Recent ucsc_postprints items

Improving coastal ocean pH estimates through assimilation of glider observations and hybrid statistical methods

Fri, 8 May 2026 00:00:00 +0000

Abstract. Ocean acidification monitoring and carbon accounting require accurate estimates of marine carbonate system variables, particularly in dynamic coastal regions where observations remain sparse. This study presents an approach to improving carbonate system state estimates in the California Current System through the assimilation of underwater glider observations with both dynamical and statistical models. We implement a 4D-Var data assimilation system that jointly assimilates physical variables, chlorophyll, and glider-based pH and alkalinity data into a regional coupled physical-biogeochemical model. In our experiments, the assimilation of physical variables and chlorophyll alone has limited impact on pH and other carbonate system estimates, while the joint assimilation including pH and alkalinity variables successfully improves these estimates. Cross-validation experiments further demonstrate that the joint assimilation typically also improves estimates near the observation...

Book Review: Pure Excess: Capitalism and the Commodity , by Todd McGowan Pure Excess: Capitalism and the Commodity, by McGowanTodd. Columbia University Press, 2024, 270 pp.

Wed, 6 May 2026 00:00:00 +0000

Book Review: Pure Excess: Capitalism and the Commodity , by Todd McGowan Pure Excess: Capitalism and the Commodity, by McGowanTodd. Columbia University Press, 2024, 270 pp.

Probing axionlike particles near the neutral pion mass with KOTO data

Tue, 5 May 2026 00:00:00 +0000

We demonstrate that novel limits on prompt axionlike particles (ALPs) in the hard-to-probe mass range near the neutral pion—the so-called pion chimney—may be obtained from recasting K L → 3 π 0 → 6 γ data taken by the J-PARC KOTO experiment, to search for K L → 2 π 0 a → 6 γ ...

Measurement of coherent exclusive J/ψ → μ+μ− production in ultraperipheral Pb+Pb collisions at sNN=5.36 TeV with the ATLAS detector

Tue, 5 May 2026 00:00:00 +0000

The ATLAS experiment has performed a measurement of coherent exclusive J/ψ → μ+μ− production in ultraperipheral Pb+Pb collisions at sNN=5.36$$ \sqrt{s_{\textrm{NN}}}=5.36 $$ TeV. The data was recorded at the Large Hadron Collider (LHC) during 2023, and corresponds to an integrated luminosity of 79 μb−1. Exclusive J/ψ candidates were selected with a dedicated track-sensitive trigger based on the ATLAS transition radiation tracker. The analysis involves reconstruction of the dimuon invariant mass based on muon tracks from the inner detector, as the muon transverse momentum range of interest precludes the use of the standard muon reconstruction and identification algorithms. Differential cross sections are measured as a function of J/ψ rapidity and are compared with theoretical predictions. After extrapolation to sNN=5.02$$ \sqrt{s_{\textrm{NN}}}=5.02 $$ TeV, they are also compared with previous measurements performed by other experiments using data from LHC Run 2. While the results...

Measurement of the azimuthal anisotropy of charged particles in sNN=5.36TeV O16+O16 and Ne20+Ne20 collisions with the ATLAS detector

Tue, 5 May 2026 00:00:00 +0000

This paper presents the first measurements of the azimuthal anisotropy coefficients , which quantify the -order Fourier modulation of charged-particle azimuthal distributions, for in and collisions recorded with the ATLAS detector at the CERN Large Hadron Collider in 2025. The coefficients are measured as a function of transverse momentum ( ), collision centrality, and event multiplicity. They are extracted using two complementary methods: two-particle correlations with a template-fit subtraction of short-range nonflow contributions, and four-particle subevent cumulants, which intrinsically suppress nonflow effects and provide sensitivity to flow fluctuations. The results show a clear hierarchy and a nonmonotonic dependence on , reaching a maximum around , consistent with trends observed in heavy-ion collisions. Detailed comparisons between the two collision systems reveal an enhanced in central collisions, consistent with theory expectations based on the predicted...

