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Serine hydrolases play important roles in signaling and human metabolism, yet little is known about their functions in gut commensal bacteria. Using bioinformatics and chemoproteomics, we identify serine hydrolases in the gut commensal Bacteroides thetaiotaomicron that are specific to the Bacteroidetes phylum. Two are predicted homologs of the human protease dipeptidyl peptidase 4 (hDPP4), a key enzyme that regulates insulin signaling. Functional studies reveal that BT4193 is a true homolog of hDPP4 that can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other is a misannotated proline-specific triaminopeptidase. We demonstrate that BT4193 is important for envelope integrity and that loss of BT4193 reduces B. thetaiotaomicron fitness during in vitro growth within a diverse community. However, neither function is dependent on BT4193 proteolytic activity, suggesting a scaffolding or signaling function for this bacterial protease.

Neuropeptide S (NPS) is a highly conserved peptide found in all tetrapods that functions in the brain to promote heightened arousal; however, the subpopulations mediating these phenomena remain unknown. We generated mice expressing Cre recombinase from the Nps gene locus (NpsCre) and examined populations of NPS+ neurons in the lateral parabrachial area (LPBA), the peri-locus coeruleus (peri-LC) region of the pons, and the dorsomedial thalamus (DMT). We performed brain-wide mapping of input and output regions of NPS+ clusters and characterized expression patterns of the NPS receptor (NPSR1). While the activity of all three NPS+ subpopulations tracked with vigilance state, only NPS+ neurons of the LPBA exhibited both increased activity prior to wakefulness and decreased activity during REM sleep, similar to the behavioral phenotype observed upon NPSR1 activation. Accordingly, we found that activation of LPBA, but not peri-LC NPS+ neurons increased wake and reduced REM sleep. Furthermore, given the extended role of the LPBA in respiration, and the link between behavioral arousal and breathing rate, we demonstrated that LPBA-, but not peri-LC-NPS+ neuronal activation increased respiratory rate. Together, our data suggests that NPS+ neurons of the LPBA represent an unexplored subpopulation regulating breathing and they are sufficient to recapitulate the sleep/wake phenotypes observed with broad NPS system activation.

Potassium K-edge XANES spectra used in 'A Combined Spectroscopic and Theoretical Analysis of Organic Potassium Compounds' by Richardson et al.

We present an ice-penetrating radar dataset acquired over the Greenland ice sheet by aircraft during the years 1971, 1972, 1974, 1978, and 1979. The dataset comprises over 177,000 km of flight lines and contains a wealth of information on the state of the Greenland ice sheet including information on ice thickness and englacial properties. During data collection in the 1970s, the data were recorded on optical film rolls and in this manuscript, we document the digitization of these film 5 rolls and their associated geographical information. Our digitization of the data enables interaction with and analysis of the data and facilitates comparison with modern-day radar observations. The complete dataset in full resolution with associated scanned notes is available here.

This document is an archive of an electronic portfolio (ePortfolio) produced as a capstone requirement for the Notation in Science Communication. In their ePortfolios, NSC students demonstrate how they have met the NSC learning outcomes. These learning portfolios detail students’ growth and development as scientists and science communicators rather than showcasing only their best work. ePortfolios are reviewed and approved by faculty, earning students a special designation on their official Stanford transcript that reflects their science communication acumen.

PDB files of AlphaFold predictions of test cases, IgSFs or high ranking receptors for orphan ligands

Although it is heavily relied on to study genetic contributors to health and disease, the current human reference genome (GRCh38) is incomplete in two major ways: firstly, it is missing large sections of heterochromatic sequence, and secondly, as a singular, linear reference genome it does not represent the full spectrum of genetic diversity that exists in the human species. In order to better understand and characterize gaps in GRCh38 and genetic diversity, we developed a method - ASLAN, an Algorithm for Sequence Location Approximation using Nuclear families - that identifies the region of origin of short reads that do not align to the GRCh38. Using unmapped reads and variant calls from whole genome sequencing (WGS) data from nuclear families, ASLAN relies on a maximum likelihood model to identify the most likely region of the genome that a subsequence belongs to, given the phasing information of family and the distribution of the subsequence in the unmapped reads. Validating ASLAN on a synthetically generated dataset, and on true reads originating from the alternative haplotypes in the decoy genome, we show that ASLAN can localize more than 90% of 100-basepair sequences with above 92% accuracy and around 1 megabase of resolution. We then run ASLAN on 100-mers from unmapped reads from WGS from over 700 families, and compare ASLAN localizations to alignment of the 100-mers to the T2T-CHM13 assembly, recently released by the Telomere-to-telomere (T2T) consortia. We find that many unmapped reads in GRCh38 originate from telomeres and centromeres that are gaps in the GRCh38 reference. We also confirm that ASLAN localizations are in high concordance with T2T-CHM13 alignments, except in the centromeres of the acrocentric chromosomes. Comparing ASLAN localizations and T2T-CHM13 alignments, we identify sequences missing from T2T-CHM13 or sequences with high divergence from their aligned region in T2T-CHM13, thus highlighting new hotspots for genetic diversity. This deposit consists of: (1) A list of non-singleton 100mers extracted from the iHART cohort from the unmapped reads (kmer_sequences.txt.zip) (2) The corresponding regions in the genome that ASLAN mapped each sequence to (GRCh38 coordinates) (ASLAN_localizations.bed) (3) The loci to which the each sequence aligned to on the CHM13-T2T assembly (CHM13-T2T coordinates) (T2T_mappings.bed)

