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Article: Manufactured housing communities and climate change: Understanding key vulnerabilities and recommendations for emergency managers.

Hamshaw, Kelly A / Baker, Daniel

Journal of emergency management (Weston, Mass.)

2024 Volume 22, Issue 7, Page(s) 87–99

Abstract: Manufactured housing communities (MHCs), commonly referred to as mobile home parks, provide an estimated 2.7 million American households with largely unsubsidized, affordable housing. Climate change threatens those who call these communities home by ... ...

Abstract	Manufactured housing communities (MHCs), commonly referred to as mobile home parks, provide an estimated 2.7 million American households with largely unsubsidized, affordable housing. Climate change threatens those who call these communities home by exacerbating known structural and social vulnerabilities associated with this housing type-including but not limited to increased risks to flooding, extreme temperatures, high winds, and wildfires. Climate change requires emergency managers to understand the diverse, integrated, and complex vulnerabilities of MHCs that affect their exposure to climate change risk. This article presents findings from an integrative literature review focused on the climate-related vulnerabilities of these communities described at three levels of scale: household, housing structure, and park community. It then draws on 15 years of engagement and action research with MHC residents and stakeholders in Vermont, including several federally declared flooding disasters, to distill key recommendations for emergency managers for assisting MHCs to prepare for and respond to emergencies. As climate change accelerates, emergency managers can increase efficacy by learning about the MHCs in their jurisdictions by leveraging the best available data to characterize risks, integrating MHCs into planning and mitigation activities, and engaging in conversations with stakeholders, including MHC residents and their trusted partners.
MeSH term(s)	Humans ; Climate Change ; Housing ; Communication ; Disasters ; Floods
Language	English
Publishing date	2024-04-04
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	2799989-0
ISSN	1543-5865
ISSN	1543-5865
DOI	10.5055/jem.0845
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Wave-particle interaction effects in the Van Allen belts.

Baker, Daniel N

Earth, planets, and space : EPS

2021 Volume 73, Issue 1, Page(s) 189

Abstract: Discovering such structures as the third radiation belt (or "storage ring") has been a major observational achievement of the NASA Radiation Belt Storm Probes program (renamed the "Van Allen Probes" mission in November 2012). A goal of that program was ... ...

Abstract	Discovering such structures as the third radiation belt (or "storage ring") has been a major observational achievement of the NASA Radiation Belt Storm Probes program (renamed the "Van Allen Probes" mission in November 2012). A goal of that program was to understand more thoroughly how high-energy electrons are accelerated deep inside the radiation belts-and ultimately lost-due to various wave-particle interactions. Van Allen Probes studies have demonstrated that electrons ranging up to 10 megaelectron volts (MeV) or more can be produced over broad regions of the outer Van Allen zone on timescales as short as a few minutes. The key to such rapid acceleration is the interaction of "seed" populations of ~ 10-200 keV electrons (and subsequently higher energies) with electromagnetic waves in the lower band (whistler-mode) chorus frequency range. Van Allen Probes data show that "source" electrons (in a typical energy range of one to a few tens of keV energy) produced by magnetospheric substorms play a crucial role in feeding free energy into the chorus waves in the outer zone. These chorus waves then, in turn, rapidly heat and accelerate the tens to hundreds of keV seed electrons injected by substorms to much higher energies. Hence, we often see that geomagnetic activity driven by strong solar storms (coronal mass ejections, or CMEs) commonly leads to ultra-relativistic electron production through the intermediary step of waves produced during intense magnetospheric substorms. More generally, wave-particle interactions are of fundamental importance over a broad range of energies and in virtually all regions of the magnetosphere. We provide a summary of many of the wave modes and particle interactions that have been studied in recent times.
Language	English
Publishing date	2021-10-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2087663-4
ISSN	1880-5981 ; 1343-8832
ISSN (online)	1880-5981
ISSN	1343-8832
DOI	10.1186/s40623-021-01508-y
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Article ; Online: H. Ralph Schumacher.

