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At least 127 records · Page 7

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.

59 BASIC BIOLOGICAL SCIENCES↗

Disproportionate impacts of COVID-19 in a large US city

COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021 and fine-grain infection hospitalization rates, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 23.7% (95% CrI: 22.5–24.8%) infection rate and 29.4% (95% CrI: 28.0–31.0%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (11.2% [95% CrI: 10.3–12.0%] vs 25.1% [95% CrI: 23.7–26.4%]), but more likely to be hospitalized (1,965 per 100,000 vs 376 per 100,000) and have their infections reported (53% [95% CrI: 49–57%] vs 28% [95% CrI: 27–30%]). We used a mixed effect poisson regression model to estimate disparities in infection and reporting rates as a function of social vulnerability. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0–3.0) times the infection rate and only 70% (95% CrI: 60%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. Our results suggest that further public health efforts are needed to mitigate local COVID-19 disparities and that the CDC’s social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.

60 APPLIED LIFE SCIENCES↗

Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy

With a dataset of testing and case counts from over 1,400 institutions of higher education (IHEs) in the United States, we analyze the number of infections and deaths from SARS-CoV-2 in the counties surrounding these IHEs during the Fall 2020 semester (August to December, 2020). We find that counties with IHEs that remained primarily online experienced fewer cases and deaths during the Fall 2020 semester; whereas before and after the semester, these two groups had almost identical COVID-19 incidence. Additionally, we see fewer cases and deaths in counties with IHEs that reported conducting any on-campus testing compared to those that reported none. To perform these two comparisons, we used a matching procedure designed to create well-balanced groups of counties that are aligned as much as possible along age, race, income, population, and urban/rural categories—demographic variables that have been shown to be correlated with COVID-19 outcomes. We conclude with a case study of IHEs in Massachusetts—a state with especially high detail in our dataset—which further highlights the importance of IHE-affiliated testing for the broader community. The results in this work suggest that campus testing can itself be thought of as a mitigation policy and that allocating additional resources to IHEs to support efforts to regularly test students and staff would be beneficial to mitigating the spread of COVID-19 in a pre-vaccine environment.

60 APPLIED LIFE SCIENCES↗

Quantile-specific heritability of plasma fibrinogen concentrations

Fibrinogen is a moderately heritable blood protein showing different genetic effects by sex, race, smoking status, pollution exposure, and disease status. These interactions may be explained in part by “quantile-dependent expressivity”, where the effect size of a genetic variant depends upon whether the phenotype (e.g. plasma fibrinogen concentration) is high or low relative to its distribution. Determine whether fibrinogen heritability (h 2 ) is quantile-specific, and whether quantile-specific h 2 could account for fibrinogen gene-environment interactions. Plasma fibrinogen concentrations from 5689 offspring-parent pairs and 1932 sibships from the Framingham Heart Study were analyzed. Quantile-specific heritability from offspring-parent (β OP , h 2 = 2β OP /(1+r spouse )) and full-sib regression slopes (β FS , h 2 = {(1+8r spouse β FS ) 0.05 –1}/(2r spouse )) were robustly estimated by quantile regression with nonparametric significance assigned from 1000 bootstrap samples. Quantile-specific h 2 (±SE) increased with increasing percentiles of the offspring’s age- and sex-adjusted fibrinogen distribution when estimated from β OP (P trend = 5.5x10 -6 ): 0.30±0.05 at the 10 th , 0.37±0.04 at the 25 th , 0.48±0.05 at the 50 th , 0.61±0.06 at the 75 th , and 0.65±0.08 at the 90 th percentile, and when estimated from β FS (P trend = 0.008): 0.28±0.04 at the 10 th , 0.31±0.04 at the 25 th , 0.36±0.03 at the 50 th , 0.41±0.05 at the 75 th , and 0.50±0.06 at the 90 th percentile. The larger genetic effect at higher average fibrinogen concentrations may contribute to fibrinogen’s greater heritability in women than men and in Blacks than Whites, and greater increase from smoking and air pollution for the FGB -455G>A A-allele. It may also explain greater fibrinogen differences between: 1) FGB -455G>A genotypes during acute phase reactions than usual conditions, 2) GTSM1 and IL-6 -572C>G genotypes in smokers than nonsmokers, 3) FGB -148C>T genotypes in untreated than treated diabetics, and LPL PvuII genotypes in macroalbuminuric than normoalbuminuric patients. Fibrinogen heritability is quantile specific, which may explain or contribute to its gene-environment interactions. The analyses do not disprove the traditional gene-environment interpretations of these examples, rather quantile-dependent expressivity provides an alternative explanation that warrants consideration.

