中国貉(Nyctereutes procyonoides)线粒体DNA多态性及其与亚种分化的关系

我们用8种限制性核酸内切酶(Hpa I、Bgl I、EcoR I、Sca I、BamH I、EcoRV、Stu I、和Apa I)分析来自东北、华北、华东、西南、华南地区的中国貉(Nyctereutes procyonoides)5个地理群体共11只个体的mtDNA多态性，计算各群体间的遗传距离。分别用UPG法和NJ法构建中国貉的系统发生关系。结果表明，云南、广西、安徽群体与华北、东北群体分别构成中国貉的南、北两个支系；根据遗传距离的计算，华北貉可以构成一个独立的亚种；指名亚种中的广西、安徽两群体间的遗传差异较大(p=o.oo97)，而广西貉与西南亚种（云南貉）则非常接近(p=o.0047)。这提示，指名亚种内已发生明显的遗传分化。华东（福建）、华南群体（两广）的分类地位及其与其它各群体的遗传关系有待进一步探讨。在所研究的5个群体中，MtDNA差异与群体间的地理距离表现出某种相关性。

Species identification in salted products of red snappers by semi-nested PCR-RFLP based on the mitochondria 12S rRNA gene sequence

A molecular approach was developed to distinguish species of red snappers among commercial salted fish products. The specific fragments of the mitocliondrial 12S rRNA gene, which were about 450 bp, were obtained using the semi-nested polymerase chain reaction (semi-nested PCR). Subsequently, PCR amplicons were sequenced, aiming to select restriction endonucleases that generated species-specific restriction fragment length polymorphism (RFLP) profiles. Discrimination of red snappers Lutjanus sanguineus, L. erythopterus from L. argentintaculatus, L. malabarius and other morphologically similar fishes such as Lethrinus leutjanus and Pinjalo pinjalo was feasible by one restriction digestion reaction with three endonucleases Hae III, Sca I and SnaB I, however, for differentiation of L. sattguineus and L. erythopterus, another restriction digestion reaction with single restriction endonuclease Mae II was needed. The seminested PCR-RFLP was demonstrated to be reliable in species identification of salted fish products in this study. (c) 2005 Published by Elsevier Ltd.

Species identification in salted products of red snappers by semi-nested PCR-RFLP based on the mitochondrial 12S rRNA gene sequence

A molecular approach was developed to distinguish species of red snappers among commercial salted fish products. The specific fragments of the mitochondrial 12S rRNA gene, which were about 450bp, were obtained using the semi-nested polymerase chain reaction (semi-nested PCR). Subsequently, PCR arnplicons were sequenced, aiming to select restriction endonucleases that generated species-specific restriction fragment length polymorphism (RFLP) profiles. Discrimination of red snappers Lutjanus sanguineus, Lutjanus erythopterus from Lutjanus argentimaculatus, Lutjanus malabarius and other morphologically similar fishes such as Lethrinus leutjanus and Pinjalo pinjalo was feasible by one restriction digestion reaction with three endonucleases Hae III, Sca I and SnaB I, however, for discrimination of L. sanguineus and L. erythopterus, another restriction digestion reaction with single restriction endonuclease Mae II was needed. The semi-nested PCR-RFLP was demonstrated to be reliable in species identification of salted fish products in this study. (c) 2005 Elsevier Ltd. All rights reserved.