Search for Higgs bosons produced in association with a high-energy photon via vector-boson fusion and decaying to a pair of b-quarks in the ATLAS detector

Tue, 5 May 2026 00:00:00 +0000

A search for Standard Model Higgs bosons produced in association with a high-energy photon and decaying to b b ¯ is performed using 133 fb − 1 of s = 13 TeV pp collision data collected with the ATLAS detector at the Large Hadron Collider at CERN. The photon requirement reduces the multijet background, and the H → b b ¯ decay is the dominant decay mode. Event selection requirements target events produced by vector-boson fusion, the dominant production mode in this channel. Several improvements enhance the search sensitivity compared to previous measurements. These improvements include better background modelling and characterization, the use of a neural-network classifier, and an updated signal extraction strategy adopting a direct binned-likelihood fit to the classifier output. With these improvements, the Higgs boson signal strength is measured to be 0.2 ± 0.7 relative to the Standard Model prediction. This corresponds to an observed significance of 0.3 standard deviations, compared...

Erratum: The environmental impact, carbon emissions and sustainability of computing in the ATLAS experiment

Tue, 5 May 2026 00:00:00 +0000

The worldwide distribution of ATLAS computing, based on the amount of CPU provided, in HS23 (see Sect. 4.1 for the precise definition of HS23), on average in 2023–2024. Countries in gray did not contribute significant CPU One correction is noted for the paper [1], which does not affect the results reported. The vertical axis range of the legend of Fig. 1 is corrected as it was reversed in the original publication.

Nanopore Sequencing: A Way to Explore Life's Origins.

Sun, 3 May 2026 00:00:00 +0000

In future years, it seems likely that someone will claim they have discovered a process that allows a mixture of simple molecules to assemble into structures and systems with the fundamental properties of life. A useful exercise for researchers is to imagine what those properties might be and then design experiments to test ideas about how those properties could emerge on early Earth and other habitable planets. A variety of polymers play key roles in living systems, and we now have powerful analytical tools to analyze their structure and functions. One of these tools is the ability to determine base sequences of nucleic acids by gel electrophoresis, which led to the publication of the human genome in 2001 by the International Human Genome Sequencing Consortium. Another is nanopore sequencing, which has the unique ability to sequence not just fragments from a purified source of DNA but also individual molecules in mixed populations of nucleic acid polymers. Here, I will describe...

Icelandic Hot Springs as a Prebiotic Analog: Wet-Dry Cycling Effects on the Stability of Nucleotides and Nucleic Acids.

Sun, 3 May 2026 00:00:00 +0000

The hot spring hypothesis for the origin of life proposes that naturally occurring wet-dry cycles in small bodies of water could have driven condensation reactions on prebiotic Earth. Mononucleotides exposed to wet-dry cycles in the laboratory have been shown to generate RNA oligomers. We tested whether similar reactions occur after wet-dry cycling in the laboratory of mononucleotides mixed with natural hot spring waters. Nucleotide solutions were prepared in the laboratory with effluent samples collected from hot springs of the Seltún (SE) and Hveradalir (HV) geothermal areas in Iceland. Sixteen wet-dry cycles with water collected from SE resulted in degradation of adenosine-5'-monophosphoric acid (95%), uridine 5'-monophosphate (63%) mononucleotides, while four wet-dry cycles were enough to destroy around 90% of both A10 and U10; thus, they displayed uniquely destructive properties for both purine and pyrimidine bases. Meanwhile, mononucleotides suspended in water collected...

"The Nerve Garden": Plant a Seed in Cyberspace

Fri, 1 May 2026 00:00:00 +0000

"The Nerve Garden": Plant a Seed in Cyberspace

The circadian isoform landscape of mouse livers.

Wed, 29 Apr 2026 00:00:00 +0000

The mammalian circadian clock is an autoregulatory feedback process that is responsible for homeostasis in mouse livers. These circadian processes are well understood at the gene level; however, they are not well understood at the isoform level. To investigate circadian oscillations at the isoform level, we used the nanopore-based R2C2 method to create over 78 million highly accurate, full-length complementary DNA reads for 12 RNA samples extracted from mouse livers collected at 2 h intervals. To generate a circadian mouse liver isoform-level transcriptome, we processed these reads using the Mandalorion tool, which identified and quantified 58 612 isoforms, 1806 of which showed circadian oscillations. We performed detailed analysis on the circadian oscillation of these isoforms, their coding sequences, and transcription start sites and compiled easy-to-access resources for other researchers. This study and its results add a new layer of detail to the quantitative analysis of transcript...

