猴和人T淋巴细胞表面TRBC受体和E受体的比较研究

1985年贲昆龙等首次发现人和猴T淋巴细胞能与树鼩(Tupaia belangeri)的红细胞(TRBC)形成亲和力极强的玫瑰花结，它与绵羊红细胞(SRBC)玫瑰花结(E花结)明显不同。例如，TRBC经神经氨酸酶处理之后，结花率明显下降，TRBC与T淋巴细胞所形成的玫瑰花结，经45℃保温，仍不受影响，为了进一步探讨TRBC受体和SRBC受体(CD2)，以及与其它T细胞表面分化搞原(CD)的系。我用某些抗人T细胞CD的单克隆抗体(McAb)对人和猴淋巴细胞进行玫瑰花结抑制试验，抗原调变和共调变(Antigenic modulation or co-modulation)实验，并且研究了TRBC受体在其它免疫细胞和某些人类和长臂猿细胞系的分布。结果表明，TRBC与外周血E~+-PBL形成玫瑰花结的百分率为88.8%。而E~--PBL仅为4.16%。TRBC受体存在于所有被试T细胞系(CEM, H33JHJA1, Jurkat, MLA-144, Molt-3, Molt-4, Molt-4 clone-8 和PEER)，但不存在于外周血粒细胞，B细胞，以及B细胞系的绝大多数细胞表面(Daudi, Raji和Reh)。分布于全T细胞的CD3, TCR, CD5, CD6和CD7的相McAb OKT3, T108(F1), T136(F101-15), T149(M-T604)和T152(7G5)均不能调变和共调变TRBC受体。猴和人外周血淋巴细胞与TRBC玫瑰花结的形成，不被T11.1 McAb OKT11所阻断，相反，OKT11显著地阻断猴和人外周血淋巴细胞E玫瑰花结的形成，最大抑制率分别为49.3%和77.7%。在世界各地10个实验室送交第四次国际人白细胞化化抗原讨论会待鉴定的13个CD2 McAb中，除T089 (39C1.5)因抗体量不够未作实验外，对其他12种McAb都进行试验，T081 (x/3)，T082 (GLB-T11.2/1)，T083 (GLB-T11.1/1)，T085 (RPA-2.10)，T1088 (0-275)和T092 (M-T201)对TRBC玫瑰花结和E玫瑰花结都呈现明显的阻断作用，T084 (F110.08)，T091 (AICD2.1)以及已知参数CD2 McAb-T086 (D-66 clonel)和T087 (GT-2)都不阻TRBC玫瑰花结的形成，亦不调变TRBC受体，而对E玫瑰花结则有不同程度阻断效应，并且调变E变体，使E玫瑰花结形成细胞百分率下降。T090 (6F10.3)和T198 (JOR-T2)即不阻TRBC玫瑰花结的形成，也不抑制E玫瑰花结的形成。由此可见，TRBC受体分布于全T细胞，它不同于已知的全T细胞表面分化抗原CD2 (gp50), CD3/TCR复合物，CD5, CD6和CD7。CD2分子不与TRBC玫瑰花结的形成，也不是介导E玫瑰花结的唯一分子。至少有二个或三个以上的蛋白质与E玫瑰花结和TRBC玫瑰花结的形成有关，其中有的分子为E受体和TRBC受体所共有。TRBC受体很有可能包括新的T淋巴细胞分化抗原。

Characterization of linear epitope of the beta(2)-microglobulin via combination of MALDI-TOF-MS with immunoaffinity

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry(MALDI-TOF-MS), in combination with immunoaffinity provided a powerful tool for determining epitope (antigenic determinant) in protein. The linear epitope of the beta(2)-microglobulin was characterized in the paper. The method as follows: at first beta(2)-microglobulin was digested by a proteolytic enzyme to produce an appropriate set of peptide fragments, then peptide fragments containing the linear epitope were selected and separated from the pool of peptide fragments by immunoprecipitation with the monoclonal antibody. The agarose beads were collected carefully after the reaction. Unbound peptides would be washed away, while the peptides containing the epitope would remain bound to the immobilized antibody after. the beads were washed several times with appropriate buffer. At last the masses of the bound peptides were identified directly by MALDI-TOF MS. Using Endoproteinase Glu-C Endoproteinase Lys-C and Trypsin in the experiment, the linear epitope of beta(2)-microglobulin was located within peptide fragment 59-69, that is, DWSFYLLYYTE.