皱纹盘鲍的遗传育种与养殖技术研究

优良的种质是产业发展的重要保证，品种更新和养殖技术的发展已经给世界农业带来了令人瞩目的成就，然而我国水产生物的育种工作刚处于起步阶段，而育种技术的研究则更是滞后。借鉴陆生生物中发展起来的相对成熟的研究方法，可以帮助加快海洋生物遗传育种相关研究的进度。本研究以我国北方海区重要的海洋经济动物－皱纹盘鲍为研究对象，从表型遗传、数量性状遗传等2个方面开展了皱纹盘鲍的遗传育种研究，同时从幼鲍培育密度与分选效应等方面研究了皱纹盘鲍的中间培育技术。 主要结果如下： 1. 皱纹盘鲍的贝壳颜色遗传、食物对贝壳颜色表现型的影响，贝壳颜色与生长速度间的关系 将贝壳颜色为橘红色（O表型）的突变型皱纹盘鲍与贝壳颜色为绿色（G表型）的野生型皱纹盘鲍进行了连续2代的交配实验。结果表明：皱纹盘鲍橘红色的贝壳颜色相对于绿色的贝壳颜色为隐性性状，皱纹盘鲍的贝壳颜色表型受单位点、2个等位基因遗传控制，其中基因型为oo的个体，贝壳颜色的表现型为橘红色（O表型），而基因型为GG或Go的个体，贝壳颜色的表现型为野生型（G表型）。 为探讨食物类型对不同基因型皱纹盘鲍贝壳颜色表现型的影响，对不同贝壳颜色表型的个体投喂不同种类的食物，结果表明，除遗传因素外，皱纹盘鲍的贝壳颜色表现型显著地受食物类型的调控。其中oo基因型的个体，在摄食底栖硅藻（Navicula sp.）和红藻时，贝壳颜色的表型为橘红色；而在摄食褐藻、绿藻和以海带粉为唯一海藻源的人工配合饵料时，贝壳颜色的表型为黄色。GG和Go基因型的个体，在摄食底栖硅藻、红藻时，贝壳颜色的表型为褐红色；在摄食褐藻、绿藻和以海带粉为唯一海藻源的人工配合饵料时，贝壳颜色的表型为绿色。该结果表明，相同基因型的皱纹盘鲍在摄食不同类型的食物时，贝壳表现型不同，即不同类型的食物可以导致2种基因型皱纹盘鲍的贝壳颜色表现型在一定范围内发生转换：oo基因型的个体，贝壳的颜色可以表现为橘红色或者黄色，不会出现野生型皱纹盘鲍的褐红色或绿色；而GG与Go基因型的个体，相应的贝壳颜色表型只能是褐红色或者绿色，不会出现oo基因型可能表现的橘红色或黄色。特定基因型的皱纹盘鲍，在摄食特定类型的食物时贝壳的相应部位可表现出特定的颜色。皱纹盘鲍的这种“食物－贝壳颜色”的相关性可作为一种形态标记，用于标识皱纹盘鲍的个体和群体，该标记技术可用于皱纹盘鲍的养殖技术和遗传学研究。 此外，选用了贝壳颜色遗传学实验中建立的贝壳颜色发生分离的家系为实验材料，以壳长为指标，分析比较了来自相同家系的O表型与G表型个体之间的生长速度。结果表明，在幼鲍发育至412天止的3-5个统计时段内，没有在同一家系来源的2种贝壳颜色表型个体之间检验到生长速度的显著差异。 2. 皱纹盘鲍不同选育群体及杂交群体的贝壳形态参数分析 在皱纹盘鲍的7个群体中（包括已经对生长速度为指标进行了多代人工选育的群体4个、野生群体之间直接杂交繁育的杂交F1群体3个），测量了4-6龄成体样本的壳长（L）、壳宽（W）、壳高（H）和壳重（Sw），并计算了L/（L+W+H）、W/（L+W+H）、H/（L+W+H）和Sw/（L×W×H）等4个壳形态学参数。用方差分析方法（MANOVA、ANOVA）统计并比较了这些壳形态参数在皱纹盘鲍群体间的遗传变异。结果表明，4个壳形态参数在不同群体间变异系数分别为0.34、0.74、2.62和6.54，其中，H/（L+W+H）与Sw/（L×W×H）在各供试群体间均具有较高的多态性且差异达显著水平，表明这2个参数在不同群体间存在较高的遗传变异。由于在活体情况下无法测量壳重（Sw）性状，建议以参数H/（L+W+H）为指标对皱纹盘鲍贝壳形态（如壳型）等进行人工选择。 3. 皱纹盘鲍成体阶段生长性状的遗传参数估计 采用巢式设计，分析了成体阶段不同发育期皱纹盘鲍的壳长与生长速率的遗传力、不同发育期的壳长性状之间的遗传相关、以及不同发育期的生长速率之间的遗传相关，结果表明：（1）壳长遗传力在受精后第70 、130、320、320、380、490与550天的雄性组分估计值分别为0.161 ± 0.075、0.312 ± 0.131、0.326 ± 0.331、0.135 ± 0.228、0.153 ± 0.185和0.180 ± 0.106；雌亲组分估计分别为0.312 ± 0.172、0.699 ± 0.168、0.695 ± 0.168、0.977 ± 0.407、0.427 ± 0.195和0.449 ± 0.027。（2）生长速率遗传力在受精后第320~380天、490 ~ 550天，雄、雌组分估计值分别为0.080 ± 0.120（雄）、 0.210 ± 0.191（雌）以及0.299 ± 0.146（雄）、0.306± 0.148（雌）。雌亲组分的壳长遗传力和生长速率遗传力估计值较大且均达显著水平，表明皱纹盘鲍在成体阶段依然受母性效应的影响。成体阶段生长性状遗传力水平的估计对制定科学的皱纹盘鲍育种方案有指导意义。（3）雄亲组分估计的不同发育期（第390 ~ 550天）壳长间遗传相关为0.597 ~ 1.000，雌亲组分估计为0.589 ~ 1.177。由雄亲、雌亲组分估计，受精后第320~380天与第490 ~ 550天两个发育阶段生长速率间遗传相关均接近于0。雌亲组分估计不同发育期壳长间遗传相关均达显著水平（t0.05, d.f.=13 = 4.33 ~ 11.69，P<0.01），表明壳长性状早期选择有效，即在皱纹盘鲍早期阶段依据壳长性状对个体进行择优或去劣可在后期阶段获得壳长较大的个体。由于使用的雄亲数目少（8个父系半同胞），实验中以雄亲组分估计的遗传参数误差较大。 4. 皱纹盘鲍选育系间的群体杂交 进行了皱纹盘鲍4个人工选育系之间的完全双列杂交实验，以群体交配的方式共建立了16个组合；此外，以大连“98”选群与汕头“S”选群为亲本，以群体交配的方式建立了4个交配组合。对不同方向的杂交组合进行了中亲杂种优势、超亲杂种优势以及配合力等方面的评价。 （1）测量了4个选育群体（R、97、S和J）及其各杂交组合在受精后第9、20和30天时的壳长，统计分析了不同选育系间壳长性状的差异、评价了不同方向杂交组合的中亲与超亲杂种优势、以及配合力。结果如下： 选育系群体内交配繁育的4个组合，在受精后第9、20和30天的壳长均有显著差异，其中，97  97组合在早期发育各阶段均为最小，分别为0.462 ± 0.023mm、0.698 ± 0.057mm和1.476 ± 0.234mm；S  S组合的3次测量值均为最大，分别为0.522 ± 0.023mm、0.824 ± 0.084mm和1.798 ± 0.229mm。 