Favorite Model Research Articles

Beyond Formal Structure: A Mechanistic Perspective on Computation and Implementation

In this article, after presenting the basic idea of causal accounts of implementation and the problems they are supposed to solve, I sketch the model of computation preferred by Chalmers and argue that it is too limited to do full justice to computational theories in cognitive science. I also argue that it does not suffice to replace Chalmers’ favorite model with a better abstract model of computation; it is necessary to acknowledge the causal structure of physical computers that is not accommodated by the models used in computability theory. Additionally, an alternative mechanistic proposal is outlined.

Long‐range signaling systems controlling glial migration in the Drosophila eye

The Drosophila compound eye comprises about 750 individual ommatidia arranged into an almost crystalline array. The eye is not needed for viability and thus served as a favorite model organ to decipher many signaling systems controlling diverse aspects such as cell fate allocation or cell-cycle control. Here, we review that the Drosophila eye can also serve to study the interaction between neurons and glial cells. In the Drosophila eye, all glial cells originate from the brain lobes and need to migrate onto the larval eye disc as neurogenesis is initiated during the third instar stage. Although we do have a relatively good understanding of the sequential progression of neurogenesis in the eye disc, we are still at the beginning in our dissection of the molecular pathways orchestrating the coordinated development of neurons and glial cells.

Kinematics of obstacle clearance in the rat

Although the rat has become the favourite animal model in preclinical research on locomotion, studies designed to assess the strategy used by rats to avoid obstacle are lacking. Using an optoelectronic 3D motion analysis system, we therefore, compared the step pattern, timing and length variables of locomotor cycles, trajectories and joint angles of limbs when rats step between and over obstacles (3 cm-high) fixed on a treadmill belt (25 cm/s). Motion in all four limbs of adult animals with an initial age of 11 weeks was serially recorded for a period of 10 weeks. The results showed that obstacle clearance is associated with the reorganization of the basic step pattern resulting in increased stride length of all limbs, increased duration of the swing phase of the hindlimbs only, and the appearance of two quadrupedal stance phases. They also revealed that the elevation of limbs above the obstacle not only involves flexion but also displacement of the corresponding girdles. Remarkably, the trajectory of the trailing forelimb to get over the obstacle is almost a mirror image of the trajectory of the leading forelimb. Lastly, all of the parameters measured remained stable over the observation period during which body weight gain reached 100 g (one third of the initial body weight). In conclusion, our study may provide a basis for future studies aimed at understanding the neural pathways involved in pathologies associated with deficit/recovery of challenged locomotion in rats.

Pavement rehabilitation and maintenance prioritization of urban roads using fuzzy logic

With regard to limits in budget, inevitably, one must choose prioritized projects in pavements rehabilitation and maintenance process. This paper looks into prioritization based upon a model including all effects of important factors like pavement condition index, traffic volume, road width as well as rehabilitation and maintenance cost. Since defining a model that introduces all those factors was difficult, a more advanced modeling named fuzzy logic was referred for the problem of prioritization. Although analytical hierarchy process can be used for decision making process as well, fuzzy modeling lets one have more precise choices for the outcome. Finally with the help of MATLAB software and coded M-files, inference engines such as Product engine, Dienes–Rescher and Lukasiewicz were all tested and the logical favorite separation for this application was found in product inference engine. As a case study some streets located in district No. 6 of Tehran municipality were selected and the favorite mathematical model was executed on those streets. This model was used for prioritizing these 131 sections.