59 BASIC BIOLOGICAL SCIENCES↗

A novel framework for increasing research transparency: Exploring the connection between diversity and innovation

A split sample/dual method research protocol is demonstrated to increase transparency while reducing the probability of false discovery. We apply the protocol to examine whether diversity in ownership teams increases or decreases the likelihood of a firm reporting a novel innovation using data from the 2018 United States Census Bureau’s Annual Business Survey. Transparency is increased in three ways: 1) all specification testing and identifying potentially productive models is done in an exploratory subsample that 2) preserves the validity of hypothesis test statistics fromde novoestimation in the holdout confirmatory sample with 3) all findings publicly documented in an earlier registered report and in this journal publication. Bayesian estimation procedures that leverage information from the exploratory stage included in the confirmatory stage estimation replace traditional frequentist null hypothesis significance testing. In addition to increasing statistical power by using information from the full sample, Bayesian methods directly estimate a probability distribution for the magnitude of an effect, allowing much richer inference. Estimated magnitudes of diversity along academic discipline, race, ethnicity, and foreign-born status dimensions are positively associated with innovation. A maximally diverse ownership team on these dimensions would be roughly six times more likely to report new-to-market innovation than a homophilic team.

Science & Technology - Other Topics↗

Opiate Sensitivity in Fruit Flies

Substance use disorder is a debilitating clinical condition in which behavioral dependence results from biological, environmental, genetic, and psychosocial factors. An epidemic surrounding the use and abuse of opioids is ravaging the world. While considerable efforts have explored the social drivers of addiction, a deeper understanding of biological causes and genetic vulnerabilities, preventative interventions, and effective treatments, have all proven elusive. This perspective article aims to remind readers that addictive natural compounds such as cocaine, nicotine, cathinone, or morphine, evolved as defensive metabolites to deter insect herbivory. The molecular mechanisms underlying motivational seeking and learning/reward show remarkable conservation since their early emergence in bilateral metazoans. An extended coevolutionary arms race subsequently weaponized these compounds into disruptors of learning, motivation, and incentivized attention. When plant chemical defenses attack insect physiology, humans are rendered susceptible due to strong conservation in the underlying molecular machinery. This perspective addresses the paradox that opiates were shaped to target insect neuropharmacology, even though this taxon appears to lack the recognized opioid receptor clade of mammals. We argue that the link is to be found in the allatostatin receptor, a basal ortholog of opioid receptors. Moreover, preliminary evidence indicates that morphine reduces Drosophila feeding and locomotion, concordant with a purported role as a defensive compound reducing herbivory. An implementation via allatostatin-mediated mechanisms is likely. This research argues for a broader heuristic perspective of substance abuse and a recognition of the evolutionary constraints that have likely shaped the biological drivers of opioid sensitivity and of its behavioral targets.

59 BASIC BIOLOGICAL SCIENCES↗

Study of Conduction-Cooled Superconducting Quadrupole Magnets Combined with Dipole Correctors for the ILC Main Linac

A superconducting rf (SRF) cryomodule for International Linear Collider(ILC) Main Linac equips focus/steering magnets. The magnets are "superferric" magnets with four superconducting (SC) race track coils conductively cooled from the cryomodule LHe supply pipe. The quadrupole field gradient and dipole field are 40 T/m and 0.1 T, respectively. The magnet length and iron-pole radius are 1 m and 0.045 m, respectively. It is known that dark current is generated at SRF cavities and accelerated through the following linac string. The dark current reaches and heats the SC magnets. It is estimated that the power deposition in the magnet may reach more than a few watts and temperature of the SC coils may locally reach to critical temperature of NbTi. It is important to make the magnet not reach quench with sufficient conduction cooling. We aim to realize the SC magnet which can stably operate under such condition. We plan to develop test coils made of three types of SC materials, NbTi, Nb₃Sn, and MgB₂ and study thermal characteristics and stability . We will develop a short model magnet, based on the test coil results. Here, we will present the magnet design study and the R&D plan.

43 PARTICLE ACCELERATORS↗

Magnetic design of the commutational magnet and quadrupoles for PERLE accelerator

ER@CEBAF is an effort to demonstrate multi-GeV multipass energy recovery with a low beam current in CEBAF. The CEBAF race-track-shaped geometry allows its linacs to accommodate multiple energy beams simultaneously. However, five energy recovery passes complicate the beamline optics design process. Individual recirculating arcs each transport one beam energy, and are shared between accelerating/decelerating beams. This paper presents a CEBAF optics redesign to accommodate the ER@CEBAF multi-pass ER scheme. Isochronous arcs were retuned to match into optics solutions for optimized 10-pass linacs. In this paper, we discuss the optics re-design process for ER@CEBAF based on the existing CEBAF layout.

