, drugs, etc. Traverse different macro and micro environments - blood, extracellular/intracellular space, and interior of organelles; and also biological barriers such as walls of blood vessels and membranes of cells and organelles. Many aspects of this mass transport remain unknown, particularly the biophysical mechanisms governing drug delivery. The main research approach relies on laboratory and clinical investigations. In parallel, considerable efforts have been directed to develop computational tools for additional insight into the intricate process of mass exchange and transport. Along these lines, we have recently formulated a composite smeared finite element (CSFE) which is composed of the smeared continuum pressure and concentration fields of the capillary and lymphatic system, and of these fields within tissue. The element offers an elegant and simple procedure which opens up new lines of inquiry and can be applied to large systems such as organs and tumors models. Here, we extend this concept to a multiscale scheme which concurrently couples domains that span from large blood vessels, capillaries and lymph, to cell cytosol and further to organelles of nanometer size. These spatial physical domains are coupled by the appropriate connectivity elements representing biological barriers. The composite finite element has "degrees of freedom" which include pressures and concentrations of all compartments of the vessels-tissue assemblage. The overall model uses the standard, measurable material properties of the continuum biological environments and biological barriers. It can be considered as a framework into which we can incorporate various additional effects (such as electrical or biochemical) for transport through membranes or within cells. This concept and the developed FE software within our package PAK offers a computational tool that can be applied to whole-organ systems, while also including specific domains such as tumors. The solved examples demonstrate the accuracy of this model and its applicability to large biological systems.

Imaging findings of recurrent pancreatic cancer following resection.

Pancreatic cancer is a challenging malignancy to treat, largely due to aggressive regional involvement, early systemic dissemination, high recurrence rate, and subsequent low patient survival. Generally, 15-20% of newly diagnosed pancreatic cancers are candidates for possible curative resection. Eighty percent of these patients, however, will experience locoregional or distant recurrence in first 2 years. Although there is no strong evidence-based guideline for optimal surveillance after pancreatic cancer resection, careful comparison of surveillance follow-up multi-detector CT (MDCT) studies with a postoperative baseline MDCT examination aids detection of early recurrent pancreatic cancer. In this review article, we describe imaging findings suggestive of recurrent pancreatic cancer and review routine and alternative imaging options.

Mass release curves as the constitutive curves for modeling diffusive transport within biological tissue.

In diffusion governed by Fick's law, the diffusion coefficient represents the phenomenological material parameter and is, in general, a constant. In certain cases of diffusion through porous media, the diffusion coefficient can be variable (i.e. non-constant) due to the complex process of solute displacements within microstructure, since these displacements depend on porosity, internal microstructural geometry, size of the transported particles, chemical nature, and physical interactions between the diffusing substance and the microstructural surroundings. In order to provide a simple and general approach of determining the diffusion coefficient for diffusion through porous media, we have introduced mass release curves as the constitutive curves of diffusion. The mass release curve for a selected direction represents cumulative mass (per surface area) passed in that direction through a small reference volume, in terms of time. We have developed a methodology, based on numerical Finite Element (FE) and Molecular Dynamics (MD) methods, to determine simple mass release curves of solutes through complex media from which we calculate the diffusion coefficient. The diffusion models take into account interactions between solute particles and microstructural surfaces, as well as hydrophobicity (partitioning). We illustrate the effectiveness of our approach on several examples of complex composite media, including an imaging-based analysis of diffusion through pancreatic cancer tissue. The presented work offers an insight into the role of mass release curves in describing diffusion through porous media in general, and further in case of complex composite media such as biological tissue.

A composite smeared finite element for mass transport in capillary systems and biological tissue.