In the underdoped n-type cuprate Nd2-xCexCuO4, long-ranged antiferromagnetic order reconstructs the Fermi surface, resulting in a putative antiferromagnetic metal with small pockets. Using angle-resolved photoemission spectroscopy, we observe an anomalous energy gap, an order of magnitude smaller than the antiferromagnetic gap, in a wide range of the underdoped regime and smoothly connecting to the superconducting gap at optimal doping. After carefully considering all the known ordering tendencies in tandem with the phase diagram, we hypothesize that the normal state gap in the underdoped n-type cuprates originates from Cooper pairing. The high temperature scale of the normal state gap raises the prospect of engineering higher transition temperatures in the n-type cuprates comparable to that of the p-type cuprates.

Aircraft collision avoidance systems rely on sensor information to detect and track intruding aircraft so that they may issue proper collision avoidance advisories. While typical surveillance sensors for manned aircraft include transponders and onboard radar, autonomous aircraft will require additional sensors both for redundancy and to replace the visual acquisition typically performed by the pilot. As a result, the community has proposed detecting other aircraft using vision-based sensors such as cameras. These sensors require the development of techniques to process images of the environment to detect intruding aircraft. To boost this development, this artifact provides a dataset of 72,000 labeled images of intruder aircraft with various lighting conditions, weather conditions, relative geometries, and geographic locations. For more information on the structure of this dataset as well as benchmark models and a full simulator, see https://github.com/sisl/VisionBasedAircraftDAA.

Over 20 weeks, I partnered Bay Ed Fund, a philanthropy that seeks to partner with and improve local, suburban school districts. Through a trust-based or power-shifting philanthropic model, the Bay Ed Fund looks to empower the district stakeholders to engage in a long term, change making process over seven to ten years for the sake of student-centered, district improvements. During my time with the Bay Ed Fund, I worked on two congruent projects: first with the consulting company Estrada Darley Miller Group and next with the Bay Ed Fund itself. In partnership with South San Francisco Unified School District, both projects focused on aspects of district change. I began by examining the literature on community driven, K-12, district change efforts. I also led a project regarding the acquisition and retention of talented individuals at key district leadership positions, that can be leveraged for long-term change. My time with the Bay Ed Fund exposed me to the intricacies and challenges involved in educational philanthropic work, and I am equipped with new skills in research, literature reviews, interviewing, and systems thinking. Among the materials, you will find a visualization of the artifacts, a district profile, a literature review, the themes from the Talent Project, and a team strategy meeting agenda.

Photographs taken of terra-cotta tiles with simulated parrotfish divots after being out in the field for one year. 10 of the tiles were caged and 10 were un-caged. Each zip file contains 10 photos of an individual tile. One is the whole view of the tile followed by close ups of each of four quadrates. Each of the 5 photos are saved in both .JPG and .CR2 (Canon raw 2) formats. Photos were taken in the lab with a Canon EOS Rebel SL1. file names for the photos are: site&depth.YYMMDD.tile#&treatment.photo#.photo coverage FR9S.140623.1C.2632.W = FR9, shallow, 6/23/14, tile 1, caged, number assigned by the camera, whole plate • sites are FR3, FR7, FR9 (FR stands for fore-reef) • depths are S=shallow, M=middle, D=deep • dates are formatted as YYMMDD, for example 140623 is June 23, 2014 • tile numbers as written on the tiles • treatments are C=caged, U=uncaged • photo# is number assigned by the camera • photo coverages are: W=whole plate, A=upper right, B=lower right, C=lower left, D=upper left this is with the tile oriented so divot #1 is in upper right (A)

