Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

The 26S proteasome is at the executive end of the ubiquitin-proteasome pathway for the controlled degradation of intracellular proteins. While the structure of its 20S core particle (CP) has been determined by X-ray crystallography, the structure of the 19S regulatory particle (RP), which recruits substrates, unfolds them, and translocates them to the CP for degradation, has remained elusive. Here, we describe the molecular architecture of the 26S holocomplex determined by an integrative approach based on data from cryoelectron microscopy, X-ray crystallography, residue-specific chemical cross-linking, and several proteomics techniques. The “lid” of the RP (consisting of Rpn3/5/6/7/8/9/11/12) is organized in a modular fashion. Rpn3/5/6/7/9/12 form a horseshoe-shaped heterohexamer, which connects to the CP and roofs the AAA-ATPase module, positioning the Rpn8/Rpn11 heterodimer close to its mouth. Rpn2 is rigid, supporting the lid, while Rpn1 is conformationally variable, positioned at the periphery of the ATPase ring. The ubiquitin receptors Rpn10 and Rpn13 are located in the distal part of the RP, indicating that they were recruited to the complex late in its evolution. The modular structure of the 26S proteasome provides insights into the sequence of events prior to the degradation of ubiquitylated substrates.
Towards a Data-driven Ontology Engineering Framework

The dynamic nature of ontology requires a new methodology to discover the evolving semantics of a particular conceptualization and maintain the novelty of specific ontology with minimal human intervention. This paper posits a conceptual framework that supports a data-driven, iterative, and self-correcting ontology engineering methodology for developing application-oriented and light-weight ontology. The method is being tested and implemented in a work-in-progress intelligent educational system (IES) project that serves an agent-based and ontology-driven academic advising system.
Corporate Social Responsibility In Diverse Environments: A Comparative Study of Managerial Attitudes in Australia and Bangladesh

The issue of the social responsibility of business has been hotly debated in the last several decades. Opinions about business's social responsi bilities He mainly between two extremes. At the one extreme is the view that business is an economic institution directed towards profit whose only responsibility to society is to provide goods and services and to return maximum benefits to investors (Friedman, 1968; 1970; 1989; Gaski, 1985; Hass, 1979; Chamberlain, 1973; Levitt, 1958). This classical view was strongly endorsed by the Nobel prize winning economist Milton Friedman. According to Friedman, the responsibility of business is
Fiery frills: carotenoid-based coloration predicts contest success in frillneck lizards

Conspicuous color signals are commonly used by a wide diversity of animals to advertise some specific aspect of their competitive ability. In particular, orange and red colors are often used as an aggressive signal to potential rivals. The iconic Australian frillneck lizard (Chlamydosaurus kingii) has a large and extensible frill that varies geographically in the extent of yellow, orange, and red present. Focusing on the red-orange lizards found in Western Australia, we first established that, in contrast to most lizards studied to date, the red-orange–colored frill is carotenoid rather than pterin based. Second, we measured chromatic and achromatic aspects of male frills before staging dyadic contests between males to determine whether color is used to signal fighting ability. Both chromatic and achromatic measures of the red-orange patches on the lizard’s frills, as well as similarly colored patches on their throats, were reliable predictors of competitive ability; males possessing more colorful displays dominated size-matched competitors in dyadic contests. Apart from large differences in body size and mass (>10%), no other colorimetrics (e.g., white patches), frill traits (e.g., size, relative and absolute patch sizes), or morphological measures (e.g., head size, bite force) were found to predict the outcome of contests. To the best of our knowledge, this is the first example of carotenoid-based patches signaling male fighting ability in a lizard.
Simulating photon scattering effects in structurally detailed ventricular models using a Monte Carlo approach

