Uncovering the rules for protein-protein interactions from yeast genomic data

Identifying protein-protein interactions is crucial for understanding cellular functions. Genomic data provides opportunities and challenges in identifying these interactions. We uncover the rules for predicting protein-protein interactions using a frequent pattern tree (FPT) approach modified to generate a minimum set of rules (mFPT), with rule attributes constructed from the interaction features of the yeast genomic data. The mFPT prediction accuracy is benchmarked against other commonly used methods such as Bayesian networks and logistic regressions under various statistical measures. Our study indicates that mFPT outranks other methods in predicting the protein-protein interactions for the database used. We predict a new protein-protein interaction complex whose biological function is related to premRNA splicing and new protein-protein interactions within existing complexes based on the rules generated.

Generation of internal and surface waves by seafloor movement in a two layer fluid system

Internal and surface waves generated by the deformations of the solid bed in a two layer fluid system of infinite lateral extent and uniform depth are investigated. An integral solution is developed for an arbitrary bed displacement on the basis of a linear approximation of the complete description of wave motion using a transform method (Laplace in time and Fourier in space) analogous to that used to study the generation of tsunamis by many researchers. The theoretical solutions are presented for three interesting specific deformations of the seafloor; the spatial variation of each seafloor displacement consists of a block section of the seafloor moving vertically either up or down while the time-displacement history of the block section is varied. The generation process and the profiles of the internal and surface waves for the case of the exponential bed movement are numerically illustrated, and the effects of the deformation parameters, densities and depths of the two layers on the solutions are discussed. As expected, the solutions derived from the present work include as special cases that obtained by Kervella et al. [Theor Comput Fluid Dyn 21:245-269, 2007] for tsunamis cased by an instantaneous seabed deformation and those presented by Hammack [J Fluid Mech 60:769-799, 1973] for the exponential and the half-sine bed displacements when the density of the upper fluid is taken as zero.

THE VARIATION AND MOVEMENT OF A KIND OF EDDIES IN SHELF SLOPE WATER

Considering the characteristics of the time and space scales of the eddies we established a quasi-static and quasi-geostrophic model to describe their variation and movement in shelf slope water. The analytical solution revealed the main properties of the variation: slow expansion and fast stagnation processes and the law of the eddy motion affected under the background field. All theoretical results are proved by satellite image measurements.

基于乐理的蛇形机器人控制方法研究

根据生物蛇和蛇形机器人的结构及运动特点 ,提出了基于乐理的蛇形机器人控制方法 ,定义了乐理的符号、规则与蛇形机器人控制过程的对应关系 ,编写了蜿蜒运动步态谱 .“勘查者—I”蛇形机器人上实现了蜿蜒运动的控制 .给出了今后的研究方向 .