The Biological Productivity of the Ocean

Thu, 23 Apr 2026 00:00:00 +0000

Productivity fuels life in the ocean, drives its chemical cycles, and lowers atmospheric carbon dioxide. Nutrient uptake and export interact with circulation to yield distinct ocean regimes.

Effects of Daily Discrimination and Microaggressions on Alcohol Use and Related Consequences Among Latine College Students at a Predominantly White Institution

Thu, 23 Apr 2026 00:00:00 +0000

OBJECTIVE: Latine college students at predominantly White institutions face discriminatory stress, increasing their risk for problematic alcohol use. The specific impact of daily discrimination and microaggressions on alcohol use and related consequences, relative to other college stressors (e.g., academics, finances), remains understudied. This study used an intensive daily longitudinal design to examine whether these experiences independently affect alcohol use and related consequences. METHOD: The study enrolled 109 Latine student drinkers (M_age = 19.95; 77% female) from a large predominantly White institution in the northeastern United States. Participants completed a baseline survey, an in-person training session, and 28 consecutive daily surveys. Multilevel models analyzed the data, examining within- and between-person effects while controlling for college stress, trauma history, and relevant demographic variables. RESULTS: Participants had an average survey...

Greenhouse gas effects on Quaternary climates

Thu, 23 Apr 2026 00:00:00 +0000

Slight but regular changes in Earth's orbit paced the rhythm of recurring ice age climate cycles that define the Quaternary period, and from detailed reconstructions we now understand that many of these changes were mediated by climate/carbon cycle feedbacks that changed the concentration of greenhouse gasses (GHGs) in the atmosphere to warm and cool the planet. Among the various GHGs the strongest effect came from changing atmospheric carbon dioxide (CO2), as supported by an expanding body of available reconstructions. Reconciling the orbital and CO2 theory is an open challenge for researchers of Quaternary climate change, and a significant opportunity to improve projections of future carbon cycle feedbacks in response to anthropogenic climate change.

The Sentani variation

Thu, 23 Apr 2026 00:00:00 +0000

Abstract This article examines the default stress pattern of Sentani (Papuan), situates it within the typology of iambic stress patterns, and provides an analysis within the Weak Bracketing framework for metrical stress theory. Sentani is unique in sometimes employing clash (adjacent stressed syllables) and other times employing lapse (adjacent stressless syllables) in an effort to avoid final stress in even-parity forms. Clash is employed in four-syllable forms, but lapse is employed in longer even-parity forms. Key to the analysis are constraints insisting that both the initial foot and the final foot carry a stress. When the initial and final foot are adjacent (i.e., in four-syllable forms), insisting that both be stressed results in a clash. When the initial and final foot are not adjacent (i.e., in longer even-parity forms), a medial foot emerges without stress in order to avoid clash.

Dissociating the Hallucinogenic and Neuroplastic Effects of Psilocybin.

Thu, 23 Apr 2026 00:00:00 +0000

It is unclear how serotonin 2A receptors (5-HT _2A Rs) in cortical layer 5 pyramidal neurons (L5 PyrNs) differentially contribute to psilocybin-induced hallucinations versus neuroplasticity. Our longitudinal in vivo imaging revealed that psilocybin promotes new synapse formation and maturation while accelerating the elimination of pre-existing synapses. Cell type-specific manipulation of 5-HT _2A R expression in L5 PyrNs further demonstrated that it is necessary and sufficient for psilocybin-induced neuroplasticity but dispensable for hallucinations.

