Sequence classification with side effect machines evolved via ring optimization

The explosion of available sequence data necessitates the development of sophisticated machine learning tools with which to analyze them. This study introduces a sequence-learning technology called side effect machines. It also applies a model of evolution which simulates the evolution of a ring species to the training of the side effect machines. A comparison is done between side effect machines evolved in the ring structure and side effect machines evolved using a standard evolutionary algorithm based on tournament selection. At the core of the training of side effect machines is a nearest neighbor classifier. A parameter study was performed to investigate the impact of the division of training data into examples for nearest neighbor assessment and training cases. The parameter study demonstrates that parameter setting is important in the baseline runs but had little impact in the ring-optimization runs. The ring optimization technique was also found to exhibit improved and also more reliable training performance. Side effect machines are tested on two types of synthetic data, one based on GC-content and the other checking for the ability of side effect machines to recognize an embedded motif. Three types of biological data are used, a data set with different types of immune-system genes, a data set with normal and retro-virally derived human genomic sequence, and standard and nonstandard initiation regions from the cytochrome-oxidase subunit one in the mitochondrial genome.     

植物核心种质研究进展

丰富的植物遗传资源为作物育种和遗传研究提供广阔的遗传基础,然而资源庞大的数量也给植物遗传资源的收集、保存、研究和利用带来了困难。Frankel首先提出并与Brown等人完善了核心种质(core collection)的概念,即通过一定的方法从整个种质资源中选择一部分样本,以最小的资源数量和遗传重复,尽可能最大限度的代表整个资源的多样性。核心种质的提出,为遗传资源的研究和利用提供了崭新的解决途径。目前,已在多年生野生大豆、硬粒小麦、花生等20种植物上开展了核心种质研究。本围绕核心种质具有四个显特点即代表性、实用性、有效性、动态性,介绍在不同植物构建核心种质时,所利用的数据、分组原则及取样方法等,并介绍了核心种质的评价进展。通过比较发现,不同植物在构建核心种质各有区别,但是以根据地理来源分组,按聚类法取样为主。目前,对植物核心种质的研究,多处于取样策略的研究阶段。对建成的核心种质评价研究较少,主要集中在农艺性状遗传多样性方面的验证,而时分子水平的验证较少,构建的核心种质还有待于实践的检验。     

“A carnival of promiscuous carnal indulgence”: bureaucrats’ ambivalence in reconciling capitalist production with native American habitus

In 1921 the U.S. Office of Indian Affairs (OIA) attempted to suppress ritual public performances in the Southwestern Pueblos. Several reams of documenting text were used to support this authorizing text. These documenting texts were affidavits purporting to describe “degrading tendencies” and “immoral relations” in the Puebloan habitus. The OIA used these sensationalized representations of the habitus of Native Americans’ communities to promote and justify the policy of forced acculturation in the waning days of its implementation. What is perplexing is that these supporting texts were trotted out so late, decades after the major thrusts of the forced acculturation program had first been put into play. My purpose is to analyze the place of these texts in the forced acculturation program. I suggest, following Anne McClintock (1995) that the obsessive fascination that the public performances seem to have held for those who reported on and condemned them, represent a layered and complex intertwining of ambivalence about domestic social relations and gender with confusion about culture and labor. Examining a slice of the U.S. Government’s policy of forced acculturation in a corner of the Native American world reveals a potentially implosive anxiety of reconciling the imposition of a desired mode of production with the persistence of a habitus perceived as celebrating the violation of appropriate domesticity.

Representing Culture in Malaysian Cultural Theme Parks: Tensions and Contradictions

Cultural representation is nowhere more significant than in multi-cultural countries, where the mode of representation is instrumental in determining the progress of integration. Ultimately, in the Malaysian context this reflects on the success of, and is intrinsically linked to, the affirmative action policies that benefit the majority Malays. This paper highlights the representation of culture through the medium of three cultural theme parks in Peninsular Malaysia, built to promote ‘unity through diversity’ and a re-imaging of the past traditions and mythical landscape of this Southeast Asian economic powerhouse. A central aim is to bring together and make sense of how the notions of nostalgia, nationalism and economic success in cultural tourism all come to bear on representations in cultural theme parks.     

