Mathematical Modeling of Multi-Level Behavior of the Embryonic Stem Cell System during Self-Renewal and Differentiation

Embryonic stem cells (ESC) are pluripotent cells derived from the inner cell mass of the blastocyst. These cells have the unique properties of unlimited self-renewal and differentiation capability. ESC therefore hold huge potential for use in therapeutic applications in regenerative medicine. This potential has been demonstrated in vitro by directing differentiation of ESC to various cell types by modulating the soluble and insoluble cues to which the cells are exposed. Despite their great potential, current differentiation methods are still limited in the yield and functionality of the ESC-derived mature phenotype. We hypothesize the lack of mechanistic understanding of the complex differentiation process to be the primary reason behind their restricted success. Mathematical models, coupled to experimental data, can aid in this understanding. While the past several decades have seen advances in the mathematical analysis of biological systems, mathematical approaches to the ESC system have received limited attention. Furthermore, variability of ESC restricts direct application of deterministic approaches towards drawing mechanistic insight. The goal of the current work is to obtain a more thorough mechanistic understanding of the ESC system through mathematical modeling. In ESC, extracellular cues guide single cell behavior in a non-deterministic fashion, giving rise to heterogeneous populations. Therefore, in this work we focus on modeling three levels of the ESC system: intracellular, extracellular, and population. We first developed an optimization framework to identify intracellular gene regulatory interactions from time series data. We show that incorporation of the bootstrapping technique into the formulism allows for accurate prediction of robust interactions from noisy data. A regression approach was then utilized to identify extracellular substrate features influential to cellular behavior. We apply this model to identify fibrin microstructural features which guide differentiation of mESC. Finally, we developed a stochastic model to capture heterogeneous population dynamics of hESC. We demonstrate the usefulness of the model to obtain mechanistic information of cell cycle transition and lineage commitment during differentiation. Through development and utilization of different mathematical approaches to analyze multilevel behavior and variability of ESC self-renewal and differentiation, we demonstrate the applicability of mathematical models in extracting mechanistic information from the ESC system

Computerized data-driven interpretation of the intrapartum cardiotocogram: a cohort study.

INTRODUCTION: Continuous intrapartum fetal monitoring remains a significant clinical challenge. We propose using cohorts of routinely collected data. We aim to combine non-classical (data-driven) and classical cardiotocography features with clinical features into a system (OxSys), which generates automated alarms for the fetus at risk of intrapartum hypoxia. We hypothesize that OxSys can outperform clinical diagnosis of "fetal distress", when optimized and tested over large retrospective data sets. MATERIAL AND METHODS: We studied a cohort of 22 790 women in labor (≥36 weeks of gestation). Paired umbilical blood analyses were available. Perinatal outcomes were defined by objective criteria (normal; severe, moderate or mild compromise). We used the data retrospectively to develop a prototype of OxSys, by relating its alarms to perinatal outcome, and comparing its performance against standards achieved by bedside diagnosis. RESULTS: OxSys1.5 triggers an alarm if the initial trace is nonreactive or the decelerative capacity (a nonclassical cardiotocography feature), exceeds a threshold, adjusted for preeclampsia and thick meconium. There were 187 newborns with severe, 613 with moderate and 3197 with mild compromise; and 18 793 with normal outcome. OxSys1.5 increased the sensitivity for compromise detection: 43.3% vs. 38.0% for severe (p = 0.3) and 36.1% vs. 31.0% for moderate (p = 0.06); and reduced the false-positive rate (14.4% vs. 16.3%, p < 0.001). CONCLUSIONS: Large historic cohorts can be used to develop and optimize computerized cardiotocography monitoring, combining clinical and cardiotocography risk factors. Our simple prototype has demonstrated the principle of using such data to trigger alarms, and compares well with clinical judgment

Home-based therapy programmes for upper limb functional recovery following stroke

