Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncoupling of Membrane Ruffling and Pinocytosis during Ras Signal Transduction*

Activation of Ras stimulates cell surface membrane ruffling and pinocytosis. Although seen as coupled events, our study demonstrates that membrane ruffling and pinocytosis are regulated by distinct Ras signal transduction pathways. Ras controls membrane ruffling via the small GTPase Rac. In BHK-21 cells, expression of the constitutively active Rac1(G12V) mutant, via a Sindbis virus vector, resulted in a dramatic stimulation of membrane ruffling without affecting the uptake of horseradish peroxidase. Expression of Ha-Ras(G12V), an activated Ras mutant, stimulated both membrane ruffling and horseradish peroxidase uptake. The Ha-Ras(G12V)-stimulated pinocytosis but not membrane ruffling was abolished by either wortmannin or co-expression with a dominant negative mutant of Rab5, Rab5(S34N). Expression of the activated Rab5(Q79L) mutant mimics the stimulatory effect of Ha-Ras(G12V) on pinocytosis but not membrane ruffling. Our data indicate that Ha-Ras(G12V) separately activates Rab5-dependent pinocytosis and Rac1-dependent membrane ruffling.
A Disability Culture Perspective on Early Intervention with Parents with Physical or Cognitive Disabilities and Their Infants.

Through the Looking Glass, 2198 Sixth Street, Suite 100, Berkeley, CA 94710. (800) 644-2666 (voice); (800) 804-1616 (TTY); tlg@berkeley.org; www.lookingglass. org [Note: This is the original manuscript that was published in Infants and Young Children, 13(2), 9-20. (2000). ] Introduction The intent of this article is two-fold: (1) to describe how a disability culture perspective has informed research and early intervention serving parents with physical disabilities and their babies, and (2) to articulate how this perspective is also guiding intervention for parents with cognitive disabilities and their babies. The term “disability culture” refers to the social model, civil rights or minority model of disability: disability as socially constructed, with an emphasis on its social meaning, and on social obstacles as the primary problem for people with disabilities and their families. This article identifies themes that have emerged from research and intervention in a disability culture-based organization, Through the Looking Glass (TLG), and which seem particularly salient for improving practice with parents with disabilities and their children. Differentiating is an appropriate theme to consider initially. There has been a persistent problem in research and practice of blurring distinctions between parents with diverse disabilities. One can consider this over-generalizing a manifestation of the concept of “spread”. Recently Olkin discussed the power of the negatively valenced disability characteristic to “spread” and evoke inferences about an individual’s other characteristics, leading to stereotyping: “A negative value attached to the fact of disability spreads to other unrelated
An Empirical Study of Software Reuse with Special Attention to Ada

Over the past several decades, numerous software technologies have been developed for overcoming the software crisis. Among these technologies, reuse has been recognized as one of the most important software technologies. Recently, it has gained substantial attention as a possible solution to the software crisis in Ada and other software communities. The purpose of this empirical study is to examine how organizations actually exploit reuse technologies and evaluates how reuse factors affect the rate of reuse in an organization. This study is an attempt to enhance the measurement of the rate of reuse and the effectiveness of reuse by establishing conceptual foundations in the literature for reuse and conducting an empirical investigation of organizations using Ada technology. This study differentiated software reuse into six criteria: domain, human, tool, organization, software metrics, and environment. The results of this study show that the rate of reuse significantly depends upon reuse capability, software development effort, object-oriented design capability, repository development effort, Ada technology capability, and domain capability.
The UCSC Genome Browser: What Every Molecular Biologist Should Know

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one's understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. Curr. Protoc. Mol. Biol. 88:19.9. 1‐19.9. 28. © 2009 by John Wiley & Sons, Inc.
Droplet ejector using surface acoustic waves

The present study aims to investigate droplet ejection using Surface Acoustic Waves (SAW). The interests in droplet ejection microsystems have dramatically grown in recent years due to inkjet printhead demand (Drop-On-Demand). Among several actuating methods (thermal, piezoelectric, etc.), the thermally driven inkjet printhead is the most successful (low cost, easy fabrication and high printing quality). Almost all of the current ink jet printers eject ink droplets through nozzles, with a direction of ejection always perpendicular to the nozzle surface. Surface acoustic waves devices are widely used for frequency filtering and are mainly devoted to cellular phones and telecommunication handset. Nowadays, recently published works have demonstrated the interest of SAW for guiding and positioning small liquid droplet atop a flat surface. This paper describes a new way to eject droplets (water, ink, etc.) using SAW. The surface acoustic waves devices used to eject droplets are carried out on lithium niobate substrates (LiNbO3 cut Y+128°, X propagation). The Rayleigh waves are excited using classical inter-digital transducers (IDT). The design of IDT has been simulated with finite element analysis and boundary element methods. The computations on the design of the IDT have been compared with measurements. The vibration amplitude of the wave necessary to droplet ejection is measured using a heterodyne laser probe. The range of the droplets volume ejected is between 100nl and 1μl. The influence of the supply voltage on the ejection is described.
Practical limitations of superresolution imaging due to conventional sample preparation revealed by a direct comparison of CLSM, SIM and dSTORM