Neththikumara, I.↗

Generating Mixed Patterns of Residential Segregation: An Evolutionary Approach

The Schelling model of residential segregation has demonstrated that even the slightest preference for neighbors of the same race can be amplified into community-wide segregation. However, these models are unable to simulate mixed, coexisting patterns of segregation and integration, which have been seen to exist in cities. Using evolutionary model discovery we demonstrate how including social factors beyond racial bias when modeling relocation behavior enables the emergence of strongly mixed patterns. Our results indicate that the emergence of mixed patterns is better explained by multiple factors influencing the decision to relocate; the most important being the interaction of nonlinear, rapidly diminishing racial bias with a recent, historical tendency to move. Additionally, preference for less isolated neighborhoods or preference for neighborhoods with longer residing neighbors may produce weaker mixed patterns. Finally, this work highlights the importance of exploring the influence of multiple hypothesized factors of decision making, and their interactions, within agent rules, when studying emergent outcomes generated by agent-based models of complex social systems.

97 MATHEMATICS AND COMPUTING↗

A Mixed-Method Design Approach for Empirically Based Selection of Unbiased Data Annotators

Implicit bias embedded in the annotated data is by far the greatest impediment in the effectual use of supervised machine learning models in tasks involving race, ethics, and geopolitical polarization. For societal good and demonstrable positive impact on wider society, it is paramount to carefully select data annotators and rigorously validate the annotation process. Current approaches to selecting annotators are not sufficiently grounded in scientific principles and are limited at the policy-guidance level, thereby rendering them unusable for machine learning practitioners. This work proposes a new approach based on the mixed-methods design that is functional, adaptable, and simpler to implement in selecting unbiased annotators for any machine learning problem. By demonstrating it on a real-world geopolitical problem, we also identified and ranked key inane profile characteristics towards an empirically-based selection of unbiased data annotators.

Thakur, Gautam Malviya↗

Of Clouds and Craters: The History of U.S. Nuclear Weapons Testing

“Now!” With that word, the Atomic Age – and the era of nuclear weapons testing – dawned. The advent of World War II’s first irresistible weapon, which had been secretly tested in the New Mexico desert in July 1945, would help hasten the inevitable: complete victory for the Allies. Codenamed Trinity, the test was the first of over a thousand conducted by the United States between 1945 and 1992. Nuclear weapons would change future clashes as well. The looming Cold War, with roots stretching all the way back to 1917, was history’s first conflict between two, major nations armed with nuclear weapons. It is clear the existence of those weapons played an important role in maintaining a tenuous peace between the United States and the Soviet Union; it is also clear nuclear weapons testing played a prominent role in fueling both the arms race and the success of deterrence. Yet, the history of nuclear weapons testing is rarely remembered, even though nuclear tests have been performed in the very recent past. Of the estimated 2,000-plus nuclear tests ever performed, the U.S. is responsible for approximately half. This is the story of U.S. full-scale nuclear weapons testing.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

A Whirlwind History of Cryptography

This presentation provides an overview of cryptography starting with the Spartan Scytale used extensively during the Peloponnesian wars up through present day. Cryptography and cryptanalysis developed side by side in arms race. Algorithm development stagnated pending cracking. Once a method of crypto was cracked, development took off. Cryptography and cryptanalysis drove developments in math, linguistics, information theory, and quantum theory, and pushed development of the first computers.

97 MATHEMATICS AND COMPUTING↗

Preserving Manhattan Project historic sites

Beginning in 1943, Project Y – the code name for Los Alamos during World War II – transformed the isolated Pajarito Plateau. The sounds of construction equipment replaced the voices of the Los Alamos Ranch School boys and local homesteaders. Construction crews hurriedly built many structures on mesa tops and in the canyons of Los Alamos. Countless concerns flooded Manhattan Project staff, but designing structures to withstand the test of time was not one of them. The top-secret race to develop an atomic bomb before Nazi Germany was on and everyone felt the pressure. Over the next 75 years, some of the structures slumped into disrepair from exposure to the harsh northern New Mexico environment - concrete cracking and spalling, wood frames rotting. That’s where Los Alamos National Laboratory’s historic preservation team enters the Manhattan Project story.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

A Valentine’s tribute to Lab love: Watch clips from 1943 wedding of two staff

She was a secretary for Director J. Robert Oppenheimer. He was a physicist who helped create the world’s first atomic bombs. And for 65 years they were Mr. and Mrs. Bradner. Hugh Bradner was the first person that Marjorie Hall met upon arrival to join the Lab’s clandestine war-time efforts. He happened to be in Dorothy McKibbin’s Santa Fe office when Marjorie walked in. It was love at first sight, Marjorie recalled years later in an interview. The Bradners were married in September 1943 at McKibbin’s home. It was one of many weddings there during the Manhattan Project era. Los Alamos was fenced and guarded during this time, as staff raced to secretly develop nuclear weapons to help end World War II. Most were young – the average age was late 20s – and many, like the Bradners, met their lifelong partners then. The Bradners left Los Alamos after the war ended in 1945. Hugh is credited with inventing the neoprene wetsuit in 1951. The couple had one daughter. Marjorie, 89, and Hugh, 92, died just a few weeks apart in 2008 in California. Many of their home movies from their time in Los Alamos are preserved at the Lab. They are part of the collections in the National Security Research Center, which is the Lab’s classified library and also houses unclassified artifacts.