Light scattering during optical imaging of electrical activation within the heart is known to significantly distort the optically-recorded action potential (AP) upstroke, as well as affecting the magnitude of the measured response of ventricular tissue to strong electric shocks. Modeling approaches based on the photon diffusion equation have recently been instrumental in quantifying and helping to understand the origin of the resulting distortion. However, they are unable to faithfully represent regions of non-scattering media, such as small cavities within the myocardium which are filled with perfusate during experiments. Stochastic Monte Carlo (MC) approaches allow simulation and tracking of individual photon “packets” as they propagate through tissue with differing scattering properties. Here, we present a novel application of the MC method of photon scattering simulation, applied for the first time to the simulation of cardiac optical mapping signals within unstructured, tetrahedral, finite element computational ventricular models. The method faithfully allows simulation of optical signals over highly-detailed, anatomically-complex MR-based models, including representations of fine-scale anatomy and intramural cavities. We show that optical action potential upstroke is prolonged close to large subepicardial vessels than further away from vessels, at times having a distinct “humped” morphology. Furthermore, we uncover a novel mechanism by which photon scattering effects around vessels cavities interact with “virtual-electrode” regions of strong de-/hyper-polarized tissue surrounding cavities during shocks, significantly reducing the apparent optically-measured epicardial polarization. We therefore demonstrate the importance of this novel optical mapping simulation approach along with highly anatomically-detailed models to fully investigate electrophysiological phenomena driven by fine-scale structural heterogeneity.
A multitracer stable isotope quantification of the effects of arginine intake on whole body arginine metabolism in neonatal piglets.

We have previously shown that deficient arginine intake increased the rate of endogenous arginine synthesis from proline. In this paper, we report in vivo quantification of the effects of arginine intake on total endogenous arginine synthesis, on the rates of conversion between arginine, citrulline, ornithine, and proline, and on nitric oxide synthesis. Male piglets, with gastric catheters for diet and isotope infusion and femoral vein catheters for blood sampling, received a complete diet for 2 days and then either a generous (+Arg; 1.80 g x kg(-1) x day(-1); n = 5) or deficient (-Arg; 0.20 g.kg(-1). day(-1); n = 5) arginine diet for 5 days. On day 7, piglets received a primed, constant infusion of [guanido-(15)N(2)]arginine, [ureido-(13)C;5,5-(2)H(2)]citrulline, [U-(13)C(5)]ornithine, and [(15)N;U-(13)C(5)]proline in an integrated study of the metabolism of arginine and its precursors. Arginine synthesis (micromol x kg(-1) x h(-1)) from both proline (+Arg: 42, -Arg: 74, pooled SE: 5) and citrulline (+Arg: 67, -Arg: 120; pooled SE: 15) were higher in piglets receiving the -Arg diet (P < 0.05); and for both diets proline accounted for approximately 60% of total endogenous arginine synthesis. The conversion of proline to citrulline (+Arg: 39, -Arg: 67, pooled SE: 6) was similar to the proline-to-arginine conversion, confirming that citrulline formation limits arginine synthesis from proline in piglets. Nitric oxide synthesis (micromol x kg(-1) x h(-1)), measured by the rate conversion of [guanido-(15)N(2)]arginine to [ureido-(15)N]citrulline, was greater in piglets receiving the +Arg diet (105) than in those receiving the -Arg diet (46, pooled SE: 10; P < 0.05). This multi-isotope method successfully allowed many aspects of arginine metabolism to be quantified simultaneously in vivo.
A survey of spatial deformation from a user-centered perspective

The spatial deformation methods are a family of modeling and animation techniques for indirectly reshaping an object by warping the surrounding space, with results that are similar to molding a highly malleable substance. They have the virtue of being computationally efficient (and hence interactive) and applicable to a variety of object representations. In this article we survey the state of the art in spatial deformation. Since manipulating ambient space directly is infeasible, deformations are controlled by tools of varying dimension—points, curves, surfaces and volumes—and it is on this basis that we classify them. Unlike previous surveys that concentrate on providing a single underlying mathematical formalism, we use the user-centered criteria of versatility, ease of use, efficiency and correctness to compare techniques.
A modular software architecture for simulating mechanical systems involving Coulomb friction integrable by the Runge-Kutta method