吐合盆地鲁克沁构造带断块油藏形成机制及油藏预测

Lukeqin arc belt is a compound structure generated by multi-movements and composed of 6 sub-structural zones, which are connected by Huoyanshan Mountain. General characteristics of the arc belt are multi-patterns of structure, multi-phases for petroleum, multi-types of trap and multi-layers for reservoirs. As a part of the eastern Lukeqin arc belt located on the south of Taibei depression, Lukeqin structural zone behaves as a complex faulted-fold zone, in which the formation and distribution of hydrocarbons are controlled by structures. As the dominant source of dynamics for the second migration of hydrocarbon, structure stress field is closely related with the potentials of hydrodynamics. Results derived from the simulations of stress field by finite element method indicate that the northwest tending faults prefer seal to the northeast tending ones. The reason is that the northwest tending faults were squeezed more strongly than the northeast tending ones. Therefor, the northeast tending faults become always the paths for oil to migrate southeastward. Lukeqin structural zone is the main site for oil to concentration because it is surrounded by high stress. Situated on the front of the foreland basin of Turpan-Hami, Lukeqing arc belt is a dam to hold back the southward migrating oil from Shengbei depression. The axis line of Shenquan-Shengnan-Yanmuxi, Lukeqin and Yubei controls the migrating paths and concentrating process of oil and gas. Results derived from stress simulation and structure analyses indicate consistently that both Yubei and Lukeqin structural zones are the favorite areas for oil to migrate. The generally southward paths for oil to migrate out of Taibei depression can be two ways. One of them is from Taibei depression to Yubei structural zone and the other is from Taibei depression to Lukeqin structural zone. By the both ways, oil migrated upward along the faults and southeastward along the structural axis to concentrate in either Permian or Triassic system. The newly ascertained path for oil migration, which is accurately southeastward instead of coarsely southward, indicates the directions for further explorations on the compound Lukeqin block zone. Five kinds of seal models of fault are all found in Lukeqin block zone by studying the seal features of faults occurred in the zone. Having studied the fault seal and their controlling factors by fuzzy set method, the paper deems that the northwest tended faults are better than the northeast tended ones for oil to concentrate. The most important factors to decide the seal extent of faults in this zone are the characteristics of main stress and fluids instead of capillary pressure differences between the two sides of fault and smear mud factors. There exist seal differences not only between the faults of different time but also between the sections within a fault due to the variation of depths, strata and positions. The general distribution rules of reservoirs were dominated by the seal characteristics of a fault during the time reservoirs formed. While the current features of fault seal decide the conservation of reservoirs and heights of oil accumulations. Seal or not of a fault is not absolute because the essential for fault to seal is the distribution of permeability of fault zone. Therefor, the multi cyclical activities of faults create the space-time variation of seal features of the fault. Totally, the seal extent of the faults within the area is not as perfect as to accumulate ordinary crude. Crude oil can only be sealed when it becomes viscous. Process for crude oil to become viscous and viscous happened strongly because of the fault-fold movements. Shallowly burying and even revealing of the objective layers of the reservoirs made the crude oil to be thickened by water washing biologically degradation and oxidation degradation. The northwestward deepening during or after the reservoir formation of the structural zone provided the power for oil to migrate one or more times. The main reason for oil accumulation is the formation of Lukeqin block zone during Xishanyao stage, middle Jurassic Period, Early Yanshanian Movement. While the main reason for reservoir conservation is the placidity of Triassic blocks after the formation of reservoirs. Contrasting to former opinions, it is concluded that the reservoirs in Lukeqin zone, including viscous reservoirs, were formed by one time but not more times. So the author proposes the opinion that the reservoirs of viscous oil were formed by viscous oil migration under the conditions of aptitude sets of fault seals controlled by fluid and other factors. To grope the distribution rules outside Taibei depression and discuss the formation mechanism of Anjurassic reservoirs, it is necessary to study the dominate factors for the formation of reservoirs in Lukeqin structural zone such as structural stress, fault seals and thickening mechanism of crude oil. Also, the necessary studies are the key to break through the Taibei depression and Anjurassic systems. Therefor, they are significant for the future exploration and reserve increasing of hydrocarbon within the Turpan-Hami basin. The paper studied the distribution rules of block reservoirs and forecasted the favorable zones for further exploration in Turpan-Hami basin. Conclusions can be useful for not only the exploration in the area but also the theory consult in the adjacent areas.