Greenhouse gas effects on Quaternary climates

Thu, 23 Apr 2026 00:00:00 +0000

Recovery of habitat heterogeneity in restored and remnant riparian forests along the Sacramento River, California, United States

Thu, 23 Apr 2026 00:00:00 +0000

Abstract Introduction Ecosystems are naturally heterogeneous, though humans often homogenize them through land use practices. Increasing physical heterogeneity in degraded ecosystems can enhance biodiversity and habitat resilience but is rarely a focus in restoration. Objectives We compared topographic and vegetation structural heterogeneity in 3251 ha of restored and remnant riparian forests along 100 km of the Sacramento River, California, which was degraded by intensive agriculture and flood control and has undergone large‐scale restoration since the late 1980s. Methods We used Light Detection and Ranging (LiDAR) data to derive three measures of topographic and vegetation structural heterogeneity that influence plant and wildlife diversity—topographic ruggedness index (TRI), overstory rugosity, and foliage height diversity (FHD)—at 2‐m (fine) and 10‐m (coarse) resolution. Results Fine‐scale TRI was 76% lower in restored than remnant forests and slowly recovered with...

Signs of Disability by Stephanie L. Kerschbaum (review)

Thu, 23 Apr 2026 00:00:00 +0000

Signs of Disability by Stephanie L. Kerschbaum (review)

Earth system carbon cycle dynamics through time

Thu, 23 Apr 2026 00:00:00 +0000

Earth's carbon cycle controls the concentration of the greenhouse gas carbon dioxide (CO2) in the atmosphere, which influences the climate on our planet and thereby affects the many processes that control the carbon cycle. These climate-carbon cycle feedbacks determine the long-term Earth System response to biological evolution, geologic drivers, and events such as anthropogenic fossil fuel use. In Section “Earth's carbon cycle” of this chapter we outline the reservoirs and chemistry of carbon in Earth's surface environment; in Section “Carbon fluxes and dynamic balances” we describe the dynamics underpinning carbon cycle feedbacks, including a discussion of carbon cycle models, and in Section “Climate and the carbon cycle” we survey the observational evidence base for our current understanding of long-term Earth System change by focusing on available proxy records and reconstructions of the climate and carbon cycle across the Cenozoic Era. In facing our collective impacts on...

Ethnic identity and religiosity are related to lower alcohol use and cannabis use in Arab American college students

Thu, 23 Apr 2026 00:00:00 +0000

Background: Although religious and cultural factors have been related to substance use in various populations, research is needed regarding associations for Arab Americans.Objectives: We examined how ethnic identity and religiosity relate to the odds and frequency of alcohol and cannabis use in Arab American college students during the COVID-19 pandemic, as well as differences by biological sex and Muslim upbringingMethods:Arab American college students (N = 173; M_age = 20.1, range 17-23; 60.7% female; 44.5% Christian upbringing, 43.9% Muslim upbringing) were recruited through electronic flyers and a psychology subject pool in California. Participants reported their ethnic identity affirmation (i.e. feeling positively about being Arab American) and search (i.e. learning about Arab culture), religiosity, and past-year alcohol and cannabis useResults: Greater ethnic identity affirmation was related to less frequent alcohol (OR = .68,...

Theoretical framework for soft X‐ray Fourier transform spectroscopy using the Wigner function

Wed, 22 Apr 2026 00:00:00 +0000

This work presents a theoretical framework for the propagation of partially coherent Gaussian radiation in a modified Mach–Zehnder interferometer designed for Fourier transform spectroscopy (FTS) applications. Using the Wigner function formalism, we analytically propagate the radiation through the system and benchmark our approach by comparing the resulting interference pattern and interferogram with previous works in the diffraction limit. Our analysis reveals that the transverse coherence length requirement of the incident light field for detectable modulation is less stringent than previously assumed. Additionally, we provide theoretical demonstrations of FTS performance across various wavelengths using the proposed setup. These findings underscore the potential of this interferometer to achieve high‐resolution FTS in the soft X‐ray regime. A theoretical framework for the propagation of partially coherent Gaussian radiation in a modified Mach–Zehnder interferometer designed...

David Deamer: Five Decades of Research on the Question of How Life Can Begin

Mon, 20 Apr 2026 00:00:00 +0000

David Deamer served as editor-in-chief of Life from 2014 to 2016. [...].