We evaluate the suitability of conventional sample preparation and labelling methods for two superresolution techniques, structured illumination microscopy and direct stochastic optical reconstruction microscopy, by a comparison to established confocal laser scanning microscopy. We show that SIM is compatible with standard fixation procedures and immunofluorescence labelling protocols and improves resolution by a factor of two compared to confocal laser scanning microscopy. With direct stochastic optical reconstruction microscopy, fluorophores can theoretically be localized with much higher precision. However, in practice, with indirect immunofluorescence labelling density can be insufficient due to the bulky probes to reveal biological structures with high resolution. Fine structures like single actin fibres are in fact resolved with direct stochastic optical reconstruction microscopy when using small affinity probes, but require proper adjustment of the fixation protocol. Finally, by a direct comparison of immunofluorescent and genetic labelling with fluorescent proteins, we show that target morphology in direct stochastic optical reconstruction microscopy data sets can differ significantly depending on the labelling method and the molecular environment of the target.
Plasmonics induced absorption enhancement in silicon nanowires coated with metallic nanoparticles

The optical properties of silicon nanowires (Si NWs) coated with metallic nanoparticles (NPs) were theoretically investigated. A three dimensional (3D) model of a solar cell has been proposed, in which the Si NWs were geometrically modeled to be periodically aligned nano-pillars in a square lattice. Hemispherical metallic NPs were coated onto a sidewall of Si NWs. We numerically studied the optical properties of the structure with the finite element method (FEM) by using the commercial software COMSOL Multiphysics. It is demonstrated that the electromagnetic field is strongly localized around the metallic NPs as well as between the metallic NPs and Si NWs. Localized surface plasmons (LSPs) are generated around the metallic NPs, coupling and scattering a large amount of light into the Si NWs. A significant enhancement of the light absorption is observed, especially in the long wavelength range of the solar spectrum. These theoretical investigations agree well with our experimental data while providing a fundamental background for improving the efficiency of Si NWs solar cells.
Dynamic Eigenstates of Parametric Interactions in Randomly Birefringent Fibers

In fiber-based parametric devices employing nondegenerate four-wave mixing, there exist dynamic eigenstates for the signal and idler, for which there is no change of polarization as the waves propagate. For the case of parametric amplifiers with two pumps of arbitrary polarization, the eigenstates are the sum of the Stokes vectors of the pumps. For nonlinear Bragg scattering, the eigenstate polarizations are determined by the sum of two Stokes vectors of one pump plus one of the other pump. Separated coupled-wave solutions for the evolution of the signal and idler are obtained for each eigenstate.
Sulfolobus Turreted Icosahedral Virus c92 Protein Responsible for the Formation of Pyramid-Like Cellular Lysis Structures

ABSTRACT Host cells infected by Sulfolobus turreted icosahedral virus (STIV) have been shown to produce unusual pyramid-like structures on the cell surface. These structures represent a virus-induced lysis mechanism that is present in Archaea and appears to be distinct from the holin/endolysin system described for DNA bacteriophages. This study investigated the STIV gene products required for pyramid formation in its host Sulfolobus solfataricus. Overexpression of STIV open reading frame (ORF) c92 in S. solfataricus alone is sufficient to produce the pyramid-like lysis structures in cells. Gene disruption of c92 within STIV demonstrates that c92 is an essential protein for virus replication. Immunolocalization of c92 shows that the protein is localized to the cellular membranes forming the pyramid-like structures.
Investigating non-filament type conduction mechanism of indium-tin-oxide resistance random access memory by varying forming current compliance

In this letter, we investigated a new interface-type conduction mechanism in ITO/Ga2O3:ITO/TiN resistance random access memory induced by varying forming current compliance. This conduction showed a typical bipolar resistive switching (RS) and a size effect experiment was applied to confirm that the conduction mechanism was an interface-type when forming current compliance was set below 1mA. Current fittings of both high resistance state (HRS) and low resistance state (LRS) showed Schottky emission. Furthermore, a conduction model was provided to separate this new conduction mechanism in ITO material relevant research from traditional filament-type.
Artin algebraization and quotient stacks