This paper presents a modular architecture of simulation software that is capable of properly capturing Coulomb friction in mechanical systems. The presented architecture is built upon Kikuuwe et al.psilas discrete-time friction model, which is based on the implicit Euler method. The paper reformulates the model into a form that can be integrable through the standard fourth order Runge-Kutta method. Some examples based on the presented architecture are presented.
Respiratory Epithelial Adenomatoid Hamartoma in the Nasal Cavity

We report a 65-year-old male with a hamartoma in the left nasal cavity. A mass was found in the left nasal cavity and was diagnosed as a benign tumor on the basis of preoperative findings. Left lateral rhinotomy was performed to completely remove it and the lesion was found to have arisen from the inferior turbinate. The pathological diagnosis was respiratory epithelial adenomatoid hamartoma. We discuss the pathological features of this disease.
A novel sequential approximate optimization approach using data mining for engineering design optimization

For most engineering design optimization problems, it is hard or even impossible to find the global optimum owing to the unaffordable computational cost. To overcome this difficulty, a sequential approximate optimization (SAO) approach that integrates the hybrid optimization algorithm with data mining and surrogate models is proposed to find the global optimum in engineering design optimization. The surrogate model is used to replace expensive simulation analysis and the data mining is applied to obtain the reduced search space. Thus, the efficiency of finding and quality of the global optimum will be increased by reducing the search space using data mining. The validity and efficiency of the proposed SAO approach are examined by studying typical numerical examples.
Glutathione Peroxidase-Catalase Cooperativity Is Required for Resistance to Hydrogen Peroxide by Mature Rat Oligodendrocytes

Oxidative mechanisms of injury are important in many neurological disorders, including hypoxic-ischemic brain damage. Cerebral palsy after preterm birth is hypothesized to be caused by hypoxic-ischemic injury of developing oligodendrocytes (OLs). Here we examined the developmental sensitivity of OLs to exogenous hydrogen peroxide (H2O2) with stage-specific rat oligodendrocyte cultures. We found that H2O2 itself or that generated by glucose oxidase was more toxic to developing than to mature OLs. Mature OLs were able to degrade H2O2 faster than developing OLs, suggesting that higher antioxidant enzyme activity might be the basis for their resistance. Catalase expression and activity were relatively constant during oligodendrocyte maturation, whereas glutathione peroxidase (GPx) was upregulated with a twofold to threefold increase in its expression and activity. Thus, it appeared that the developmental change in resistance to H2O2 was caused by modulation of GPx but not by catalase expression. To test the relative roles of catalase and GPx in the setting of oxidative stress, we measured enzyme activity in cells exposed to H2O2 and found that H2O2 induced a decrease in catalase activity in developing but not in mature OLs. Inhibition of GPx by mercaptosuccinate led to an increase in the vulnerability of mature OLs to H2O2 as well as a reduction in catalase activity. Finally, H2O2-dependent inactivation of catalase in developing OLs was prevented by the GPx mimic ebselen. These data provide evidence for a key role for GPx-catalase cooperativity in the resistance of mature OLs to H2O2-induced cell death.
Binding Modes of Zaragozic Acid A to Human Squalene Synthase and Staphylococcal Dehydrosqualene Synthase*

Background: Fungal metabolites, zaragozic acids, are potent inhibitors against squalene synthase and S. aureus dehydro-squalene synthase. Results: Here we reported the zaragozic acid A binding mode for the head-to-head prenyltransferase drug targets. Conclusion: Zaragozic acid A presents an unexpected binding mode from the cyclopropyl-containing intermediate in both enzymes. Significance: Our structures provide a structural basis for development of potential drugs for hyperlipidemias and bacterial infection treatments. Zaragozic acids (ZAs) belong to a family of fungal metabolites with nanomolar inhibitory activity toward squalene synthase (SQS). The enzyme catalyzes the committed step of sterol synthesis and has attracted attention as a potential target for antilipogenic and antiinfective therapies. Here, we have determined the structure of ZA-A complexed with human SQS. ZA-A binding induces a local conformational change in the substrate binding site, and its C-6 acyl group also extends over to the cofactor binding cavity. In addition, ZA-A effectively inhibits a homologous bacterial enzyme, dehydrosqualene synthase (CrtM), which synthesizes the precursor of staphyloxanthin in Staphylococcus aureus to cope with oxidative stress. Size reduction at Tyr248 in CrtM further increases the ZA-A binding affinity, and it reveals a similar overall inhibitor binding mode to that of human SQS/ZA-A except for the C-6 acyl group. These structures pave the way for further improving selectivity and development of a new generation of anticholesterolemic and antimicrobial inhibitors.
Regulation of follicle growth and apoptosis in cultured mouse ovaries by NGF and oxygen

