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Categorical perception in animal communication and decision-making
No full textThe information an animal gathers from its environment, including that associated with signals, often varies continuously. Animals may respond to this continuous variation in a physical stimulus as lying in discrete categories rather than along a continuum, a phenomenon known as categorical perception. Categorical perception was first described in the context of speech and thought to be uniquely associated with human language. Subsequent work has since discovered that categorical perception functions in communication and decision-making across animal taxa, behavioral contexts, and sensory modalities. We begin with an overview of how categorical perception functions in speech perception and, then, describe subsequent work illustrating its role in nonhuman animal communication and decision-making. We synthesize this work to suggest that categorical perception may be favored where there is a benefit to 1) setting consistent behavioral response rules in the face of variation and potential overlap in the physical structure of signals, 2) especially rapid decision-making, or 3) reducing the costs associated with processing and/or comparing signals. We conclude by suggesting other systems in which categorical perception may play a role as a next step toward understanding how this phenomenon may influence our thinking about the function and evolution of animal communication and decision-making
Graphene-based Josephson Triode
No full textThere has been a growing interest to the materials with broken time-reversal and inversion symmetry, which can support non-reciprocal superconducting currents [1]. This search for an intrinsic superconducting diode has so far resulted in devices that typically show a few percent difference between the magnitudes of the supercurrent flowing in the positive and negative directions. We show that required time-reversal symmetry breaking can be achieved in multiterminal Josephson junctions [2], resulting in supercurrent rectification approaching 100%
Detecting a Majorana-fermion zero mode using a quantum dot
No full textWe propose an experimental setup for detecting a Majorana zero mode consisting of a spinless quantum dot coupled to the end of a p-wave superconducting nanowire. The Majorana bound state at the end of the wire strongly influences the conductance through the quantum dot: Driving the wire through the topological phase transition causes a sharp jump in the conductance by a factor of 1/2. In the topological phase, the zero-temperature peak value of the dot conductance (i.e., when the dot is on resonance and symmetrically coupled to the leads) is e2/2h. In contrast, if the wire is in its trivial phase, the conductance peak value is e2/h, or if a regular fermionic zero mode occurs on the end of the wire, the conductance is 0. The system can also be used to tune Flensberg's qubit system to the required degeneracy point. © 2011 American Physical Society
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.
No full textMorphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies-structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge-in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.]
Bayesian Nonparametric Methods for Epidemiology and Clustering
No full textBayesian nonparametric methods employ prior distributions with large support in the space of probabilistic models. The flexibility of these methods enables them to address challenging inference tasks. This thesis develops Bayesian nonparametric methodologies for problems in epidemiology and clustering. During an infectious disease outbreak, there is interest in (1) understanding the impact of environmental conditions, human behavior, genetic variants, and public policy on transmission; (2) monitoring the rate of transmissions across regions and over time; and (3) producing short-term forecasts of disease incidence to facilitate decision making and planning by policy makers and members of the public. The data which are typically available to address these questions are incidence data – cases, hospitalizations, or deaths occurring in a certain population during a certain time interval – pose a challenge to methodology as they have an indirect and nonlinear relationship with the transmission rate, and they may suffer from artifacts and systematic biases that can vary across time and across regions. In Chapter 2 we exploit the flexibility of Bayesian nonparametric models to account for the many irregularities in these data. Cluster analysis is the task of identifying meaningful subgroups in data. A large variety of algorithms for clustering have been developed, but within the Bayesian paradigm, clustering has nearly always been performed by associating observations with components of a mixture distribution. These mixture models are inherently limited by a tradeoff between component flexibility and identifiability. Thus, relatively inflexible components are used, often leading to disappointing results. In Chapter 3, we develop a decision theoretic framework for Bayesian Level-Set (BALLET) clustering, which exploits Bayesian nonparametric density posteriors. The approach avoids some pitfalls of classical Bayesian clustering methods by leveraging ideas from the algorithmic and frequentist literature. Finally, we note that level-set clustering represents a simple example of clustering into non-exchangeable subsets, since one part is designated as noise points. In Chapter 4, we develop loss functions for non-exchangeable partitions with an arbitrary number of categories. We show that the notion of Categorized Partitions (CaPos) is useful in practical situations and that our novel loss functions yield sensible decision-theoretic point estimates.</p
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.
