University of Central Florida

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

Abstract: SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

Social exchange theory (SET) is one the most influential conceptual paradigms in organizational behavior. Despite its usefulness, theoretical ambiguities within SET remain. As a consequence, tests of the model, as well as its applications, tend to rely on an incompletely specified set of ideas. The authors address conceptual difficulties and highlight areas in need of additional research. In so doing, they pay special attention to four issues: (a) the roots of the conceptual ambiguities, (b) norms and rules of exchange, (c) nature of the resources being exchanged, and (d) social exchange relationships.

A sensitive single-beam technique for measuring both the nonlinear refractive index and nonlinear absorption coefficient for a wide variety of materials is reported. The authors describe the experimental details and present a comprehensive theoretical analysis including cases where nonlinear refraction is accompanied by nonlinear absorption. In these experiments, the transmittance of a sample is measured through a finite aperture in the far field as the sample is moved along the propagation path (z) of a focused Gaussian beam. The sign and magnitude of the nonlinear refraction are easily deduced from such a transmittance curve (Z-scan). Employing this technique, a sensitivity of better than lambda /300 wavefront distortion is achieved in n/sub 2/ measurements of BaF/sub 2/ using picosecond frequency-doubled Nd:YAG laser pulses.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

The goal of this article is to review the state-of-the-art tracking methods, classify them into different categories, and identify new trends. Object tracking, in general, is a challenging problem. Difficulties in tracking objects can arise due to abrupt object motion, changing appearance patterns of both the object and the scene, nonrigid object structures, object-to-object and object-to-scene occlusions, and camera motion. Tracking is usually performed in the context of higher-level applications that require the location and/or shape of the object in every frame. Typically, assumptions are made to constrain the tracking problem in the context of a particular application. In this survey, we categorize the tracking methods on the basis of the object and motion representations used, provide detailed descriptions of representative methods in each category, and examine their pros and cons. Moreover, we discuss the important issues related to tracking including the use of appropriate image features, selection of motion models, and detection of objects.

Abstract This book contributes to the idea that to have an understanding of the mind, consciousness, or cognition, a detailed scientific and phenomenological understanding of the body is essential. There is still a need to develop a common vocabulary that is capable of integrating discussions of brain mechanisms in neuroscience, behavioral expressions in psychology, design concerns in artificial intelligence and robotics, and debates about embodied experience in the phenomenology and philosophy of mind. This book helps to formulate this common vocabulary by developing a conceptual framework that avoids both the overly reductionistic approaches that explain everything in terms of bottom-up neuronal mechanisms, and the inflationistic approaches that explain everything in terms of Cartesian, top-down cognitive states. Through discussions of neonate imitation, the Molyneux problem, gesture, self-awareness, free will, social cognition and intersubjectivity, as well as pathologies such as deafferentation, unilateral neglect, phantom limb, autism and schizophrenia, the book proposes to remap the conceptual landscape by revitalizing the concepts of body image and body schema, proprioception, ecological experience, intermodal perception, and enactive concepts of ownership and agency for action. Informed by both philosophical theory and scientific evidence, it addresses two basic sets of questions that concern the structure of embodied experience. First, questions about the phenomenal aspects of that structure, specifically the relatively regular and constant phenomenal features found in the content of experience. Second, questions about aspects of the structure of consciousness that are more hidden, those that may be more difficult to get at because they happen before one knows it, and do not normally enter into the phenomenal content of experience in an explicit way.

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

In 1998, Bender and Boettcher found that a wide class of Hamiltonians, even though non-Hermitian, can still exhibit entirely real spectra provided that they obey parity-time requirements or PT symmetry. Here we demonstrate experimentally passive PT-symmetry breaking within the realm of optics. This phase transition leads to a loss induced optical transparency in specially designed pseudo-Hermitian guiding potentials.

The rigorous coupled-wave analysis technique for describing the diffraction of electromagnetic waves by periodic grating structures is reviewed. Formulations for a stable and efficient numerical implementation of the analysis technique are presented for one-dimensional binary gratings for both TE and TM polarization and for the general case of conical diffraction. It is shown that by exploitation of the symmetry of the diffraction problem a very efficient formulation, with up to an order-of-magnitude improvement in the numerical efficiency, is produced. The rigorous coupled-wave analysis is shown to be inherently stable. The sources of potential numerical problems associated with underflow and overflow, inherent in digital calculations, are presented. A formulation that anticipates and preempts these instability problems is presented. The calculated diffraction efficiencies for dielectric gratings are shown to converge to the correct value with an increasing number of space harmonics over a wide range of parameters, including very deep gratings. The effect of the number of harmonics on the convergence of the diffraction efficiencies is investigated. More field harmonics are shown to be required for the convergence of gratings with larger grating periods, deeper gratings, TM polarization, and conical diffraction.