One of the key processes in living organisms is mass transport occurring from blood vessels to tissues for supplying tissues with oxygen, nutrients, drugs, immune cells, and - in the reverse direction - transport of waste products of cell metabolism to blood vessels. The mass exchange from blood vessels to tissue and vice versa occurs through blood vessel walls. This vital process has been investigated experimentally over centuries, and also in the last decades by the use of computational methods. Due to geometrical and functional complexity and heterogeneity of capillary systems, it is however not feasible to model in silico individual capillaries (including transport through the walls and coupling to tissue) within whole organ models. Hence, there is a need for simplified and robust computational models that address mass transport in capillary-tissue systems. We here introduce a smeared modeling concept for gradient-driven mass transport and formulate a new composite smeared finite element (CSFE). The transport from capillary system is first smeared to continuous mass sources within tissue, under the assumption of uniform concentration within capillaries. Here, the fundamental relation between capillary surface area and volumetric fraction is derived as the basis for modeling transport through capillary walls. Further, we formulate the CSFE which relies on the transformation of the one-dimensional (1D) constitutive relations (for transport within capillaries) into the continuum form expressed by Darcy's and diffusion tensors. The introduced CSFE is composed of two volumetric parts - capillary and tissue domains, and has four nodal degrees of freedom (DOF): pressure and concentration for each of the two domains. The domains are coupled by connectivity elements at each node. The fictitious connectivity elements take into account the surface area of capillary walls which belongs to each node, as well as the wall material properties (permeability and partitioning). The overall FE model contains geometrical and material characteristics of the entire capillary-tissue system, with physiologically measurable parameters assigned to each FE node within the model. The smeared concept is implemented into our implicit-iterative FE scheme and into FE package PAK. The first three examples illustrate accuracy of the CSFE element, while the liver and pancreas models demonstrate robustness of the introduced methodology and its applicability to real physiological conditions.

Prolonged exposure to extracellular lumican restrains pancreatic adenocarcinoma growth.

We previously demonstrated that pancreatic stellate cells within pancreatic ductal adenocarcinoma (PDAC) stroma secrete lumican and its presence is associated with prolonged survival of patients with localized PDAC. Here, we observed that extracellular lumican decreases PDAC tumour cell growth in xenograft and syngeneic orthotopic animal models, and induces growth inhibition of low-passage human PDAC cells in a species-specific manner. PDAC cells grown in variant culture conditions and exposed to extracellular lumican display typical characterizations of cancer cell in a quiescent state, such as growth inhibition, apoptosis, G0/G1 arrest and chemoresistance. Importantly, extracellular lumican is associated with diminished ERK1/2 phosphorylation and increased p38 phosphorylation within PDAC cells. We further demonstrated that extracellular lumican physically binds with EGFR to trigger EGFR internalization and downregulation of EGFR and its downstream signal molecule ERK. Lumican enhances casitas B-lineage lymphoma expression, which stabilized the TGFß Type II receptor sensitizing PDAC cells to TGFß-mediated activation of p38 and SMAD signals. These provide a mechanism for the shift in signalling and phenotypic changes we observed after prolonged exposure to lumican. Together, our findings demonstrate that stromal lumican restrains PDAC cell growth through mediating cell entry into a quiescent state.

Recommendations for MRI-based contouring of gross tumor volume and organs at risk for radiation therapy of pancreatic cancer.

PURPOSE: Local recurrence is a common and morbid event in patients with unresectable pancreatic adenocarcinoma. A more conformal and targeted radiation dose to the macroscopic tumor in nonmetastatic pancreatic cancer is likely to reduce acute toxicity and improve local control. Optimal soft tissue contrast is required to facilitate delineation of a target and creation of a planning target volume with margin reduction and motion management. Magnetic resonance imaging (MRI) offers considerable advantages in optimizing soft tissue delineation and is an ideal modality for imaging and delineating a gross tumor volume (GTV) within the pancreas, particularly as it relates to conformal radiation planning. Currently, no guidelines have been defined for the delineation of pancreatic tumors for radiation therapy treatment planning. Moreover, abdominal MRI sequences are complex and the anatomy relevant to the radiation oncologist can be challenging. The purpose of this study is to provide recommendations for delineation of GTV and organs at risk (OARs) using MRI and incorporating multiple MRI sequences. METHODS AND MATERIALS: Five patients with pancreatic cancer and 1 healthy subject were imaged with MRI scans either on 1.5T or on 3T magnets in 2 separate institutes. The GTV and OARs were contoured for all patients in a consensus meeting. RESULTS: An overview of MRI-based anatomy of the GTV and OARs is provided. Practical contouring instructions for the GTV and the OARs with the aid of MRI were developed and included in these recommendations. In addition, practical suggestions for implementation of MRI in pancreatic radiation treatment planning are provided. CONCLUSIONS: With this report, we attempt to provide recommendations for MRI-based contouring of pancreatic tumors and OARs. This could lead to better uniformity in defining the GTV and OARs for clinical trials and in radiation therapy treatment planning, with the ultimate goal of improving local control while minimizing morbidity.

Building pharmacogenetics into a pharmacovigilance program in Singapore: using serious skin rash as a pilot study.