Abstract Cryopreservation of ovarian tissue has been proposed for use in preserving female fertility before anticancer chemo-radiotherapy, because ovarian tissue contains a large pool of non-growing, primordial follicles. The mechanisms that regulate the exit of follicles from the pool are poorly understood. To determine optimal conditions for in vitro ovarian culture, we investigated the effects of nerve growth factor (NGF) and oxygen concentration on follicle growth and apoptosis. Oxygen concentration affected both cell proliferation and apoptosis. Under 20% oxygen, but not 1.5% or 5%, NGF decreased apoptosis in mouse ovaries by down-regulating the pro-apoptotic genes Bax and p53. In conclusion, high oxygen tension during in vitro ovarian culture promotes follicle growth and, in conjunction with NGF, suppresses apoptosis. The efficiency of this method to preserve fertility depends in part on the level of atresia. These results suggest that oxygen and NGF may be used to increase numbers of preantral follicles and mature oocytes in the culture of mammalian ovarian cortical strips.
WAIS-IV - Échelle d'intelligence de Wechsler pour adultes

Version pour francophones du Canada. Administration des sous-tests - Edition de recherche. -- Livret de reponses 1 : Reperage des symboles (25). -- Livret de reponses 2 : Annulation (25). -- WAIS-IV : Cahier de notation (25). -- WAIS-IV : Stimulus Book 1.
WORKING PAPER NO . 1347 ASSESSING DSGE MODEL NONLINEARITIES

We develop a new class of nonlinear time-series models to identify nonlinearities in the data and to evaluate nonlinear DSGE models. U.S. output growth and the federal funds rate display nonlinear conditional mean dynamics, while inflation and nominal wage growth feature conditional heteroskedasticity. We estimate a DSGE model with asymmetric wage/price adjustment costs and use predictive checks to assess its ability to account for nonlinearities. While it is able to match the nonlinear inflation and wage dynamics, thanks to the estimated downward wage/price rigidities, these do not spill over to output growth or the interest rate. (JEL C11, C32, C52, E32) ∗ Correspondence: B. Aruoba: University of Maryland, Department of Economics, University of Maryland, College Park, MD 20742. Email: aruoba@econ.umd. edu. L. Bocola, F. Schorfheide: University of Pennsylvania, Department of Economics, 3718 Locust Walk, University of Pennsylvania, Philadelphia, PA 19104. Email: lbocola@sas.upenn. edu (Bocola), schorf@ssc.upenn. edu (Schorfheide). We thank Jaroslav Borovicka, Frank Diebold, Gianni Lombardo, and Karel Mertens, as well as seminar participants at the 2011 FRB-NBER DSGE Conference, the 2011 (EC)2 Conference, the ECB, the Federal Reserve Bank of Chicago, the University of Pennsylvania, the University of Maryland, the University of Wisconsin, and Washington University of St. Louis for helpful comments. Much of this paper was written while the authors visited the Federal Reserve Bank of Philadelphia, whose hospitality they are thankful for. Aruoba and Schorfheide gratefully acknowledge financial support from the National Science Foundation under Grant SES 1061725. The views expressed in this paper are those of the authors and do not necessarily reflect the views of the Federal Reserve Bank of Philadelphia or the Federal Reserve System. This paper is available free of charge at www.philadelphiafed. org/research-and-data/publications/working-papers/.
Contextual Cues in Multiple-Item Recognition

