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At least 955 records · Page 53

Globular clusters, ultracompact dwarfs, and dwarf galaxies in Abell 2744 at a redshift of 0.308

We report a photometric study of globular clusters (GCs), ultracompact dwarfs (UCDs), and dwarf galaxies in the giant merging galaxy cluster Abell 2744 at z = 0.308. Color–magnitude diagrams of the point sources derived from deep F814W (rest frame r′) and F105W (rest frame I) images of Abell 2744 in the Hubble Space Telescope Frontier Field show a rich population of point sources, which have colors that are similar to those of typical GCs. These sources are as bright as −14.9<M{sub r{sup ′}}⩽−11.4 (26.0 < F814W(Vega) ≤ 29.5) mag, being mostly UCDs and bright GCs in Abell 2744. The luminosity function (LF) of these sources shows a break at M{sub r{sup ′}}≈−12.9 (F814W ≈ 28.0) mag, indicating a boundary between UCDs and bright GCs. The numbers of GCs and UCDs are estimated to be 1,711,640{sup +589,760} {sub −430,500} and 147 ± 26, respectively. The clustercentric radial number density profiles of the UCDs and bright GCs show similar slopes, but these profiles are much steeper than those of the dwarf galaxies and the mass density profile based on gravitational lensing analysis. We derive an LF of the red sequence galaxies for −22.9<M{sub r{sup ′}}⩽−13.9 mag. The faint end of this LF is fit well by a flat power law with α=−1.14±0.08, showing no faint upturn. These results support the galaxy-origin scenario for bright UCDs: they are the nuclei of dwarf galaxies that are stripped when they pass close to the center of massive galaxies or a galaxy cluster, while some of the faint UCDs are at the bright end of the GCs.

79 ASTRONOMY AND ASTROPHYSICS↗

Lessons from the Onset of a Common Envelope Episode: the Remarkable M31 2015 Luminous Red Nova Outburst

This paper investigates the recent stellar-merger transient M31LRN 2015 in the Andromeda galaxy. We analyze published optical photometry and spectroscopy along with a Hubble Space Telescope detection of the color and magnitude of the pre-outburst source. The transient outburst is consistent with dynamically driven ejecta at the onset of a common envelope episode, which eventually leads to the complete merger of a binary system. The light curve appears to contain two components: first ∼10{sup −2} M{sub ⊙} of fast ejecta driven by shocks at the onset of common envelope, and later, ∼0.3 M {sub ⊙} of further ejecta as the secondary becomes more deeply engulfed within the primary. Just prior to merger, we find that the primary star is a 3–5.5 M {sub ⊙} subgiant-branch primary star with a radius of 30–40 R {sub ⊙}. Its position in the color–magnitude diagram shows that it is growing in radius, consistent with a picture where it engulfs its companion. By matching the properties of the primary star to the transient outburst, we show that the optical transient lasts less than 10 orbits of the original binary, which had a pre-merger period of ∼10 days. We consider the possible orbital dynamics leading up to the merger, and argue that if the system merged due to the Darwin tidal instability it implies a lower mass main-sequence companion of 0.1–0.6 M {sub ⊙}. This analysis represents a promising step toward a more detailed understanding of flows in common envelope episodes through direct observational constraints.

79 ASTRONOMY AND ASTROPHYSICS↗

In‐depth comparative analysis of Illumina ® MiSeq run metrics: Development of a wet‐lab quality assessment tool

Abstract Whole genome sequencing of bacterial isolates has become a daily task in many laboratories, generating incredible amounts of data. However, data acquisition is not an end in itself; the goal is to acquire high‐quality data useful for understanding genetic relationships. Having a method that could rapidly determine which of the many available run metrics are the most important indicators of overall run quality and having a way to monitor these during a given sequencing run would be extremely helpful to this effect. Therefore, we compared various run metrics across 486 MiSeq runs, from five different machines. By performing a statistical analysis using principal components analysis and a K ‐means clustering algorithm of the metrics, we were able to validate metric comparisons among instruments, allowing for the development of a predictive algorithm, which permits one to observe whether a given MiSeq run has performed adequately. This algorithm is available in an Excel spreadsheet: that is, MiSeq Instrument & Run (In‐Run) Forecast. Our tool can help verify that the quantity/quality of the generated sequencing data consistently meets or exceeds recommended manufacturer expectations. Patterns of deviation from those expectations can be used to assess potential run problems and plan preventative maintenance, which can save valuable time and funding resources.

