bluuebunny/crossref_metadata_2025 huggingface dataset:
A Bayesian valuation framework for catastrophe bonds
Authors: Domfeh Dixon , Chatterjee Arpita , Dixon Matthew
Published: August 2024

Catastrophe (CAT) bond markets are incomplete and hence carry uncertainty in instrument pricing. Various pricing approaches have been proposed, but none treats the uncertainty in catastrophes and interest rates in a sufficiently flexible and statistically reliable way within an asset valuation framework. Consequently, little is known empirically about the expected risk premium of CAT bonds. The primary contribution of this article is to present a Bayesian CAT bond valuation framework based on uncertainty quantification of catastrophes and interest rates. We leverage this framework to estimate fair value prices and expected risk premiums for CAT bonds with varying catastrophe risk profiles.
Unravelling the secrets of non-host resistance in plant–insect interactions
Authors: Pinheiro Daniel Gonçalves da Silva , Espirito-Santo Ana Beatriz Moreira Menezes do , Fasoli José Vitor Botter , Sobral-Souza Thadeu , Campos Marcelo Lattarulo
Published: August 2024

Despite the existence of over half a million species of plant-eating insects, our planet remains predominantly green. In fact, susceptibility to herbivory is the exception, as plants are resistant to most insect species. This phenomenon is known as non-host resistance (NHR), where every individual of a plant species is resistant to all variants of a pest or pathogen. While NHR represents the most common and durable outcome of the plant immune system, several aspects of this type of plant defence remain elusive, particularly in plant–insect interactions. In this review, we clarify the concept of NHR in plant–insect interactions. We emphasize that NHR is a phenomenon arising as a consequence of effective plant defences providing invulnerability to most insect herbivores. This underscores that NHR is one of the main ecological features delimiting the range of plant–insect interactions on Earth. We further highlight the traits and molecular components of the plant immune system known to participate in NHR against insects. Finally, we discuss how NHR can be leveraged as a tool to develop pest-resilient crops. Given the significant threat insects pose to global food security, research in plant NHR represents a crucial focal point with immense potential for ensuring food security worldwide.
Ray-tracing versus Born approximation in full-sky weak lensing simulations of the MillenniumTNG project
Authors: Ferlito Fulvio , Davies Christopher T , Springel Volker , Reinecke Martin , Greco Alessandro , Delgado Ana Maria , White Simon D M , Hernández-Aguayo César , Bose Sownak , Hernquist Lars
Published: August 2024

Weak gravitational lensing is a powerful tool for precision tests of cosmology. As the expected deflection angles are small, predictions based on non-linear N-body simulations are commonly computed with the Born approximation. Here, we examine this assumption using DORIAN, a newly developed full-sky ray-tracing scheme applied to high-resolution mass-shell outputs of the two largest simulations in the MillenniumTNG suite, each with a 3000 Mpc box containing almost 1.1 trillion cold dark matter particles in addition to 16.7 billion particles representing massive neutrinos. We examine simple two-point statistics like the angular power spectrum of the convergence field, as well as statistics sensitive to higher order correlations such as peak and minimum statistics, void statistics, and Minkowski functionals of the convergence maps. Overall, we find only small differences between the Born approximation and a full ray-tracing treatment. While these are negligibly small at power-spectrum level, some higher order statistics show more sizeable effects; ray-tracing is necessary to achieve per cent level precision. At the resolution reached here, full-sky maps with 0.8 billion pixels and an angular resolution of 0.43 arcmin, we find that interpolation accuracy can introduce appreciable errors in ray-tracing results. We therefore implemented an interpolation method based on non-uniform fast Fourier transforms (NUFFT) along with more traditional methods. Bilinear interpolation introduces significant smoothing, while nearest grid point sampling agrees well with NUFFT, at least for our fiducial source redshift, $z_s=1.0$, and for the 1 arcmin smoothing we use for higher order statistics.
Angular momentum transfer in cosmological simulations of Milky Way-mass discs
Authors: Trapp Cameron W , Kereš Dušan , Hopkins Philip F , Faucher-Giguère Claude-André , Murray Norman
Published: August 2024