Can Life Begin on Enceladus? A Perspective from Hydrothermal Chemistry

Mon, 20 Apr 2026 00:00:00 +0000

Enceladus is a target of future missions designed to search for existing life or its precursors. Recent flybys of Enceladus by the Cassini probe have confirmed the existence of a long-lived global ocean laced with organic compounds and biologically available nitrogen. This immediately suggests the possibility that life could have begun and may still exist on Enceladus. Here we will compare the properties of two proposed sites for the origin of life on Earth-hydrothermal vents on the ocean floor and hydrothermal volcanic fields at the surface-and ask whether similar conditions could have fostered the origin of life on Enceladus. The answer depends on which of the two sites would be more conducive for the chemical evolution leading to life's origin. A hydrothermal vent origin would allow life to begin in the Enceladus ocean, but if the origin of life requires freshwater hydrothermal pools undergoing wet-dry cycles, the Enceladus ocean could be habitable but lifeless. These arguments...

Factoring Origin of Life Hypotheses into the Search for Life in the Solar System and Beyond

Mon, 20 Apr 2026 00:00:00 +0000

Two widely-cited alternative hypotheses propose geological localities and biochemical mechanisms for life's origins. The first states that chemical energy available in submarine hydrothermal vents supported the formation of organic compounds and initiated primitive metabolic pathways which became incorporated in the earliest cells; the second proposes that protocells self-assembled from exogenous and geothermally-delivered monomers in freshwater hot springs. These alternative hypotheses are relevant to the fossil record of early life on Earth, and can be factored into the search for life elsewhere in the Solar System. This review summarizes the evidence supporting and challenging these hypotheses, and considers their implications for the search for life on various habitable worlds. It will discuss the relative probability that life could have emerged in environments on early Mars, on the icy moons of Jupiter and Saturn, and also the degree to which prebiotic chemistry could have...

A Multilamellar Lipid-Polymer Progenitor Can Promote the Assembly of Improbable Functional Polymer Complexes at Life's Origins.

Mon, 20 Apr 2026 00:00:00 +0000

The original conditions from which primitive life emerged on the early Earth were likely to be dilute mixtures of organic compounds in aqueous solutions. A significant challenge for origins of life research is to discover the reactions that allowed such mixtures to become increasingly complex with products such as polymers that had structural and functional properties related to biology. The chances are low that potential reactants could find one another in dilute solutions composed of thousands of different molecular species. To improve the probability of such encounters, we have investigated a novel condition that both concentrates and organizes potential reactants and encapsulates polymeric products to form protocells. The condition involves a source of freshwater that falls as rainfall precipitation on land masses such as volcanic islands. The water dissolves exogenously and endogenously available organic compounds and feeds into hydrothermal fields where the solutions undergo...

A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond

Mon, 20 Apr 2026 00:00:00 +0000

Charles Darwin's original intuition that life began in a "warm little pond" has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and the difficulty of forming stable membranous compartments in seawater suggest that Darwin's original insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines field observations and laboratory results to provide a novel and testable model in which life begins as protocells assembling in inland fresh water hydrothermal fields. Hydrothermal fields are associated with volcanic landmasses resembling Hawaii and Iceland today and could plausibly have existed on similar land masses rising out of Earth's first oceans. I will report on a field trip to the living and ancient stromatolite fossil localities of Western Australia, which provided key insights into how life...

Hydrothermal Chemistry and the Origin of Cellular Life

Mon, 20 Apr 2026 00:00:00 +0000

Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe...

Revisiting Darwin's Warm Little Pond in the 21st Century: Land-Based Scenarios for Life's Origins.

Mon, 20 Apr 2026 00:00:00 +0000

Revisiting Darwin's Warm Little Pond in the 21st Century: Land-Based Scenarios for Life's Origins.

AFM Images of Viroid-Sized Rings That Self-Assemble from Mononucleotides through Wet–Dry Cycling: Implications for the Origin of Life

Mon, 20 Apr 2026 00:00:00 +0000

It is possible that early life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet-dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers. The aim of the study reported here was to visualize the products by atomic force microscopy. In addition to globular oligomers, ring-like structures ranging from 10-200 nm in diameter, with an average around 30-40 nm, were abundant, particularly when nucleotides capable of base pairing were present. The thickness of the rings was consistent with single stranded products, but some had thicknesses indicating base pair stacking. Others had more complex structures in the form of short polymer attachments and pairing of rings. These observations suggest the possibility that base-pairing may promote polymerization during wet-dry cycling...