To study the possible genetic associations with adverse drug reactions (ADR), the Singapore Health Sciences Authority (HSA) has piloted a program to collect DNA and phenotype data of ADR cases as part of its pharmacovigilance program. Between 2009 and 2012, HSA screened 158 cases of Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). To assess the association between HLA-B*1502 and carbamazepine (CBZ)-induced SJS/TEN, 13 cases and 26 drug-tolerant controls were analyzed. All 13 CBZ-SJS/TEN cases and 3/26 controls were HLA-B*1502 positive (odds ratio 181, 95% confidence interval: 8.7-3785, P=6.9 × 10(-8)). Discussions of the finding with the Ministry of Health and an expert panel led to the decision to make HLA-B*1502 testing the standard of care prior to first use of CBZ in Asians and to subsidize the genotyping test at public hospitals. This program illustrates the role of a regulatory authority in advancing the use of pharmacogenetics for drug safety.

Resolution of adefovir-related nephrotoxicity by adefovir dose-reduction in patients with chronic hepatitis B.

BACKGROUND: Chronic hepatitis B patients (CHB) treated with adefovir were followed up to evaluate nephrotoxicity and its outcome. AIM: To assess the incidence of renal dysfunction during adefovir therapy in Asian patients and factors associated with it, and evaluate strategies to improve adefovir-related renal dysfunction and their impact on viral suppression. METHODS: Chronic hepatitis B clinic patients from a tertiary hospital on adefovir treatment, with their clinical and laboratory parameters were extracted from the hospital electronic clinical database in an observational study design. Patients were excluded if they had liver/renal transplant, baseline renal impairment or were on dialysis. Adefovir-related renal dysfunction was defined as adefovir-related abnormal serum creatinine (ARASC) > 125 µmol/L (males), >90 µmol/L (females); adefovir-related abnormal GFR <60 mL/min; and adefovir-related increased serum creatinine >0.5 mg/dL, without other known causes of nephrotoxicity. RESULTS: A total of 271/383 adefovir-treated patients were suitable for analysis and 33(12%) patients developed abnormal serum creatinine. Cumulative increase in proportion of patients with ARASC was 33.8% and GFR ≤60 mL/min was 38.3% by 6 years, while serum creatinine increase ≥0.5 mg/dL was 21.48% by 5 years. Using multivariate analysis, the only independent baseline predictor of ARASC was GFR ≤76.1 mL/min. Patients who had ARASC had similar levels of viral suppression to those who did not have ARASC. Those who had ARASC either continued adefovir (24%), switched therapy (24%) or had adefovir dose reduction (52%). ARASC resolved and GFR normalised in almost all patients after either switching therapy or reducing adefovir dose, with no difference between the two strategies (P = 0.737). Those with adefovir dose reduction had no significant increase in HBV DNA (P = 0.170). CONCLUSIONS: Adefovir-related renal dysfunction occurred in a significant number of adefovir-treated patients, but reduction of the dose led to renal improvement without compromising treatment efficacy.

Missed diagnosis of influenza B virus due to nucleoprotein sequence mutations, Singapore, April 2011.

A new influenza B variant was discovered in Singapore in April 2011 during diagnostic testing of a 3-year-old boy with respiratory symptoms. Influenza B virus was isolated from culture and confirmed by standard immunofluorescence testing, but was not detected by the routine, in-house influenza screening reverse-transcription polymerase chain reaction assay that targets the nucleoprotein (NP) gene. Subsequent sequencing investigations demonstrated that several other published assays targeting NP could also fail to detect this novel variant.

JAK2 mutations in Asian patients with essential thrombocythaemia.

BACKGROUND/AIM: JAK2V617F is an acquired mutation present in a considerable proportion of patients with chronic myeloproliferative disorders. Its reported prevalence in European and US studies of patients with essential thrombocythaemia (ET) is 23-57%. This study was conducted to determine the prevalence of the JAK2 mutation in Asian ET patients, and to examine their disease profile. METHODS: Asian patients with ET were either recruited to the study or registry data were analysed retrospectively. Blood samples were collected for analysis of JAK2 mutation status during routine patient follow up. Clinical data on these patients (including demographics and disease profiles) and complications at diagnosis were recorded. RESULTS: The JAK2 mutation was detected in 35/102 (34%) patients. Females were more likely than males to have JAK2 mutation (P = 0.031). At diagnosis, JAK2-mutated patients were found to be older (P = 0.012), have higher leucocyte counts (P = 0.036) and high-risk disease (P = 0.039). There were no other statistically significant differences between mutated and wild-type JAK2 ET patients. CONCLUSION: The prevalence of JAK2 mutations in this population of Asian ET patients was 34%. Patients with the JAK2 mutation were significantly more likely to have high-risk disease. Further studies are required to assess the role of JAK2 mutations in risk stratification in ET and compare the phenotype of Asian patients with other populations.