This article contains a slightly expanded version of the lectures given by the author at the summer school "Algebraic stacks and related topics" in Mainz, Germany from August 31 to September 4, 2015. The content of these lectures is purely expository and consists of two main goals. First, we provide a treatment of Artin's approximation and algebraization theorems following the ideas of Conrad and de Jong which rely on a deep desingularization result due to Neron and Popescu. Second, we prove that under suitable hypotheses, algebraic stacks are etale locally quotients stacks in a neighborhood of a point with a linearly reductive stabilizer.
Market Power and Transferable Property Rights

The appeal of using markets as a means of allocating scarce resources stems in large part from the assumption that a market will approximate the competitive ideal. When competition is not a foregone conclusion, the question naturally arises as to how a firm might manipulate the market to its own advantage. This paper analyzes the issue of market power in the context of markets for transferable property rights. First, a model is developed that explains how a single firm with market power might exercise its influence. This is followed by an examination of the model in the context of a particular policy problem—the control of particulate sulfates in the Los Angeles region.
Suicidal ideations and attempts in juvenile delinquents.

BACKGROUND Suicidality among adolescents is a common focus of clinical attention. In spite of links to disruptive behaviors and other types of psychopathology, it is not clear whether other factors commonly associated with suicide, such as personality and parenting, predict suicidality over and above psychopathology. The purpose of the present study was to assess suicidal ideations and attempts and their relationship to psychopathology, violence exposure, personality traits and parental rearing in Russian male juvenile delinquents with conduct disorder (CD). METHOD Suicidality and psychopathology were assessed using a semi-structured psychiatric interview in 271 incarcerated male juvenile delinquents diagnosed with CD. Violence exposure, personality characteristics and perceived parental rearing were assessed via self-reports. RESULTS Thirty-four percent of those diagnosed with CD (92 subjects) reported a lifetime history of either suicidal thoughts or attempts. Suicidal ideators and attempters did not differ significantly on any variable of interest, but both reported significantly higher rates of psychopathology and violence exposure than the non-suicidal group, as well as higher levels of harm avoidance, lower self-directedness, and higher rates of perceived negative parental rearing. Finally, even when controlling for the relationship with psychopathology, personality and perceived parental rearing factors showed significant associations with suicidality. CONCLUSIONS Juvenile delinquents with CD have high rates of suicidal ideations and attempts, related to a wide spectrum of psychopathology and specific personality traits. These findings suggest that a combination of intrinsic and extrinsic factors create vulnerability to stressors, which under the influence of situational factors (e.g., repeated traumatization) may lead to suicidal thoughts and acts. Factors potentially contributing to vulnerability for suicidality should be identified when planning prevention and rehabilitation efforts for troubled youth.
Engineering ultrafast spin currents and terahertz transients by magnetic heterostructures

1. Department of Physical Chemistry, Fritz Haber Institute, Berlin, Germany. 2. Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden. 3. I. Physikalisches Institut, Georg-August-Universität Göttingen, Göttingen, Germany. 4. Helmholtz-Zentrum Berlin fϋr Materialien und Energie, Berlin, Germany. 5. Peter Grünberg Institute and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, Jülich, Germany.
T-type calcium channels inhibitors: a patent review

Importance of the field: T-type calcium channels are transmembrane proteins that regulate calcium entry in the cell in a voltage-dependent manner. Intracellular calcium levels are the key to many physiological processes, ranging from neuron firing to cardiac pacemaking. Inhibition of T-type calcium channels is heralded as a potential treatment to peripheral and CNS disorders, including hypertension, heart failure, sleep, epilepsy, drug addiction and neuropathic pain. Areas covered in this review: A comprehensive summary of patent literature disclosing T-type calcium channels inhibitors is provided. What the reader will gain: In all, 46 patent applications including 15 chemical structure classes are reviewed. Available in vitro, in vivo and clinical results are also discussed. Take home message: Several selective T-type calcium channels inhibitors with demonstrated in vitro and in vivo effects, including one Phase I clinical candidate, are now available. While future clinical results will be paramount to assess target validity in patients, these novel inhibitors represent excellent tools to further investigate the role of T-type channels in pathophysiological conditions.
Risk and Price in the Bidding Process of Contractors

Formal and analytical risk models prescribe how risk should be incorporated into construction bids. However, the actual process of how contractors and their clients negotiate and agree to price is complex and not clearly articulated in the literature. With participant observation, the entire tender process was shadowed in two leading U.K. construction firms. This was compared with propositions in analytical models, and significant differences were found. A total of 670 h of work observed in both firms revealed three stages of the bidding process. Bidding activities were categorized and their extent estimated as deskwork (32%), calculations (19%), meetings (14%), documents (13%), off-days (11%), conversations (7%), correspondence (3%), and travel (1%). Risk allowances of 1–2% were priced in some bids, and three tiers of risk apportionment in bids were identified. However, priced risks may be excluded from the final bid to enhance competitiveness. Although risk apportionment affects a contractor’s pricing s.
p16INK4a Immunohistochemistry Improves Interobserver Agreement in the Diagnosis of Cervical Intraepithelial Neoplasia

