What determines the folding of the chromatin fiber?

In this review, we attempt to summarize, in a critical manner, what is currently known about the processes of condensation and decondensation of chromatin fibers. We begin with a critical analysis of the possible mechanisms for condensation, considering both old and new evidence as to whether the linker DNA between nucleosomes bends or remains straight in the condensed structure. Concluding that the preponderance of evidence is for straight linkers, we ask what other fundamental process might allow condensation, and argue that there is evidence for linker histone-induced contraction of the internucleosome angle, as salt concentration is raised toward physiological levels. We also ask how certain specific regions of chromatin can become decondensed, even at physiological salt concentration, to allow transcription. We consider linker histone depletion and acetylation of the core histone tails, as possible mechanisms. On the basis of recent evidence, we suggest a unified model linking targeted acetylation of specific genomic regions to linker histone depletion, with unfolding of the condensed fiber as a consequence.

Characterization of the osmotic response element of the human aldose reductase gene promoter.

Aldose reductase (EC 1.1.1.21) catalyzes the NADPH-mediated conversion of glucose to sorbitol. The hyperglycemia of diabetes increases sorbitol production primarily through substrate availability and is thought to contribute to the pathogenesis of many diabetic complications. Increased sorbitol production can also occur at normoglycemic levels via rapid increases in aldose reductase transcription and expression, which have been shown to occur upon exposure of many cell types to hyperosmotic conditions. The induction of aldose reductase transcription and the accumulation of sorbitol, an organic osmolyte, have been shown to be part of the physiological osmoregulatory mechanism whereby renal tubular cells adjust to the intraluminal hyperosmolality during urinary concentration. Previously, to explore the mechanism regulating aldose reductase levels, we partially characterized the human aldose reductase gene promoter present in a 4.2-kb fragment upstream of the transcription initiation start site. A fragment (-192 to +31 bp) was shown to contain several elements that control the basal expression of the enzyme. In this study, we examined the entire 4.2-kb human AR gene promoter fragment by deletion mutagenesis and transfection studies for the presence of osmotic response enhancer elements. An 11-bp nucleotide sequence (TGGAAAATTAC) was located 3.7 kb upstream of the transcription initiation site that mediates hypertonicity-responsive enhancer activity. This osmotic response element (ORE) increased the expression of the chloramphenicol acetyltransferase reporter gene product 2-fold in transfected HepG2 cells exposed to hypertonic NaCl media as compared with isoosmotic media. A more distal homologous sequence is also described; however, this sequence has no osmotic enhancer activity in transfected cells. Specific ORE mutant constructs, gel shift, and DNA fragment competition studies confirm the nature of the element and identify specific nucleotides essential for enhancer activity. A plasmid construct containing three repeat OREs and a heterologous promoter increased expression 8-fold in isoosmotic media and an additional 4-fold when the transfected cells are subjected to hyperosmotic stress (total approximately 30-fold). These findings will permit future studies to identify the transcription factors involved in the normal regulatory response mechanism to hypertonicity and to identify whether and how this response is altered in a variety of pathologic states, including diabetes.

A long-range regulatory element of Hoxc8 identified by using the pClasper vector.

Hox genes are located in highly conserved clusters. The significance of this organization is unclear, but one possibility is that regulatory regions for individual genes are dispersed throughout the cluster and shared with other Hox genes. This hypothesis is supported by studies on several Hox genes in which even large genomic regions immediately surrounding the gene fail to direct the complete expression pattern in transgenic mice. In particular, previous studies have identified proximal regulatory regions that are primarily responsible for early phases of mouse Hoxc8 expression. To locate additional regulatory regions governing expression during the later periods of development, a yeast homologous recombination-based strategy utilizing the pClasper vector was employed. Using homologous recombination into pClasper, we cloned a 27-kb region around the Hoxc8 gene from a yeast artificial chromosome. A reporter gene was introduced into the coding region of the isolated gene by homologous recombination in yeast. This large fragment recapitulates critical aspects of Hoxc8 expression in transgenic mice. We show that the regulatory elements that maintain the anterior boundaries of expression in the neural tube and paraxial mesoderm are located between 11 and 19 kb downstream of the gene.

The pattern articulation unit of Illiac III; homogenous Boolean functions in the iterative array,

"Supported in part by Contract AT(11-1) 1018 with the U.S. Atomic Energy Commission and the Advanced Research Projects Agency."

