The Graduate Center, CUNY

Abstract The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy , which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project.

In 2008 we published the fi rst set of guidelines for standardiz- ing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the fi eld. Our knowledge base and relevant new tech- nologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in differ- ent 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 that there is a difference between meas urements that monitor the num- bers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the com- plete process including the amoun t and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accu mulation must be differentiated from stimuli that increas e autophagic activity, de fi ned as increased autophagy induction coupled with in creased delivery to, and degra- dation within, lysosomes (in most higher eukaryotes and some pro- tists such as Dictyostelium ) or the vacuole (in plants and fungi). In otherwords,itisespeciallyimportantthatinvestigatorsnewtothe fi eld understand that the appearance of more autophagosomes does not necessarily equate with mo re autophagy. In fact, in many cases, autophagosomes accumu late because of a block in traf fi cking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may re fl ect a reductionindegradativeactivity .Itisworthemphasizingherethat lysosomal digestion is a stage of au tophagy and evaluating its com- petence is a crucial part of the evaluation of autophagic fl ux, 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 for reviewers 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 appro- priate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no indi- vidual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays 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 autophagy- related 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 speci fi c marker for an autophagic process. In these guidelines, we con- sider 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 fi eld

During the past decade a number of variations in the simple up-down procedure have been used in psychoacoustic testing. A broad class of these methods is described with due emphasis on the related problems of parameter estimation and the efficient placing of observations. The advantages of up-down methods are many, including simplicity, high efficiency, robustness, small-sample reliability, and relative freedom from restrictive assumptions. Several applications of these procedures in psychoacoustics are described, including examples where conventional techniques are inapplicable.

The topic of how students become self-regulated as learners has attracted researchers for decades. Initial attempts to measure self-regulated learning (SRL) using questionnaires and interviews were successful in demonstrating significant predictions of students’ academic outcomes. The present article describes the second wave of research, which has involved the development of online measures of self-regulatory processes and motivational feelings or beliefs regarding learning in authentic contexts. These innovative methods include computer traces, think-aloud protocols, diaries of studying, direct observation, and microanalyses. Although still in the formative stage of development, these online measures are providing valuable new information regarding the causal impact of SRL processes as well as raising new questions for future study.

This book addresses how the new linguistic concept of 'Translanguaging' has contributed to our understandings of language, bilingualism and education, with potential to transform not only semiotic systems and speaker subjectivities, but also social structures.

A review and tutorial of the fundamental ideas and methods of joint time-frequency distributions is presented. The objective of the field is to describe how the spectral content of a signal changes in time and to develop the physical and mathematical ideas needed to understand what a time-varying spectrum is. The basic gal is to devise a distribution that represents the energy or intensity of a signal simultaneously in time and frequency. Although the basic notions have been developing steadily over the last 40 years, there have recently been significant advances. This review is intended to be understandable to the nonspecialist with emphasis on the diversity of concepts and motivations that have gone into the formation of the field.>

There is increasing evidence that subjective cognitive decline (SCD) in individuals with unimpaired performance on cognitive tests may represent the first symptomatic manifestation of Alzheimer's disease (AD). The research on SCD in early AD, however, is limited by the absence of common standards. The working group of the Subjective Cognitive Decline Initiative (SCD-I) addressed this deficiency by reaching consensus on terminology and on a conceptual framework for research on SCD in AD. In this publication, research criteria for SCD in pre-mild cognitive impairment (MCI) are presented. In addition, a list of core features proposed for reporting in SCD studies is provided, which will enable comparability of research across different settings. Finally, a set of features is presented, which in accordance with current knowledge, increases the likelihood of the presence of preclinical AD in individuals with SCD. This list is referred to as SCD plus.

The principal limitations of the terms NAFLD and NASH are the reliance on exclusionary confounder terms and the use of potentially stigmatising language. This study set out to determine if content experts and patient advocates were in favor of a change in nomenclature and/or definition. A modified Delphi process was led by three large pan-national liver associations. The consensus was defined a priori as a supermajority (67%) vote. An independent committee of experts external to the nomenclature process made the final recommendation on the acronym and its diagnostic criteria. A total of 236 panelists from 56 countries participated in 4 online surveys and 2 hybrid meetings. Response rates across the 4 survey rounds were 87%, 83%, 83%, and 78%, respectively. Seventy-four percent of respondents felt that the current nomenclature was sufficiently flawed to consider a name change. The terms "nonalcoholic" and "fatty" were felt to be stigmatising by 61% and 66% of respondents, respectively. Steatotic liver disease was chosen as an overarching term to encompass the various aetiologies of steatosis. The term steatohepatitis was felt to be an important pathophysiological concept that should be retained. The name chosen to replace NAFLD was metabolic dysfunction-associated steatotic liver disease. There was consensus to change the definition to include the presence of at least 1 of 5 cardiometabolic risk factors. Those with no metabolic parameters and no known cause were deemed to have cryptogenic steatotic liver disease. A new category, outside pure metabolic dysfunction-associated steatotic liver disease, termed metabolic and alcohol related/associated liver disease (MetALD), was selected to describe those with metabolic dysfunction-associated steatotic liver disease, who consume greater amounts of alcohol per week (140-350 g/wk and 210-420 g/wk for females and males, respectively). The new nomenclature and diagnostic criteria are widely supported and nonstigmatising, and can improve awareness and patient identification.