Kastanis, George John↗

Governing in Time: Temporal Capacity and the Feasibility of Energy Transitions

Energy systems function as both technological systems and temporal institutions that shape how societies coordinate, justify, and support collective choices over time. This paper introduces the concept of governance horizons to explain why energy transitions can remain morally supported yet become institutionally weak under increasing pressure. We argue that governability depends on institutions' capacity to synchronize across multiple timeframes - aligning short-term decisions with intermediate coordination and long-term commitments. When this synchronization fails, transitions struggle not because their goals are dismissed, but because governance lacks sufficient time to justify, coordinate, and uphold decisions. Comparative analysis of San Antonio, Texas, and Interior Alaska reveals how energy system pressures generate distinct temporal configurations: San Antonio exhibits governance horizon stretching, where institutions must simultaneously meet near-term reliability demands and long-term transformation goals, while Interior Alaska exhibits horizon compression, where extreme environmental constraints force decision-making into short stabilization cycles. In both contexts, public support for sustainability goals coexists with institutional strain because evaluative judgments are unevenly distributed over time. A temporal configuration analysis is introduced as a diagnostic analytic stance for identifying these patterns. By treating temporal alignment as an explanatory variable rather than a background condition, this approach clarifies how feasibility, sequencing, and legitimacy are shaped by constraints on institutional time. The analysis demonstrates that successful energy transitions depend not only on technological innovation or institutional support, but on governance systems’ ability to sustain credible coordination across multiple time horizons.

Comparative case study↗

SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structural variant Annotation and analysis (SvAnna) assesses all classes of SVs and their intersection with transcripts and regulatory sequences, relating predicted effects on gene function with clinical phenotype data. SvAnna places 87% of deleterious SVs in the top ten ranks. The interpretable prioritizations offered by SvAnna will facilitate the widespread adoption of long-read sequencing in diagnostic genomics. SvAnna is available at https://github.com/TheJacksonLaboratory/SvAnna.

59 BASIC BIOLOGICAL SCIENCES↗

Prioritizing Uncertainties in Hydrogen Contribution to Risk in Post-Crash Outcomes for Rail

This report presents analysis from Sandia National Laboratories predicting contributions to risk associated with the use of hydrogen technology for rail. Event sequence diagrams are used to describe possible accident scenarios and progressions. Initiating event frequencies and branch event probabilities for each scenario are quantified with uncertainty using distributions fit to Federal Railroad Administration and U.S. Department of Transportation Pipeline and Hazardous Materials Safety Administration data on applicable accidents from 2000 to 2020. Uncertainty is propagated through the event sequence diagram to estimate the frequency and conditional probability of accident end states. The analysis identifies four scenarios with significant contributions to risk from hydrogen that are predicted to occur relatively frequently, which may inform priorities for reducing uncertainty. These scenarios are 1) overpressure events resulting from collisions with hydrogen release due to mechanical damage and delayed ignition, 2) jet fire events resulting from collisions with hydrogen release due to mechanical damage and immediate ignition, 3) jet fires resulting from fire or explosion initiating events involving the hydrogen tank and correct operation of the thermally-activated pressure relief device (TPRD) subsequent to the thermal insult, and 4) pressure burst resulting from fire or explosion initiating events involving the hydrogen tank and failure of the TPRD. Delayed and immediate hydrogen ignition probabilities are identified as being highly uncertain and potential candidates for reducing conservatism in the predicted frequencies for these two scenarios.

08 HYDROGEN↗

MiR-328 suppresses the survival of esophageal cancer cells by targeting PLCE1

Esophageal cancer (EC) is the sixth leading cause of death worldwide. Recent studies have highlighted the vital role of microRNAs (miRNAs) in EC development and diagnosis. In our study, qPCR analysis showed that miRNA-328 was expressed at significantly low levels in EC109 and EC9706 cells. The results also showed that overexpression of miR-328 by lentivirus-mediated gene transfer markedly inhibited cell proliferation and invasion, and enhanced apoptosis; whereas, inhibition of miR-328 significantly promoted cell proliferation and invasion, and suppressed apoptosis in EC109 and EC9706 cells. Dual-luciferase reporter assay confirmed that miR-328 directly targeted phospholipase C epsilon 1 (PLCE1) by binding to target sequences in the 3′-UTR. qPCR and Western blot analysis showed that the PLCE1 was overexpressed in EC109 and EC9706 cells. Additionally, we found that miR-328 overexpression decreased PLCE1 mRNA and protein levels, while miR-328 inhibition enhanced the PLCE1 expression. Further analysis showed that PLCE1 overexpression rescued the inhibitory effect of miR-328 on cell proliferation and invasion, and repressed the promotive effect of miR-328 on cell apoptosis. In conclusion, our results suggest that miR-328 suppresses the survival of EC cells by regulating PLCE1 expression, which might be a potential therapeutic method for EC. - Highlights: • PLCE1 was a target gene of miR-328. • MiR-328 overexpression decreased PLCE1 expression. • PLCE1 overexpression rescued the inhibitory effect of miR-328 on the survival of EC cells.

60 APPLIED LIFE SCIENCES↗

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

A global view of structure–function relationships in the tautomerase superfamily

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure–function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase–like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.