The isolation of graphene in 2004 from graphite was a defining moment for the "birth" of a field: two-dimensional (2D) materials. In recent years, there has been a rapidly increasing number of papers focusing on non-graphene layered materials, including transition-metal dichalcogenides (TMDs), because of the new properties and applications that emerge upon 2D confinement. Here, we review significant recent advances and important new developments in 2D materials "beyond graphene". We provide insight into the theoretical modeling and understanding of the van der Waals (vdW) forces that hold together the 2D layers in bulk solids, as well as their excitonic properties and growth morphologies. Additionally, we highlight recent breakthroughs in TMD synthesis and characterization and discuss the newest families of 2D materials, including monoelement 2D materials (i.e., silicene, phosphorene, etc.) and transition metal carbide- and carbon nitride-based MXenes. We then discuss the doping and functionalization of 2D materials beyond graphene that enable device applications, followed by advances in electronic, optoelectronic, and magnetic devices and theory. Finally, we provide perspectives on the future of 2D materials beyond graphene.

We present a simple yet highly sensitive single-beam experimental technique for the determination of both the sign and magnitude of n(2). The sample is moved along the z direction of a focused Gaussian beam while the repetitively pulsed laser energy is held fixed. The resultant plot of transmittance through an aperture in the far field yields a dispersion-shaped curve from which n(2) is easily calculated. A transmittance change of 1% corresponds to a phase distortion of approximately lambda/250. We demonstrate this method on several materials using both CO(2) and Nd:YAG laser pulses.

A review of supercapacitor electrode materials with 0, 1, 2, and 3 dimensional nanostructures.

BACKGROUND: Low muscle mass and weakness are common and potentially disabling in older adults, but in order to become recognized as a clinical condition, criteria for diagnosis should be based on clinically relevant thresholds and independently validated. The Foundation for the National Institutes of Health Biomarkers Consortium Sarcopenia Project used an evidence-based approach to develop these criteria. Initial findings were presented at a conference in May 2012, which generated recommendations that guided additional analyses to determine final recommended criteria. Details of the Project and its findings are presented in four accompanying manuscripts. METHODS: The Foundation for the National Institutes of Health Sarcopenia Project used data from nine sources of community-dwelling older persons: Age, Gene/Environment Susceptibility-Reykjavik Study, Boston Puerto Rican Health Study, a series of six clinical trials, Framingham Heart Study, Health, Aging, and Body Composition, Invecchiare in Chianti, Osteoporotic Fractures in Men Study, Rancho Bernardo Study, and Study of Osteoporotic Fractures. Feedback from conference attendees was obtained via surveys and breakout groups. RESULTS: The pooled sample included 26,625 participants (57% women, mean age in men 75.2 [±6.1 SD] and in women 78.6 [±5.9] years). Conference attendees emphasized the importance of evaluating the influence of body mass on cutpoints. Based on the analyses presented in this series, the final recommended cutpoints for weakness are grip strength <26kg for men and <16kg for women, and for low lean mass, appendicular lean mass adjusted for body mass index <0.789 for men and <0.512 for women. CONCLUSIONS: These evidence-based cutpoints, based on a large and diverse population, may help identify participants for clinical trials and should be evaluated among populations with high rates of functional limitations.

We report the first observation of Airy optical beams. This intriguing class of wave packets, initially predicted by Berry and Balazs in 1979, has been realized in both one- and two-dimensional configurations. As demonstrated in our experiments, these Airy beams can exhibit unusual features such as the ability to remain diffraction-free over long distances while they tend to freely accelerate during propagation.

The endogenous two-break unit root test of Lumsdaine and Papell is derived assuming no structural breaks under the null. Thus, rejection of the null does not necessarily imply rejection of a unit root per se, but may imply rejection of a unit root without break. Similarly, the alternative does not necessarily imply trend stationarity with breaks, but may indicate a unit root with breaks. In this paper, we propose an endogenous two-break Lagrange multiplier unit root test that allows for breaks under both the null and alternative hypotheses. As a result, rejection of the null unambiguously implies trend stationarity.

Transepithelial/transendothelial electrical resistance (TEER) is a widely accepted quantitative technique to measure the integrity of tight junction dynamics in cell culture models of endothelial and epithelial monolayers. TEER values are strong indicators of the integrity of the cellular barriers before they are evaluated for transport of drugs or chemicals. TEER measurements can be performed in real time without cell damage and generally are based on measuring ohmic resistance or measuring impedance across a wide spectrum of frequencies. The measurements for various cell types have been reported with commercially available measurement systems and also with custom-built microfluidic implementations. Some of the barrier models that have been widely characterized using TEER include the blood-brain barrier (BBB), gastrointestinal (GI) tract, and pulmonary models. Variations in these values can arise due to factors such as temperature, medium formulation, and passage number of cells. The aim of this article is to review the different TEER measurement techniques and analyze their strengths and weaknesses, determine the significance of TEER in drug toxicity studies, examine the various in vitro models and microfluidic organs-on-chips implementations using TEER measurements in some widely studied barrier models (BBB, GI tract, and pulmonary), and discuss the various factors that can affect TEER measurements.