两个方向杂交组合与选育系亲本群体内交配组合的平均值和高亲值比较，得到如下结果：（A）受精后第9天壳长表现正向中亲杂种优势的组合有6个、表现负向中亲杂种优势的组合6个，其中J  97组合的中亲优势率最高，为9.05%；R  S组合最低，为-6.61%。正向高亲杂种优势组合有4个、负向高亲杂种优势组合有8个，其中S  J组合的高亲优势率最高，为5.77%；R  S组合最低，为-7.96%。（B）受精后第20天壳长表现正向中亲杂种优势的组合有7个、表现负向中亲杂种优势的组合5个，其中J  97组合的中亲优势率最高，为12.60%；J  R组合最低，为-8.72%。正向高亲杂种优势组合有3个、负向高亲杂种优势组合有11个，其中J  97组合的高亲优势率最高，为12.20%；J  R组合最低，为-12.67%。（C）受精后第30天壳长表现正向中亲杂种优势的组合有7个、负向中亲杂种优势的组合5个，其中97  S组合的中亲优势率最高，为24.08%；S  97组合最低，为-12.69%。正向高亲杂种优势组合有6个、负向高亲杂种优势组合有6个，其中97  S组合的高亲优势率最高，为15.95%；S  J组合最低，为-19.44%。上述结果表明，皱纹盘鲍不同选育系之间的交配组合，杂种优势率差异很大，因此，通过组配实验，将杂种优势率高的交配组合选择出来应用于生产，可望显著提高目标性状的产量。 对早期发育阶段各生长期壳长性状，亲本一般配合力（GCA）、各杂交组合间特殊配合力（SCA）以及正反交（REC）效应值进行方差分析，结果表明：各亲本GCA差异显著，说明各选育群体存在显著的遗传差异，其中汕头选群“S”在测量的各个生长期均为正值且显著大于其它各亲本；特殊配合力（SCA）以及正反交（REC）效应值较大在各杂交组合间存在显著差异，说明在早期生长发育阶段非加性遗传效应（显性和上位效应）占主导地位。综合各个生长期亲本GCA和杂交组特殊配合力（SCA）以及正反交（REC）效应值，杂交组合97×S在早期生长阶段不仅有较高SCA值而且两个亲本也具有较大的GCA值，表明选育系97和S较适宜作为杂交亲本使用。 （2）大连“98”选群与汕头“S”选群进行2×2因子设计的群体杂交实验，比较了各交配组合早期存活相关性状如受精率、孵化率、变态率以及壳长性状，评价了两个方向杂交组合平均以及不同方向杂交组合的中亲杂种优势率。结果表明早期发育阶段各组合间的受精率无显著差异，而孵化率、变态率等两个杂交方向平均的中亲杂种优势率为5.49%与12.53%，高于壳长性状的优势率（0.936-1.534%）。方差分析结果表明不同方向的杂交组合在早期发育阶段存活相关性状以及壳长性状存在显著差异。孵化率、变态率性状，S×98的中亲杂种优势率分别为13.21%与21.10%，均高于98×S的-3.84%与3.85%；而第10和25d壳长性状，S×98的中亲杂种优势率为1.14%与-2.52%，低于98×S的1.93%与4.41%。 为进一步评价“98”选群与“S”选群不同交配组合在不同温度条件下的生长，进行了基因型与环境的互作研究。从“98”选群与“S”选群的4个交配组合中分别取5月龄幼鲍100头，各组合随机分成3组，每组1个重复，分别于12°C、16°C和 22°C温度条件下进行培育，比较各交配组合基因型与温度对幼鲍生长的影响。不同温度条件下，各组合壳长生长的方差分析结果表明，基因型和温度都能够对幼鲍生长以及最终壳长产生极显著的影响（P < 0. 01），它们的交互作用也达到显著水平（P < 0.05）。杂交子代的幼鲍壳长在12°C、16°C和 22°C温度条件下均表现出杂种优势，双向杂交的中亲杂种优势率分别为5.32%、5.55%和0.03%，表明低温条件（12°C），比高温条件（22°C）下有更强的杂种优势。汕头“S”选群的早期孵化率、变态率、生长性状以及低温条件下幼鲍生长性状的单亲杂种优势率分别为16.64%、42.49%、3.42~5.79%和5.73~9.15%，单亲杂种优势率较大，表明可通过杂交手段，显著地改良汕头“S”选群在早期发育阶段的生长速度、存活率以及幼鲍期的生长性状。本研究的结果支持了Lerner（1954）杂种优势的基因与环境互作学说。 5. 皱纹盘鲍幼鲍的中间培育技术研究 （1）对南方越冬方式的评价 目前，每年的11月前后，将6-7月龄幼鲍运往南方的闽东、闽中、闽南沿海越冬，翌年4月至6月再运回到北方（大连、山东半岛）的养殖模式已经普遍应用于皱纹盘鲍的实际生产，为评价南方越冬的幼鲍培育方式，本研究分别以不同幼鲍材料在闽东三都海湾进行了越冬培育实验。 选择生产上壳长分别为18.37 ± 1.28 mm、15.89 ± 1.10 mm、14.55 ± 1.10 mm与10.59 ± 0.84 mm的幼鲍进行了为期6.5个月的越冬培育，实验结束时，存活率分别为95.56 ± 2.21%、90.55 ± 1.96%、83.97 ± 1.63%与63.30 ± 2.79%。回归分析表明，供试幼鲍在实验起始时的壳长与越冬阶段的存活率成正相关（P = 0.018 < 0.05）。该结果表明，提高幼鲍的规格可显著提高皱纹盘鲍的越冬成活率，因此对于实际生产而言，采取适当措施提高皱纹盘鲍越冬苗种的规格将大幅增加生产的收益，而采用生长速率快的品种、品系或提早采苗均可实现该目标。综合各规格组幼鲍，幼鲍在南方开放性水域进行越冬培育的平均存活率较高，可达到91.38±0.01%，从幼鲍南方越冬的存活曲线可以看出，幼鲍的死亡主要集中在从大连运至福建某地后的15天内，出现死亡高峰的原因可能是由于运输过程的胁迫。此外，2月及4月中下旬水温出现显著降低或回升时也有较明显的死亡出现。该部分结果，对皱纹盘鲍幼鲍的养成管理有指导意义，可以通过合理安排越冬时间、避开死亡的敏感期等措施减少苗种越冬阶段的死亡量。 以中国大连野生群体繁育的子一代为亲本（10♀，10♂），以群体交配的方式繁育F2代个体为实验材料，分别于南方海区以及北方室内升温水方式下进行生长、存活比较，结果表明南方越冬培育方式下，幼鲍壳长的日增长率为81.37-108.89 µm•day-1，与北方室内升温培育条件相比，壳长生长提高了1.08 ~ 1.68倍；而存活率无显著差异。皱纹盘鲍幼鲍南方越冬方式的优势主要体现在鲍鱼幼鲍的生长速度加快，同时节约养殖场的能耗 （2）幼鲍培育过程中的养殖密度与分选效应评价 以3种规格皱纹盘鲍幼鲍为材料比较幼鲍在4个培育密度以及分选或混养条件下壳长的平均日生长及特定生长率。在南方越冬培育方式下实验进行106天，多因素方差分析结果表明实验初始幼鲍的壳长以及培育密度对壳长的生长有显著影响，而且密度效应在不同幼鲍起始规格组中有不同表现；分选没有能够提高不同规格组的生长。本研究的结果对皱纹盘鲍幼鲍的越冬培育有一定的指导作用。

Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study

INTRODUCTION:Subclinical atherosclerosis (SCA) measures in multiple arterial beds are heritable phenotypes that are associated with increased incidence of cardiovascular disease. We conducted a genome-wide association study (GWAS) for SCA measurements in the community-based Framingham Heart Study.METHODS:Over 100,000 single nucleotide polymorphisms (SNPs) were genotyped (Human 100K GeneChip, Affymetrix) in 1345 subjects from 310 families. We calculated sex-specific age-adjusted and multivariable-adjusted residuals in subjects tested for quantitative SCA phenotypes, including ankle-brachial index, coronary artery calcification and abdominal aortic calcification using multi-detector computed tomography, and carotid intimal medial thickness (IMT) using carotid ultrasonography. We evaluated associations of these phenotypes with 70,987 autosomal SNPs with minor allele frequency [greater than or equal to] 0.10, call rate [greater than or equal to] 80%, and Hardy-Weinberg p-value [greater than or equal to] 0.001 in samples ranging from 673 to 984 subjects, using linear regression with generalized estimating equations (GEE) methodology and family-based association testing (FBAT). Variance components LOD scores were also calculated.RESULTS:There was no association result meeting criteria for genome-wide significance, but our methods identified 11 SNPs with p < 10-5 by GEE and five SNPs with p < 10-5 by FBAT for multivariable-adjusted phenotypes. Among the associated variants were SNPs in or near genes that may be considered candidates for further study, such as rs1376877 (GEE p < 0.000001, located in ABI2) for maximum internal carotid artery IMT and rs4814615 (FBAT p = 0.000003, located in PCSK2) for maximum common carotid artery IMT. Modest significant associations were noted with various SCA phenotypes for variants in previously reported atherosclerosis candidate genes, including NOS3 and ESR1. Associations were also noted of a region on chromosome 9p21 with CAC phenotypes that confirm associations with coronary heart disease and CAC in two recently reported genome-wide association studies. In linkage analyses, several regions of genome-wide linkage were noted, confirming previously reported linkage of internal carotid artery IMT on chromosome 12. All GEE, FBAT and linkage results are provided as an open-access results resource at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007.CONCLUSION:The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.