It has been repeatedly shown that there is a substantial lack of interobserver reproducibility in the histologic diagnosis of cervical intraepithelial neoplasia (CIN), which might be improved by a more specific diagnostic biomarker. Cervical cancer and CIN, but not other cervical epithelia, express high levels of the cyclin-dependent kinase inhibitor p16INK4a, suggesting that staining for this marker could help to more precisely identify CIN in tissue sections and therefore reduce variation in interpretation of cervical lesions. To test this hypothesis, 194 cervical cone biopsy samples were selected from a routine histopathology laboratory. Two consecutive sections from each biopsy were stained with hematoxylin and eosin and with a p16INK4a-specific monoclonal antibody, respectively. Five experienced cervical pathologists examined the slides. The agreement in the diagnosis between pairs or groups of observers was calculated by kappa statistics. Significant discrepancies were observed in the diagnostic interpretation of hematoxylin and eosin-stained slides, particularly for low-grade lesions (kappa value 0.60 [95% confidence interval 0.58–0.63]). There was significantly better agreement in the interpretation of p16INK4a expression (kappa value 0.91 [95% confidence interval 0.84–0.99]). Expression of p16INK4a was restricted to CIN 2/CIN 3, CIN 1 associated with high-risk human papillomavirus, or cervical cancer. p16INK4a immunostaining allowed precise identification of even small CIN or cervical cancer lesions in biopsy sections and helped to reduce interobserver variation in the histopathologic interpretation of cervical biopsy specimens. Thus, p16INK4a immunohistochemistry can reduce false-negative and false-positive biopsy interpretation and thereby significantly improve cervical (pre)-cancer diagnosis.
Modulation of Bordetella pertussis by nicotinic acid

Growth of Bordetella pertussis in a high concentration of nicotinic acid (NA) had a modulating effect on several properties and activities of the bacteria. Compared with normally grown cells, those grown in a high concentration of NA had reduced capacity for taking up both NA and nicotinamide (ND); they had reduced adenylate cyclase activity and showed loss of agglutinogen factors 2 and 3, but an increase in factor 1. By contrast, cells grown in a high concentration of ND showed only a slightly decreased capacity for uptake of ND and none of the other changes. Modulation of B. pertussis by NA varied with the strain and culture conditions and appeared to be distinct from the antigenic modulation induced by high Mg2+ in the culture medium. Evidence is presented for the association of a small proportion of the extracytoplasmic adenylate cyclase with the outer membrane of B. pertussis.
The Biological Mechanisms and Behavioral Functions of Opsin-Based Light Detection by the Skin

Light detection not only forms the basis of vision (via visual retinal photoreceptors), but can also occur in other parts of the body, including many non-rod/non-cone ocular cells, the pineal complex, the deep brain, and the skin. Indeed, many of the photopigments (an opsin linked to a light-sensitive 11-cis retinal chromophore) that mediate color vision in the eyes of vertebrates are also present in the skin of animals such as reptiles, amphibians, crustaceans and fishes (with related photoreceptive molecules present in cephalopods), providing a localized mechanism for light detection across the surface of the body. This form of non-visual photosensitivity may be particularly important for animals that can change their coloration by altering the dispersion of pigments within the chromatophores (pigment containing cells) of the skin. Thus, skin coloration may be directly color matched or “tuned” to both the luminance and spectral properties of the local background environment, thereby facilitating behavioral functions such as camouflage, thermoregulation, and social signaling. This review examines the diversity and sensitivity of opsin-based photopigments present in the skin and considers their putative functional roles in mediating animal behavior. Furthermore, it discusses the potential underlying biochemical and molecular pathways that link shifts in environmental light to both photopigment expression and chromatophore photoresponses. Although photoreception that occurs independently of image formation remains poorly understood, this review highlights the important role of non-visual light detection in facilitating the multiple functions of animal coloration.
Performance of MPEG codecs in the presence of errors

MPEG is emerging as a major international standard for applications in compressed video storage, transmission, and interactive communications. MPEG will be used in applications which involve imperfect channel conditions or storage defects. This work studies the effects of different types of errors on the compressed MPEG bit streams and possible approaches to minimize such effects. The use of forward error correction, block interleaving, error concealment, and their inter-relationship and applicability to MPEG bit streams, were investigated.