The Study of New Trend for DSC Scene Effects Technology

Since early 2007, many ambitious DSC manufactures in Japan have paid special attention for built in digital effects, in order to create better quality of picture, such as: Face Detection, Smile Shutter Mode, Full frame CCD, Anti Shake system, Live View, CMOS sensor..., which were highly appreciated by many photo fans around the world, and created hot-selling record on favorite model. In fact, these fancy “Digital Technologies” could be standardized in selected new cameras right now. In late 2009, new artificial intelligence image chips such as: back-illuminated CMOS image sensor, 30x Optical Zoom (or more), Full HD Video, Sweep Panorama, Interchangeable Unit Camera System,Super High Speed ISO, Super Steady, Motion Remover.., have been promoted in new generation of camera. It could change not only the performance of new camera (DSC/DC) but to challenge the current DV market seriously, and may inspire new record-high selling again. In our experiment, we collect more than 300 cases from the telephone survey during Sep, 2010 and Dec, 2010. Total of 220 cases comply with the conditions. To probe mainly into the relationship between new generation DC Confidence level and 3 potential customers: Amateur Photographer (AP), Senior Photographer (SP), and college student (CS). That is the reason what we are probe into this highly competitively market with brilliant creative design, and hope to offer an objective suggestion for both industry and education administers.

Analysis of a salinity induced BjSOS3 protein from Brassica indicate it to be structurally and functionally related to its ortholog from Arabidopsis

Arabidopsis has been a favorite model system for plant biologist. It is anticipated that comparative analysis of this plant with other members of Brassicaceae may aid in identification of orthologs playing role as key genetic determinants for salinity response. In this endeavor, we have recently identified SOS family members from Brassica juncea in our laboratory and reported their salinity responsive transcriptional induction in seedlings of various diploid and amphidiploids species. In the present study, we have carried out detailed time kinetics for BjSOS3 expression in a salinity tolerant B.juncea var. CS52. Transcript analysis at the sensitive growth stages of plants viz. seedling and reproductive stage indicated clear differential transcriptional regulation of BjSOS3 under non-induced as well as salinity induced conditions in a time and organ specific manner, mirroring their respective tolerance physiology. Similar to its ortholog from Arabidopsis thaliana, the modeled BjSOS3 protein show typical features of a Ca(2+) binding protein with four conserved EF-hands. We have also attempted to study the binding of SOS3 protein with the modeled SOS2 protein. It has been established that SOS3 protein senses Ca(2+) though the binding is very weak; we show the down regulation of BjSOS3 mRNA in presence of calcium chelator - EGTA under the various stress conditions including ABA. In situ localization of BjSOS3-GFP fusion protein in onion peel has shown its presence strongly in plasma membrane as well as cytosol. The leads presented in the paper will assist in understanding and establishing the SOS signaling machinery in B.juncea.

Strangers no more: Uterine NK cell recognition of the placenta in mice

Successful pregnancy requires a series of coordinated interactions between the developing placenta, the uterus, and the maternal immune system (1). At the maternal/fetal interface, where the placenta contacts the uterus, a specialized type of lymphocyte known as a uterine natural killer (uNK) cell is thought to play a critical role in mediating the uterine vascular adaptations to pregnancy. Epidemiological data have suggested that this function is modified by the response of uNK cells to the paternally inherited classical class I major histocompatibility complex (MHC I) molecules (i.e., the HLA-A, -B, and -C antigens in humans) expressed by placental trophoblasts invading into the uterus, as inopportune genetic combinations of the mother and father expected to alter uNK cell activity increase the risk of certain obstetrical complications (i.e., preeclampsia, fetal growth restriction, and recurrent miscarriage). In mice, however, direct evidence for such uNK cell-mediated “allorecognition” of the placenta has so far been lacking, and as a result the biomedical researcher's favorite model organism has yet to be used to study how levels of uNK cell activity influence reproductive success. In PNAS, Hemberger and colleagues now present strong evidence that murine uNK cells do indeed recognize paternal MHC I molecules expressed by invasive trophoblasts and that this recognition has significant implications for uterine vascular remodeling and ultimate pregnancy outcome (2). This work thus opens up use of the mouse as a means to study the key interactions that underlie some of the more serious complications of pregnancy.