Biochemistry & Molecular Biology↗

Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18

Bacteriophages are useful nonantibiotic therapeutics for bacterial infections as well as threats to industries utilizing bacterial agents. This study identified Phaeobacter virus MD18 , a phage antagonist of Phaeobacter inhibens , a bacterium with promising use as a probiotic for aquatic farming industries. Genomic analysis suggested that Phaeobacter phage MD18 has evolved to enhance its replication in P. inhibens by adopting favorable tRNA genes as well as through genomic sequence adaptation to resemble host codon usage. Lastly, a high-throughput analysis of P. inhibens transposon insertion mutants identified genes that modulate host susceptibility to phage MD18 and implicated the type IV pilus as the likely receptor recognized for adsorption. This study marks the first characterization of the relationship between P. inhibens and an environmentally sampled phage, which informs our understanding of natural threats to the bacterium and may promote the development of novel phage technologies for genetic manipulation of this host.

59 BASIC BIOLOGICAL SCIENCES↗

TracKlinic: Diagnosis of Challenge Factors in Visual Tracking

Generic visual object tracking is difficult due to many challenge factors (e.g., occlusion, blur, etc.). Each of these factors may cause serious problems for a tracker, and when they work together can make things even more complicated. Despite a great amount of efforts devoted to understanding the behavior of trackers, reliable and quantifiable ways for studying the per factor tracking behavior remain barely available. Addressing this issue, in this paper we contribute to the community a tracking diagnosis toolkit, TracKlinic, for diagnosis of challenge factors of tracking algorithms. TracKlinic consists of two novel components focusing on the data and analysis aspects, respectively. For the data component, we carefully prepare a set of 2,390 annotated videos, each involving one and only one major challenge factor. When analyzing an algorithm for a specific challenge factor, such one-factor-per-sequence rule greatly inhibits the disturbance from other factors and consequently leads to more faithful analysis. For the analysis component, given the tracking results on all sequences, it investigates the behavior of the tracker under each individual factor and generates the report automatically. With TracKlinic, a thorough study is conducted on ten state-of-the-art trackers on nine challenge factors (including two compound ones). The results suggest that, heavy shape variation and occlusion are the two most challenging factors faced by most trackers. Besides, out-of-view, though does not happen frequently, is often fatal. By sharing TracKlinic1, we expect to make it much easier for diagnosing tracking algorithms, and to thus facilitate developing better ones.

97 MATHEMATICS AND COMPUTING↗

Crystal Structure of USP7 Ubiquitin-like Domains with an ICP0 Peptide Reveals a Novel Mechanism Used by Viral and Cellular Proteins to Target USP7

Herpes simplex virus-1 immediate-early protein ICP0 activates viral genes during early stages of infection, affects cellular levels of multiple host proteins and is crucial for effective lytic infection. Being a RING-type E3 ligase prone to auto-ubiquitination, ICP0 relies on human deubiquitinating enzyme USP7 for protection against 26S proteasomal mediated degradation. USP7 is involved in apoptosis, epigenetics, cell proliferation and is targeted by several herpesviruses. Several USP7 partners, including ICP0, GMPS, and UHRF1, interact through its C-terminal domain (CTD), which contains five ubiquitin-like (Ubl) structures. Despite the fact that USP7 has emerged as a drug target for cancer therapy, structural details of USP7 regulation and the molecular mechanism of interaction at its CTD have remained elusive. Here, we mapped the binding site between an ICP0 peptide and USP7 and determined the crystal structure of the first three Ubl domains bound to the ICP0 peptide, which showed that ICP0 binds to a loop on Ubl2. Sequences similar to the USP7-binding site in ICP0 were identified in GMPS and UHRF1 and shown to bind USP7-CTD through Ubl2. In addition, co-immunoprecipitation assays in human cells comparing binding to USP7 with and without a Ubl2 mutation, confirmed the importance of the Ubl2 binding pocket for binding ICP0, GMPS and UHRF1. Therefore we have identified a novel mechanism of USP7 recognition that is used by both viral and cellular proteins. Our structural information was used to generate a model of near full-length USP7, showing the relative position of the ICP0/GMPS/UHRF1 binding pocket and the structural basis by which it could regulate enzymatic activity.