Secure architectures for pairing based public key cryptography

Along with the growing demand for cryptosystems in systems ranging from large servers to mobile devices, suitable cryptogrophic protocols for use under certain constraints are becoming more and more important. Constraints such as calculation time, area, efficiency and security, must be considered by the designer. Elliptic curves, since their introduction to public key cryptography in 1985 have challenged established public key and signature generation schemes such as RSA, offering more security per bit. Amongst Elliptic curve based systems, pairing based cryptographies are thoroughly researched and can be used in many public key protocols such as identity based schemes. For hardware implementions of pairing based protocols, all components which calculate operations over Elliptic curves can be considered. Designers of the pairing algorithms must choose calculation blocks and arrange the basic operations carefully so that the implementation can meet the constraints of time and hardware resource area. This thesis deals with different hardware architectures to accelerate the pairing based cryptosystems in the field of characteristic two. Using different top-level architectures the hardware efficiency of operations that run at different times is first considered in this thesis. Security is another important aspect of pairing based cryptography to be considered in practically Side Channel Analysis (SCA) attacks. The naively implemented hardware accelerators for pairing based cryptographies can be vulnerable when taking the physical analysis attacks into consideration. This thesis considered the weaknesses in pairing based public key cryptography and addresses the particular calculations in the systems that are insecure. In this case, countermeasures should be applied to protect the weak link of the implementation to improve and perfect the pairing based algorithms. Some important rules that the designers must obey to improve the security of the cryptosystems are proposed. According to these rules, three countermeasures that protect the pairing based cryptosystems against SCA attacks are applied. The implementations of the countermeasures are presented and their performances are investigated.

Induced pluripotent stem cell-derived cardiac progenitors differentiate to cardiomyocytes and form biosynthetic tissues.

The mammalian heart has little capacity to regenerate, and following injury the myocardium is replaced by non-contractile scar tissue. Consequently, increased wall stress and workload on the remaining myocardium leads to chamber dilation, dysfunction, and heart failure. Cell-based therapy with an autologous, epigenetically reprogrammed, and cardiac-committed progenitor cell source could potentially reverse this process by replacing the damaged myocardium with functional tissue. However, it is unclear whether cardiac progenitor cell-derived cardiomyocytes are capable of attaining levels of structural and functional maturity comparable to that of terminally-fated cardiomyocytes. Here, we first describe the derivation of mouse induced pluripotent stem (iPS) cells, which once differentiated allow for the enrichment of Nkx2-5(+) cardiac progenitors, and the cardiomyocyte-specific expression of the red fluorescent protein. We show that the cardiac progenitors are multipotent and capable of differentiating into endothelial cells, smooth muscle cells and cardiomyocytes. Moreover, cardiac progenitor selection corresponds to cKit(+) cell enrichment, while cardiomyocyte cell-lineage commitment is concomitant with dual expression of either cKit/Flk1 or cKit/Sca-1. We proceed to show that the cardiac progenitor-derived cardiomyocytes are capable of forming electrically and mechanically coupled large-scale 2D cell cultures with mature electrophysiological properties. Finally, we examine the cell progenitors' ability to form electromechanically coherent macroscopic tissues, using a physiologically relevant 3D culture model and demonstrate that following long-term culture the cardiomyocytes align, and form robust electromechanical connections throughout the volume of the biosynthetic tissue construct. We conclude that the iPS cell-derived cardiac progenitors are a robust cell source for tissue engineering applications and a 3D culture platform for pharmacological screening and drug development studies.

Micro-Anatomical Quantitative Imaging Towards Enabling Automated Diagnosis of Thick Tissues at the Point of Care

Histopathology is the clinical standard for tissue diagnosis. However, histopathology has several limitations including that it requires tissue processing, which can take 30 minutes or more, and requires a highly trained pathologist to diagnose the tissue. Additionally, the diagnosis is qualitative, and the lack of quantitation leads to possible observer-specific diagnosis. Taken together, it is difficult to diagnose tissue at the point of care using histopathology.