Background: With an increased focus on home-based stroke services and the undertaking of programmes, targeted at upper limb recovery within clinical practice, a systematic review of home-based therapy programmes for individuals with upper limb impairment following stroke was required. Objectives: To determine the effects of home-based therapy programmes for upper limb recovery in patients with upper limb impairment following stroke. Search methods: We searched the Cochrane Stroke Group's Specialised Trials Register (May 2011), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2011, Issue 2), MEDLINE (1950 to May 2011), EMBASE (1980 to May 2011), AMED (1985 to May 2011) and six additional databases. We also searched reference lists and trials registers. Selection criteria: Randomised controlled trials (RCTs) in adults after stroke, where the intervention was a home-based therapy programme targeted at the upper limb, compared with placebo, or no intervention or usual care. Primary outcomes were performance in activities of daily living (ADL) and functional movement of the upper limb. Secondary outcomes were performance in extended ADL and motor impairment of the arm. Data collection and analysis: Two review authors independently screened abstracts, extracted data and appraised trials. We undertook assessment of risk of bias in terms of method of randomisation and allocation concealment (selection bias), blinding of outcome assessment (detection bias), whether all the randomised patients were accounted for in the analysis (attrition bias) and the presence of selective outcome reporting. Main results: We included four studies with 166 participants. No studies compared the effects of home-based upper limb therapy programmes with placebo or no intervention. Three studies compared the effects of home-based upper limb therapy programmes with usual care. Primary outcomes: we found no statistically significant result for performance of ADL (mean difference (MD) 2.85; 95% confidence interval (CI) -1.43 to 7.14) or functional movement of the upper limb (MD 2.25; 95% CI -0.24 to 4.73)). Secondary outcomes: no statistically significant results for extended ADL (MD 0.83; 95% CI -0.51 to 2.17)) or upper limb motor impairment (MD 1.46; 95% CI -0.58 to 3.51). One study compared the effects of a home-based upper limb programme with the same upper limb programme based in hospital, measuring upper limb motor impairment only; we found no statistically significant difference between groups (MD 0.60; 95% CI -8.94 to 10.14). Authors' conclusions: There is insufficient good quality evidence to make recommendations about the relative effect of home-based therapy programmes compared with placebo, no intervention or usual care

The Mock LISA Data Challenges: from Challenge 3 to Challenge 4

The Mock LISA Data Challenges are a program to demonstrate LISA data-analysis capabilities and to encourage their development. Each round of challenges consists of one or more datasets containing simulated instrument noise and gravitational waves from sources of undisclosed parameters. Participants analyze the datasets and report best-fit solutions for the source parameters. Here we present the results of the third challenge, issued in Apr 2008, which demonstrated the positive recovery of signals from chirping Galactic binaries, from spinning supermassive--black-hole binaries (with optimal SNRs between ~ 10 and 2000), from simultaneous extreme-mass-ratio inspirals (SNRs of 10-50), from cosmic-string-cusp bursts (SNRs of 10-100), and from a relatively loud isotropic background with Omega_gw(f) ~ 10^-11, slightly below the LISA instrument noise.Comment: 12 pages, 2 figures, proceedings of the 8th Edoardo Amaldi Conference on Gravitational Waves, New York, June 21-26, 200

Potential for pancreatic maturation of differentiating human embryonic stem cells is sensitive to the specific pathway of definitive endoderm commitment

This study provides a detailed experimental and mathematical analysis of the impact of the initial pathway of definitive endoderm (DE) induction on later stages of pancreatic maturation. Human embryonic stem cells (hESCs) were induced to insulin-producing cells following a directed-differentiation approach. DE was induced following four alternative pathway modulations. DE derivatives obtained from these alternate pathways were subjected to pancreatic progenitor (PP) induction and maturation and analyzed at each stage. Results indicate that late stage maturation is influenced by the initial pathway of DE commitment. Detailed quantitative analysis revealed WNT3A and FGF2 induced DE cells showed highest expression of insulin, are closely aligned in gene expression patterning and have a closer resemblance to pancreatic organogenesis. Conversely, BMP4 at DE induction gave most divergent differentiation dynamics with lowest insulin upregulation, but highest glucagon upregulation. Additionally, we have concluded that early analysis of PP markers is indicative of its potential for pancreatic maturation. © 2014 Jaramillo et al

Conservation status of oyster reef ecosystem of Southern and Eastern Australia

Reef ecosystems all over the world are in decline and managers urgently need information that can assess management interventions and set national conservation targets. We assess the conservation status and risk of ecosystem collapse for the Oyster Reef Ecosystem of Southern and Eastern Australia, which comprises two community sub-types established by Saccostrea glomerata (Sydney rock oyster) and Ostrea angasi (Australian flat oyster), consistent with the IUCN Red List of Ecosystems risk assessment process. We established: (i) key aspects of the ecosystem including: ecological description, biological characteristics, condition and collapse thresholds, natural and threatening processes; (ii) previous and current extent of occurrence and current area of occupancy; and (iii) its likelihood of collapse within the next 50e100 years. The most severe risk rating occurred for Criterion A: Reduction in Extent (since 1750) and Criterion D: Disruption of biotic processes (since 1750), although assessment varied from Least Concern to Critically Endangered amongst the four criteria assessed. Our overall assessment ranks the risk of collapse for the ecosystem (including both community sub-types) as Critically Endangered with a high degree of confidence. Our results suggest the need for rapid intervention to protect remaining reefs and undertake restoration at suitable sites. Several restoration projects have already demonstrated this is feasible, and Australia is well equipped with government policies and regulatory mechanisms to support the future conservation and recovery of temperate oyster ecosystems

Population Based Model of Human Embryonic Stem Cell (hESC) Differentiation during Endoderm Induction

