University of California, Santa Cruz
  • Santa Cruz, California, United States
Recent publications
Social isolation is defined, in psychological terms, as the absence of meaningful social interactions, contacts, and relationships with family and friends, with neighbors. It can occur on an individual level and, on a broader level, within “society at large.” In the United States, three main groups of socially isolated individuals can be identified: people who reside in assisted-living facilities, nursing homes, or hospices, people suffering from “persistent loneliness” and people incarcerated in jails or prisons who are housed in involuntary solitary confinement. In this chapter, we discuss the psychological and neurobiological effects of isolation, using both animal models as well as direct studies of humans experiencing these conditions. Only by understanding the impact of isolation on the brain and the mechanisms that underlie these changes can we hope to develop interventions that prevent them from occurring in the first place. This knowledge may also contribute to the efforts of psychologists, clinicians, and community health leaders to employ evidence-based prevention programs to mitigate the risk of isolation-induced physical and psychological damage in humans.
The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are presampled, independent of the hard scatter, and stored as combined events. Consequently, for each hard-scatter interaction, only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.
Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.
The ATLAS experiment at the Large Hadron Collider has a broad physics programme ranging from precision measurements to direct searches for new particles and new interactions, requiring ever larger and ever more accurate datasets of simulated Monte Carlo events. Detector simulation with Geant4 is accurate but requires significant CPU resources. Over the past decade, ATLAS has developed and utilized tools that replace the most CPU-intensive component of the simulation—the calorimeter shower simulation—with faster simulation methods. Here, AtlFast3, the next generation of high-accuracy fast simulation in ATLAS, is introduced. AtlFast3 combines parameterized approaches with machine-learning techniques and is deployed to meet current and future computing challenges, and simulation needs of the ATLAS experiment. With highly accurate performance and significantly improved modelling of substructure within jets, AtlFast3 can simulate large numbers of events for a wide range of physics processes.
In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.
Understanding the relative contributions of different spawning habitats to adult fish populations is central to effective fisheries management and species conservation. The Tarek (Alburnus tarichi) is an adfluvial cyprinid that is endemic to the alkaline-saline waters of Lake Van, Turkey. Tarek are culturally and economically important to the region, and also threatened by anthropogenic impacts, including poaching, dams, water diversions, pollution, and habitat degradation. Here we analyzed otoliths from 120 adult fish caught in Lake Van in 2016–2017 to reconstruct the age structure and natal origins of this Tarek population. Ages ranged from 2 to 10 years, with most fish belonging to the 2011–2014 cohorts (age 3–5). We analyzed strontium isotope ratios from water samples collected in 2016 and 2018 to build a baseline map and then used linear discriminant function analysis to classify Tarek to their likely natal origins. We found that adult Tarek originated from at least 7 different major tributaries of Lake Van, with a majority of fish originating from the Gevas and Engil tributaries in the south. Furthermore, the relative contributions of fish from each tributary varied among years, suggesting that a mosaic of natal habitats may be important for population stability. These results suggest that protection of all Lake Van watersheds from anthropogenic disturbance could be valuable for maintaining the stability of the Lake Van Tarek population and fishery.
Motivated by the contradiction between a government's hard budget constraints and artificial intelligence, this study constructs a computable general equilibrium model embedded with various fiscal and tax policies to study the impact of artificial intelligence development on the Chinese economy under government budget constraints with different intensities. This paper seeks to find a reasonable policy that takes into account China's employment, income distribution, and budget constraints to achieve common prosperity. It finds that the softer the government's budget constraints, the smaller the negative impact of artificial intelligence on the economy. More specifically, allowing the government to increase its debts and spending is more effective than tax cuts. It is suggested that if the goal is to reconcile the contradiction between hard budget constraints and artificial intelligence, fiscal and tax policy combinations, together with an improvised soft budget constraint, are required to increase the taxation of capital to an appropriate degree. In order to resolve the contradiction between the government's hard budget constraints and the development of artificial intelligence in pursuit of common prosperity, a robot tax should be levied and automation capital taxed.
With growing evidence of labor violations and exploitative working conditions in fisheries, ensuring decent work is imperative to protect fishers and fishworkers in the global seafood sector. This study provides the first evaluation of decent work in a shared, transboundary fishery – the shrimp and groundfish fishery of the Guianas-Brazil Shelf. Decent work in fisheries has gained increasing attention and research, yet gaps exist in our understanding of the elements of decent work, how we evaluate it, and how to enable decent work. To date, there has been limited analysis of decent work in a range of geographies and diverse fisheries contexts, including small-scale fisheries and transboundary fisheries. This study will address this gap by evaluating decent work, utilizing a new fishery-specific, holistic evaluation framework drawing from existing frameworks including the ILO Work in Fishing Convention (C188), the Monterey Framework for Social Responsibility, and the FAO Voluntary Guidelines for Securing Sustainable Small-Scale Fisheries. This evaluation details country-level challenges that put fishers and fishworkers at risk in their occupation, including illegal fishing, vessel safety, and worker representation. This paper concludes with recommendations, to be advanced with a transboundary, regional approach, to ensure decent work and strengthen existing progress, including 1) addressing widespread illegal activities, 2) adopting fisheries-specific standards like C188, 3) implementing and enforcing policies at the country and regional level, and 4) ensuring worker representation and participation leveraging cooperatives and collectives.