The principal limitations of the terms NAFLD and NASH are the reliance on exclusionary confounder terms and the use of potentially stigmatising language. This study set out to determine if content experts and patient advocates were in favour of a change in nomenclature and/or definition. A modified Delphi process was led by three large pan-national liver associations. The consensus was defined a priori as a supermajority (67%) vote. An independent committee of experts external to the nomenclature process made the final recommendation on the acronym and its diagnostic criteria. A total of 236 panellists from 56 countries participated in 4 online surveys and 2 hybrid meetings. Response rates across the 4 survey rounds were 87%, 83%, 83%, and 78%, respectively. Seventy-four percent of respondents felt that the current nomenclature was sufficiently flawed to consider a name change. The terms "nonalcoholic" and "fatty" were felt to be stigmatising by 61% and 66% of respondents, respectively. Steatotic liver disease was chosen as an overarching term to encompass the various aetiologies of steatosis. The term steatohepatitis was felt to be an important pathophysiological concept that should be retained. The name chosen to replace NAFLD was metabolic dysfunction-associated steatotic liver disease (MASLD). There was consensus to change the definition to include the presence of at least 1 of 5 cardiometabolic risk factors. Those with no metabolic parameters and no known cause were deemed to have cryptogenic steatotic liver disease. A new category, outside pure metabolic dysfunction-associated steatotic liver disease, termed metabolic and alcohol related/associated liver disease (MetALD), was selected to describe those with metabolic dysfunction-associated steatotic liver disease, who consume greater amounts of alcohol per week (140-350 g/wk and 210-420 g/wk for females and males, respectively). The new nomenclature and diagnostic criteria are widely supported and non-stigmatising, and can improve awareness and patient identification.

This software note announces a new open‐source release of the Maxent software for modeling species distributions from occurrence records and environmental data, and describes a new R package for fitting such models. The new release (ver. 3.4.0) will be hosted online by the American Museum of Natural History, along with future versions. It contains small functional changes, most notably use of a complementary log‐log (cloglog) transform to produce an estimate of occurrence probability. The cloglog transform derives from the recently‐published interpretation of Maxent as an inhomogeneous Poisson process (IPP), giving it a stronger theoretical justification than the logistic transform which it replaces by default. In addition, the new R package, maxnet, fits Maxent models using the glmnet package for regularized generalized linear models. We discuss the implications of the IPP formulation in terms of model inputs and outputs, treating occurrence records as points rather than grid cells and interpreting the exponential Maxent model (raw output) as as an estimate of relative abundance. With these two open‐source developments, we invite others to freely use and contribute to the software.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Some 70 years after its development in Frankfurt, Germany, critical theory retains its ability to disrupt and hallenge the status quo. In the process, it elicits highlycharged emotions of all types—fierce loyalty from its roponents, vehement hostility from its detractors. Such vibrantly polar reactions indicate at the very least that critical theory still matters. We can be against critical theory or for it, but, especially at the present historical uncture, we cannot be without it. These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Spatial thinning of species occurrence records can help address problems associated with spatial sampling biases. Ideally, thinning removes the fewest records necessary to substantially reduce the effects of sampling bias, while simultaneously retaining the greatest amount of useful information. Spatial thinning can be done manually; however, this is prohibitively time consuming for large datasets. Using a randomization approach, the ‘thin’ function in the spThin R package returns a dataset with the maximum number of records for a given thinning distance, when run for sufficient iterations. We here provide a worked example for the Caribbean spiny pocket mouse, where the results obtained match those of manual thinning.

Exceptional points are branch point singularities in the parameter space of a system at which two or more eigenvalues, and their corresponding eigenvectors, coalesce and become degenerate. Such peculiar degeneracies are distinct features of non-Hermitian systems, which do not obey conservation laws because they exchange energy with the surrounding environment. Non-Hermiticity has been of great interest in recent years, particularly in connection with the quantum mechanical notion of parity-time symmetry, after the realization that Hamiltonians satisfying this special symmetry can exhibit entirely real spectra. These concepts have become of particular interest in photonics because optical gain and loss can be integrated and controlled with high resolution in nanoscale structures, realizing an ideal playground for non-Hermitian physics, parity-time symmetry, and exceptional points. As we control dissipation and amplification in a nanophotonic system, the emergence of exceptional point singularities dramatically alters their overall response, leading to a range of exotic optical functionalities associated with abrupt phase transitions in the eigenvalue spectrum. These concepts enable ultrasensitive measurements, superior manipulation of the modal content of multimode lasers, and adiabatic control of topological energy transfer for mode and polarization conversion. Non-Hermitian degeneracies have also been exploited in exotic laser systems, new nonlinear optics schemes, and exotic scattering features in open systems. Here we review the opportunities offered by exceptional point physics in photonics, discuss recent developments in theoretical and experimental research based on photonic exceptional points, and examine future opportunities in this area from basic science to applied technology.