The Cold War and the Social and Economic History of the Twentieth Century

냉전은 권력정치(power politics)와 안보, 패권에 대한 문제만이 아닌, 산업발전의 여러 단계에서 경제와 사회를 어떻게 조직해야 하는가에 대한 서로 다른 이론들 간의 갈등이기도 했다. 물론 이념과 신념체계가 냉전을 형성하는 데 가장 큰 기여를 했지만, 사회 갈등 역시 광범위하게 냉전의 경과와 결과를 결정하는 데 중요한 영향을 끼쳤다. 냉전시기에는 자본주의에 대한 마르크스주의자들의 도전에서 시작해 다양한 사회적 개념이 출현했지만, 특별히 대중적으로 선호하는 모델이 부상하지는 않았다. 그러나 장기적으로 보자면, 집단주의적 중앙계획경제는 커다란 비용에도 불구하고 저개발 사회들을 근대화하는 데에는 어느 정도 강점을 보였다. 반면에 자유시장경제는 적어도 국가가 운영하는 사회복지제도와 일국적, 국제적 수준의 계획을 일정한 정도 수용한 이후에 훨씬 더 높은 생산성을 보여주었다. 정치적 자유가 생산성과 혁신에 유리하게 작용했다는 점이 20세기의 가장 중요한 교훈일 것이다.

Preparation of Drosophila Polytene Chromosome Squashes for Antibody Labeling

Drosophila has long been a favorite model system for studying the relationship between chromatin structure and gene regulation due to the cytological advantages provided by the giant salivary gland polytene chromosomes of third instar larvae. In this tissue the chromosomes undergo many rounds of replication in the absence of cell division giving rise to approximately 1000 copies. The DNA remains aligned after each replicative cycle resulting in greatly enlarged chromosomes that provide a unique opportunity to correlate chromatin morphology with the localization of specific proteins. Consequently, there has been a high level of interest in defining the epigenetic modifications present at different genes and at different stages of the transcription process. An important tool for such studies is the labeling of polytene chromosomes with antibodies to the enzyme, transcription factor, or histone modification of interest. This video protocol illustrates the squash technique used in the Johansen laboratory to prepare Drosophila polytene chromosomes for antibody labeling.

Regulation of metabolism in Caenorhabditis elegans longevity

The nematode Caenorhabditis elegans is a favorite model for the study of aging. A wealth of genetic and genomic studies show that metabolic regulation is a hallmark of life-span modulation. A recent study in BMC Biology identifying metabolic signatures for longevity suggests that amino-acid pools may be important in longevity.See research article http://www.biomedcentral.com/1741-7007/8/14.

High-resolution synchrotron infrared spectroscopy of thiophosgene: The ν2 and ν4 fundamental bands near 500 cm −1

Thiophosgene (Cl 2CS) is a favorite model system for studies of photophysics, vibrational dynamics, and intersystem interaction effects. But there are no previous rotationally-resolved infrared studies because the spectra are very congested due to hot bands and multiple isotopic species. This paper reports a detailed study of the ν 2 (∼504 cm −1) and ν 4 (∼471 cm −1) fundamental bands for the two most abundant isotopomers, 35Cl 2CS and 35Cl 37ClCS, based on spectra with observed line widths of ∼0.0008 cm −1 obtained at the Canadian Light Source far-infrared beamline using synchrotron radiation and a Bruker IFS125 Fourier transform spectrometer.

Advances in Genetical Genomics of Plants

Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research.