Endothelial cells release phenotypically and quantitatively distinct microparticles in activation and apoptosis

Background: Endothelial cells (EC) shed endothelial microparticles (EMP) in activation and apoptosis. Objectives: We compared the antigenic expression of EMP species released during activation as compared to apoptosis, in three cell lines. Methods: EC from renal and brain microvascular (MiVEC) and coronary macrovascular (MaVEC) origin were incubated with TNF-alpha to induce activation, or deprived of growth factors to induce apoptosis. Antigens expressed on EMP and EC were assayed flow cytometrically and included constitutive markers (CD31, CD51/61, CD105), inducible markers (CD54, CD62E and CD106), and annexin V binding. Results: It was found that in apoptosis, constitutive markers in EMP were markedly increased (CD31>CD105), with a concomitant decrease in expression in EC. Annexin V EC surface binding and annexin V+ EMP were more sharply increased in apoptosis than in activation. In contrast, in activation, inducible markers in EMP were markedly increased in both EMP and EC (CD62E>CD54>CD 106). Coronary MaVEC released significantly less EMP than MiVEC. Conclusion: EC release qualitatively and quantitatively distinct EMP during activation compared to apoptosis. Analysis of EMP phenotypic signatures may provide clinically useful information on the status of the endothelium. (C) 2003 Elsevier Science Ltd. All rights reserved.

博兴洼陷西部砂体成因与油气成藏研究

Based on achievements of thirty years of hydrocarbon exploration, this paper uses the modern theories and methods of sedimentology and oil accumulation to study the origin and distribution features of four sandbodies of Gaoqing, Fanjia, Zhenglizhuang and Jinjia from the third member to the lower second member of Shahejie Formation in detail. Various geophysical methods are also used to explain and to predict the spatial distribution of sandbodies, which further shows mechanism and the model of oil accumulation and illuminates the disciplinarians of oil enrichment and its controlling factors in the study area. The most favourable oil pools predicted by this paper have significant economic and social benefits, which has been confirmed by the exploration. The main conclusions and knowledge includes: (1) Resolving the problems, which remain unresolvable for a long time in the western area of Boxing depression, about the original environment and the spatial distribution of sandbodies of Gaoqing, Fanjia, Zhenglizhuang and Jinjia, and illuminating their relationships. It is suggested that two deltas or delta-related sandbody sediments, which include the delta sandbodies of Jinjia and Gaoqing and their frontal turbidite fan sandbody, are developed in the second and third members of Shahejie Formation. The sandbodies of Fanjia, Gaoqing and Zhenglizhuang are components of Gaoqing delta and belong to the sediments of various periods in different part of the delta. Whereas, the sandbody of Jinjia belong to the Jinjia delta or fan-delta created by the uplift of the Western Shandong and in some areas shows the features of juxtaposition, superimposed deposition and fingeration with the sandbodies of Gaoqing and Zhenglizhuang. (2)Proposing that the sandbodies of different origins in the deltas of Gaoqing and Jinjia have obvious different reservoir qualities, among which the delta frontal bedded sandbodies in the second member of Shahejie Formation in Zhenglizhuang are the best ones and the turbidite sandbody of Fanjia is relatively worse. This shows the direction of further reservoir prediction. (3) According to modern petroleum system theory and continental pool-formation theory, the author divided the western area of Boxing depression into the Jinjia—Zhenglizhuang—Fanjia nose structure belt pool-formation system and the Gaoqing fracture belt pool-formation system. The study area is predominantly located in the former belt and subdivided into pool-formation sub-systems of Zhenglizhuang-Fanjia and Jinjia, which have the source rock of mudstone and oil shale from the upper forth member and the third member of Shahejie Formation in Boxing depression. The hydrocarbon migration and accumulation are controlled by Jinjia-Zhenglizhuang-fanjia nose structure and Gaoqing fracture. (4)Proposing that compared with the best developed sandbodies and traps in the west area of Boxing, the source from the Boxing depression is not sufficient, which is the fundamental reason that the hydrocarbon resources in mid-west area is less than in the east of Boxing. (5) Under the direction of the new theory (fluid compartments theory) and new method of modern pool-formation mechanism, two kinds of pool-formation model are established in study, i.e. inner-compartment model and outer-compartment model. The former has abnormal pressure and is the antigenic source seal pool-forming mechanism, whereas the latter has normal pressure and is of the allochthonous source opening pool-formation mechanism. (6)The study shows that the four sandbodies of Gaoqing, Fanjia, Jinjia and Zhenglizhuang sand are all very benefit for pool-formation, among which the Fanjia sandbody is the best favourable one and is likely to form lithological reservoir and fault-lithological reservoir. But the main step of exploration in Gaoqing, Zhenglizhuang sandbodies should be finding out the fault block, reversed roof and stratum-lithological oil reservoir. (7)Established a set of guidelines and techniques for the research and exploration in the large scale of sandbodies. Proposing that the various traps related to reversed fault and basin-ward fault should be found in step slopes and gentle slopes respectively, and the lithological oil reservoir should mainly be found in the sandstone updip pinch out. It is also suggested that Fanjia sandbody is most favourable to form the lithological and fault-lithological and the Gaoqing, Zhenglizhuang and Jinjia sandbodies have the potential of forming fault block, reversed roof and stratum-lithological oil reservoir. (8) Interpretation and prediction the spatial distribution of main sandbodies based on various geophysical methods suggestion that Fanxi, Gao28 south and Gao27 east have better exploration potential.