Several clinical situations could benefit from more rapid and automated histological processing, which could reduce the time and the number of steps required between obtaining a fresh tissue specimen and rendering a diagnosis. For example, there is need for rapid detection of residual cancer on the surface of tumor resection specimens during excisional surgeries, which is known as intraoperative tumor margin assessment. Additionally, rapid assessment of biopsy specimens at the point-of-care could enable clinicians to confirm that a suspicious lesion is successfully sampled, thus preventing an unnecessary repeat biopsy procedure. Rapid and low cost histological processing could also be potentially useful in settings lacking the human resources and equipment necessary to perform standard histologic assessment. Lastly, automated interpretation of tissue samples could potentially reduce inter-observer error, particularly in the diagnosis of borderline lesions.

To address these needs, high quality microscopic images of the tissue must be obtained in rapid timeframes, in order for a pathologic assessment to be useful for guiding the intervention. Optical microscopy is a powerful technique to obtain high-resolution images of tissue morphology in real-time at the point of care, without the need for tissue processing. In particular, a number of groups have combined fluorescence microscopy with vital fluorescent stains to visualize micro-anatomical features of thick (i.e. unsectioned or unprocessed) tissue. However, robust methods for segmentation and quantitative analysis of heterogeneous images are essential to enable automated diagnosis. Thus, the goal of this work was to obtain high resolution imaging of tissue morphology through employing fluorescence microscopy and vital fluorescent stains and to develop a quantitative strategy to segment and quantify tissue features in heterogeneous images, such as nuclei and the surrounding stroma, which will enable automated diagnosis of thick tissues.

To achieve these goals, three specific aims were proposed. The first aim was to develop an image processing method that can differentiate nuclei from background tissue heterogeneity and enable automated diagnosis of thick tissue at the point of care. A computational technique called sparse component analysis (SCA) was adapted to isolate features of interest, such as nuclei, from the background. SCA has been used previously in the image processing community for image compression, enhancement, and restoration, but has never been applied to separate distinct tissue types in a heterogeneous image. In combination with a high resolution fluorescence microendoscope (HRME) and a contrast agent acriflavine, the utility of this technique was demonstrated through imaging preclinical sarcoma tumor margins. Acriflavine localizes to the nuclei of cells where it reversibly associates with RNA and DNA. Additionally, acriflavine shows some affinity for collagen and muscle. SCA was adapted to isolate acriflavine positive features or APFs (which correspond to RNA and DNA) from background tissue heterogeneity. The circle transform (CT) was applied to the SCA output to quantify the size and density of overlapping APFs. The sensitivity of the SCA+CT approach to variations in APF size, density and background heterogeneity was demonstrated through simulations. Specifically, SCA+CT achieved the lowest errors for higher contrast ratios and larger APF sizes. When applied to tissue images of excised sarcoma margins, SCA+CT correctly isolated APFs and showed consistently increased density in tumor and tumor + muscle images compared to images containing muscle. Next, variables were quantified from images of resected primary sarcomas and used to optimize a multivariate model. The sensitivity and specificity for differentiating positive from negative ex vivo resected tumor margins was 82% and 75%. The utility of this approach was further tested by imaging the in vivo tumor cavities from 34 mice after resection of a sarcoma with local recurrence as a bench mark. When applied prospectively to images from the tumor cavity, the sensitivity and specificity for differentiating local recurrence was 78% and 82%. The results indicate that SCA+CT can accurately delineate APFs in heterogeneous tissue, which is essential to enable automated and rapid surveillance of tissue pathology.

Two primary challenges were identified in the work in aim 1. First, while SCA can be used to isolate features, such as APFs, from heterogeneous images, its performance is limited by the contrast between APFs and the background. Second, while it is feasible to create mosaics by scanning a sarcoma tumor bed in a mouse, which is on the order of 3-7 mm in any one dimension, it is not feasible to evaluate an entire human surgical margin. Thus, improvements to the microscopic imaging system were made to (1) improve image contrast through rejecting out-of-focus background fluorescence and to (2) increase the field of view (FOV) while maintaining the sub-cellular resolution needed for delineation of nuclei. To address these challenges, a technique called structured illumination microscopy (SIM) was employed in which the entire FOV is illuminated with a defined spatial pattern rather than scanning a focal spot, such as in confocal microscopy.

Thus, the second aim was to improve image contrast and increase the FOV through employing wide-field, non-contact structured illumination microscopy and optimize the segmentation algorithm for new imaging modality. Both image contrast and FOV were increased through the development of a wide-field fluorescence SIM system. Clear improvement in image contrast was seen in structured illumination images compared to uniform illumination images. Additionally, the FOV is over 13X larger than the fluorescence microendoscope used in aim 1. Initial segmentation results of SIM images revealed that SCA is unable to segment large numbers of APFs in the tumor images. Because the FOV of the SIM system is over 13X larger than the FOV of the fluorescence microendoscope, dense collections of APFs commonly seen in tumor images could no longer be sparsely represented, and the fundamental sparsity assumption associated with SCA was no longer met. Thus, an algorithm called maximally stable extremal regions (MSER) was investigated as an alternative approach for APF segmentation in SIM images. MSER was able to accurately segment large numbers of APFs in SIM images of tumor tissue. In addition to optimizing MSER for SIM image segmentation, an optimal frequency of the illumination pattern used in SIM was carefully selected because the image signal to noise ratio (SNR) is dependent on the grid frequency. A grid frequency of 31.7 mm-1 led to the highest SNR and lowest percent error associated with MSER segmentation.