New school in liver development: Lessons from zebrafish #

There is significant overlap in the genes and pathways that control liver development and those that regulate liver regeneration, hepatic progenitor cell expansion, response to injury, and cancer. Additionally, defects in liver development may underlie some congenital and perinatal liver diseases. Thus, studying hepatogenesis is important for understanding not only how the liver forms, but also how it functions. Elegant work in mice has uncovered a host of transcription factors and signaling molecules that govern the early steps of hepatic specification; however, the inherent difficulty of studying embryogenesis in utero has driven developmental biologists to seek new systems. The rapidly developing vertebrate zebrafish is a favorite model for embryology. The power of forward genetic screens combined with live real-time imaging of development in transparent zebrafish embryos has highlighted conserved processes essential for hepatogenesis and has uncovered some exciting new players. This review presents the advantages of zebrafish for studying liver development, underscoring how studies in zebrafish and mice complement each other. In addition to their value for studying development, zebrafish models of hepatic and biliary diseases are expanding, and using these small, inexpensive embryos for drug screening has become de rigueur. Zebrafish provide a shared platform for developmental biology and translational research, offering innovative methods for studying liver development and disease. The story of hepatogenesis has something for everyone. It involves transcriptional regulation, cell-cell interaction, signaling pathways, control of cell proliferation and apoptosis, plus morphogenic processes that sculpt vasculature, parenchymal cells, and mesenchyme to form the multifaceted liver. Decades of research on liver development in mice and other vertebrates offer valuable lessons in how the multipotent endoderm is programmed to form a functional liver. Of equal importance are insights that have illuminated the mechanisms by which hepatic progenitors are activated in a damaged liver, how the adult liver regenerates, and, possibly, the basis for engineering liver cells in vitro for cell transplantation to sustain patients with liver failure. Moreover, processes that are key to liver development are often co-opted during pathogenesis. Therefore, reviewing hepatogenesis is informative for both basic and translational researchers. In this review, we bring to light the many advantages offered by the tropical freshwater vertebrate zebrafish (Danio rerio) in studying hepatogenesis. By comparing zebrafish and mice, we highlight how work in each system complements the other and emphasize novel paradigms that have been uncovered using zebrafish. Finally, we highlight exciting efforts using zebrafish to model hepatobiliary diseases.

Galactic vs. extragalactic origin of the peculiar transient SCP 06F6

We study four scenarios for the SCP 06F6 transient event that was announced recently. Some of these were previously briefly discussed as plausible models for SCP 06F6, in particular with the claimed detection of a z=0.143 cosmological redshift of a Swan spectrum of a carbon rich envelope. We adopt this value of z for extragalactic scenarios. We cannot rule out any of these models, but can rank them from most to least preferred. Our favorite model is a tidal disruption of a CO white dwarf (WD) by an intermediate-mass black hole (IMBH). To account for the properties of the SCP 06F6 event, we have to assume the presence of a strong disk wind that was not included in previous numerical simulations. If the IMBH is the central BH of a galaxy, this explains the non-detection of a bright galaxy in the direction of SCP 06F6. Our second favorite scenario is a type Ia-like SN that exploded inside the dense wind of a carbon star. The carbon star is the donor star of the exploded WD. Our third favorite model is a Galactic source of an asteroid that collided with a WD. Such a scenario was discussed in the past as the source of dusty disks around WDs, but no predictions exist regarding the appearance of such an event. Our least favorite model is of a core collapse SN. The only way we can account for the properties of SCP 06F6 with a core collapse SN is if we assume the occurrence of a rare type of binary interaction.

A canonical dynamics view of the Newtonian limit of general relativity

The Newtonian limit of general relativity was Jurgen Ehlers favourite model for limit relations between theories of physics. In this contribution, for the case of isolated systems, the Newtonian limit of general relativity will be illuminated from a canonical dynamics point of view. The canonical dynamics approach naturally supplies a post-Newtonian expansion of general relativity.

Amy Kiger: Abuzz on cell biology

From flattened epithelial cells to elongated neurons, cell morphology is heavily intertwined with cell growth and function. Understanding the genetic factors that govern cell shape might therefore provide insights into the processes underlying development and disease. Figure 1 Amy Kiger Amy Kiger has focused on these and other fundamental questions of cell biology in Drosophila throughout her career. She first worked on circadian rhythm in Drosophila as a research technician in a laboratory at The Rockefeller University, then studied male germ line stem cell biology in flies as a graduate student at Stanford (1, 2). Her postdoctoral studies in Norbert Perrimon's laboratory at Harvard on the genetic basis of cell morphology and growth in Drosophila have yielded several novel insights (3–5). With the results of these massive genome-wide screens (5), Kiger is now striking out on her own at the University of California, San Diego (UCSD), investigating the genetic basis for cell shape in her favorite model system—the fruit fly. She discussed with us the dizzying possibilities presented by her work.