Biofilms are a widely observed growth mode in which microbial communities are spatially structured and embedded in a polymeric extracellular matrix. Here, we focus on the model bacterium Vibrio cholerae and summarize the current understanding of biofilm formation, including initial attachment, matrix components, community dynamics, social interactions, molecular regulation, and dispersal. The regulatory network that orchestrates the decision to form and disperse from biofilms coordinates various environmental inputs. These cues are integrated by several transcription factors, regulatory RNAs, and second-messenger molecules, including bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP). Through complex mechanisms, V. cholerae weighs the energetic cost of forming biofilms against the benefits of protection and social interaction that biofilms provide. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
The retrieval of a subset of items can cause the forgetting of other, non-retrieved items, a phenomenon known as retrieval-induced forgetting. Initial work suggested that giving people the opportunity to restudy non-retrieved items following retrieval practice is sufficient to eliminate the effect of retrieval-induced forgetting, but more recent work has suggested otherwise. If retrieval-induced forgetting is not eliminated by restudy, then such a finding would have important implications for understanding the theoretical nature of retrieval-induced forgetting. It would suggest, for example, that retrieval-induced forgetting reflects more than the temporary reduction in the accessibility of non-retrieved items in memory. The two experiments reported here sought to clarify this issue, with the results suggesting that retrieval-induced forgetting can be eliminated by restudy. Indeed, retrieval-induced forgetting was eliminated by restudy even when the forgetting effect was produced by three rounds of retrieval practice instead of one round of retrieval practice. These findings are consistent with the idea that retrieval-induced forgetting, at least under the conditions of the current experiments, reflects a temporary reduction in the accessibility of non-retrieved items in memory.
This paper uses Cultural Historical Activity Theory (CHAT) to examine the boundary zone of teacher professional development within a multi-agency collaborative project. It highlights different goals, histories, and commitments that collided and intermingled to create tensions, contradictions, and opportunities for expansive learning. Although a policy mandate, use of the English Language Arts-Common Core State Standards created a common goal, however, interagency participants acted under strikingly different conceptions of effective teacher professional development. In an era of increased collaboration among agencies, this paper reconceptualizes interagency teacher professional development, serving as both a cautionary tale and a vision for the future.
Let V be a vertex operator superalgebra and G a finite automorphism group of V. Let σ be the order 2 automorphism of V associated with the superstructure of V. A sequence of associative algebras AG,n(V) are constructed to study the twisted representations of V for nonnegative n∈1T′Z where T′ is the order of group generated by G and σ. This result which generalizes many previous results on Zhu's algebras is then used to investigate the super orbifold theory. If V is a simple vertex operator superalgebra and S is a finite set of inequivalent irreducible twisted V-modules which is closed under the action of G, a duality theorem of Schur-Weyl type is obtained for the actions of certain finite dimensional semisimple associated algebra Aα(G,S) and VG on the direct sum of twisted V-modules in S. In particular, for any g∈G every irreducible g-twisted V-module is completely reducible VG-module.
In pluralistic societies, encounters with individuals, contexts, and norms of other religions can prompt conflict. We test a novel framework for explaining how individuals apply religious norms across individuals and contexts. In Studies 1 and 2, adolescents and adults in India and the United States judged events in which religious norms were violated by protagonists of different religions in different religious contexts. Participants often judged that norm violations were wrong even when the norm religion matched only the protagonist or context religion. Study 3 presented dilemmas that pitted religious norms against non-religious concerns. Participants favored following the religious norm yet accepted the protagonist's right to violate it. In each adult sample, more religious participants more often judged that protagonists were obligated to follow the protagonist's own religious norms. These findings reveal individual and contextual determinants of judgments about religious violations with implications for peaceful coexistence in pluralistic societies.
Plant residue input plays a vital role in cropland carbon (C) balance, which can be greatly affected by climate change. Our knowledge of the effect of plant residue on soil respiration is crucial for evaluating C exchange between the atmosphere and terrestrial ecosystems, but large uncertainties remain in the effect of plant input on the temperature sensitivity (Q10) of soil organic C (SOC) decomposition in cropland ecosystems. Here, soils were sampled from two bare fallow plots (including a Mollisol and an Alfisol with different climate and land-use history) and their adjacent old field plots, and were incubated at 10 °C and 20 °C for 815 days. The ‘equal-time’, ‘equal-C’, ‘one-pool model’ and ‘two-pool model’ methods were used to evaluate the Q10 of SOC decomposition. Results indicated that in the early stage of incubation, exclusion of plant input increased the Q10 (Alfisol) or had minor effect on the Q10 (Mollisol), which may be related to the interactions between substrate quality decrease (increase of chemical stability) and clay mineral suppression on microbial decomposition. However, in the later stage of incubation, plant residue removal decreased the Q10 values in both soils possibly due to the limitation of substrate availability on microbial decomposition. Overall, the role of plant input in the temperature sensitivity of SOC decomposition should be considered when predicting SOC stocks in a future warmer world.