Baker, Joshua F / Baker, Daniel G

Rheumatic diseases clinics of North America

2023 Volume 50, Issue 1, Page(s) 103–111

Abstract: Dr Schumacher was a force in rheumatology for more than half a century through his multiple roles as a researcher, clinician, mentor, and educator. He is not likely to be soon forgotten by the rheumatology community; however, it is hoped that this ... ...

Abstract	Dr Schumacher was a force in rheumatology for more than half a century through his multiple roles as a researcher, clinician, mentor, and educator. He is not likely to be soon forgotten by the rheumatology community; however, it is hoped that this chapter can provide a faithful recollection that will help bring his memory to life for some and that rings true to those who knew him and learned from him.
MeSH term(s)	Male ; Humans ; Rheumatology ; Mentors
Language	English
Publishing date	2023-09-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	92118-x
ISSN	1558-3163 ; 0889-857X
ISSN (online)	1558-3163
ISSN	0889-857X
DOI	10.1016/j.rdc.2023.08.008
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Article ; Online: Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.

Baker, Daniel N / Langmead, Ben

Genome research

2023 Volume 33, Issue 7, Page(s) 1218–1227

Abstract: A genomic sketch is a small, probabilistic representation of the set of k-mers in a sequencing data set. Sketches are building blocks for large-scale analyses that consider similarities between many pairs of sequences or sequence collections. Although ... ...

Abstract	A genomic sketch is a small, probabilistic representation of the set of k-mers in a sequencing data set. Sketches are building blocks for large-scale analyses that consider similarities between many pairs of sequences or sequence collections. Although existing tools can easily compare tens of thousands of genomes, data sets can reach millions of sequences and beyond. Popular tools also fail to consider k-mer multiplicities, making them less applicable in quantitative settings. Here, we describe a method called Dashing 2 that builds on the SetSketch data structure. SetSketch is related to HyperLogLog (HLL) but discards use of leading zero count in favor of a truncated logarithm of adjustable base. Unlike HLL, SetSketch can perform multiplicity-aware sketching when combined with the ProbMinHash method. Dashing 2 integrates locality-sensitive hashing to scale all-pairs comparisons to millions of sequences. It achieves superior similarity estimates for the Jaccard coefficient and average nucleotide identity compared with the original Dashing, but in much less time while using the same-sized sketch. Dashing 2 is a free, open source software.
MeSH term(s)	Genomics/methods ; Software ; Genome ; Nucleotides ; Algorithms ; Sequence Analysis, DNA/methods
Chemical Substances	Nucleotides
Language	English
Publishing date	2023-07-06
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.277655.123
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Article ; Online: Object Image Size Is a Fundamental Coding Dimension in Human Vision: New Insights and Model.

Meese, Tim S / Baker, Daniel H

Neuroscience

2023 Volume 514, Page(s) 79–91

Abstract: In previous psychophysical work we found that luminance contrast is integrated over retinal area subject to contrast gain control. If different mechanisms perform this operation for a range of superimposed retinal regions of different sizes, this could ... ...