The Personal Structure of Personal Need for Structure

Abstract. This study investigated the responses of N = 1,789 participants to a set of 12 Likert-type items for the assessment of personal need for structure (PNS). Mixture-distribution Rasch models were used to analyze the homogeneity of the response format across items and the homogeneity of the item parameters and category parameters across persons. Model selection yielded a two-class rating scale model as the favorite model. This model contains the assumptions that the Likert response scale is used in a constant way for all items but that the item or category parameters differ between two latent subpopulations. The parameter estimates revealed large differences in the threshold parameters for the response categories between the two subpopulations. While the larger subpopulation showed a tendency to avoid extreme response categories, the smaller subpopulation used the whole range of the response scale. The different response styles identified by the mixture-distribution Rasch analysis were validated by significantly higher Extraversion scores for participants in the smaller subpopulation that showed more extreme and impulsive rating behavior. The results confirmed that PNS reflects quantitative interindividual differences, and they also showed that the total score of the 12 PNS items forms a combination of the latent PNS trait and response style.

High‐frequency ultrasonographic imaging of avian cardiovascular development

The chick embryo has long been a favorite model system for morphologic and physiologic studies of the developing heart, largely because of its easy visualization and amenability to experimental manipulations. However, this advantage is diminished after 5 days of incubation, when rapidly growing chorioallantoic membranes reduce visibility of the embryo. Using high-frequency ultrasound, we show that chick embryonic cardiovascular structures can be readily visualized throughout the period of Stages 9-39. At most stages of development, a simple ex ovo culture technique provided the best imaging opportunities. We have measured cardiac and vascular structures, blood flow velocities, and calculated ventricular volumes as early as Stage 11 with values comparable to those previously obtained using video microscopy. The endocardial and myocardial layers of the pre-septated heart are readily seen as well as the acellular layer of the cardiac jelly. Ventricular inflow in the pre-septated heart is biphasic, just as in the mature heart, and is converted to a monophasic (outflow) wave by ventricular contraction. Although blood has soft-tissue density at the ultrasound resolutions and developmental stages examined, its movement allowed easy discrimination of perfused vascular structures throughout the embryo. The utility of such imaging was demonstrated by documenting changes in blood flow patterns after experimental conotruncal banding.

Amoebae as Exemplary Cells: The Protean Nature of an Elementary Organism

In the nineteenth century protozoology and early cell biology intersected through the nexus of Darwin's theory of evolution. As single-celled organisms, amoebae offered an attractive focus of study for researchers seeking evolutionary relationships between the cells of humans and other animals, and their primitive appearance made them a favourite model for the ancient ancestor of all living things. Their resemblance to human and other metazoan cells made them popular objects of study among morphologists, physiologists, and even those investigating animal behaviour. The amoeba became the exemplar of the new protoplasmic cell concept of mid-century and because its apparent simplicity made it widely generalizable it became a popular subject in a breadth of experimental investigations and theoretical speculations. It was able to do this because "the amoeba" denotes not a particular organism, but a general type of behaviour common to the cells of a range of protozoa, simple plants and higher animals. Its status as an exemplary cell also rested upon auxiliary philosophical assumptions about what constitutes a primitive characteristic and the thesis that evolution is a progressive development of order from chaos.

Changing Places: A Novel Type of Niche and Stem Cell Coordination in the Drosophila Ovary

The Drosophila ovary has been a favorite model for the study of stem cells within their niche. In this issue of Cell Stem Cell, Nystul and Spradling (2007) study somatic stem cells within a novel kind of niche and reveal the complexity and coordination of stem cell behavior.