Metabolic costs of submerged activity in three species of Arctic seals.

Fri, 17 Apr 2026 00:00:00 +0000

Arctic seals live in dynamic environments characterized by the seasonal advancement and retreat of sea ice. These amphibious marine mammals rely on sea ice as a haul-out substrate for rest and key life-history events, but they spend the majority of their time in the water. Current and predicted sea ice loss highlights the importance of estimating the costs of in-water activities when modelling the energy budgets of free-ranging seals under changing conditions. Yet, activity-specific costs are not available for many affected species. We used open-flow respirometry to measure and compare resting metabolic rates with the energetic costs of submerged diving and swimming in spotted (Phoca largha; n = 3), ringed (Pusa hispida; n = 1) and bearded seals (Erignathus barbatus; n = 1). Individuals were trained to voluntarily complete a sustained stationary breath hold under water or a continuous submerged swim before surfacing in a metabolic dome...

Phase I/II Study of Combined BCL-xL and MEK Inhibition with Navitoclax and Trametinib in KRAS or NRAS Mutant Advanced Solid Tumors.

Mon, 13 Apr 2026 00:00:00 +0000

Purpose

MEK inhibitors (MEKi) lack monotherapy efficacy in most RAS-mutant cancers. BCL-xL is an anti-apoptotic protein identified by a synthetic lethal shRNA screen as a key suppressor of apoptotic response to MEKi.

Patients and methods

We conducted a dose escalation study (NCT02079740) of the BCL-xL inhibitor navitoclax and MEKi trametinib in patients with RAS-mutant tumors with expansion cohorts for: pancreatic, gynecologic (GYN), non-small cell lung cancer (NSCLC), and other cancers harboring KRAS/NRAS mutations. Paired pretreatment and day 15 tumor biopsies and serial cell-free (cf)DNA were analyzed.

Results

A total of 91 patients initiated treatment, with 38 in dose escalation. Fifty-eight percent had ≥3 prior therapies. A total of 15 patients (17%) had colorectal cancer, 19 (11%) pancreatic, 15 (17%) NSCLC, and 32 (35%) GYN cancers. The recommended phase II dose (RP2D) was established as trametinib 2 mg daily days 1 to 14 and navitoclax 250 mg daily...

Post-translational modification of H2B C-terminal helix regulates nucleosome interactions and chromatin signaling

Mon, 13 Apr 2026 00:00:00 +0000

Histone H2B contains a highly conserved C-terminal (H2B αC) helix that has been implicated in chromatin interactions and dynamics. The H2B αC helix comprising residues 105-125 is positioned adjacent to a major site of nucleosome interactions called the acidic patch. Despite individual structural studies highlighting interactions between chromatin proteins and the H2B αC helix, the general role of the helix in mediating nucleosome recognition has not been explored. Moreover, many post-translational modifications (PTMs) have been identified within the H2B αC helix, but significant gaps exist in our understanding of their regulatory potential. In this study, we employed nucleosome affinity proteomics using a library of nucleosomes with mutations or PTMs of the H2B αC helix to investigate contributions to nucleosome binding. Our work uncovers new spatial patterns of H2B αC helix engagement across the proteome. We also demonstrate that H2B K120 mono-ubiquitylation (H2B K120ub)...

A global decision framework for reducing bat fatalities at wind energy facilities

Mon, 13 Apr 2026 00:00:00 +0000

Abstract: Ensuring wind energy development does not cause biodiversity loss is a global priority. Wind turbines kill large numbers of bats, raising concern that global expansion of wind energy increases the threat of extinction of vulnerable bat species. Uncertainty about bat population size and status has hindered efforts to implement regulatory policies based on solutions known to reduce bat fatalities at wind energy facilities, in large part because the amount of fatality reduction necessary to protect bats has been difficult to define. Adoption of the full mitigation hierarchy for bats is urgently needed, including informed siting to avoid impacts to bats, minimization of bat fatalities using fatality thresholds to set operational conditions (e.g. curtailment) and compensation through offsets. We introduce a method...