The Illinois pattern recognition computer (Illiac III) /

"Presented at the 18th Annual ACM National Conference, Denver, Colorado August 27, 1963"

The pattern articulation unit of ILLIAC III : implementation of the homogeneous instruction "BOOLE" /

Supported by: Contract AT (11-1)-1018 with the U.S. Atomic Energy Commission and the Advanced Research Projects Agency.

Pattern recognition as knowledge-guided computer induction /

Bibliography: p. 39-41.

What is the Impact of the Underserved Pathway program on Entering an Underserved Family Medicine Residency? A Comparison of Three Approaches for Estimating the Average Treatment Effect

Thesis (Master's)--University of Washington, 2016-06

What You Get Out of Memory Depends on the Question You Ask

Following study, participants received 2 tests. The 1st was a recognition test; the 2nd was designed to tap recollection. The objective was to examine performance on Test I conditional on Test 2 performance. In Experiment 1, contrary to process dissociation assumptions, exclusion errors better predicted subsequent recollection than did inclusion errors. In Experiments 2 and 3, with alternate questions posed on Test 2, words having high estimates of recollection with one question had high estimates of familiarity with the other question. Results supported the following: (a) the 2-test procedure has considerable potential for elucidating the relationship between recollection and familiarity; (b) there is substantial evidence for dependency between such processes when estimates are obtained using the process dissociation and remember-know procedures; and (c) order of information access appears to depend on the question posed to the memory system.

Pattern-based reuse of successful designs: usability ofsafety-critical systems

Users of safety-critical systems are expected to effectively control or monitor complex systems, with errors potentially leading to catastrophe. For such systems, safety is of paramount importance and must be designed into the human-machine interface. While many case studies show how inadequate design practice led to poor safety and usability, concrete guidance on good design practices is scarce. The paper argues that the pattern language paradigm, widely used in the software design community, is a suitable means of documenting appropriate design strategies. We discuss how typical usability-related properties (e.g., flexibility) need some adjustment to be used for assessing safety-critical systems, and document a pattern language, based on corresponding "safety-usability" principles

An investigation into children’s inductive reasoning strategies:What drives the development of category induction?

In a series of studies, I investigated the developmental changes in children’s inductive reasoning strategy, methodological manipulations affecting the trajectory, and driving mechanisms behind the development of category induction. I systematically controlled the nature of the stimuli used, and employed a triad paradigm in which perceptual cues were directly pitted against category membership, to explore under which circumstances children used perceptual or category induction. My induction tasks were designed for children aged 3-9 years old using biologically plausible novel items. In Study 1, I tested 264 children. Using a wide age range allowed me to systematically investigate the developmental trajectory of induction. I also created two degrees of perceptual distractor – high and low – and explored whether the degree of perceptual similarity between target and test items altered children’s strategy preference. A further 52 children were tested in Study 2, to examine whether children showing a perceptual-bias were in fact basing their choice on maturation categories. A gradual transition was observed from perceptual to category induction. However, this transition could not be due to the inability to inhibit high perceptual distractors as children of all ages were equally distracted. Children were also not basing their strategy choices on maturation categories. In Study 3, I investigated category structure (featural vs. relational category rules) and domain (natural vs. artefact) on inductive preference. I tested 403 children. Each child was assigned to either the featural or relational condition, and completed both a natural kind and an artefact task. A further 98 children were tested in Study 4, on the effect of using stimuli labels during the tasks. I observed the same gradual transition from perceptual to category induction preference in Studies 3 and 4. This pattern was stable across domains, but children developed a category-bias one year later for relational categories, arguably due to the greater demands on executive function (EF) posed by these stimuli. Children who received labels during the task made significantly more category choices than those who did not receive labels, possibly due to priming effects. Having investigated influences affecting the developmental trajectory, I continued by exploring the driving mechanism behind the development of category induction. In Study 5, I tested 60 children on a battery of EF tasks as well as my induction task. None of the EF tasks were able to predict inductive variance, therefore EF development is unlikely to be the driving factor behind the transition. Finally in Study 6, I divided 252 children into either a comparison group or an intervention group. The intervention group took part in an interactive educational session at Twycross Zoo about animal adaptations. Both groups took part in four induction tasks, two before and two a week after the zoo visits. There was a significant increase in the number of category choices made in the intervention condition after the zoo visit, a result not observed in the comparison condition. This highlights the role of knowledge in supporting the transition from perceptual to category induction. I suggest that EF development may support induction development, but the driving mechanism behind the transition is an accumulation of knowledge, and an appreciation for the importance of category membership.