Deep generative modeling for protein design

Deep learning approaches have produced substantial breakthroughs in fields such as image classification and natural language processing and are making rapid inroads in the area of protein design. Many generative models of proteins have been developed that encompass all known protein sequences, model specific protein families, or extrapolate the dynamics of individual proteins. Those generative models can learn protein representations that are often more informative of protein structure and function than hand-engineered features. Furthermore, they can be used to quickly propose millions of novel proteins that resemble the native counterparts in terms of expression level, stability, or other attributes. The protein design process can further be guided by discriminative oracles to select candidates with the highest probability of having the desired properties. In this review, we discuss five classes of generative models that have been most successful at modeling proteins and provide a framework for model guided protein design.     

Sensory representation abnormalities that parallel focal hand dystonia in a primate model

In our hypothesis of focal dystonia, attended repetitive behaviors generate aberrant sensory representations. Those aberrant representations interfere with motor control. Abnormal motor control strengthens sensory abnormalities. The positive feedback loop reinforces the dystonic condition. Previous studies of primates with focal hand dystonia have demonstrated multi-digit or hairy-glabrous responses at single sites in area 3b, receptive fields that average ten times larger than normal, and high receptive field overlap as a function of horizontal distance. In this study, we strengthen and elaborate these findings. One animal was implanted with an array of microelectrodes that spanned the border between the face and digits. After the animal developed hand dystonia, responses in the initial hand representation increasingly responded to low threshold stimulation of the face in a columnar substitution. The hand-face border that is normally sharp became patchy and smeared over 1 mm of cortex within 6 weeks. Two more trained animals developed a focal hand dystonia variable in severity across the hand. Receptive field size, presence of multi-digit or hairy-glabrous receptive fields, and columnar overlap covaried with the animal's ability to use specific digits. A fourth animal performed the same behaviors without developing dystonia. Many of its physiological measures were similar to the dystonic animals, but receptive field overlap functions were minimally abnormal, and no sites shared response properties that are normally segregated such as hairy-glabrous combined fields, or multi-digit fields. Thalamic mapping demonstrated proportionate levels of abnormality in thalamic representations as were found in cortical representations.     

Using topographic networks to build a representation of consciousness

The subject of consciousness has intrigued both psychologists and neuroscientists for many years. Recently, following many recent advances in the emerging field of cognitive neuroscience, there is the possibility that this fundamental process may soon be explained. In particular, there have been dramatic insights gained into the mechanisms of attention, cognition and perception in recent decades. Here, simple network models are proposed which are used to create a representation of consciousness. The models are inspired by the structure of the thalamus and all incorporate topographic layers in their structure. Operation of the models allows filtering of the information reaching the representation according to (1) modality and/or (2) sub-modality, in addition several of the models allowing filtering at the topographic level. The models presented have different structures and employ different integrative mechanisms to produce gating or amplification at different levels; the resultant representations of consciousness are discussed.     

Functional classification of protein structures by local structure matching in graph representation

As a result of high‐throughput protein structure initiatives, over 14,400 protein structures have been solved by Structural Genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP‐Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP‐Func method to our previously reported method, Structurally Aligned Local Sites of Activity (SALSA), using the Ribulose Phosphate Binding Barrel (RPBB), 6‐Hairpin Glycosidase (6‐HG), and Concanavalin A‐like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP‐Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP‐Func methods to predict function. Forty‐one SG proteins in the RPBB superfamily, nine SG proteins in the 6‐HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community.     

Driving integration: how is it done

ABSTRACT

The present dilemma of immigrant integration in the West is, that for previous generations of immigrants in Europe and the United States, education and politics were strong engines that drove integration. However, these engines have not worked so well for this current wave of immigration, despite emerging progress. In this review, I examine the chapters on education and politics. Two questions emerge: first, with regard to education, how much can the ineffectiveness of the education system be attributed to the cultural challenges of immigration, compared to the challenges of class, with implications for immigrants and natives as well? and second, with regard to politics, is the problem not just the numbers of minority representatives, but how they are organized, and for what purpose – indeed, if they have a purpose?     

Signs of Anger: Representation of Agonistic Behaviour in Invertebrate Cognition

In this essay I shall examine the representation of aggression and its issues in the model animal, the Fruit Fly, Drosophila melanogaster. The Fruit Fly is the model animal for genetics and more recently neuroscience. On the basis of its behaviour conclusions are being drawn that will help in the development of new treatments for clinical entities like aggression and anxiety disorders—the author questions those findings and asks whether more should be done to focus on the actual biology and behaviour—the Umwelt, instead of trying to bridge the gulf between invertebrate and human behaviours.