Coupled phases and combinatorial selection in fluctuating hydrothermal pools: a scenario to guide experimental approaches to the origin of cellular life.

Mon, 13 Apr 2026 00:00:00 +0000

Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an experiment in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively...

PELP1 coordinates the modular assembly and enzymatic activity of the rixosome complex

Mon, 13 Apr 2026 00:00:00 +0000

The rixosome is a large multisubunit complex that initiates RNA decay during critical nuclear transactions including ribosome assembly and heterochromatin maintenance. The overall architecture of the complex remains undefined because several subunits contain intrinsically disordered regions (IDRs). Here, we combined structural and functional approaches to establish PELP1 as the central scaffold of the rixosome upon which the enzymatic subunits modularly assemble. The C-terminal half of PELP1 is composed of a proline-rich IDR that mediates association with the AAA-ATPase MDN1, histones, and the SUMO-specific protease SENP3. The PELP1 IDR contains a glutamic acid-rich region that we establish can chaperone the histone octamer in vitro. Last, the x-ray structure of a small linear motif (SLiM) from the PELP IDR bound to SENP3 reveals how PELP1 allosterically activates SUMO protease activity. This work provides an integrated structural model for understanding the rixosome's dynamic...

Small cell transformation of ROS1 fusion-positive lung cancer resistant to ROS1 inhibition.

Mon, 13 Apr 2026 00:00:00 +0000

Histologic transformation from non-small cell to small cell lung cancer has been reported as a resistance mechanism to targeted therapy in EGFR-mutant and ALK fusion-positive lung cancers. Whether small cell transformation occurs in other oncogene-driven lung cancers remains unknown. Here we analyzed the genomic landscape of two pre-mortem and 11 post-mortem metastatic tumors collected from an advanced, ROS1 fusion-positive lung cancer patient, who had received sequential ROS1 inhibitors. Evidence of small cell transformation was observed in all metastatic sites at autopsy, with inactivation of RB1 and TP53, and loss of ROS1 fusion expression. Whole-exome sequencing revealed minimal mutational and copy number heterogeneity, suggestive of hard clonal sweep. Patient-derived models generated from autopsy retained features consistent with small cell lung cancer and demonstrated resistance to ROS1 inhibitors. This case supports small cell transformation...

APC/C-mediated ubiquitylation of extranucleosomal histone complexes lacking canonical degrons

Mon, 13 Apr 2026 00:00:00 +0000

Non-degradative histone ubiquitylation plays a myriad of well-defined roles in the regulation of gene expression and choreographing DNA damage repair pathways. In contrast, the contributions of degradative histone ubiquitylation on genomic processes has remained elusive. Recently, the APC/C has been shown to ubiquitylate histones to regulate gene expression in pluripotent cells, but the molecular mechanism is unclear. Here we show that despite directly binding to the nucleosome through subunit APC3, the APC/C is unable to ubiquitylate nucleosomal histones. In contrast, extranucleosomal H2A/H2B and H3/H4 complexes are broadly ubiquitylated by the APC/C in an unexpected manner. Using a combination of cryo-electron microscopy (cryo-EM) and biophysical and enzymatic assays, we demonstrate that APC8 and histone tails direct APC/C-mediated polyubiquitylation of core histones in the absence of traditional APC/C substrate degron sequences. Taken together, our work implicates APC/C-nucleosome...

A Field Trip to the Archaean in Search of Darwins Warm Little Pond.

Mon, 13 Apr 2026 00:00:00 +0000

Charles Darwins original intuition that life began in a warm little pond has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and the difficulty of forming stable membranous compartments in seawater suggest that Darwins original insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines field observations and laboratory results to provide a novel and testable model in which life begins as protocells assembling in inland fresh water hydrothermal fields. Hydrothermal fields are associated with volcanic landmasses resembling Hawaii and Iceland today and could plausibly have existed on similar land masses rising out of Earths first oceans. I will report on a field trip to the living and ancient stromatolite fossil localities of Western Australia, which provided key insights into how life may have...