Development of quantitative-fluorescence polymerase chain reaction for the rapid prenatal diagnosis of common chromosomal aneuploidies in 1,000 samples in Singapore.

INTRODUCTION: We aimed to develop a rapid quantitative-fluorescence polymerase chain reaction (QF-PCR) to detect common foetal aneuploidies in the Singapore population within 48 hours of sample collection in order to alleviate parental anxiety. METHODS: DNA from 1,000 foetal samples (978 amniotic fluids, 14 chorion villi and eight foetal blood samples) was analysed using a QF-PCR of 19 microsatellite markers located on chromosomes 13, 18, 21, X and Y. A total of 523 samples were archived before the QF-PCR analysis (archived), while QF-PCR was performed and the results obtained within 48 hours of sample collection in the remaining 477 samples (live). The results were confirmed with their respective karyotypes. RESULTS: In total, 47 autosomal trisomies (T) were found: 30 among the archived (three T13, 12 T18, 15 T21) and 17 among the live (four T18, 13 T21) samples. The QF-PCR results were verified with their respective karyotypes. We achieved 100 percent sensitivity (lower 95 percent confidence interval [CI], 92.8 percent) and specificity (lower 95 percent CI, 99.5 percent), and the time taken from sample collection to the obtaining of results for the 477 live samples was less than 48 hours. CONCLUSION: Prenatal diagnostic results of common chromosomal abnormalities can be released within 48 hours of sample collection using QF-PCR. Parental anxiety is alleviated and clinical management is enhanced with this short waiting time.

How well do serum sTREM-1 measurements prognosticate in septic shock?

The soluble triggering receptor expressed on myeloid cells (sTREM)-1 has emerged as a potentially useful biomarker for the diagnosis of sepsis. This study aimed to evaluate the prognostic utility of serum sTREM-1 in septic shock, in comparison with that of procalcitonin measurements. Thirty-one consecutive patients in a tertiary medical intensive care unit with septic shock were studied. sTREM-1 levels in blood were measured using a modified immunoblot array technique on days one to three of intensive care unit admission. Serum procalcitonin and interleukin (IL)-1beta, IL-6, IL-IO and tumour necrosis factor-alpha levels were also measured. No significant difference was observed in the sTREM-1 levels on the first three days between survivors and nonsurvivors. sTREM-1 levels moderately correlated with the Acute Physiology and Chronic Health Evaluation II and Sequential Organ Failure Assessment scores on day three, but did not correlate with vasopressor requirements, cytokine levels and the presence of bacteraemia. In contrast, procalcitonin levels were significantly higher in nonsurvivors than in survivors on days two and three. A significant relationship also existed between procalcitonin levels and the other variables. In conclusion, this study found that the prognostic utility of serum sTREM-1 in septic shock is poor and that procalcitonin measurements perform better in this regard.

Hypoxic chondrogenic differentiation of human embryonic stem cells enhances cartilage protein synthesis and biomechanical functionality.

BACKGROUND: Engineering musculoskeletal cartilages with stem cells remains a challenge because researchers must control many factors, including differentiation and cartilage matrix synthesis, particularly collagen II production. Hypoxia has effects on many cellular processes, though few investigations with hypoxia provide quantitative functional data on engineered cartilage. OBJECTIVE: This study investigated the effects of hypoxia on chondrogenesis with human embryonic stem cells (hESCs). METHODS: The experiment comprised two phases, embryoid body (EB) differentiation for 3 wks followed by a scaffold-less tissue engineering strategy called self-assembly for 4 wks. During each phase, hypoxic conditions (2% O(2)) or normoxic conditions (20% O(2)) were applied, and engineered constructs were analyzed for cellular, morphological, biochemical, and biomechanical properties. RESULTS: Hypoxic conditions significantly altered the chondrogenic differentiation process, whereby cells cultured in these conditions had an enhanced ability to produce collagen II (up to 3.4-times), collagen I (up to 2.9-times), and glycosaminoglycans (GAGs) (up to 1.9-times), resulting in better biomechanical functionality (up to three times in tensile modulus and up to four times in compressive properties). Hypoxic cells had a different expression profile than normoxic cells for cluster of differentiation (CD)44, CD105, and platelet derived growth factor receptor (PDGFR)alpha, further emphasizing that hypoxia altered hESC differentiation and suggesting that these markers may be used to predict an hESC-derived cell population's chondrogenic potential. Also, normoxic self-assembly outperformed hypoxic self-assembly in tensile and compressive biomechanical characteristics. CONCLUSIONS: These results show that oxygen availability has dramatic effects on the differentiation and synthetic potentials of hESCs and may have important implications for the development of strategies to engineer cartilage.