Once MSER was optimized for SIM image segmentation and the optimal grid frequency was selected, a quantitative model was developed to diagnose mouse sarcoma tumor margins that were imaged ex vivo with SIM. Tumor margins were stained with acridine orange (AO) in aim 2 because AO was found to stain the sarcoma tissue more brightly than acriflavine. Both acriflavine and AO are intravital dyes, which have been shown to stain nuclei, skeletal muscle, and collagenous stroma. A tissue-type classification model was developed to differentiate localized regions (75x75 µm) of tumor from skeletal muscle and adipose tissue based on the MSER segmentation output. Specifically, a logistic regression model was used to classify each localized region. The logistic regression model yielded an output in terms of probability (0-100%) that tumor was located within each 75x75 µm region. The model performance was tested using a receiver operator characteristic (ROC) curve analysis that revealed 77% sensitivity and 81% specificity. For margin classification, the whole margin image was divided into localized regions and this tissue-type classification model was applied. In a subset of 6 margins (3 negative, 3 positive), it was shown that with a tumor probability threshold of 50%, 8% of all regions from negative margins exceeded this threshold, while over 17% of all regions exceeded the threshold in the positive margins. Thus, 8% of regions in negative margins were considered false positives. These false positive regions are likely due to the high density of APFs present in normal tissues, which clearly demonstrates a challenge in implementing this automatic algorithm based on AO staining alone.

Thus, the third aim was to improve the specificity of the diagnostic model through leveraging other sources of contrast. Modifications were made to the SIM system to enable fluorescence imaging at a variety of wavelengths. Specifically, the SIM system was modified to enabling imaging of red fluorescent protein (RFP) expressing sarcomas, which were used to delineate the location of tumor cells within each image. Initial analysis of AO stained panels confirmed that there was room for improvement in tumor detection, particularly in regards to false positive regions that were negative for RFP. One approach for improving the specificity of the diagnostic model was to investigate using a fluorophore that was more specific to staining tumor. Specifically, tetracycline was selected because it appeared to specifically stain freshly excised tumor tissue in a matter of minutes, and was non-toxic and stable in solution. Results indicated that tetracycline staining has promise for increasing the specificity of tumor detection in SIM images of a preclinical sarcoma model and further investigation is warranted.

In conclusion, this work presents the development of a combination of tools that is capable of automated segmentation and quantification of micro-anatomical images of thick tissue. When compared to the fluorescence microendoscope, wide-field multispectral fluorescence SIM imaging provided improved image contrast, a larger FOV with comparable resolution, and the ability to image a variety of fluorophores. MSER was an appropriate and rapid approach to segment dense collections of APFs from wide-field SIM images. Variables that reflect the morphology of the tissue, such as the density, size, and shape of nuclei and nucleoli, can be used to automatically diagnose SIM images. The clinical utility of SIM imaging and MSER segmentation to detect microscopic residual disease has been demonstrated by imaging excised preclinical sarcoma margins. Ultimately, this work demonstrates that fluorescence imaging of tissue micro-anatomy combined with a specialized algorithm for delineation and quantification of features is a means for rapid, non-destructive and automated detection of microscopic disease, which could improve cancer management in a variety of clinical scenarios.

Evaluation of Random Delay Insertion against DPA on FPGAs

Side-channel attacks (SCA) threaten electronic cryptographic devices and can be carried out by monitoring the physical characteristics of security circuits. Differential Power Analysis (DPA) is one the most widely studied side-channel attacks. Numerous countermeasure techniques, such as Random Delay Insertion (RDI), have been proposed to reduce the risk of DPA attacks against cryptographic devices. The RDI technique was first proposed for microprocessors but it was shown to be unsuccessful when implemented on smartcards as it was vulnerable to a variant of the DPA attack known as the Sliding-Window DPA attack.Previous research by the authors investigated the use of the RDI countermeasure for Field Programmable Gate Array (FPGA) based cryptographic devices. A split-RDI technique wasproposed to improve the security of the RDI countermeasure. A set of critical parameters wasalso proposed that could be utilized in the design stage to optimize a security algorithm designwith RDI in terms of area, speed and power. The authors also showed that RDI is an efficientcountermeasure technique on FPGA in comparison to other countermeasures.In this article, a new RDI logic design is proposed that can be used to cost-efficiently implementRDI on FPGA devices. Sliding-Window DPA and realignment attacks, which were shown to beeffective against RDI implemented on smartcard devices, are performed on the improved RDIFPGA implementation. We demonstrate that these attacks are unsuccessful and we also proposea realignment technique that can be used to demonstrate the weakness of RDI implementations.