Two experiments were conducted to determine whether performance on a multiple-item recognition (verbal discrimination) list was dependent on contextual cues as has been demonstrated using other memory paradigms. Experiment 1 used two different backgrounds during presentation of the study list. During the recognition task this background was either held constant or varied. The results suggested the context affected the recognition of incorrect items. In Experiment 2 the context variable was list membership. The results indicated that the recognition of list membership was limited to correct items. These results were interpreted in light of current models of multiple-item recognition.
Intercellular communication in bacteria

Bacteria have been long considered primitive organisms, with a lifestyle focused on the survival and propagation of single cells. However, in the past few decades it became obvious that bacteria can display sophisticated group behaviors. For instance, bacteria can communicate amongst themselves and with their hosts, by producing, sensing, and responding to chemical signals. By doing so, they can sense their surroundings and adapt as to increase their chances of survival and propagation. Here, we review the discovery of bacterial intercellular communication, some of the signaling molecules identified to date, the role of intercellular signaling in symbiotic and pathogenic relationships between bacteria and their hosts and its implications for the development of new therapeutic strategies against human disease.
Carcinoma of the endometrium: Effect of stage and grade on survival

Of 523 patients with endometrial carcinoma, 324 were FIGO stage Ia, 85 stage Ib, 24 stage II, 44 stage III, and 46 stage IV. High‐grade lesions were present in 7.1% with stage Ia, 18.8% with stage Ib, 37.5% with stage II, 29.6% with stage III, and 55.3% with stage IV. There was no significant difference from expected survival at 5, 10, and 15 years for patients with IaG1 or IbG1 disease. Patients with IaG2 and IbG2 disease showed similar survival, as did patients with IaG3 and IbG3 disease. Thus, uterine size seemed to make no difference in patient survival at comparable grades of disease. Deaths due to cancer at 5 years increased from 63% for stage Ia disease to 100% for stage IV disease. By absolute measurement of penetration, with increasing stage of disease there was greater penetration whether the disease was low or high in grade. Also, as the grade increased within a given stage, so did penetration of the myometrium.
A broadband modified differential phase shifter for microwave applications

In this paper, a novel broadband differential phase shifter is presented. In this design, multi-section coupled-lines are connected to a mirrored one to create a double-section to have a better coupling coefficient and frequency bandwidth of the phase shifter. In addition, the reference line of the conventional shiffman phase shifter is replaced with a similar structure of double coupled-lines to improve the phase and amplitude balance and the frequency response. The proposed design is simulated using the full-wave electromagnetic software IE3D and validated by the measurements. Compared with the cascading microstrip multi-section coupled-line configuration, the presented planar structure is symmetric and has a better performance. In order to prove the idea, the proposed structure is fabricated on a three plate stripline printed circuit and measured. The measured amplitude and phase imbalance between the two paths are within 0.4 dB and 1 degree over the frequency band of 2 to 6 GHz.
Bio-harmonized Dynamic Model of a Biology Inspired Carangiform Robotic Fish Underwater Vehicle

Abstract This paper presents a novel dynamic model of a bio-inspired robotic fish underwater vehicle by unifying conventional rigid body dynamics and bio-fluid-dynamics of a carangiform fish swimming given by Lighthill's (LH) slender body theory It proposes an inclusive mathematical design for better control and energy efficient path travel for the robotic fish. The system is modeled as an 2-link robot manipulator (caudal tail) with a mobile base (head). Lighthill caudal-tail reactive forces and moments are shown to contribute towards thrust generation and yaw balance. These LH reactive forces are shown to generate the inertial added mass during the robotic fish locomotion. This forward thrust drives the robotic fish head represented by a unified non-linear equation of motion in earth fixed frame. Using the proposed dynamic model an open-loop (manual) operating region for the identified kinematic parameter tail beat frequency (TBF) is established. Obtained Kinematic results also resemble with real fish kinematic results. The objective is to mimic the propulsion technique of the carangiform swimming style and to show the fish behavior navigating efficiently over large distances at impressive speeds and its exceptional character in fluid environment.