Abstract	In previous psychophysical work we found that luminance contrast is integrated over retinal area subject to contrast gain control. If different mechanisms perform this operation for a range of superimposed retinal regions of different sizes, this could provide the basis for size-coding. To test this idea we included two novel features in a standard adaptation paradigm to discount more pedestrian accounts of repulsive size-aftereffects. First, we used spatially jittering luminance-contrast adaptors to avoid simple contour displacement aftereffects. Second, we decoupled adaptor and target spatial frequency to avoid the well-known spatial frequency shift aftereffect. Empirical results indicated strong evidence of a bidirectional size adaptation aftereffect. We show that the textbook population model is inappropriate for our results, and develop our existing model of contrast perception to include multiple size mechanisms with divisive surround-suppression from the largest mechanism. For a given stimulus patch, this delivers a blurred step-function of responses across the population, with contrast and size encoded by the height and lateral position of the step. Unlike for textbook population coding schemes, our human results (N = 4 male, N = 4 female) displayed two asymmetries: (i) size aftereffects were greatest for targets smaller than the adaptor, and (ii) on that side of the function, results did not return to baseline, even when targets were 25% of adaptor diameter. Our results and emergent model properties provide evidence for a novel dimension of visual coding (size) and a novel strategy for that coding, consistent with previous results on contrast detection and discrimination for various stimulus sizes.
MeSH term(s)	Female ; Humans ; Male ; Contrast Sensitivity/physiology ; Figural Aftereffect/physiology ; Form Perception/physiology ; Photic Stimulation/methods ; Psychophysics/methods ; Retina/physiology ; Size Perception/physiology
Language	English
Publishing date	2023-02-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	196739-3
ISSN	1873-7544 ; 0306-4522
ISSN (online)	1873-7544
ISSN	0306-4522
DOI	10.1016/j.neuroscience.2023.01.025
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Article ; Online: CAR T therapy extends its reach to autoimmune diseases.

Baker, Daniel J / June, Carl H

Cell

2022 Volume 185, Issue 24, Page(s) 4471–4473

Abstract: CAR T therapy has revolutionized the treatment of hematologic cancers. In their recent Nature Medicine paper, Mackensen et al. report the use of CAR T cells to treat systemic lupus erythematosus in five patients. This provides enthusiasm to further ... ...

Abstract	CAR T therapy has revolutionized the treatment of hematologic cancers. In their recent Nature Medicine paper, Mackensen et al. report the use of CAR T cells to treat systemic lupus erythematosus in five patients. This provides enthusiasm to further explore CAR T therapy beyond oncology.
MeSH term(s)	Humans ; Receptors, Chimeric Antigen ; Autoimmune Diseases/therapy ; Lupus Erythematosus, Systemic/drug therapy
Chemical Substances	Receptors, Chimeric Antigen
Language	English
Publishing date	2022-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Comment
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2022.10.026
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Book ; Online: Statistical analysis of periodic data in neuroscience

Baker, Daniel H.

2021

Abstract: Many experimental paradigms in neuroscience involve driving the nervous system with periodic sensory stimuli. Neural signals recorded using a variety of techniques will then include phase-locked oscillations at the stimulation frequency. The analysis of ... ...

Abstract	Many experimental paradigms in neuroscience involve driving the nervous system with periodic sensory stimuli. Neural signals recorded using a variety of techniques will then include phase-locked oscillations at the stimulation frequency. The analysis of such data often involves standard univariate statistics such as T-tests, conducted on the Fourier amplitude components (ignoring phase), either to test for the presence of a signal, or to compare signals across different conditions. However, the assumptions of these tests will sometimes be violated because amplitudes are not normally distributed, and furthermore weak signals might be missed if the phase information is discarded. An alternative approach is to conduct multivariate statistical tests using the real and imaginary Fourier components. Here the performance of two multivariate extensions of the T-test are compared: Hotelling's $T^2$ and a variant called $T^2_{circ}$. A novel test of the assumptions of $T^2_{circ}$ is developed, based on the condition index of the data (the square root of the ratio of eigenvalues of a bounding ellipse), and a heuristic for excluding outliers using the Mahalanobis distance is proposed. The $T^2_{circ}$ statistic is then extended to multi-level designs, resulting in a new statistical test termed $ANOVA^2_{circ}$. This has identical assumptions to $T^2_{circ}$, and is shown to be more sensitive than MANOVA when these assumptions are met. The use of these tests is demonstrated for two publicly available empirical data sets, and practical guidance is suggested for choosing which test to run. Implementations of these novel tools are provided as an R package and a Matlab toolbox, in the hope that their wider adoption will improve the sensitivity of statistical inferences involving periodic data. Comment: 18 pages, 10 figures
Keywords	Statistics - Methodology ; Quantitative Biology - Neurons and Cognition
Subject code	310
Publishing date	2021-01-12
Publishing country	us
Document type	Book ; Online
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Article ; Online: Application of computational methods for class A GPCR Ligand discovery.

