Fabrication of an Atom Chip for Rydberg Atom-Metal Surface Interaction Studies

This thesis outlines the fabrication of two atom chips for the study of interactions between ⁸⁷Rb Rydberg atoms and a Au surface. Atom chips yield tightly confined, cold samples of an atomic species by generating magnetic fields with high gradients using microfabricated current-carrying wires. These ground state atoms may in turn be excited to Rydberg states. The trapping wires of Chip 1 are fabricated using thermally evaporated Cr/Au and patterned using lift-off photolithography. Chip 2 uses a Ti/Pd/Au tri-layer, instead of Cr/Au, to minimize interdiffusion. The chip has a thermally evaporated Au surface layer for Rydberg atom-surface interactions, which is separated from the underlying trapping wires by a planarizing polyimide dielectric. The polyimide was patterned using reactive ion etching. Special attention was paid to the edge roughness and electrical properties of the trapping wires, the planarization of the polyimide, and the grain structure of the Au surface

For What it is Worth: Meditations on the Meaning of Life with Camus and Nozick

The meaning of life is an enduring philosophical question. This paper seeks to explore the thought of Albert Camus and Robert Nozick on the meaning of life and critically examine their contributions to philosophy. Camus begins with contemplating whether life is worth ending or worth living and concludes that only an eternal revolt against the absurdity of the universe makes life worth living. Nozick begins with examining the link between questions of meaning and a finite existence and concludes with a theory of meaning as a constant interplay of value and meaning creating ‘worth’, but on a foundation of free choice. Each gives unique analyses and conclusions, but both founder on the inability of their theories of meaning to build an objective philosophical basis for meaning. This leads to a contemplation of balancing unresolved tension between philosophical tensions and life as we live it.Key Words: Camus, Nozick, meaning, life, value, purpose, worth, suicide, philosoph

Towards BioDBcore: a community-defined information specification for biological databases

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological database

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis

Computational approaches have promised to organize collections of functional genomics data into testable predictions of gene and protein involvement in biological processes and pathways. However, few such predictions have been experimentally validated on a large scale, leaving many bioinformatic methods unproven and underutilized in the biology community. Further, it remains unclear what biological concerns should be taken into account when using computational methods to drive real-world experimental efforts. To investigate these concerns and to establish the utility of computational predictions of gene function, we experimentally tested hundreds of predictions generated from an ensemble of three complementary methods for the process of mitochondrial organization and biogenesis in Saccharomyces cerevisiae. The biological data with respect to the mitochondria are presented in a companion manuscript published in PLoS Genetics (doi:10.1371/journal.pgen.1000407). Here we analyze and explore the results of this study that are broadly applicable for computationalists applying gene function prediction techniques, including a new experimental comparison with 48 genes representing the genomic background. Our study leads to several conclusions that are important to consider when driving laboratory investigations using computational prediction approaches. While most genes in yeast are already known to participate in at least one biological process, we confirm that genes with known functions can still be strong candidates for annotation of additional gene functions. We find that different analysis techniques and different underlying data can both greatly affect the types of functional predictions produced by computational methods. This diversity allows an ensemble of techniques to substantially broaden the biological scope and breadth of predictions. We also find that performing prediction and validation steps iteratively allows us to more completely characterize a biological area of interest. While this study focused on a specific functional area in yeast, many of these observations may be useful in the contexts of other processes and organisms

Recent Applications of Fluorescence Recovery after Photobleaching (FRAP) to Membrane Bio-Macromolecules

This review examines some recent applications of fluorescence recovery after photobleaching (FRAP) to biopolymers, while mainly focusing on membrane protein studies. Initially, we discuss the lateral diffusion of membrane proteins, as measured by FRAP. Then, we talk about the use of FRAP to probe interactions between membrane proteins by obtaining fundamental information such as geometry and stoichiometry of the interacting complex. Afterwards, we discuss some applications of FRAP at the cellular level as well as the level of organisms. We conclude by comparing diffusion coefficients obtained by FRAP and several other alternative methods

History, power, and electricity: American popular magazine accounts of electroconvulsive therapy, 1940–2005

Electroconvulsive therapy (ECT) is a psychiatric treatment that has been in use in the United States since the 1940s. During the whole of its existence, it has been extensively discussed and debated within American popular magazines. While initial reports of the treatment highlighted its benefits to patients, accounts by the 1970s and 1980s were increasingly polarized. This article analyzes the popular accounts over time, particularly the ways in which the debates over ECT have revolved around different interpretations of ECT's history and its power dynamics. © 2008Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57903/1/20283_ftp.pd