东营凹陷辛镇复杂断块油藏形成机制和剩余油分布规律研究

In this paper, the complex faulted-block oil reservoir of Xinzhen area in Dongying depression is systematically studied from basic conditions forming faulted-block oil and gas reservoir integrating geology, seismic, logging and reservoir engineering information and computer; guided by petroleum geology, geomechanics, structural geology and geophysics and other theories. Based on analysis of background condition such as regional strata, structure and petroleum geology, structural research on geometry, kinemaitcs and dynamics, oil-controlling fault research on the seal features, sealing mechanism and sealing pattern, and research on enrichment rules and controlling factors of complex faulted-block oil reservoir are carried out to give out the formation mechanics of oil reservoir of Xinzhen complex faulted-block oil reservoir. As a result, the reservoir formation pattern is established. At the same time, through dissecting the characteristics and hydrocarbon enrichment law of complex faulted-block oil reservoir, and studying its distribution law of remaining oil after entering extra high water-cut period, a set of technologies are formed to predict complex faulted-block oil reservoir and its remaining oil distribution and to enhance oil recovery (EOR). Based on the time relationship between migration of hydrocarbon and trap formation, accumulating period of Xinzhen oil reservoir is determined. The formation of Xinzhen anticlinal trap was prior to the primary migration. This is favorable to formation of Xinzhen anticlinal hydrocarbon reservoir. Meanwhile, because anticline top caving isn't at the sane time as that of moving or faulted-trap forming inner anticline, oil and gas migrated many times and Xinzhen complex faulted-block oil reservoir formed from ES_3~(upper) to EG. Accumulating law and controlling factors of complex faulted-block reservoir are analyzed from many aspects such as regional structure background controlling hydrocarbon accumulating, plastic arch-open structure controlling oil-bearing series and reservoir types, sealing-opening of fault controlling hydrocarbon distribution and structure pattern controlling enriched trap types. Also, we established the structure pattern in Xinzhen a'ea: the arch-open of underlying strata cause expanding fracture. The main block groups developed here are shovel-like normal fault block group in the north area of Xinzhen and its associated graben block group. Block groups dominate the formation and distribution of reservoirs. We studied qualitatively and quantitatively the sealing characteristics, sealing history and sealing mechanism of faults, too. And, the sealing characteristics are evaluated and the distribution pattern of hydrocarbon controlled by faults is researched. Due to movement intensity of big faults, deep falling of downthrown block, high degree of repture and development of fracture, shallow layers close to the downthrown block of secondary faults are unfavorable to hydrocarbon accumulation. This is confirmed by the exploration practice in Xinzhen anticline. In terms of the downthrown blocks of sencondary contemporaneous faults lied in the south and north area of Xinzhen, hydrocarbon is poor close to fracture belt, while it is relatively abundant in tertiary companion faults. Because of long-term movement of faults that control hydrocarbon, fi'om ES3 to EG, six set of oil-bearing series formed. And their opening causes the inhomogeneity in hydrocarbon abundance among each block--in two flanks of anticline reservoirs are abundant while in the axial area, oil and gas are sporadic. There the sealing characteristics control oil-bearing area of oil/gas accumulation and the height of oil reservoir. Longitudinally, oil and gas are enriched in dip-flat areas in mid-plane of faults. It is established that there are four types of accumulating patterns in complex faulted-block oil reservoirs in Xinzhen. The first is accumulating pattern of lithologic oil reservoirs in E~S_3~(mid-lowwer), that is, self-generating-self-reserving-self-covering lithologic trap pattern. The second is drag-anticline accumulating pattern in Xinzhen. The structure traps are drag anticlines formed by the contemporaneous faults of the second basement in the north of Xinzhen, and the multiple source rocks involve Ek_2, Es_4, Es_3 and Es_1 members. The reservoirs are fluvial-delta sandstones of the upper member of Shahejie formation and Guantao formation, covered by regional thick mudstone of the upper member of Guantao formation and MingHuazhen formation. The third is the accumulating pattern of reverse listric fault, the third-degree fault of Xinzhen anticline limb and the reservoirs form reservoir screened by reverse listric faults. The forth is accumulating pattern of crossing faults which form closing or semi-closing faulted-blocks that accumulate hydrocarbon. The technologies of predicting remaining oil in complex faulted-block reservoir during the mid and late development stage is formed. Remaining oil in simple large faulted-blocks enriches in structural high, structural middle, structural low of thick bottom water reservoirs, points near bent edge-fault oftertiary faults and part the fourth ones with big falling displacement, microstructure high place of oil-sandbodies and areas where local well pattern isn't perfect. While that in small complex faulted-blocks enriches near small nose, small high point, angle of small faults, small oil-bearing faulted-blocks without well and areas with non-perfect well pattern. The technologies of enhancing recovery factor in complex faulted-block reservoir during the mid and late development stage is formed as follows: fine reservoir description, drilling adjust wells, designing directional wells, sub-dividing layer series of development, improving flooding pattern, changing water-injection direction and enhancing swept volume, cyclic waterflooding and gas-injection, etc. Here, directional wells include directional deflecting wells, lateral-drilling wells, lateral-drilling horizontal wells and horizontal wells. The results of this paper have been used in exploration and development of Shengli oilfield, and have achieved great social and economic profit, especially in predicting distribution of complex faulted-block reservoir, remaining oil distribution during middle and late stage of development, and in EOR. Applying the achievement of fault-closure research, new hydrocarbon-bearing blocks are discovered in flanks of Dongying central uplift and in complex blocks with proved reserves 15 million tons. With the study of remaining oil distribution law in complex faulted-block reservoirs, recovery factors are increased greatly in Dongxin, Xianhe and Linpan complex faulted-block reservoirs and accumulated oil production increment is 3 million tons.