Anthropologists have been committed, at least since Franz Boas, to investigating relationships between nature and culture. At the dawn of the 21st century, this enduring interest was inflected with some new twists. An emergent cohort of “multispecies ethnographers” began to place a fresh emphasis on the subjectivity and agency of organisms whose lives are entangled with humans. Multispecies ethnography emerged at the intersection of three interdisciplinary strands of inquiry: environmental studies, science and technology studies (STS), and animal studies. Departing from classically ethnobiological subjects, useful plants and charismatic animals, multispecies ethnographers also brought understudied organisms—such as insects, fungi, and microbes—into anthropological conversations. Anthropologists gathered together at the Multispecies Salon, an art exhibit, where the boundaries of an emerging interdiscipline were probed amidst a collection of living organisms, artifacts from the biological sciences, and surprising biopolitical interventions.

We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise (CP) method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G(d,p) and D95++(d,p) basis sets at both the Hartree–Fock and second-order Mo/ller–Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the (more traditional) single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative (before vibrational corrections) and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone.

Summary Recent studies have demonstrated a need for increased rigour in building and evaluating ecological niche models ( ENM s) based on presence‐only occurrence data. Two major goals are to balance goodness‐of‐fit with model complexity (e.g. by ‘tuning’ model settings) and to evaluate models with spatially independent data. These issues are especially critical for data sets suffering from sampling bias, and for studies that require transferring models across space or time (e.g. responses to climate change or spread of invasive species). Efficient implementation of procedures to accomplish these goals, however, requires automation. We developed ENM eval , an R package that: (i) creates data sets for k ‐fold cross‐validation using one of several methods for partitioning occurrence data (including options for spatially independent partitions), (ii) builds a series of candidate models using Maxent with a variety of user‐defined settings and (iii) provides multiple evaluation metrics to aid in selecting optimal model settings. The six methods for partitioning data are n −1 jackknife, random k ‐folds ( = bins), user‐specified folds and three methods of masked geographically structured folds. ENM eval quantifies six evaluation metrics: the area under the curve of the receiver‐operating characteristic plot for test localities ( AUC TEST ), the difference between training and testing AUC ( AUC DIFF ), two different threshold‐based omission rates for test localities and the Akaike information criterion corrected for small sample sizes ( AIC c). We demonstrate ENM eval by tuning model settings for eight tree species of the genus Coccoloba in Puerto Rico based on AIC c. Evaluation metrics varied substantially across model settings, and models selected with AIC c differed from default ones. In summary, ENMeval facilitates the production of better ENM s and should promote future methodological research on many outstanding issues.

Abstract The concept of translanguaging is clarified, establishing it as a particular conception of the mental grammars and linguistic practices of bilinguals. Translanguaging is different from code switching . Under translanguaging, the mental grammars of bilinguals are structured but unitary collections of features, and the practices of bilinguals are acts of feature selection, not of grammar switch. A proper understanding of translanguaging requires a return to the well known but often forgotten idea that named languages are social, not linguistic, objects. Whereas the idiolect of a particular individual is a linguistic object defined in terms of lexical and structural features, the named language of a nation or social group is not; its boundaries and membership cannot be established on the basis of lexical and structural features. The two named languages of the bilingual exist only in the outsider’s view. From the insider’s perspective of the speaker, there is only his or her full idiolect or repertoire, which belongs only to the speaker, not to any named language. Translanguaging is the deployment of a speaker’s full linguistic repertoire without regard for watchful adherence to the socially and politically defined boundaries of named (and usually national and state) languages . In schools, the translanguaging of bilinguals tends to be severely restricted. In addition, schools confuse the assessment of general linguistic proficiency, which is best manifested in bilinguals while translanguaging, with the testing of proficiency in a named language, which insists on inhibiting translanguaging. The concept of translanguaging is of special relevance to schools interested in the linguistic and intellectual growth of bilingual students as well as to minoritized communities involved in language maintenance and revitalization efforts.

High Resolution Image Download MS PowerPoint Slide AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

Large-scale labeled data are generally required to train deep neural networks in order to obtain better performance in visual feature learning from images or videos for computer vision applications. To avoid extensive cost of collecting and annotating large-scale datasets, as a subset of unsupervised learning methods, self-supervised learning methods are proposed to learn general image and video features from large-scale unlabeled data without using any human-annotated labels. This paper provides an extensive review of deep learning-based self-supervised general visual feature learning methods from images or videos. First, the motivation, general pipeline, and terminologies of this field are described. Then the common deep neural network architectures that used for self-supervised learning are summarized. Next, the schema and evaluation metrics of self-supervised learning methods are reviewed followed by the commonly used datasets for images, videos, audios, and 3D data, as well as the existing self-supervised visual feature learning methods. Finally, quantitative performance comparisons of the reviewed methods on benchmark datasets are summarized and discussed for both image and video feature learning. At last, this paper is concluded and lists a set of promising future directions for self-supervised visual feature learning.