The launch of the James Webb Space Telescope (JWST) in late 2021 marks a new start for studies of galaxy formation at high redshift ( z ≳ 6) during the era of cosmic reionization. JWST can capture sensitive, high-resolution images and multiobject spectroscopy in the IR that will transform our view of galaxy formation during the first billion years of cosmic history. This review summarizes our current knowledge of the role of galaxies in reionizing intergalactic hydrogen ahead of JWST, achieved through observations with the Hubble Space Telescope and ground-based facilities including Keck, the Very Large Telescope, Subaru, and the Atacama Large Millimeter/Submillimeter Array. We identify outstanding questions in the field that JWST can address during its mission lifetime, including with the planned JWST Cycle 1 programs. These findings include the following: ▪ Surveys with JWST have sufficient sensitivity and area to complete the census of galaxy formation at the current redshift frontier ( z ∼ 8–10). ▪ Rest-frame optical spectroscopy with JWST of galaxies will newly enable measures of star-formation rate, metallicity, and ionization at z ∼ 8–9, allowing for the astrophysics of early galaxies to be constrained. ▪ The presence of evolved stellar populations at z ∼ 8–10 can be definitively tested by JWST, which would provide evidence of star formation out to z ∼ 15. Expected final online publication date for the Annual Review of Astronomy Volume 60 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Consider a cooperation game on a spatial network of habitat patches, where players can relocate between patches if they judge the local conditions to be unfavorable. In time, the relocation events may lead to a homogeneous state where all patches harbor the same relative densities of cooperators and defectors, or they may lead to self-organized patterns, where some patches become safe havens that maintain an elevated cooperator density. Here we analyze the transition between these states mathematically. We show that safe havens form once a certain threshold in connectivity is crossed. This threshold can be analytically linked to the structure of the patch network and specifically to certain network motifs. Surprisingly, a forgiving defector avoidance strategy may be most favorable for cooperators. Our results demonstrate that the analysis of cooperation games in ecological metacommunity models is mathematically tractable and has the potential to link topics such as macroecological patterns, behavioral evolution, and network topology.
Islands are global hotspots for biodiversity and extinction, representing ~ 5% of Earth’s land area alongside 40% of globally threatened vertebrates and 61% of global extinctions since the 1500s. Invasive species are the primary driver of native biodiversity loss on islands, though eradication of invasive species from islands has been effective at halting or reversing these trends. A global compendium of this conservation tool is essential for scaling best-practices and enabling innovations to maximize biodiversity outcomes. Here, we synthesize over 100 years of invasive vertebrate eradications from islands, comprising 1550 eradication attempts on 998 islands, with an 88% success rate. We show a significant growth in eradication activity since the 1980s, primarily driven by rodent eradications. The annual number of eradications on islands peaked in the mid-2000s, but the annual area treated continues to rise dramatically. This trend reflects increases in removal efficacy and project complexity, generating increased conservation gains. Our synthesis demonstrates the collective contribution of national interventions towards global biodiversity outcomes. Further investment in invasive vertebrate eradications from islands will expand biodiversity conservation while strengthening biodiversity resilience to climate change and creating co-benefits for human societies.
Plain Language Summary The ocean mitigates the extent of global warming by absorbing a portion of the carbon dioxide gas (CO2) released into the atmosphere by human activities. However, this comes at a cost to ocean health because the uptake of this anthropogenic CO2 causes changes in ocean chemistry, called ocean acidification (OA), that can be detrimental to marine ecosystems. This study explores how OA metrics have changed in the upper waters of the open North Pacific Ocean and coastal California Current Large Marine Ecosystem (CCLME). We focus on the CCLME due to its global importance and economically important fisheries. We find that different OA metrics exhibit different patterns of change with depth in the water column due to the natural, background ocean chemistry. One such metric shows that there is now more subsurface water containing CO2 levels elevated enough to threaten the health of marine organisms than there was before the anthropogenic CO2 addition. Our finding of expanded volumes of water with high‐CO2 levels near the coast is important to consider as a source of stress for marine organisms living both on the seafloor and in the water column.
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
We use data collected from panel phone surveys to document the changes in food security of households in rural Liberia and Malawi during the market disruptions associated with the COVID-19 lockdowns in 2020. We use two distinct empirical approaches in our analysis: (a) an event study around the date of the lockdowns (March to July 2020), and (b) a difference-in-differences analysis comparing the lockdown period in 2020 to the same months in 2021, in order to attempt to control for seasonality. In both countries, market activity was severely disrupted and we observe declines in expenditures. However, we find no evidence of declines in food security.
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6,634 members
Sasha Tozzi
  • Department of Ocean Sciences
Marc Perry
  • Genomics Institute
Diane Gifford-Gonzalez
  • Department of Anthropology
John Pearse
  • Department of Ecology & Evolutionary Biology
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