Meta-Rules: Reasoning About Control

How can we insure that knowledge embedded in a program is applied effectively? Traditionally the answer to this question has been sought in different problem solving paradigms and in different approaches to encoding and indexing knowledge. Each of these is useful with a certain variety of problem, but they all share a common problem: they become ineffective in the face of a sufficiently large knowledge base. How then can we make it possible for a system to continue to function in the face of a very large number of plausibly useful chunks of knowledge? In response to this question we propose a framework for viewing issues of knowledge indexing and retrieval, a framework that includes what appears to be a useful perspective on the concept of a strategy. We view strategies as a means of controlling invocation in situations where traditional selection mechanisms become ineffective. We examine ways to effect such control, and describe meta-rules, a means of specifying strategies which offers a number of advantages. We consider at some length how and when it is useful to reason about control, and explore the advantages meta-rules offer for doing this.

Breaking the Rules: writing reflectively for yourself.

The rules which epitomise good writing may on occasions be broken, deliberately and with what the writers judge to be good purpose. This can well occur when students or staff set out to engage effectively with their personal and professional development, through personal reflection on and in experiences. They may do this in what has been called “stream of consciousness” writing, which is deliberately compiled in a manner at variance with the general rules for best practice. The rationale for such an unusual decision, namely to engage in what is frankly disorderly writing, is set out briefly in this chapter. Its characteristics are summarised, in implicit contrast with more conventional styles of writing. Examples are included of claims for the effectiveness of this style when used for developmental purposes by students and staff; and reference is made to the publications of some of those who have endorsed this approach.

Agency and animation: the performance of interactive game characters

As an animator and practice-based researcher with a background in games development, I am interested in technological change in the video game medium, with a focus on the tools and technologies that drive game character animation and interactive story. In particular, I am concerned with the issue of ‘user agency’, or the ability of the end user to affect story development—a key quality of the gaming experience and essential to the aesthetics of gaming, which is defined in large measure by its interactive elements. In this paper I consider the unique qualities of the video game1 as an artistic medium and the impact that these qualities have on the production of animated virtual character performances. I discuss the somewhat oppositional nature of animated character performances found in games from recent years, which range from inactive to active—in other words, low to high agency. Where procedural techniques (based on coded rules of movement) are used to model dynamic character performances, the user has the ability to interactively affect characters in real-time within the larger sphere of the game. This game play creates a high degree of user agency. However, it lacks the aesthetic nuances of the more crafted sections of games: the short cut-scenes, or narrative interludes where entire acted performances are mapped onto game characters (often via performance capture)2 and constructed into relatively cinematic representations. While visually spectacular, cut-scenes involve minimal interactivity, so user agency is low. Contemporary games typically float between these two distinct methods of animation, from a focus on user agency and dynamically responsive animation to a focus on animated character performance in sections where the user is a passive participant. We tend to think of the majority of action in games as taking place via playable figures: an avatar or central character that represents a player. However, there is another realm of characters that also partake in actions ranging from significant to incidental: non-playable characters, or NPCs, which populate action sequences where game play takes place as well as cut scenes that unfold without much or any interaction on the part of the player. NPCs are the equivalent to supporting roles, bit characters, or extras in the world of cinema. Minor NPCs may simply be background characters or enemies to defeat, but many NPCs are crucial to the overall game story. It is my argument that, thus far, no game has successfully utilized the full potential of these characters to contribute toward development of interactive, high performance action. In particular, a type of NPC that I have identified as ‘pivotal’3—those constituting the supporting cast of a video game—are essential to the telling of a game story, particularly in genres that focus on story and characters: adventure games, action games, and role-playing games. A game story can be defined as the entirety of the narrative, told through non-interactive cut-scenes as well a interactive sections of play, and development of more complex stories in games clearly impacts the animation of NPCs. I argue that NPCs in games must be capable of acting with emotion throughout a game—in the cutscenes, which are tightly controlled, but also in sections of game play, where player agency can potentially alter the story in real-time. When the animated performance of NPCs and user agency are not continuous throughout the game, the implication is that game stories may be primarily told through short movies within games, making it more difficult to define video games animation as a distinct artistic medium.

Fuzzy rules from ant-inspired computation

M. Galea and Q. Shen. Fuzzy rules from ant-inspired computation. Proceedings of the 13th International Conference on Fuzzy Systems, pages 1691-1696, 2004.

FRANTIC - A system for inducing accurate and comprehensible fuzzy rules

M. Galea and Q. Shen. FRANTIC - A system for inducing accurate and comprehensible fuzzy rules. Proceedings of the 2004 UK Workshop on Computational Intelligence, pages 136-143.

Linguistic hedges for ant-generated rules

M. Galea and Q. Shen. Linguistic hedges for ant-generated rules. Proceedings of the 15th International Conference on Fuzzy Systems, pages 9105-9112, 2006.