时变环境下Chemostat中微生物连续培养食物链模型的分歧分析

研究均匀搅拌的Chemostat中微生物连续培养的单食物链模型．模型的特点是在营养输入项中引入时变环境,以便更逼真地模拟自然现象．用单特征值分歧定理得到了周期解存在的条件,用Crandall-Rabinowitz定理证明了单种群分歧解的稳定性．     

Impulsive Vaccination of an SEIRS Model with Time Delay and Varying Total Population Size

Pulse vaccination is an effective and important strategy for the elimination of infectious diseases. A delayed SEIRS epidemic model with pulse vaccination and varying total population size is proposed in this paper. We point out, if R* < 1, the infectious population disappear so the disease dies out, while if R _*; > 1, the infectious population persist. Our results indicate that a long period of pulsing or a small pulse vaccination rate is sufficient condition for the permanence of the model.     

Assessment of Transmission in Trachoma Programs over Time Suggests No Short-Term Loss of Immunity

Trachoma programs have dramatically reduced the prevalence of the ocular chlamydia that cause the disease. Some have hypothesized that immunity to the infection may be reduced because of program success in reducing the incidence of infection, and transmission may then increase. Longitudinal studies of multiple communities would be necessary to test this hypothesis. Here, we quantify transmission using an estimated basic reproduction number based on 32 communities during the first, second, and third years of an antibiotic treatment program. We found that there is little to no increase in the basic reproduction number over time. The estimated linear trend in the basic reproduction number, , was found to be −0.025 per year, 95% CI −0.167 to 0.117 per year. We are unable to find evidence supporting any loss of immunity over the course of a 3-year program. This is encouraging, as it allows the possibility that repeated mass antibiotic distributions may eliminate infection from even the most severely affected areas.     

一类具年龄结构和接种的非终生免疫型传染病模型

研究一类具年龄结构和接种的非终生免疫SIRS传染病模型平衡解的稳定性.首先利用特征线法讨论了模型平衡解的存在性,然后利用比较定理和逐次迭代法得到无病平衡解与地方病平衡解全局稳定性的充分条件.     

Immunity,Age and Loss of Immunohomeostasis1

An interpretative discussion on the cellular basis of the association between immunosenescence and loss of immunologic homeostasis was developed from results of studies performed to resolve the issues (a) of whether cells in certain stages of differentiation are more vulnerable to aging than those in other stages and (b) whether the regulatory cells participating in modulating immune responses are prime targets of aging. Young and old mice were exposed to (1) 6-thioguanine (6-TG) to study the activity of their mitotically active and inactive cells and (2) 500R of irradiation to study regeneration of their immune cells. Many alterations were detected in old mice including the existence of a relatively large pool of mitotically inactive pluripotent stem cells in the bone marrow, heightened stem cell regenerative activity, and altered patterns of immunologic regeneration. These kinetic abnormalities reflect age-related changes in stem cells and their progenies, and in the lymphohematopoietic stromal cells.     

一个具暂时免疫且总人数可变的传染病动力学模型

建立了一个具常恢复率和接触率依赖于总人数的SIRS传染病动力学模型,讨论了系统平衡点的存在性和稳定性,对双线性传染率的特殊情形,给出了传染病平衡点的全局稳定性结论,推广和改进了已有的相应结果。     

Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data

Time series data provided by single-molecule Förster resonance energy transfer (smFRET) experiments offer the opportunity to infer not only model parameters describing molecular complexes, e.g., rate constants, but also information about the model itself, e.g., the number of conformational states. Resolving whether such states exist or how many of them exist requires a careful approach to the problem of model selection, here meaning discrimination among models with differing numbers of states. The most straightforward approach to model selection generalizes the common idea of maximum likelihood—selecting the most likely parameter values—to maximum evidence: selecting the most likely model. In either case, such an inference presents a tremendous computational challenge, which we here address by exploiting an approximation technique termed variational Bayesian expectation maximization. We demonstrate how this technique can be applied to temporal data such as smFRET time series; show superior statistical consistency relative to the maximum likelihood approach; compare its performance on smFRET data generated from experiments on the ribosome; and illustrate how model selection in such probabilistic or generative modeling can facilitate analysis of closely related temporal data currently prevalent in biophysics. Source code used in this analysis, including a graphical user interface, is available open source via http://vbFRET.sourceforge.net.     