Photographs taken of terra-cotta tiles with simulated parrotfish divots after being out in the field for three years. 10 of the tiles were caged and 10 were un-caged. Each zip file contains 10 photos of an individual tile. One is the whole view of the tile followed by close ups of each of four quadrates. Each of the 5 photos are saved in both .JPG and .CR2 (Canon raw 2) formats. Photos were taken in the lab with a Canon EOS Rebel SL1. file names for the photos are: site&depth.YYMMDD.tile#&treatment.photo#.photo coverage FR9S.140623.1C.2632.W = FR9, shallow, 6/23/14, tile 1, caged, number assigned by the camera, whole plate • sites are FR3, FR7, FR9 (FR stands for fore-reef) • depths are S=shallow, M=middle, D=deep • dates are formatted as YYMMDD, for example 140623 is June 23, 2014 • tile numbers as written on the tiles • treatments are C=caged, U=uncaged • photo# is number assigned by the camera • photo coverages are: W=whole plate, A=upper right, B=lower right, C=lower left, D=upper left this is with the tile oriented so divot #1 is in upper right (A)

Electron-doped cuprates consistently exhibit strong antiferromagnetic correlations, leading to the prevalent belief that antiferromagnetic spin fluctuations mediate Cooper pairing in these unconventional superconductors. However, early investigations showed that while antiferromagnetic spin fluctuations create the largest pseudogap at hot spots in momentum space, the superconducting gap is also maximized at these locations. This presented a paradox for spin-fluctuation-mediated pairing: Cooper pairing is strongest at momenta where normal state low energy spectral weight is most suppressed. Here we investigate this paradox and find evidence that a gossamer – meaning very faint – Fermi surface can provide an explanation for these observations. We study Nd2-xCexCuO4 using angle-resolved photoemission spectroscopy and directly observe the Bogoliubov quasiparticles. First, we resolve the previously-observed reconstructed main band and the states gapped by the antiferromagnetic pseudogap around the hot spots. Within the antiferromagnetic pseudogap, we also observe gossamer states with distinct dispersion, from which Bogoliubov quasiparticle coherence peaks emerge below the superconducting critical temperature. We propose that orientation fluctuations in the antiferromagnetic order parameter are responsible for the gossamer states. Moreover, we find that the largest superconducting gap is an order of magnitude smaller than the pseudogap, establishing the distinct nature of these two gaps.

This is a list of California law enforcement agencies that we have gathered and curated for the purpose of finding and tracking policy manuals and military equipment inventories. Each row represents a law enforcement agency. The reason for compiling this list is to have a base set of URLs and related information for California LEAs that will be incorporated into the Know Systemic Racism Knowledge Graph. Stanford Libraries' KNOW Systemic Racism project began work in collaboration with the Electronic Frontier Foundation (EFF) to gather this list and details about California law enforcement agencies between 2018-2022. We continued to refine the list and add details into August 2023. ## Methodology This dataset includes a list of POST (Peace Officer Standards and Training) participating law enforcement agencies (LEAs) in California. This list is based on the [California's Commision on Police Officer Standards and Training](https://post.ca.gov/le-agencies). Some LEAs on that list do not appear on this list because our primary interest is in identifying the policy manuals. For example, some LEAs, particularly community college police departments, are part of a shared resource and use the same policy. We added the website URL for each agency as well as an archived version of that URL at the point in time when we gathered it. We are very grateful to Archive.org for webarchving this and other material on the Web and encourage others to support their work. These LEAs now all have entries within Wikidata and we have added the Wikidata QID to this list to make this dataset more durable and to make it open to continual development by the community.

Atlantic bluefin tuna (ABT) are large, wide-ranging pelagic predators which typically migrate between foraging regions in the North Atlantic and two principal spawning regions, the Gulf of Mexico and the Mediterranean Sea. A new spawning area has been described in the Slope Sea (SS) region off New England; however, the relationship between ABT that spawn in the SS and ABT using the principal spawning regions remains poorly understood. We used electronic tags to examine the location, temperature, and diving behavior of ABT in the SS, and identified 24 individuals that were present during the spawning season (June-August) with tag data showing temperatures and behavior consistent with spawning ABT. In general, the SS spawners had similar spatial ranges to Mediterranean-spawning ABT; however, some individuals displayed distinct behaviours that were identified first in Gulf of Mexico spawners. Using monthly spatial distributions, we estimated that the SS spawners have high exposure to fishing pressure relative to other ABT and may represent a disproportionate share of the West Atlantic catch. This analysis provides the first description of the behavior of ABT frequenting this spawning ground, creating a foundation for integrating this region into multi-stock management and, potentially, conserving an important source of genetic diversity.

Concentrations of rotavirus, human adenovirus, enteroviruses, and human noroviruses in wastewater solids at two wastewater treatment plants in the Bay Area of California

Concentrations of nucleic-acid markers of the targets mentioned in the title in wastewater solids measured by digital droplet (RT-)PCR