Using simulation to assess cardiac first-responder schemes exhibiting stochastic and spatial complexities

A Monte-Carlo simulation-based model has been constructed to assess a public health scheme involving mobile-volunteer cardiac First-Responders. The scheme being assessed aims to improve survival of Sudden-Cardiac-Arrest (SCA) patients, through reducing the time until administration of life-saving defibrillation treatment, with volunteers being paged to respond to possible SCA incidents alongside the Emergency Medical Services. The need for a model, for example, to assess the impact of the scheme in different geographical regions, was apparent upon collection of observational trial data (given it exhibited stochastic and spatial complexities). The simulation-based model developed has been validated and then used to assess the scheme's benefits in an alternative rural region (not a part of the original trial). These illustrative results conclude that the scheme may not be the most efficient use of National Health Service resources in this geographical region, thus demonstrating the importance and usefulness of simulation modelling in aiding decision making.

Adaptor protein-2 sigma subunit mutations causing familial hypocalciuric hypercalcaemia type 3 (FHH3) demonstrate genotype-phenotype correlations, codon bias and dominant-negative effects

The adaptor protein-2 sigma subunit (AP2sigma;2) is pivotal for clathrin-mediated endocytosis of plasma membrane constituents such as the calcium-sensing receptor (CaSR). Mutations of the AP2sigma;2 Arg15 residue result in familial hypocalciuric hypercalcaemia type 3 (FHH3), a disorder of extracellular calcium (Ca<inf>o</inf>²⁺) homeostasis. To elucidate the role of AP2sigma;2 in Ca<inf>o</inf>²⁺ regulation, we investigated 65 FHH probands, without other FHH-associated mutations, for AP2sigma;2 mutations, characterized their functional consequences and investigated the genetic mechanisms leading to FHH3. AP2sigma;2 mutations were identified in 17 probands, comprising 5 Arg15Cys, 4 Arg15His and 8 Arg15Leu mutations. A genotype-phenotype correlation was observed with the Arg15Leu mutation leading to marked hypercalcaemia. FHH3 probands harboured additional phenotypes such as cognitive dysfunction. All three FHH3-causing AP2sigma;2 mutations impaired CaSR signal transduction in a dominant-negative manner. Mutational bias was observed at the AP2sigma;2 Arg15 residue as other predicted missense substitutions (Arg15Gly, Arg15Pro and Arg15Ser), which also caused CaSR loss-of-function, were not detected in FHH probands, and these mutations were found to reduce the numbers of CaSR-expressing cells. FHH3 probands had significantly greater serum calcium (sCa) and magnesium (sMg) concentrations with reduced urinary calcium to creatinine clearance ratios (CCCR) in comparison with FHH1 probands with CaSR mutations, and a calculated index of sCa × sMg/100 × CCCR, which was ≥ 5.0, had a diagnostic sensitivity and specificity of 83 and 86%, respectively, for FHH3. Thus, our studies demonstrate AP2sigma;2 mutations to result in a more severe FHH phenotype with genotype-phenotype correlations, and a dominant-negative mechanism of action with mutational bias at the Arg15 residue.

c-Kit+ progenitors generate vascular cells for tissue-engineered grafts through modulation of the Wnt/Klf4 pathway

The development of decellularised scaffolds for small diameter vascular grafts is hampered by their limited patency, due to the lack of luminal cell coverage by endothelial cells (EC) and to the low tone of the vessel due to absence of a contractile smooth muscle cells (SMC). In this study, we identify a population of vascular progenitor c-Kit+/Sca-1- cells available in large numbers and derived from immuno-privileged embryonic stem cells (ESCs). We also define an efficient and controlled differentiation protocol yielding fully to differentiated ECs and SMCs in sufficient numbers to allow the repopulation of a tissue engineered vascular graft. When seeded ex vivo on a decellularised vessel, c-Kit+/Sca-1-derived cells recapitulated the native vessel structure and upon in vivo implantation in the mouse, markedly reduced neointima formation and mortality, restoring functional vascularisation. We showed that Krüppel-like transcription factor 4 (Klf4) regulates the choice of differentiation pathway of these cells through β-catenin activation and was itself regulated by the canonical Wnt pathway activator lithium chloride. Our data show that ESC-derived c-Kit+/Sca-1-cells can be differentiated through a Klf4/β-catenin dependent pathway and are a suitable source of vascular progenitors for the creation of superior tissue-engineered vessels from decellularised scaffolds.

As capacidades dinâmicas das empresas nacionais de maior sucesso no online gaming:modelo para a indústria nacional

Dissertação, Mestrado, Marketing, Instituto Politécnico de Santarém, Escola Superior de Gestão e Tecnologia, 2014

The dynamics of fibroblasts/ECM in neonatal cardiac injury

Tese de mestrado. Biologia (Biologia Evolutiva e do Desenvolvimento). Universidade de Lisboa, Faculdade de Ciências, 2014

Water quality in lakes and reservoirs in China

Dissertation elaborated for the partial fulfilment of the requirements of the Master Degree in Civil Engineering in the Speciality Area of Hydarulics