Loss of Anti-Viral Immunity by Infection with a Virus Encoding a Cross-Reactive Pathogenic Epitope

T cell cross-reactivity between different strains of the same virus, between different members of the same virus group, and even between unrelated viruses is a common occurrence. We questioned here how an intervening infection with a virus containing a sub-dominant cross-reactive T cell epitope would affect protective immunity to a previously encountered virus. Pichinde virus (PV) and lymphocytic choriomeningitis virus (LCMV) encode subdominant cross-reactive NP_205–212 CD8 T cell epitopes sharing 6 of 8 amino acids, differing only in the MHC anchoring regions. These pMHC epitopes induce cross-reactive but non-identical T cell receptor (TCR) repertoires, and structural studies showed that the differing anchoring amino acids altered the conformation of the MHC landscape presented to the TCR. PV-immune mice receiving an intervening infection with wild type but not NP205-mutant LCMV developed severe immunopathology in the form of acute fatty necrosis on re-challenge with PV, and this pathology could be predicted by the ratio of NP205-specific to the normally immunodominant PV NP_38–45 -specific T cells. Thus, cross-reactive epitopes can exert pathogenic properties that compromise protective immunity by impairing more protective T cell responses.     

一类含分布时滞的流行病模型的研究

提出了一类含分布时滞的流行病模型,利用构造李亚普诺夫泛函的方法,得到了无病平衡点和地方病平衡点全局稳定性的结论,揭示了平均时滞对各类平衡点稳定性的影响。     

A Stochastic Model of Gene Evolution with Time Dependent Pseudochaotic Mutations

We develop here a new class of stochastic models of gene evolution in which a random subset of the 64 possible trinucleotides mutates at each evolutionary time t according to some time dependent substitution probabilities. Therefore, at each time t, the numbers and the types of mutable trinucleotides are unknown. Thus, the mutation matrix changes at each time t. This pseudochaotic model developed generalizes the standard model in which all the trinucleotides mutate at each time t. It determines the occurrence probabilities at time t of trinucleotides which pseudochaotically mutate according to 3 time dependent substitution parameters associated with the 3 trinucleotide sites. The main result proves that under suitable assumptions, this pseudochaotic model converges to a uniform probability vector identical to that of the standard model. Furthermore, an application of this pseudochaotic model allows an evolutionary study of the 3 circular codes identified in both eukaryotic and prokaryotic genes. A circular code is a particular set of trinucleotides whose main property is the retrieval of the frames in genes locally, i.e., anywhere in genes and particularly without start codons, and automatically with a window of a few nucleotides. After a certain evolutionary time and with particular time dependent functions for the 3 substitution parameters, precisely an exponential decrease in the 1st and 2nd trinucleotide sites and an exponential increase in the 3rd one, this pseudochaotic model retrieves the main statistical properties of the 3 circular codes observed in genes. Furthermore, it leads to a circular code asymmetry stronger than the standard model (nonpseudochaotic) and, therefore, to a better correlation with the genes.     

Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity

tRNA is the most highly modified class of RNA species, and modifications are found in tRNAs from all organisms that have been examined. Despite their vastly different chemical structures and their presence in different tRNAs, occurring in different locations in tRNA, the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent discoveries have revealed unprecedented complexity in the modification patterns of tRNA, their regulation and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge on the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance and activation of defenses in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal SCS9 encodes a tRNA methyltransferase that mediates the 2´-O-ribose methylation of selected tRNA species in the anticodon loop. These SCS9-mediated tRNA modifications enhance during the course of infection with the bacterial pathogen Pseudomonas syringae DC3000, and lack of such tRNA modification, as observed in scs9 mutants, severely compromise plant immunity against the same pathogen without affecting the salicylic acid (SA) signaling pathway which regulates plant immune responses. Our results support a model that gives importance to the control of certain tRNA modifications for mounting an effective immune response in Arabidopsis, and therefore expands the repertoire of molecular components essential for an efficient disease resistance response.     