The mechanisms by which human embryonic stem cells (hESC) differentiate to endodermal lineage have not been extensively studied. Mathematical models can aid in the identification of mechanistic information. In this work we use a population-based modeling approach to understand the mechanism of endoderm induction in hESC, performed experimentally with exposure to Activin A and Activin A supplemented with growth factors (basic fibroblast growth factor (FGF2) and bone morphogenetic protein 4 (BMP4)). The differentiating cell population is analyzed daily for cellular growth, cell death, and expression of the endoderm proteins Sox17 and CXCR4. The stochastic model starts with a population of undifferentiated cells, wherefrom it evolves in time by assigning each cell a propensity to proliferate, die and differentiate using certain user defined rules. Twelve alternate mechanisms which might describe the observed dynamics were simulated, and an ensemble parameter estimation was performed on each mechanism. A comparison of the quality of agreement of experimental data with simulations for several competing mechanisms led to the identification of one which adequately describes the observed dynamics under both induction conditions. The results indicate that hESC commitment to endoderm occurs through an intermediate mesendoderm germ layer which further differentiates into mesoderm and endoderm, and that during induction proliferation of the endoderm germ layer is promoted. Furthermore, our model suggests that CXCR4 is expressed in mesendoderm and endoderm, but is not expressed in mesoderm. Comparison between the two induction conditions indicates that supplementing FGF2 and BMP4 to Activin A enhances the kinetics of differentiation than Activin A alone. This mechanistic information can aid in the derivation of functional, mature cells from their progenitors. While applied to initial endoderm commitment of hESC, the model is general enough to be applicable either to a system of adult stem cells or later stages of ESC differentiation

The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation.

OBJECTIVES: The interaction between the immune system and tumor cells is an important feature for the prognosis and treatment of cancer. Multiplex immunohistochemistry (mIHC) and multiplex immunofluorescence (mIF) analyses are emerging technologies that can be used to help quantify immune cell subsets, their functional state, and their spatial arrangement within the tumor microenvironment. METHODS: The Society for Immunotherapy of Cancer (SITC) convened a task force of pathologists and laboratory leaders from academic centers as well as experts from pharmaceutical and diagnostic companies to develop best practice guidelines for the optimization and validation of mIHC/mIF assays across platforms. RESULTS: Representative outputs and the advantages and disadvantages of mIHC/mIF approaches, such as multiplexed chromogenic IHC, multiplexed immunohistochemical consecutive staining on single slide, mIF (including multispectral approaches), tissue-based mass spectrometry, and digital spatial profiling are discussed. CONCLUSIONS: mIHC/mIF technologies are becoming standard tools for biomarker studies and are likely to enter routine clinical practice in the near future. Careful assay optimization and validation will help ensure outputs are robust and comparable across laboratories as well as potentially across mIHC/mIF platforms. Quantitative image analysis of mIHC/mIF output and data management considerations will be addressed in a complementary manuscript from this task force

The Mock LISA Data Challenges: from Challenge 1B to Challenge 3

The Mock LISA Data Challenges are a programme to demonstrate and encourage the development of LISA data-analysis capabilities, tools and techniques. At the time of this workshop, three rounds of challenges had been completed, and the next was about to start. In this article we provide a critical analysis of entries to the latest completed round, Challenge 1B. The entries confirm the consolidation of a range of data-analysis techniques for Galactic and massive--black-hole binaries, and they include the first convincing examples of detection and parameter estimation of extreme--mass-ratio inspiral sources. In this article we also introduce the next round, Challenge 3. Its data sets feature more realistic waveform models (e.g., Galactic binaries may now chirp, and massive--black-hole binaries may precess due to spin interactions), as well as new source classes (bursts from cosmic strings, isotropic stochastic backgrounds) and more complicated nonsymmetric instrument noise.Comment: 20 pages, 3 EPS figures. Proceedings of the 12th Gravitational Wave Data Analysis Workshop, Cambridge MA, 13--16 December 2007. Typos correcte

Obesity and immune function relationships.

The immunological processes involved in the collaborative defence of organisms are affected by nutritional status. Thus, a positive chronic imbalance between energy intake and expenditure leads to situations of obesity, which may influence unspecific and specific immune responses mediated by humoral and cell mediated mechanisms. Furthermore, several lines of evidence have supported a link between adipose tissue and immunocompetent cells. This interaction is illustrated in obesity, where excess adiposity and impaired immune function have been described in both humans and genetically obese rodents. However, limited and often controversial information exist comparing immunity in obese and non-obese subjects as well as about the cellular and molecular mechanisms implicated. In general terms, clinical and epidemiological data support the evidence that the incidence and severity of specific types of infectious illnesses are higher in obese persons as compared to lean individuals together with the occurrence of poor antibody responses to antigens in overweight subjects. Leptin might play a key role in linking nutritional status with T-cell function. The complexities and heterogeneity of the host defences concerning the immune response in different nutritional circumstances affecting the energy balance require an integral study of the immunocompetent cells, their subsets and products as well as specific and unspecific inducer/regulator systems. In this context, more research is needed to clarify the clinical implications of the alterations induced by obesity on the immune function