各向异性扩散的迭代停止时间问题研究

各向异性扩散在抑制噪声与保留边缘方面具有良好的性能，它实际上是一个微分迭代的过程，一个重要问题是这种迭代过程何时停止。根据原始图像与噪声的相关信息，应用最小均方误差、信噪比与相关系数最小原则确定微分停止时间。并应用信息论中的熵与互信息，提出了一种基于互信息的微分停止原则。通过实验验证各种微分停止原则的性能，并讨论了它们各自的特点与适用条件。     

基于各向异性散布的医学图像非线性滤波法

为了向临床医生提供清晰准确的诊断依据 ,在对医学断层图像 (CT、MRI)进行滤波处理时 ,须保留具有重要诊断意义的微细结构。然而 ,绝大多数滤波技术在去噪的同时却滤出了细小结构。本文介绍了一个改进的非线性各向异性散布滤波算法 ,图像滤波被认为是一种散布迭代过程 ,通过自动确定最优散布常数和迭代次数 ,散布过程在遇到边界时就会被抑制或停下来 ,从而保留了边缘信息和微小结构。通过对实际医学图像(CT、MRI)的实验表明 ,本文算法既能提高信噪比又可保留重要的解剖结构     

基于扩散张量成像技术的大脑组织核磁共振电导率重构的仿真研究

将核磁共振电阻抗成像(MREIT)技术应用于人体头部大脑组织电导率重构上.采用基于径向基函数(RBF)神经网络的均质电导率重构MREIT算法,对建立在扩散张量核磁共振成像(DT-MRI)数据基础上的白质组织各向异性电导率和各向同性的灰质、脑脊液目标电导率进行重构.在五层真实形状头模型(包括头皮、颅骨、脑脊液、灰质和白质组织)上进行的仿真实验结果表明,该算法具有一定的抗噪声能力,重构的头部电导率分布图像具有较高的精确性.研究证明了MREIT技术用于头部复杂组织结构电导率重构上的合理性与可行性,在无创头部组织电导率检测领域具有潜在的应用价值.     

由水分子扩散张量计算脑组织电导率张量的新方法

脑组织电导率在脑电/磁研究中是一个重要参数.为了获取脑组织电导率,本研究利用扩散张量成像(DTI)技术,从电化学角度出发,提出了基于Stokes-Einstein与Nernst-Einstein方程的计算脑组织电导率的一种新方法,以三个正交方向上的电导率作为不同脑组织的电导率张量特征值.在人体头部DTI数据上进行计算,并与不同脑组织(白质、灰质、脑脊液)的经验电脑率值进行了对比,发现扩散各向异性越严重的组织,其电导率张量特征值偏离经验值越远,进一步证明了在脑电,磁计算中要考虑脑组织电导率各向异性的必要性.所提出的方法,基于扩散张量,考虑脑液体中各种离子浓度等因素,为获取脑组织各向异性电导率分布提供了一种新的有效途径.     

A strategy for cloning infectious molecular clones of retroviruses from serum or plasma

To enable biological characterisation of lentiviral variants which emerge during infection and development of AIDS, a method was developed to construct molecular clones from circulating simian immunodeficiency virus (SIV) particles present in as little as 20 microl of serum from infected rhesus monkeys. This technique uses a long distance RT-PCR method optimised for the amplification of partly overlapping 5-kb SIV (half genome) amplimers. Ligation of the genome halves resulted in the construction of full-length clones which, after transfection, were able to replicate well in rhesus peripheral blood mononuclear cells (PBMCs) and in various human T-cell lines inducing syncytia. In addition to the study of molecular cloned virus quasispecies emerging in circulation as a result of immune escape, this method may also be applied to obtain entire genes or full-length molecular clones. These clones may be present in other extracellular body fluids such as urine, saliva, tears, lymph, and bronchial or cerebral spinal fluid. Genes amplified in this way can be inserted quickly in new recombinant expression vectors and may then be applied for DNA vaccination approaches.     