No full textSince the publication of the Society for Immunotherapy of Cancer's (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients
Rod fractures in thoracolumbar fusions to the sacrum/pelvis for adult symptomatic lumbar scoliosis: long-term follow-up of a prospective, multicenter cohort of 160 patients.
No full textObjectivePrevious reports of rod fracture (RF) in adult spinal deformity are limited by heterogeneous cohorts, low follow-up rates, and relatively short follow-up durations. Since the majority of RFs present > 2 years after surgery, true occurrence and revision rates remain unclear. The objectives of this study were to better understand the risk factors for RF and assess its occurrence and revision rates following primary thoracolumbar fusions to the sacrum/pelvis for adult symptomatic lumbar scoliosis (ASLS) in a prospective series with long-term follow-up.MethodsPatient records were obtained from the Adult Symptomatic Lumbar Scoliosis-1 (ASLS-1) database, an NIH-sponsored multicenter, prospective study. Inclusion criteria were as follows: patients aged 40-80 years undergoing primary surgeries for ASLS (Cobb angle ≥ 30° and Oswestry Disability Index ≥ 20 or Scoliosis Research Society-22r ≤ 4.0 in pain, function, and/or self-image) with instrumented fusion of ≥ 7 levels that included the sacrum/pelvis. Patients with and without RF were compared to assess risk factors for RF and revision surgery.ResultsInclusion criteria were met by 160 patients (median age 62 years, IQR 55.7-67.9 years). At a median follow-up of 5.1 years (IQR 3.8-6.6 years), there were 92 RFs in 62 patients (38.8%). The median time to RF was 3.0 years (IQR 1.9-4.54 years), and 73% occurred > 2 years following surgery. Based on Kaplan-Meier analyses, estimated RF rates at 2, 4, 5, and 8 years after surgery were 11%, 24%, 35%, and 49%, respectively. Baseline radiographic, clinical, and demographic characteristics were similar between patients with and without RF. In Cox regression models, greater postoperative pelvic tilt (HR 1.895, 95% CI 1.196-3.002, p = 0.0065) and greater estimated blood loss (HR 1.02, 95% CI 1.005-1.036, p = 0.0088) were associated with increased risk of RF. Thirty-eight patients (61% of all RFs) underwent revision surgery. Bilateral RF was predictive of revision surgery (HR 3.52, 95% CI 1.8-6.9, p = 0.0002), while patients with unilateral nondisplaced RFs were less likely to require revision (HR 0.39, 95% CI 0.18-0.84, p = 0.016).ConclusionsThis study provides what is to the authors' knowledge the highest-quality data to date on RF rates following ASLS surgery. At a median follow-up of 5.1 years, 38.8% of patients had at least one RF. Estimated RF rates at 2, 4, 5, and 8 years after surgery were 11%, 24%, 35%, and 49%, respectively. Greater estimated blood loss and postoperative pelvic tilt were significant risk factors for RF. These findings emphasize the importance of long-term follow-up to realize the true prevalence and cumulative incidence of RF
Taxes and Subsidies and the Transition to Clean Cooking: A Review of Relevant Theoretical and Empirical Insights
No full textUnited Nations Sustainable Development Goal 7.1 sets a target of ensuring universal access to affordable, reliable, and modern energy services by 2030. Unfortunately, many low- and middle-income countries (LMICs) are well off course to meet this target, especially with respect to access to clean cooking energy. Though many challenges impede progress, cost barriers are perhaps most significant. This report discusses the role of subsidy and tax policies—levied on both the supply and demand side of this market—in affecting progress toward universal access to clean cooking in LMICs. Moreover, we also combat a common myth among those opposing subsidies for clean cooking: we show that a “fear of spoiling the market” with such incentives finds little empirical support in the literature. This report offers recommendations to policy makers, in addition to a case study on clean cooking transitions in Nepal
Management Prioritization in a Public-Facing Urban Wetland
No full textThe Museum of Life and Science is a nature center and science museum located in Durham, North Carolina, working to understand and improve the health of an urban wetland ecosystem located on their campus. The majority of the natural land cover within the wetland’s watershed is forested and managed by the Museum, so a forest inventory and management analysis was conducted to understand potential impacts on the wetland. Interviews and a literature review produced alternatives for community-based environmental management in urban ecosystems that formed a basis for a multi-criteria decision analysis framework. This paper provides a decision-making methodology for the Museum of Life and Science to assess potential environmental management decisions and recommendations through a forestry lens to improve watershed health while meeting their mission