The Hot Spring Hypothesis for an Origin of Life

Sun, 12 Apr 2026 00:00:00 +0000

We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first...

Determining Convergence for Expected Improvement-Based Bayesian Optimization

Fri, 10 Apr 2026 00:00:00 +0000

Bayesian optimization routines may have theoretical convergence results, but determining whether a run has converged in practice can be a subjective task. This paper provides a framework inspired by statistical process control for monitoring an optimization run for convergence. The maximum Expected Improvement (EI) tends to decrease during an optimization run, but decreasing EI is not sufficient for convergence. We consider both a decrease in EI as well as local stability of the variance in order to assess for convergence. The EI process is made more numerically stable through an expected log-normal approximation. An Exponentially Weighted Moving Average control chart is adapted for automated convergence analysis, which allows assessment of stability of both the EI and its variance. The success of the methodology is demonstrated on several examples.

Stochastic Collapsed Variational Inference for Structured Gaussian Process Regression Networks

Fri, 10 Apr 2026 00:00:00 +0000

This paper presents an efficient variational inference framework for a family of structured Gaussian process regression network (SGPRN) models. We incorporate auxiliary inducing variables in latent functions and jointly treat both the distributions of the inducing variables and hyper-parameters as variational parameters. Then we take advantage of the collapsed representation of the model and propose structured variational distributions, which enables the decomposability of a tractable variational lower bound and leads to stochastic optimization. Our inference approach is able to model data in which outputs do not share a common input set, and with a computational complexity independent of the size of the inputs and outputs to easily handle datasets with missing values. Finally, we illustrate our approach on both synthetic and real data.

Temporal Categorical Modeling Using Latent Gaussian Processes

Fri, 10 Apr 2026 00:00:00 +0000

Abstract: Latent Gaussian processes are widely used in latent variable models because they offer a flexible nonlinear mapping from a low-dimensional latent space to a high-dimensional space via Gaussian processes. However, these models are computationally intensive and do not scale well. In this paper, we propose a temporal categorical model that utilizes latent Gaussian processes, inducing-input approximation, and a regularization framework to model multivariate categorical processes, with and without priors on hyperparameters. We analyze the underlying properties and introduce two variational inference approaches: one based on a Monte Carlo method and the other on the delta method. We also found that latent dynamics tend to collapse into a constant zero, which hinders the reflection of dynamic information. To address this, we propose two strategies to regularize the latent dynamics for better alignment with observation dynamics: introducing a regularization...

Nonstationary multivariate Gaussian processes for electronic health records

Fri, 10 Apr 2026 00:00:00 +0000

Advances in the modeling and analysis of electronic health records (EHR) have the potential to improve patient risk stratification, leading to better patient outcomes. The modeling of complex temporal relations across the multiple clinical variables inherent in EHR data is largely unexplored. Existing approaches to modeling EHR data often lack the flexibility to handle time-varying correlations across multiple clinical variables, or they are too complex for clinical interpretation. Therefore, we propose a novel nonstationary multivariate Gaussian process model for EHR data to address the aforementioned drawbacks of existing methodologies. Our proposed model is able to capture time-varying scale, correlation and smoothness across multiple clinical variables. We also provide details on two inference approaches: Maximum a posteriori and Hamilton Monte Carlo. Our model is validated on synthetic data and then we demonstrate its effectiveness on EHR data from Kaiser Permanente Division...

Equivalence testing for multiple groups

Fri, 10 Apr 2026 00:00:00 +0000

Summary Testing for equivalence, rather than testing for a difference, is an important component of some scientific studies. While the focus of the existing literature is on comparing two groups for equivalence, real‐world applications arise regularly that require testing across more than two groups. This paper reviews the existing approaches for testing across multiple groups and proposes a novel framework for multigroup equivalence testing under a Bayesian paradigm. This approach allows for a more scientifically meaningful definition of the equivalence margin and a more powerful test than the few existing alternatives. This approach also allows a new definition of equivalence based on future differences.

What are the possible job opportunities/options for a college graduate with a degree in physical education?