Venous Thromboembolism in Autologous Blood or Marrow Transplantation Survivors: A Report from the Blood or Marrow Transplant Survivor Study

Hemostatic complications are commonly encountered in blood or marrow transplantation (BMT) recipients, increasing their morbidity and mortality and are well described in the immediate post-transplantation period. The risk of venous thromboembolism (VTE) in long-term survivors of autologous BMT has not been studied previously. Patients who underwent autologous BMT between January 1, 1974, and December 31, 2010 for a hematologic malignancy, lived 2 years or more after transplantation, and were age ≥18 years were surveyed for long-term outcomes. The median duration of follow-up was 9.8 years (interquartile range, 6.4 to 14.3 years). We analyzed the risk of VTE in 820 autologous BMT recipients who survived for ≥2 years, compared with 644 siblings. BMT survivors were at a 2.6-fold higher risk of VTE compared with siblings (95% confidence interval [CI], 1.6 to 4.4; P =.0004), after adjusting for sociodemographic characteristics. Conditional on surviving for ≥2 years after BMT, the mean cumulative incidence of VTE was 3.9 ± .8% at 5 years and 6.1 ± 1.1% at 10 years. A diagnosis of plasma cell disorder (hazard ratio [HR], 2.37; 95% CI, 1.3 to 4.2; P = .004) and annual household income ≤$50,000 (HR, 2.02; 95% CI, 1.2 to 3.6; P = .015) were associated with increased VTE risk. Our data indicate that autologous BMT survivors are at elevated risk for developing late-occurring VTE. The development of risk prediction models to identify autologous BMT survivors at greatest risk for VTE and thromboprophylaxis may help decrease the morbidity and mortality associated with VTE.     

Activin A circulating levels in patients with bone metastasis from breast or prostate cancer

Recent studies have highlighted that Activin A, a member of the transforming growth factor-β (TGF-β) superfamily, may be involved in the regulation of osteoblastic activity and in osteoclast differentiation. Therefore, we have investigated the clinical significance of its circulating levels in patients with bone metastasis. Activin A serum concentrations were determined, by a commercially available enzyme-linked immunosorbent assay kit, in 72 patients with breast cancer (BC) or prostatic cancer (PC) with (BM+) or without (BM−) bone metastases, in 15 female patients with age-related osteoporosis (OP), in 20 patients with benign prostatic hypertrophy (BPH) and in 48 registered healthy blood donors (HS) of both sex (25 female and 23 male). Activin A serum concentrations were significantly increased in BC or PC patients as compared to OP (P < 0.0001) or BPH (P = 0.045), respectively, or to sex matched HS (P < 0.0001). Additionally, these levels resulted more elevated in PC patients as compared to BC patients (P = 0.032). Interestingly, Activin A was significantly higher in BM+ patients than in BM− patients (BC, P = 0.047; PC, P = 0.016). In BC patients, a significant correlation was observed only between Activin A and number of bone metastases (P = 0.0065) while, in PC patients, Activin A levels were strongly correlated with the Gleason score (P = 0.011) or PSA levels (P = 0.0001) and, to a lessen extent, with the number of bone metastases (P = 0.056). Receiver operating characteristic curve (ROC) analysis showed a fair diagnostic accuracy of Activin A to discriminate between BM+ and BM− patients (BC: AUC = 0.71 ± 0.09, P = 0.03; PC: AUC = 0.73 ± 0.081, P = 0.005). These findings indicate that Activin A may be implicated in the pathogenesis of bone metastasis. Therefore, this cytokine may be considered a novel potential target for a more selective therapeutic approach in the treatment of skeletal metastasis and may be also useful as additional biochemical marker of metastatic bone disease.     

A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing

PurposeAs genome-scale sequencing is increasingly applied in clinical scenarios, a wide variety of genomic findings will be discovered as secondary or incidental findings, and there is debate about how they should be handled. The clinical actionability of such findings varies, necessitating standardized frameworks for a priori decision making about their analysis.MethodsWe established a semiquantitative metric to assess five elements of actionability: severity and likelihood of the disease outcome, efficacy and burden of intervention, and knowledge base, with a total score from 0 to 15.ResultsThe semiquantitative metric was applied to a list of putative actionable conditions, the list of genes recommended by the American College of Medical Genetics and Genomics (ACMG) for return when deleterious variants are discovered as secondary/incidental findings, and a random sample of 1,000 genes. Scores from the list of putative actionable conditions (median = 12) and the ACMG list (median = 11) were both statistically different than the randomly selected genes (median = 7) (P < 0.0001, two-tailed Mann-Whitney test).ConclusionGene–disease pairs having a score of 11 or higher represent the top quintile of actionability. The semiquantitative metric effectively assesses clinical actionability, promotes transparency, and may facilitate assessments of clinical actionability by various groups and in diverse contexts.     