59 BASIC BIOLOGICAL SCIENCES↗

'Criticality events' database for fuel cycle facilities in support of the IRSN nuclear criticality safety guide - 14384

IRSN has developed a database gathering the events which have affected the safety of French fuel cycle facilities (from conversion to waste storage, laboratories and experimental facilities, facilities under dismantling and decommissioning). Among all the recorded events, it is possible to extract in particular those impacting the criticality safety. In order to extend the analysis of these events, the IRSN criticality safety department has developed a specific database dedicated to criticality risks. The 'criticality events' database is continuously updated on the basis of the declared events and their analysis by engineers from the criticality safety department. At this time, about 380 events (on 540 identified since 1980) are described in details in this database. Thus, the number of events in facilities can be between 1 and 75. It is possible to establish a link, as a feedback, between the 'criticality events' database and the sequences of events identified in the IRSN nuclear criticality safety guide. Indeed, the purpose of this guide is to be a support for criticality safety analysis or assessment. The guide is in the form of diagrams and gives advice to perform an assessment of criticality risks for each criticality control mode and for the reference fissile medium. Thus, the guide presents the parameters to be considered in the analysis and the typical sequences (written in the form of questions) related to the most current failures to be investigated. With the objective of being able to illustrate the nuclear criticality safety guide, it was decided to select the events of the database which are representative of the sequences. Thus, 70 sequences have been illustrated up to now by one or several events analyzed in the 'criticality events' database. Furthermore, this action allows 'extending' the nuclear criticality safety guide with sequences which had not yet been identified (when an event cannot illustrate a failure listed in the diagrams). This paper will describe the approach used to build the 'criticality events' database, the criteria used to classify events and the link with the IRSN nuclear criticality safety guide. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Extreme Thermal Stabilization of Carborane–Cyanate Composites via B–N Dative-Bonded Boroxine Barriers

Enhancing the thermal stability of cyanate ester (CE) resins is crucial for high-temperature aerospace applications. This study elucidates the degradation mechanisms of CE composites reinforced with carborane additives, focusing on the formation of boron–nitrogen (B–N) dative bonds and their role in improving thermal resistance. Using thermogravimetric analysis, we examined char formation and evolved gases at multiple degradation stages. Reaction sequences and char products were characterized via Fourier transform infrared spectroscopy (FTIR), solid-state 13C and 11B NMR, and evolved gas analysis using mass spectrometry and FTIR. The solid-state 11B NMR was instrumental in detecting various boron oxidation states and the formation of B–N dative bonds during decomposition. These bonds facilitate cross-linking in the char phase, enhancing material integrity at elevated temperatures. However, in inert environments, the volatility of boron additives like carborane limits their effectiveness. These findings advance the understanding of CE composite degradation mechanisms and offer critical insights for developing high-temperature-resistant materials for aerospace applications.

Fourier transform infrared spectroscopy↗

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6× and 30.7× using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. Furthermore, to highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6×. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.

97 MATHEMATICS AND COMPUTING↗

Tuning Copolymer Microstructure Using Ring-Opening Cross-Metathesis Polymerization

The capability of ring-opening cross-metathesis (RO/CM) polymerization to produce alternating copolymers was studied. By treating commercial polybutadiene (PB) with bulky oxanorbornene monomers and Ru-based olefin metathesis catalysts, alternating copolymers were produced under mild conditions with high sequence fidelities. Here, we found that alternating copolymers could be produced starting from a variety of butadiene sources including PB, cyclooctadiene (COD), or t,t,t-1,5,9-cyclododecatriene (CDT), highlighting for the first time the kinetic pathway independence of this process. Kinetic copolymerization analysis of an oxanorbonene monomer with CDT revealed that much higher monomer conversions were obtained compared with the analogous homopolymerizations and showed evidence of alternating monomer incorporation. Copolymerization of these monomers also enabled good control when targeting different molecular weights. Copolymer thermal analysis revealed a strong correlation between thermal behavior and alternating sequence fidelity, providing a second lever beyond composition to tune thermal behavior. These data demonstrate that a broad variety of polymer microstructures can be accessed via RO/CM polymerization and highlight the potential of CDT in alternating copolymer synthesis.

Foster, Jeffrey C. [Oak Ridge National Laboratory ↗

Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX

Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV). Previous studies indicated that cleavage of messenger RNAs (mRNA) by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity.

59 BASIC BIOLOGICAL SCIENCES↗

Reinventing cell penetrating peptides using glycosylated methionine sulfonium ion sequences

Cell penetrating peptides (CPPs) are intriguing molecules that have received much attention, both in terms of mechanistic analysis and as transporters for intracellular therapeutic delivery. Most CPPs contain an abundance of cationic charged residues, typically arginine, where the amino acid compositions, rather than specific sequences, tend to determine their ability to enter cells. Hydrophobic residues are often added to cationic sequences to create efficient CPPs, but typically at the penalty of increased cytotoxicity. Here, we examined polypeptides containing glycosylated, cationic derivatives of methionine, where we found these hydrophilic polypeptides to be surprisingly effective as CPPs and to also possess low cytotoxicity. X-ray analysis of how these new polypeptides interact with lipid membranes revealed that the incorporation of sterically demanding hydrophilic cationic groups in polypeptides is an unprecedented new concept for design of potent CPPs.

59 BASIC BIOLOGICAL SCIENCES↗