The possibility of parity-time (PT) symmetric periodic potentials is investigated within the context of optics. Beam dynamics in this new type of optical structures is examined in detail for both one- and two-dimensional lattice geometries. It is shown that PT periodic structures can exhibit unique characteristics stemming from the nonorthogonality of the associated Floquet-Bloch modes. Some of these features include double refraction, power oscillations, and eigenfunction unfolding as well as nonreciprocal diffraction patterns.

IMPORTANCE: The Global Burden of Diseases, Injuries, and Risk Factors Study 2019 (GBD 2019) provided systematic estimates of incidence, morbidity, and mortality to inform local and international efforts toward reducing cancer burden. OBJECTIVE: To estimate cancer burden and trends globally for 204 countries and territories and by Sociodemographic Index (SDI) quintiles from 2010 to 2019. EVIDENCE REVIEW: The GBD 2019 estimation methods were used to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life years (DALYs) in 2019 and over the past decade. Estimates are also provided by quintiles of the SDI, a composite measure of educational attainment, income per capita, and total fertility rate for those younger than 25 years. Estimates include 95% uncertainty intervals (UIs). FINDINGS: In 2019, there were an estimated 23.6 million (95% UI, 22.2-24.9 million) new cancer cases (17.2 million when excluding nonmelanoma skin cancer) and 10.0 million (95% UI, 9.36-10.6 million) cancer deaths globally, with an estimated 250 million (235-264 million) DALYs due to cancer. Since 2010, these represented a 26.3% (95% UI, 20.3%-32.3%) increase in new cases, a 20.9% (95% UI, 14.2%-27.6%) increase in deaths, and a 16.0% (95% UI, 9.3%-22.8%) increase in DALYs. Among 22 groups of diseases and injuries in the GBD 2019 study, cancer was second only to cardiovascular diseases for the number of deaths, years of life lost, and DALYs globally in 2019. Cancer burden differed across SDI quintiles. The proportion of years lived with disability that contributed to DALYs increased with SDI, ranging from 1.4% (1.1%-1.8%) in the low SDI quintile to 5.7% (4.2%-7.1%) in the high SDI quintile. While the high SDI quintile had the highest number of new cases in 2019, the middle SDI quintile had the highest number of cancer deaths and DALYs. From 2010 to 2019, the largest percentage increase in the numbers of cases and deaths occurred in the low and low-middle SDI quintiles. CONCLUSIONS AND RELEVANCE: The results of this systematic analysis suggest that the global burden of cancer is substantial and growing, with burden differing by SDI. These results provide comprehensive and comparable estimates that can potentially inform efforts toward equitable cancer control around the world.

OBJECTIVE: to examine the clinical evidence reporting the prevalence of sarcopenia and the effect of nutrition and exercise interventions from studies using the consensus definition of sarcopenia proposed by the European Working Group on Sarcopenia in Older People (EWGSOP). METHODS: PubMed and Dialog databases were searched (January 2000-October 2013) using pre-defined search terms. Prevalence studies and intervention studies investigating muscle mass plus strength or function outcome measures using the EWGSOP definition of sarcopenia, in well-defined populations of adults aged ≥50 years were selected. RESULTS: prevalence of sarcopenia was, with regional and age-related variations, 1-29% in community-dwelling populations, 14-33% in long-term care populations and 10% in the only acute hospital-care population examined. Moderate quality evidence suggests that exercise interventions improve muscle strength and physical performance. The results of nutrition interventions are equivocal due to the low number of studies and heterogeneous study design. Essential amino acid (EAA) supplements, including ∼2.5 g of leucine, and β-hydroxy β-methylbutyric acid (HMB) supplements, show some effects in improving muscle mass and function parameters. Protein supplements have not shown consistent benefits on muscle mass and function. CONCLUSION: prevalence of sarcopenia is substantial in most geriatric settings. Well-designed, standardised studies evaluating exercise or nutrition interventions are needed before treatment guidelines can be developed. Physicians should screen for sarcopenia in both community and geriatric settings, with diagnosis based on muscle mass and function. Supervised resistance exercise is recommended for individuals with sarcopenia. EAA (with leucine) and HMB may improve muscle outcomes.