Um modelo computacional para estudar a influência dos anticorpos na manutenção da memória imunológica.

Este artigo apresenta um modelo computacional para estudar a evolução temporal do repertório clonal, incluindo populações de anticorpos. O modelo proposto também foi utilizado para estudar o comportamento da memória imunológica quando populações antigênicas são inoculadas aleatoriamente para simular um processo de mutação viral. Os resultados das simulações realizadas sugerem que um decréscimo na produção de anticorpos favorece a manutenção global da memória imunológica. O modelo aqui exposto permite representar a geração, manutenção e regulação da memória imunológica de uma forma mais completa, através de uma rede de memória, que combina as características da teoria de seleção clonal de F. M. Burnet e a hipótese de rede de N. K. Jerne, considerando somente interações idiotípicas?anti-idiotípicas.

Data mining the yeast genome in a lazy functional language

Clare, A. and King R.D. (2003) Data mining the yeast genome in a lazy functional language. In Practical Aspects of Declarative Languages (PADL'03) (won Best/Most Practical Paper award).

Adding Polymorphic Abstraction to ML (Detailed Abstract)

The ML programming language restricts type polymorphism to occur only in the "let-in" construct and requires every occurrence of a formal parameter of a function (a lambda abstraction) to have the same type. Milner in 1978 refers to this restriction (which was adopted to help ML achieve automatic type inference) as a serious limitation. We show that this restriction can be relaxed enough to allow universal polymorphic abstraction without losing automatic type inference. This extension is equivalent to the rank-2 fragment of system F. We precisely characterize the additional program phrases (lambda terms) that can be typed with this extension and we describe typing anomalies both before and after the extension. We discuss how macros may be used to gain some of the power of rank-3 types without losing automatic type inference. We also discuss user-interface problems in how to inform the programmer of the possible types a program phrase may have.

An Algorithm for Inferring Quasi-Static Types

This report presents an algorithm, and its implementation, for doing type inference in the context of Quasi-Static Typing (QST) ["Quasy-static Typing." Satish Thatte Proc. ACM Symp. on Principles of Programming Languages, 1988]. The package infers types a la "QST" for the simply typed λ-calculus.