Epstein-Barr virus nuclear antigen 1 linear epitopes that are reactive with immunoglobulin A (IgA) or IgG in sera from nasopharyngeal carcinoma patients or from healthy donors.

The entire amino acid sequence of the unique region of the EBNA 1 protein was synthesized as a set of 41 20-residue peptides with an overlap of 10 amino acids. The peptides were tested in the enzyme-linked immunosorbent assay for reactivity with immunoglobulin A (IgA) and IgG in sera from 50 patients with nasopharyngeal carcinoma (NPC) as compared with 36 serum samples from healthy Epstein-Barr virus (EBV)-seropositive donors and 5 serum samples from EBV-negative donors. The most immunoreactive peptide for both IgA and IgG binding was localized to the glycine-alanine repeat domain of the antigen. In the unique regions, 16 immunoreactive peptides were found. Of these, four were reactive with IgG but not IgA and three peptides were reactive with IgA but not IgG in NPC sera. In addition, several IgA and IgG epitopes on the carboxy-terminal region were specifically reactive with NPC sera, but unreactive with sera from healthy EBV-positive donors. The results suggest that EBV serology specific for individual epitopes may provide additional useful information not available by conventional serology with whole antigens or the EBNA complex.     

Anticoagulant substance released from human lung mast cells by stimulation with anti-IgE or Ca-ionophore A23187

A significant amount of anticoagulant substance was released along with histamine, when human lung mast cells were stimulated with anti-IgE and Ca-ionophore A23187. Its activity was lost by heparinase, not by chondroitin-ABC lyase or chondroitin-AC lyase, and also inhibited by Polybrene, suggesting it would be heparin.     

Busulfan- or Thiotepa-Based Conditioning in Myelofibrosis: A Phase II Multicenter Randomized Study from the GITMO Group

We report a randomized study comparing fludarabine in combination with busulfan (FB) or thiotepa (FT), as conditioning regimen for hematopoietic stem cell transplantation (HSCT) in patients with myelofibrosis. The primary study endpoint was progression-free survival (PFS).Sixty patients were enrolled with a median age of 56 years and an intermediate-2 or high-risk score in 65%, according to the Dynamic International Prognostic Staging System (DIPSS). Donors were HLA-identical sibling (n = 25), matched unrelated (n = 25) or single allele mismatched unrelated (n = 10). With a median follow-up of 22 months (range, 1 to 68 months), outcomes at 2 years after HSCT in the FB arm versus the FT arm were as follows: PFS, 43% versus 55% (P = .28); overall survival (OS), 54% versus 70% (P = .17); relapse/progression, 36% versus 24% (P = .24); nonrelapse mortality (NRM), 21% in both arms (P = .99); and graft failure, 14% versus 10% (P = .96). A better PFS was observed in patients with intermediate-1 DIPSS score (P = .03). Both neutrophil engraftment and platelet engraftment were significantly influenced by previous splenectomy (hazard ratio [HR], 2.28; 95% confidence interval [CI], 1.16 to 4.51; P = .02) and splenomegaly at transplantation (HR, 0.51; 95% CI, 0.27 to 0.94; P = .03). In conclusion, the clinical outcome after HSCT was comparable when using either a busulfan or thiotepa based conditioning regimen.     

中国人早发及多发糖尿病家系中HNF4A基因突变的筛查

目的探讨中国上海及周边地区早发及（或）多发糖尿病家系肝细胞核因子如基因（hepatocyte nuclear faetor-4α，HNF4A）的突变及变异发生情况。方法用PER-单链构象多态及序列分析的方法对154例早发及（或）多发糖尿病家系先证者进行HNF4A基因扫查。对发现的突变或变异采用PCR-限制性片段长度多态性方法在家系其他成员及93名正常对照者中进一步检测。结果在2例糖尿病家系先证者中发现2个同义突变，即N153N和A158A。其中N153N在1个早发性糖尿病家系中见到，且与糖尿病共分离。上述同义突变在正常者中未查到。此外，还发现3个变异位点：即IVS1＋308（A→G）（rs2071197），IVS1＋357（A→T）（rs2071198），IVS1-5（C→T）（rs745975）。3个位点基因型和等位基因频率在糖尿病先证者和正常对照者中无品著差别．结论HNF4A基因突变在中国人早发及（或）多发糖尿病家系中可能罕见。     