What does the study of the spatial patterns of pathological lesions tell us about the pathogenesis of neurodegenerative disorders?

Discrete pathological lesions, which include extracellular protein deposits, intracellular inclusions and changes in cell morphology, occur in the brain in the majority of neurodegenerative disorders. These lesions are not randomly distributed in the brain but exhibit a spatial pattern, that is, a departure from randomness towards regularity or clustering. The spatial pattern of a lesion may reflect pathological processes affecting particular neuroanatomical structures and, therefore, studies of spatial pattern may help to elucidate the pathogenesis of a lesion and of the disorders themselves. The present article reviews first, the statistical methods used to detect spatial patterns and second, the types of spatial patterns exhibited by pathological lesions in a variety of disorders which include Alzheimer's disease, Down syndrome, dementia with Lewy bodies, Creutzfeldt-Jakob disease, Pick's disease and corticobasal degeneration. These studies suggest that despite the morphological and molecular diversity of brain lesions, they often exhibit a common type of spatial pattern (i.e. aggregation into clusters that are regularly distributed in the tissue). The pathogenic implications of spatial pattern analysis are discussed with reference to the individual disorders and to studies of neurodegeneration as a whole.

Disconnected brains:what is the role of fMRI in connectivity research?

In this paper we consider how functional Magnetic Resonance Imaging (fMRI) has been used to study cortical connectivity in autism and autistic spectrum disorders (ASD). We discuss those studies that have contributed to the evidence supporting a model of disordered cortical connectivity in autism and (ASD), with a focusing emphasis on the application to research into the underconnectivity model. We note that the analytical techniques employed are limited and do not allow interpretation in terms of effective, or directional connectivity, nor do they provide information about the temporal or spectral characteristics of the functional networks being studied. We highlight how currently the features of neural generators that are being assessed by functional connectivity in fMRI are unclear. In addition, we note the importance in clinical studies of considering the consequences of task choice for the nature of the imaging data that can be collected and also of individual differences in participant state and trait characteristics for the accurate interpretation of imaging data. We discuss how alternative techniques such as EEG/MEG may address the limitations of fMRI in assessing brain connectivity, and additionally consider the potential of multimodal approaches. We conclude that fMRI has made significant contributions towards our understanding of the brain in terms of neural systems but that the conclusions drawn from its application in the sphere of autism research need to be approached with caution. It is important in research of this kind that we are aware of the need to examine the methodological and analytical techniques closely when applying findings in clinical populations, not only when they are used to support the development of theoretical models but also to inform diagnostic or treatment decisions.

Logistics Innovation in Small 3PLs:what is the Role of ICT?

For companies competing in highly dynamic markets, the search for new sources of competitive advantages is mandatory. Innovation is considered a fundamental component of a successful business as it allows companies to sustain profit margins and sales growth and to reduce pressures coming from competitors. In the knowledge-driven economy, information and communication technology (ICT) plays an important role as it enables innovation in product/service, processes and organisations especially in service companies. This paper investigates the role of ICT in logistics innovation. The focus of the paper is on the effects that ICT usage is having on the management of small third-party logistics service providers (3PLs). On the basis of quantitative and qualitative evidence emerging from a recent survey carried out on the Italian logistic service market, the paper analyses how ICT is used to support logistics innovation and the factors inhibiting/facilitate the usage of ICT in such companies. Implications for logistics innovation management will be outlined from both research and managerial perspectives.

Logic Based Pattern Recognition - Ontology Content (2)

Logic based Pattern Recognition extends the well known similarity models, where the distance measure is the base instrument for recognition. Initial part (1) of current publication in iTECH-06 reduces the logic based recognition models to the reduced disjunctive normal forms of partially defined Boolean functions. This step appears as a way to alternative pattern recognition instruments through combining metric and logic hypotheses and features, leading to studies of logic forms, hypotheses, hierarchies of hypotheses and effective algorithmic solutions. Current part (2) provides probabilistic conclusions on effective recognition by logic means in a model environment of binary attributes.