99 GENERAL AND MISCELLANEOUS↗

Data-Driven Understanding of Low-to-Moderate Income Customers’ Adoption and Financial Qualification in Community Solar (Final Technical Report)

When Solstice began working in the community solar industry, it quickly became clear that there was a wide disparity along race and class lines in terms of what kind of household traditional solar offerings benefited. Solstice is an organization that aligns itself to the principles of a Just Transition, or the concept that a transition to a green economy should benefit and prioritize historically marginalized groups of people. Given that low-income communities are disproportionately burdened by our current polluting fossil fuel economy, Solstice set out to investigate the root causes of the exclusion of low to moderate income (LMI) households in the community solar market. As we worked more and more with financiers, developers, and LMI households, we recognized that significant barriers to entry in a developer-owned project were credit threshold requirements. A FICO score of 750 and higher discriminates against LMI households that are not financially stable enough to take on multiple lines of credit (or who may not have been deemed credit worthy enough to access a line of credit) yet who may have been reliable utility customers. As Solstice began looking further into preliminary data and speaking to community-based organizations (CBOs) that serve LMI households, we found our hypothesis to be worth investigating; there was indeed a subset of LMI households with poor FICO scores (or no FICO score at all) that had perfect bill payment history. Though initially Solstice was intent on gathering a body of data to prove or disprove this hypothesis, we were also concerned that all this proof of a financially stable and reliable customer was not being incorporated into FICO, and wondered if such a score would be possible. After preliminary research into the existence of alternative scores, Solstice realized that many mission-driven lending institutions rely on alternative metrics that are formulated for their specific industry. However, we also realized that community solar did not have an alternative credit underwriting mechanism, though there was great need from solar financiers for one. We anticipated that the creation of an EnergyScore would contribute to financiers’ need to qualify more people, as these entities are desperately looking for ways to lower the cost of customer acquisition. FICO turns away nearly 50% of potential customers (according to our own acquisition experience), and much of the community solar industry is realizing that FICO is not the perfect qualifying mechanism. Additionally, with a grounding in energy justice, just transitions, and climate justice, Solstice recognizes the need for a solution that addresses a more urgent need for LMI households to access renewable energy savings and relieve energy burdens. With funding from the Department of Energy, we gathered the data necessary to build the EnergyScore, reached out to mission-driven developers willing to test the metric, and secured several demonstration projects to pilot the EnergyScore. After acquiring customers for these demo projects using the EnergyScore, we will be continuously collecting customer payment behavior data. Though it goes beyond the scope of this project, we plan to disseminate this de-identified data with the wider community solar industry, which includes not only financiers and developers, but other mission-driven nonprofits, solar cooperatives, community-based organizations, environmental justice activists, and academics. While we intend to disprove the notion that LMI households cannot be included in projects without acutely increasing the risk to project finances, we also hope the data can be used to negotiate better pricing of systems and terms of ownership for community groups seeking to build inclusive projects.

14 SOLAR ENERGY↗

Why didn’t Oppenheimer ever win a Nobel Prize?

For his scientific achievement, he would be forever known as the father of the atomic bomb – but never as a Nobel laureate. The pinnacle of global recognition, the Nobel Prize was bestowed on 18 of J. Robert Oppenheimer’s colleagues with whom he worked at the Manhattan Project site in Los Alamos. There, in just 27 months and in a perceived race with Nazi Germany, the scientists created the first nuclear weapons. Their efforts brought the world into the Atomic Age and helped end World War II. Several were awarded the prize before coming to work at the wartime lab, while most would go on to win later in life. Oppenheimer was nominated for the Nobel Prize for Physics three times: in 1946, in 1951, and in 1967. Colleagues, scholars, and surely Oppenheimer himself pondered why he was never bestowed the honor. “To understand this,” said James Kunetka, historian and author of The General and the Genius, “you have to first examine the man’s academic life before and after the war.”

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Physical Lab Security: Before and After World War II

Physical security during World War II was important to maintaining the secrecy of the Manhattan Project, the government’s wartime effort to create the atomic bomb. In a perceived race against Nazi Germany to do so, physicist J. Robert Oppenheimer, the Lab’s first director, and General Leslie Groves, head of the Manhattan Project, needed a secluded place to build the clandestine Lab.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