The concentration of IgD in blood sera of children suffering from dys- or hypogammaglobulinaemia of class A

6580 children inhabitans of selected region of Lower Silesia and 475 children with recurrent respiratory tract infections as well as 65 children with chronic active hepatitis were tested. IgA level was determined in each case. In the cases where IgA was absent or a low level of this immunoglobulin was found (0.2 g/l) IgD concentration was determined. It was established that the frequency of dysgammaglobulinaemia of class A was 1/731 tested cases in the tested population and 1/119 cases in children with respiratory tract infections and 1/65 tested children with chronic active hepatitis. Hypogammaglobulinaemia of class A was found in 1/365 cases in the tested population and 1/20 cases in children with respiratory tract infections and 2/65 children with chronic aggressive hepatitis. In children with dysgammaglobulinaemia of class A lack of IgD in serum was found in 44% of the cases--however, in hypogammaglobulinaemia IgA lack of IgD in serum was found in 38% of the cases.     

Selection of variant Borrelia burgdorferi isolates from mice immunized with outer surface protein A or B.

A nonclonal population of Borrelia burgdorferi N40 (passage 3) that survived protective immunity following challenge inoculation of outer surface protein (Osp) A- or B-hyperimmunized mice were characterized for the molecular basis of evasion of immunity. Two of six B. burgdorferi isolates, cultured from OspA-immunized mice, had antigenic diversity in the carboxyl terminus of OspA and did not bind to the protective OspA monoclonal antibody designated IXDII. However, OspA-immunized mice challenged with these variants were fully protected. Moreover, B. burgdorferi isolates with a point mutation in ospB, which results in a truncated OspB that does not bind to protective OspB monoclonal antibody 7E6C, were frequently enriched after infection of OspB-immunized mice. These studies suggest that the incomplete efficacy of an OspA- or OspB-based vaccine may be partly due to immunomediated in vivo selective pressure, resulting in the persistence of some spirochetes that do not bind to protective antibodies.     

A focused microarray to assess dopaminergic and glial cell differentiation from fetal tissue or embryonic stem cells

We designed oligonucleotide gene-specific probes to develop a focused array that can be used to discriminate between neural phenotypes, identify biomarkers, and provide an overview of the process of dopaminergic neuron and glial differentiation. We have arrayed approximately 100 genes expressed in dopaminergic neurons, oligodendrocytes, and astrocytes, an additional 200 known cytokines, chemokines, and their respective receptors, as well as markers for pluripotent and progenitor cells. The gene-specific 60-mer 3' biased oligonucleotides for these 281 genes were arrayed in a 25 x 12 format based on function. Using human adult brain substantia nigra, human embryonic stem cells (ESCs), and the differentiated progeny of pluripotent cells, we showed that this array was capable of distinguishing dopaminergic neurons, glial cells, and pluripotent cells by their gene expression profiles in a concentration-dependent manner. Using linear correlation coefficients of input RNA with output intensity, we identified a list of genes that can serve as reporting genes for detecting dopaminergic neurons, glial cells, and contaminating ESCs and progenitors. Finally, we monitored NTera2 differentiation toward dopaminergic neurons and have shown the ability of this array to distinguish stages of differentiation and provide important clues to factors regulating differentiation, the degree of contaminating populations, and stage of cell maturity. We suggest that this focused array will serve as a useful complement to other large-scale arrays in routine assessment of cell properties prior to their therapeutic use.     

A matter of life or death: how microsatellites emerge in and vanish from the human genome

Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions, and disease-associated loci. We observed that substitutions were the predominant cause for births of short microsatellites, while insertions and deletions were important for births of longer microsatellites. Substitutions were the cause for deaths of microsatellites of virtually all lengths. AT-rich L1 sequences exhibited elevated frequency of births/deaths over their entire length, while GC-rich Alus only in their 3' poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1 density, but low GC content and Alu density. The majority of the 17 disease-associated microsatellites examined are evolutionarily ancient (were acquired by the common ancestor of simians). Our genome-wide investigation of microsatellite life cycle has fundamental applications for predicting the susceptibility of birth/death of microsatellites, including many disease-causing loci.