Principality and Decidable Type Inference for Finite-Rank Intersection Types

Principality of typings is the property that for each typable term, there is a typing from which all other typings are obtained via some set of operations. Type inference is the problem of finding a typing for a given term, if possible. We define an intersection type system which has principal typings and types exactly the strongly normalizable λ-terms. More interestingly, every finite-rank restriction of this system (using Leivant's first notion of rank) has principal typings and also has decidable type inference. This is in contrast to System F where the finite rank restriction for every finite rank at 3 and above has neither principal typings nor decidable type inference. This is also in contrast to earlier presentations of intersection types where the status of these properties is not known for the finite-rank restrictions at 3 and above.Furthermore, the notion of principal typings for our system involves only one operation, substitution, rather than several operations (not all substitution-based) as in earlier presentations of principality for intersection types (of unrestricted rank). A unification-based type inference algorithm is presented using a new form of unification, β-unification.

Type Inference for Variant Object Types

Existing type systems for object calculi are based on invariant subtyping. Subtyping invariance is required for soundness of static typing in the presence of method overrides, but it is often in the way of the expressive power of the type system. Flexibility of static typing can be recovered in different ways: in first-order systems, by the adoption of object types with variance annotations, in second-order systems by resorting to Self types. Type inference is known to be P-complete for first-order systems of finite and recursive object types, and NP-complete for a restricted version of Self types. The complexity of type inference for systems with variance annotations is yet unknown. This paper presents a new object type system based on the notion of Split types, a form of object types where every method is assigned two types, namely, an update type and a select type. The subtyping relation that arises for Split types is variant and, as a result, subtyping can be performed both in width and in depth. The new type system generalizes all the existing first-order type systems for objects, including systems based on variance annotations. Interestingly, the additional expressive power does not affect the complexity of the type inference problem, as we show by presenting an O(n^3) inference algorithm.

Typed Abstraction of Complex Network Compositions

The heterogeneity and open nature of network systems make analysis of compositions of components quite challenging, making the design and implementation of robust network services largely inaccessible to the average programmer. We propose the development of a novel type system and practical type spaces which reflect simplified representations of the results and conclusions which can be derived from complex compositional theories in more accessible ways, essentially allowing the system architect or programmer to be exposed only to the inputs and output of compositional analysis without having to be familiar with the ins and outs of its internals. Toward this end we present the TRAFFIC (Typed Representation and Analysis of Flows For Interoperability Checks) framework, a simple flow-composition and typing language with corresponding type system. We then discuss and demonstrate the expressive power of a type space for TRAFFIC derived from the network calculus, allowing us to reason about and infer such properties as data arrival, transit, and loss rates in large composite network applications.

Inferring Intersection Typings that are Equivalent to Call-by-Name and Call-by-Value Evaluations

We present a procedure to infer a typing for an arbitrary λ-term M in an intersection-type system that translates into exactly the call-by-name (resp., call-by-value) evaluation of M. Our framework is the recently developed System E which augments intersection types with expansion variables. The inferred typing for M is obtained by setting up a unification problem involving both type variables and expansion variables, which we solve with a confluent rewrite system. The inference procedure is compositional in the sense that typings for different program components can be inferred in any order, and without knowledge of the definition of other program components. Using expansion variables lets us achieve a compositional inference procedure easily. Termination of the procedure is generally undecidable. The procedure terminates and returns a typing if the input M is normalizing according to call-by-name (resp., call-by-value). The inferred typing is exact in the sense that the exact call-by-name (resp., call-by-value) behaviour of M can be obtained by a (polynomial) transformation of the typing. The inferred typing is also principal in the sense that any other typing that translates the call-by-name (resp., call-by-value) evaluation of M can be obtained from the inferred typing for M using a substitution-based transformation.