A Systematic Model Specification Procedure for an Illness-Death Model without Recovery

Multi-state models are a flexible tool for analyzing complex time-to-event problems with multiple endpoints. Compared to the Cox regression model with a single endpoint or a summarizing composite endpoint, they can provide a more detailed insight into the disease process. Furthermore, prognosis can be improved by including information from intermediate events occurring during the course of the disease. Different model variants, options and additional assumptions provide many possibilities, but at the same time complicate the implementation of multi-state techniques. So far, no guiding literature is available to specify a multi-state model systematically. The objective of this work was to set up a general specification procedure for an illness-death model that optimizes the model fit and predictive accuracy by stepwise reduction of the model. As an application example, we reanalyzed data from an observational study of 434 ovarian cancer patients with progression as intermediate and death as absorbing state. The technique is described in general terms and can be applied to other illness-death models without recovery. The clock-reset approach was used, implicating that the time was reset to zero after progression. The non-homogeneous semi-Markov characteristic stated that the present time as well as the time between surgery and progression influenced survival after progression. Covariate effects on transitions were estimated and proportionality of transition baseline hazards was tested. The finally developed model optimized the accuracy of predictions for two simulated patients. This stepwise procedure yields parsimonious but targeted multi-state models with well interpretable coefficients and optimized predictive ability, even for smaller data sets.     

The Time Course of the Loss and Recovery of Contracture Ability in Frog Striated Muscle Following Exposure to Ca-Free Solutions

Using area under the contracture curve to quantitate contractures, the diffusion coefficient of calcium ions within the frog toe muscle during washout in a calcium-free solution and subsequent recovery after reintroduction of calcium to the bathing solution was calculated to be about 2 x 10^-6 cm²/sec. The diffusion coefficient measured during washout was found to be independent of temperature or initial calcium ion concentration. During recovery it was found to decrease if the temperature was lowered. This was likely due to the repolarization occurring after the depolarizing effect of the calcium-free solution. The relation between contracture area and [Ca]_o was found to be useful over a wider range than that between maximum tension and [Ca]_o. The normalized contracture areas were larger at lower calcium concentrations if the contractures were produced with cold potassium solutions or if NO₃ replaced Cl in the bathing solutions. Decreasing the potassium concentration of the contracture solution to 50 mM from 115 mM did not change the relation between [Ca]_o and the normalized area. If the K concentration of the bathing solution was increased, the areas were decreased at lower concentrations of Ca.     

Preimplantation Genetic Diagnosis and Natural Conception: A Comparison of Live Birth Rates in Patients with Recurrent Pregnancy Loss Associated with Translocation

Background

Established causes of recurrent pregnancy loss (RPL) include antiphospholipid syndrome, uterine anomalies, parental chromosomal abnormalities, particularly translocations, and abnormal embryonic karyotypes. The number of centers performing preimplantation genetic diagnosis (PGD) for patients with translocations has steadily increased worldwide. The live birth rate with PGD was reported to be 27-54%. The live birth rate with natural conception was reported to be 37-63% on the first trial and 65-83% cumulatively. To date, however, there has been no cohort study comparing age and the number of previous miscarriages in matched patients undergoing or not undergoing PGD. Thus, we compared the live birth rate of patients with RPL associated with a translocation undergoing PGD with that of patients who chose natural conception.