Szwabowski, Gregory L / Baker, Daniel L / Parrill, Abby L

Journal of molecular graphics & modelling

2023 Volume 121, Page(s) 108434

Abstract: G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for drug development due to their role in transmitting cellular signals in a multitude of biological processes. Of the six classes categorizing GPCR (A, ...

Abstract	G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for drug development due to their role in transmitting cellular signals in a multitude of biological processes. Of the six classes categorizing GPCR (A, B, C, D, E, and F), class A contains the largest number of therapeutically relevant GPCR. Despite their importance as drug targets, many challenges exist for the discovery of novel class A GPCR ligands serving as drug precursors. Though knowledge of the structural and functional characteristics of GPCR has grown significantly over the past 20 years, a large portion of GPCR lack reported, experimentally determined structures. Furthermore, many GPCR have no known endogenous and/or synthetic ligands, limiting further exploration of their biochemical, cellular, and physiological roles. While many successes in GPCR ligand discovery have resulted from experimental high-throughput screening, computational methods have played an increasingly important role in GPCR ligand identification in the past decade. Here we discuss computational techniques applied to GPCR ligand discovery. This review summarizes class A GPCR structure/function and provides an overview of many obstacles currently faced in GPCR ligand discovery. Furthermore, we discuss applications and recent successes of computational techniques used to predict GPCR structure as well as present a summary of ligand- and structure-based methods used to identify potential GPCR ligands. Finally, we discuss computational hit list generation and refinement and provide comprehensive workflows for GPCR ligand identification.
MeSH term(s)	Receptors, G-Protein-Coupled/chemistry ; Binding Sites ; Ligands ; Drug Design ; Signal Transduction
Chemical Substances	Receptors, G-Protein-Coupled ; Ligands
Language	English
Publishing date	2023-02-21
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2023.108434
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Article: The role of salinity in recovery of white sturgeon (

Shartau, Ryan B / Shu, Jacelyn / Baker, Daniel W

Conservation physiology

2023 Volume 11, Issue 1, Page(s) coad009

Abstract: White sturgeon ( ...

Abstract	White sturgeon (
Language	English
Publishing date	2023-03-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2721508-8
ISSN	2051-1434
ISSN	2051-1434
DOI	10.1093/conphys/coad009
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Article ; Online: Blurring the boundary between models and reality: Visual perception of scale assessed by performance.

Meese, Tim S / Baker, Daniel H / Summers, Robert J

PloS one

2023 Volume 18, Issue 5, Page(s) e0285423

Abstract: One of the primary jobs of visual perception is to build a three-dimensional representation of the world around us from our flat retinal images. These are a rich source of depth cues but no single one of them can tell us about scale (i.e., absolute depth ...

Abstract	One of the primary jobs of visual perception is to build a three-dimensional representation of the world around us from our flat retinal images. These are a rich source of depth cues but no single one of them can tell us about scale (i.e., absolute depth and size). For example, the pictorial depth cues in a (perfect) scale model are identical to those in the real scene that is being modelled. Here we investigate image blur gradients, which derive naturally from the limited depth of field available for any optical device and can be used to help estimate visual scale. By manipulating image blur artificially to produce what is sometimes called fake tilt shift miniaturization, we provide the first performance-based evidence that human vision uses this cue when making forced-choice judgements about scale (identifying which of an image pair was a photograph of a full-scale railway scene, and which was a 1:76 scale model). The orientation of the blur gradient (relative to the ground plane) proves to be crucial, though its rate of change is less important for our task, suggesting a fairly coarse visual analysis of this image parameter.
MeSH term(s)	Humans ; Depth Perception ; Visual Perception ; Cues ; Gravitation ; Judgment
Language	English
Publishing date	2023-05-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0285423
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