Safe Compositional Specification of Network Systems With Polymorphic, Constrained Types

In the framework of iBench research project, our previous work created a domain specific language TRAFFIC [6] that facilitates specification, programming, and maintenance of distributed applications over a network. It allows safety property to be formalized in terms of types and subtyping relations. Extending upon our previous work, we add Hindley-Milner style polymorphism [8] with constraints [9] to the type system of TRAFFIC. This allows a programmer to use for-all quantifier to describe types of network components, escalating power and expressiveness of types to a new level that was not possible before with propositional subtyping relations. Furthermore, we design our type system with a pluggable constraint system, so it can adapt to different application needs while maintaining soundness. In this paper, we show the soundness of the type system, which is not syntax-directed but is easier to do typing derivation. We show that there is an equivalent syntax-directed type system, which is what a type checker program would implement to verify the safety of a network flow. This is followed by discussion on several constraint systems: polymorphism with subtyping constraints, Linear Programming, and Constraint Handling Rules (CHR) [3]. Finally, we provide some examples to illustrate workings of these constraint systems.

Learning and Production of Movement Sequences: Behavioral, Neurophysiological, and Modeling Perspectives

A growing wave of behavioral studies, using a wide variety of paradigms that were introduced or greatly refined in recent years, has generated a new wealth of parametric observations about serial order behavior. What was a mere trickle of neurophysiological studies has grown to a more steady stream of probes of neural sites and mechanisms underlying sequential behavior. Moreover, simulation models of serial behavior generation have begun to open a channel to link cellular dynamics with cognitive and behavioral dynamics. Here we summarize the major results from prominent sequence learning and performance tasks, namely immediate serial recall, typing, 2XN, discrete sequence production, and serial reaction time. These populate a continuum from higher to lower degrees of internal control of sequential organization. The main movement classes covered are speech and keypressing, both involving small amplitude movements that are very amenable to parametric study. A brief synopsis of classes of serial order models, vis-à-vis the detailing of major effects found in the behavioral data, leads to a focus on competitive queuing (CQ) models. Recently, the many behavioral predictive successes of CQ models have been joined by successful prediction of distinctively patterend electrophysiological recordings in prefrontal cortex, wherein parallel activation dynamics of multiple neural ensembles strikingly matches the parallel dynamics predicted by CQ theory. An extended CQ simulation model-the N-STREAMS neural network model-is then examined to highlight issues in ongoing attemptes to accomodate a broader range of behavioral and neurophysiological data within a CQ-consistent theory. Important contemporary issues such as the nature of working memory representations for sequential behavior, and the development and role of chunks in hierarchial control are prominent throughout.

Functional genomics of commensal Lactobacilli

Catabolic flexibility affords a bacterium the ability to utilise different sugar sources as carbon for energy. This is important for commensal lactobacilli like Lactobacillus ruminis which can be exposed to a variety of carbohydrates in vivo. However, little is known about the fermentation capabilities, metabolic pathways, genetic diversity or potential survival mechanisms used by L. ruminis in vivo. A combination of in vitro and in silico techniques was used to identify the catabolic pathways of L. ruminis. I also compared 16 L. ruminis strains using a panel of biochemical and survival assays, genetically, whole genome sequencing and RNA sequencing. Multi locus sequence typing revealed that strains clustered according to their host sources. Transcriptome analysis by RNAseq of two motile strains under three growth conditions, including swarming, identified the up-regulation of carbohydrate-related genes under swarming conditions. This suggests that carbohydrate flexibility may have an uncharacterised role in L. ruminis swarming. Following on from the assessment of L. ruminis catabolic flexibility, the porcine diet was supplemented with galactooligosaccharides or L. ruminis ATCC 25644 plus galactooligosaccharides. Supplementation of the porcine diet with galactooligosaccharide had no effect on microbiota diversity. In contrast, the L. ruminis plus galactooligosaccharide treatment significantly reduced the microbiota diversity. Diet is a major factor that affects the diversity of the gut microbiota. In order to get a more thorough understanding of diet and gut health in animals such as racehorses and domesticated herbivores, I determined the core microbiota of animals consuming different feeds. Interestingly, the gut microbiota diversity correlated with the host phylogeny of the animal. The genome of Lactobacillus equi (2.19 Mb), isolated from a healthy Irish thoroughbred was also sequenced and annotated, and comprised 2,263 predicted genes. The large repertoire of predicted carbohydrate-related genes may offer L. equi an advantage in the complex and harsh hindgut environment. In summary, this thesis uses functional genomics to assess the effect that carbohydrates have on commensal lactobacilli and the microbiota as a whole.