Methods and Findings

After genetic counseling, 52 patients who desired natural conception and 37 patients who chose PGD were matched for age and number of previous miscarriages and these comprised the subjects of our study. PGD was performed by means of fluorescence in situ hybridization analysis. The live birth rates on the first PGD trial and the first natural pregnancy after ascertainment of the carrier status were 37.8% and 53.8%, respectively (odds ratio 0.52, 95% confidence interval 0.22-1.23). Cumulative live birth rates were 67.6% and 65.4%, respectively, in the groups undergoing and not undergoing PGD. The time required to become pregnancy was similar in both groups. PGD was found to reduce the miscarriage rate significantly. The prevalence of twin pregnancies was significantly higher in the PGD group. The cost of PGD was $7,956 U.S. per patient.

Conclusions

While PGD significantly prevented further miscarriages, there was no difference in the live birth rate. Couples should be fully informed of the similarity in the live birth rate, the similarity in time to become pregnancy, the advantages of PGD, such as the reduction in the miscarriage rate, as well as its disadvantages, such as the higher cost, and the advantages of a natural pregnancy, such as the avoidance of IVF failure. The findings presented here should be incorporated into the genetic counseling of patients with RPL and carrying a translocation.     

The Effect of Loss of Immunity on Noise-Induced Sustained Oscillations in Epidemics

The effect of loss of immunity on sustained population oscillations about an endemic equilibrium is studied via a multiple scales analysis of a SIRS model. The analysis captures the key elements supporting the nearly regular oscillations of the infected and susceptible populations, namely, the interaction of the deterministic and stochastic dynamics together with the separation of time scales of the damping and the period of these oscillations. The derivation of a nonlinear stochastic amplitude equation describing the envelope of the oscillations yields two criteria providing explicit parameter ranges where they can be observed. These conditions are similar to those found for other applications in the context of coherence resonance, in which noise drives nearly regular oscillations in a system that is quiescent without noise. In this context the criteria indicate how loss of immunity and other factors can lead to a significant increase in the parameter range for prevalence of the sustained oscillations, without any external driving forces. Comparison of the power spectral densities of the full model and the approximation confirms that the multiple scales analysis captures nonlinear features of the oscillations.     

Predictors of Time to Recovery in Infants with Probable Serious Bacterial Infection

Introduction

Serious bacterial infections continue to be an important cause of death and illness among infants in developing countries. Time to recovery could be considered a surrogate marker of severity of the infection. We therefore aimed to identify clinical and laboratory predictors of time to recovery in infants with probable serious bacterial infection (PSBI).

Methods

We used the dataset of 700 infants (7-120 days) enrolled in a randomised controlled trial in India in which 10mg of oral zinc or placebo was given to infants with PSBI. PSBI was defined as signs/symptoms of possible serious bacterial infection along with baseline C-reactive protein(CRP) level >12mg/L. Time to recovery was defined as time from enrolment to the end of a 2-day period with no symptoms/signs of PSBI and daily weight gain of at least 10g over 2 succesive days on exclusive oral feeding. Cox proportional hazard regression was used to measure the associations between relevant variables and time to recovery.

Results

Infants who were formula fed prior to illness episode had 33% longer time to recovery (HR-0.67, 95%CI-0.52, 0.87) than those who were not. Being underweight (HR-0.84, 95%CI-0.70, 0.99), lethargic (HR-0.77, 95%CI-0.62, 0.96) and irritable (HR-0.81, 95%CI-0.66, 0.99) were independent predictors of time to recovery. Baseline CRP was significantly associated with time to recovery (P<0.001), higher CRP was associated with longer time to recovery and this association was nearly linear.

Conclusion

Simple clinical and laboratory parameters such as formula feeding prior to the illness, being underweight, lethargic, irritable and having elevated CRP levels could be used for early identification of infants with PSBI at risk for protracted illness and could guide prompt referral to higher centers in resource limited settings. This also provides prognostic information to clinicians and family as longer recovery time has economic and social implications on the family in our setting.

Trial Registration

ClinicalTrials.gov NCT00347386     

The Influence of Immunity Loss on Persistence and Recurrence of Endemic Infections

Conditions for persistence of endemic infections with immunity loss are derived and shown to agree with conditions for recurrence recently established by Chaffee and Kuske (Bull. Math. Biol. 73(11):2552–2574, 2011).