Refining quantitative fluorescent polymerase chain reaction for prenatal detection of X chromosomal anomalies in the major Southeast Asian populations.

INTRODUCTION: This study aimed to refine the current quantitative fluorescent polymerase chain reaction (QF-PCR) screen to detect X chromosome anomalies for prenatal diagnosis in the major Southeast-Asian populations. METHODS: 100 amniotic fluid samples from Chinese, Malay and Indian origins were subjected to QF-PCR using the X chromosome markers, HPRT, X22 and AMXY, along with the autosomal marker D21S1411. RESULTS: Out of the 100 samples tested by markers X22 and HPRT, eight samples were homozygous for both markers, of which seven were resolved by comparison with the autosomal marker D21S1411. CONCLUSION: 99 percent of samples could be tested for X chromosome copy numbers, increasing the stringency for detection of X chromosome anomalies by QF-PCR. All results were confirmed by cytogenetics.

Soluble triggering receptor expressed on myeloid cells-1 in acute respiratory infections.

Levels of the soluble form of the triggering receptor expressed on myeloid cells (sTREM)-1 are elevated in severe sepsis. However, it is not known whether sTREM-1 measurements can distinguish milder bacterial infections from noninfectious inflammation. The present authors studied whether serum sTREM-1 levels differ in community-acquired pneumonia, exacerbations of chronic obstructive pulmonary disease (COPD), asthma and controls, and whether sTREM-1 may be used as a surrogate marker for the need for antibiotics. Serum sTREM-1 levels in 150 patients with pneumonia, COPD and asthma exacerbations and 62 healthy controls were measured. Serum sTREM-1 levels were significantly elevated in pneumonia (median 295.2 ng x mL(-1)), COPD (280.3 ng x mL(-1)) and asthma exacerbations (184.0 ng x mL(-1)) compared with controls (83.1 ng x mL(-1)). Levels were higher in pneumonia and Anthonisen type 1 COPD exacerbations than in type 2 and 3 COPD and asthma exacerbations. The area under the receiver operating characteristics curve for sTREM-1 as a surrogate marker for the need for antibiotics was 0.77. Serum levels of the soluble form of the triggering receptor expressed on myeloid cells-1 were elevated predominantly in pneumonia and Anthonisen type 1 COPD exacerbations versus type 2 and 3 chronic obstructive pulmonary disease exacerbations, asthma and controls. Serum levels of the soluble form of the triggering receptor expressed on myeloid cells-1 has moderate but insufficient accuracy as a surrogate marker for the need for antibiotics in lower respiratory tract infections.

Discordant quantitative detection of putative biomarkers in nodal micrometastases of colorectal cancer: biological and clinical implications.

AIMS: Nodal expression of the carcinoembryonic antigen (CEA), cytokeratin 20 (CK20), and guanylyl cyclase C (GCC) genes was measured in tandem in patients with colorectal cancer (CRC) to assess whether there would be sufficient agreement between these markers in their ability to detect micrometastasis to qualify one of them as a universal marker, and whether frozen and paraffin wax embedded tissues would yield similar results. METHODS: One hundred and seventy five frozen lymph nodes (FT) and 158 formalin fixed, paraffin wax embedded lymph nodes (PET) from 28 CRC cases were analysed using gene specific quantitative real time polymerase chain reaction, carried out on the LightCycler system with SYBR Green chemistry. RESULTS: There was significant disparity in positive detection of the three biomarkers in FT versus PET, with notable agreement achieved only for CEA (66.6%) in FT versus PET in Dukes' B disease, and between CK20 and GCC (44.6%) in FT, also in Dukes' B disease. One patient with full concordance in all three tumour markers with both tissue types suffered a relapse and died within two years of follow up. CONCLUSIONS: There was considerable discordance in the positive detection of the three tumour markers in both tissue types (FT versus PET). This brings into question whether using a single tumour marker to detect micrometastasis in one tissue type (FT or PET) is adequately representative, and challenges the concept of universal markers for molecular CRC metastatic detection. Multiple tumour markers would predict more accurately the metastatic potential of Dukes' B CRCs.