Acute kidney injury in patients treated with immune checkpoint inhibitors

Background: Immune checkpoint inhibitor-associated acute kidney injury (ICPi-AKI) has emerged as an important toxicity among patients with cancer. Methods: We collected data on 429 patients with ICPi-AKI and 429 control patients who received ICPis contemporaneously but who did not develop ICPi-AKI from 30 sites in 10 countries. Multivariable logistic regression was used to identify predictors of ICPi-AKI and its recovery. A multivariable Cox model was used to estimate the effect of ICPi rechallenge versus no rechallenge on survival following ICPi-AKI. Results: ICPi-AKI occurred at a median of 16 weeks (IQR 8-32) following ICPi initiation. Lower baseline estimated glomerular filtration rate, proton pump inhibitor (PPI) use, and extrarenal immune-related adverse events (irAEs) were each associated with a higher risk of ICPi-AKI. Acute tubulointerstitial nephritis was the most common lesion on kidney biopsy (125/151 biopsied patients [82.7%]). Renal recovery occurred in 276 patients (64.3%) at a median of 7 weeks (IQR 3-10) following ICPi-AKI. Treatment with corticosteroids within 14 days following ICPi-AKI diagnosis was associated with higher odds of renal recovery (adjusted OR 2.64; 95% CI 1.58 to 4.41). Among patients treated with corticosteroids, early initiation of corticosteroids (within 3 days of ICPi-AKI) was associated with a higher odds of renal recovery compared with later initiation (more than 3 days following ICPi-AKI) (adjusted OR 2.09; 95% CI 1.16 to 3.79). Of 121 patients rechallenged, 20 (16.5%) developed recurrent ICPi-AKI. There was no difference in survival among patients rechallenged versus those not rechallenged following ICPi-AKI. Conclusions: Patients who developed ICPi-AKI were more likely to have impaired renal function at baseline, use a PPI, and have extrarenal irAEs. Two-thirds of patients had renal recovery following ICPi-AKI. Treatment with corticosteroids was associated with improved renal recovery

All's well that begins Wells: Celebrating 60 years of Animal Behaviour and 36 years of research on anuran social behaviour

The scientific study of frogs and toads as important systems in behavioural ecology traces its roots to an influential review published in this journal 36 years ago (Wells 1977a, ‘The social behaviour of anuran amphibians’, Animal Behaviour, 25, 666–693). In just 28 pages, Wells summarized the state of knowledge on important behaviours associated with anuran breeding and introduced an evolutionary framework ‘for understanding the relationship between social behaviour and ecology’ (page 666) that was largely lacking in earlier treatments of this group. Not only is Wells's review one of the most cited papers ever published in Animal Behaviour, it is also responsible for setting broad research agendas and shaping much of our current thinking on social behaviour in an entire order of vertebrates. As such, it is entirely appropriate that we honour Wells's review and its contributions to the study of animal behaviour in this inaugural essay celebrating 12 papers selected by the community as the most influential papers published in the 60-year history of Animal Behaviour. In our essay, we place Wells's review in historical context at the dawn of behavioural ecology, highlight the field's progress in answering some major research questions outlined in the review, and provide our own prospectus for future research on the social behaviour of anuran amphibians. Highlights ► This essay celebrates Kent Wells's (1977, Animal Behaviour, 25, 666–693) paper, ‘The social behaviour of anuran amphibians’. ► We place the article in historical context and outline its major contributions. ► We discuss progress on anuran social behaviour since its publication in 1977. ► We provide our own prospectus on the future of anuran behavioural ecology

Calibration of ionic and cellular cardiac electrophysiology models

© 2020 The Authors. WIREs Systems Biology and Medicine published by Wiley Periodicals, Inc. Cardiac electrophysiology models are among the most mature and well-studied mathematical models of biological systems. This maturity is bringing new challenges as models are being used increasingly to make quantitative rather than qualitative predictions. As such, calibrating the parameters within ion current and action potential (AP) models to experimental data sets is a crucial step in constructing a predictive model. This review highlights some of the fundamental concepts in cardiac model calibration and is intended to be readily understood by computational and mathematical modelers working in other fields of biology. We discuss the classic and latest approaches to calibration in the electrophysiology field, at both the ion channel and cellular AP scales. We end with a discussion of the many challenges that work to date has raised and the need for reproducible descriptions of the calibration process to enable models to be recalibrated to new data sets and built upon for new studies. This article is categorized under: Analytical and Computational Methods > Computational Methods Physiology > Mammalian Physiology in Health and Disease Models of Systems Properties and Processes > Cellular Models