Fuelling star formation in large, discy galaxies requires a continuous supply of gas accreting into star-forming regions. Previously, we characterized this accretion in four Milky Way mass galaxies ($M_{\rm halo}\sim 10^{12}{\rm M}_{\odot }$) in the FIRE-2 cosmological zoom-in simulations. At $z\sim 0$, we found that gas within the inner circumgalactic medium (iCGM) approaches the disc with comparable angular momentum (AM) to the disc edge, joining in the outer half of the gaseous disc. Within the disc, gas moves inwards at velocities of $\sim$1–5 km s$^{-1}$ while fully rotationally supported. In this study, we analyse the torques that drive these flows. In all cases studied, we find that the torques in discs enable gas accreted near the disc edge to transport inwards and fuel star formation in the central few kpc. The primary sources of torque come from gravity, hydrodynamical forces, and the sub-grid $P \mathrm{ d}V$ work done by supernova (SN) remnants interacting with gas on $\lesssim$10 pc scales. These SNe remnant interactions induce negative torques within the inner disc and positive torques in the outer disc. The gas–gas gravitational, hydro, and ‘feedback’ torques transfer AM outwards to where accreting gas joins the disc, playing an important role in driving inflows and regulating disc structure. Gravitational torques from stars and dark matter provide an AM sink within the innermost regions of the disc and iCGM, respectively. Feedback torques are dominant within the disc, while gravitational and hydrodynamical torques have similar significance depending on the system/region. Torques from viscous shearing, magnetic forces, stellar winds, and radiative transfer are less significant.
Stellar formation and young clusters in NGC 2366 – main properties
Authors: Feinstein C , Baume G , Vergne M M , Rodríguez M J
Published: August 2024

The characteristics of the young stellar population in the nearby irregular galaxy NGC 2366 were investigated. In particular, we focused our attention on its hierarchical clustering distributions and the properties of the stellar groups. This galaxy exhibits a prominent blue helium-burning star feature in the colour-magnitude diagram, suggesting that it has undergone an extended period of stellar formation. The galaxy was observed in two bands by the Hubble Space Telescope covering almost its complete central and intermediate parts, including all the major stellar formation regions. Available photometric data allowed us to select the blue and young stars and, therefore, study the recent stellar formation. Through the path linkage criterion (PLC), we found 23 young star groups and estimated their fundamental parameters, such as their stellar densities, sizes, and number of members. We also performed a fractal substructure analysis to determine the clustering properties of this population, and we built a stellar density map corresponding to the galactic young population. We found that most of the young stellar groups have stars that have a distribution of locations that is compatible with a fractal dimension.
Prevalent Fast Evolution of Genes Involved in Heterochromatin Functions
Authors: Lin Leila , Huang Yuheng , McIntyre Jennifer , Chang Ching-Ho , Colmenares Serafin , Lee Yuh Chwen G
Published: August 2024

Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles in maintaining genome stability, organizing chromosomes, and suppressing transposable elements. Given the importance of these functions, it is expected that genes involved in heterochromatin regulation would be highly conserved. Yet, a handful of these genes were found to evolve rapidly. To investigate whether these previous findings are anecdotal or general to genes modulating heterochromatin, we compile an exhaustive list of 106 candidate genes involved in heterochromatin functions and investigate their evolution over short and long evolutionary time scales in Drosophila. Our analyses find that these genes exhibit significantly more frequent evolutionary changes, both in the forms of amino acid substitutions and gene copy number change, when compared to genes involved in Polycomb-based repressive chromatin. While positive selection drives amino acid changes within both structured domains with diverse functions and intrinsically disordered regions, purifying selection may have maintained the proportions of intrinsically disordered regions of these proteins. Together with the observed negative associations between the evolutionary rate of these genes and the genomic abundance of transposable elements, we propose an evolutionary model where the fast evolution of genes involved in heterochromatin functions is an inevitable outcome of the unique functional roles of heterochromatin, while the rapid evolution of transposable elements may be an effect rather than cause. Our study provides an important global view of the evolution of genes involved in this critical cellular domain and provides insights into the factors driving the distinctive evolution of heterochromatin.
N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition
Authors: Damberger Fred F , Krepl Miroslav , Arora Rajika , Beusch Irene , Maris Christophe , Dorn Georg , Šponer Jiří , Ravindranathan Sapna , Allain Frédéric H-T
Published: August 2024

The N-terminal RNA recognition motif domain (RRM1) of polypyrimidine tract binding protein (PTB) forms an additional C-terminal helix α3, which docks to one edge of the β-sheet upon binding to a stem-loop RNA containing a UCUUU pentaloop. Importantly, α3 does not contact the RNA. The α3 helix therefore represents an allosteric means to regulate the conformation of adjacent domains in PTB upon binding structured RNAs. Here we investigate the process of dynamic adaptation by stem-loop RNA and RRM1 using NMR and MD in order to obtain mechanistic insights on how this allostery is achieved. Relaxation data and NMR structure determination of the free protein show that α3 is partially ordered and interacts with the domain transiently. Stem-loop RNA binding quenches fast time scale dynamics and α3 becomes ordered, however microsecond dynamics at the protein-RNA interface is observed. MD shows how RRM1 binding to the stem-loop RNA is coupled to the stabilization of the C-terminal helix and helps to transduce differences in RNA loop sequence into changes in α3 length and order. IRES assays of full length PTB and a mutant with altered dynamics in the α3 region show that this dynamic allostery influences PTB function in cultured HEK293T cells.
Structural insights into RNA cleavage by a novel family of bacterial RNases
Authors: Wu Ruoxi , Ingle Shakti , Barnes Sarah A , Dahlin Heather R , Khamrui Susmita , Xiang Yufei , Shi Yi , Bechhofer David H , Lazarus Michael B
Published: August 2024

Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.
Clinically relevant mutations in regulatory regions of metabolic genes facilitate early adaptation to ciprofloxacin in Escherichia coli
Authors: Pal Arijit , Ghosh Dipannita , Thakur Pratyusha , Nagpal Priya , Irulappan Madhumathi , Maruthan Karthik , Mukherjee Sanket , Patil Nikita G , Dutta Tanmay , Veeraraghavan Balaji , Vivekanandan Perumal
Published: August 2024

The genomic landscape associated with early adaptation to ciprofloxacin is poorly understood. Although the interplay between core metabolism and antimicrobial resistance is being increasingly recognized, mutations in metabolic genes and their biological role remain elusive. Here, we exposed Escherichia coli to increasing gradients of ciprofloxacin with intermittent transfer-bottlenecking and identified mutations in three non-canonical targets linked to metabolism including a deletion (tRNA-ArgΔ414-bp) and point mutations in the regulatory regions of argI (ARG box) and narU. Our findings suggest that these mutations modulate arginine and carbohydrate metabolism, facilitate anaerobiosis and increased ATP production during ciprofloxacin stress. Furthermore, mutations in the regulatory regions of argI and narU were detected in over 70% of sequences from clinical E. coli isolates and were overrepresented among ciprofloxacin-resistant isolates. In sum, we have identified clinically relevant mutations in the regulatory regions of metabolic genes as a central theme that drives physiological changes necessary for adaptation to ciprofloxacin stress.
Structural basis of Cas3 activation in type I-C CRISPR-Cas system
Authors: Kim Do Yeon , Lee So Yeon , Ha Hyun Ji , Park Hyun Ho
Published: August 2024

CRISPR-Cas systems function as adaptive immune mechanisms in bacteria and archaea and offer protection against phages and other mobile genetic elements. Among many types of CRISPR-Cas systems, Type I CRISPR-Cas systems are most abundant, with target interference depending on a multi-subunit, RNA-guided complex known as Cascade that recruits a transacting helicase nuclease, Cas3, to degrade the target. While structural studies on several other types of Cas3 have been conducted long ago, it was only recently that the structural study of Type I-C Cas3 in complex with Cascade was revealed, shedding light on how Cas3 achieve its activity in the Cascade complex. In the present study, we elucidated the first structure of standalone Type I-C Cas3 from Neisseria lactamica (NlaCas3). Structural analysis revealed that the histidine–aspartate (HD) nuclease active site of NlaCas3 was bound to two Fe2+ ions that inhibited its activity. Moreover, NlaCas3 could cleave both single-stranded and double-stranded DNA in the presence of Ni2+ or Co2+, showing the highest activity in the presence of both Ni2+ and Mg2+ ions. By comparing the structural studies of various Cas3 proteins, we determined that our NlaCas3 stays in an inactive conformation, allowing us to understand the structural changes associated with its activation and their implication.
DipR, a GntR/FadR-family transcriptional repressor: regulatory mechanism and widespread distribution of the dip cluster for dipicolinic acid catabolism in bacteria
Authors: Jiang Yinhu , Wang Kexin , Xu Lu , Xu Lanyi , Xu Qimiao , Mu Yang , Hong Qing , He Jian , Jiang Jiandong , Qiu Jiguo
Published: August 2024

Dipicolinic acid is an essential component of bacterial spores for stress resistance, which is released into the environment after spore germination. In a previous study, a dip gene cluster was found to be responsible for the catabolism of dipicolinic acid in Alcaligenes faecalis JQ135. However, the transcriptional regulatory mechanism remains unclear. The present study characterized the new GntR/FadR family transcriptional factor DipR, showing that the dip cluster is transcribed as the six transcriptional units, dipR, dipA, dipBC, dipDEFG, dipH and dipJKLM. The purified DipR protein has six binding sites sharing the 6-bp conserved motif sequence 5′-GWATAC-3′. Site-directed mutations indicated that these motif sequences are essential for DipR binding. Moreover, the four key amino acid residues R63, R67, H196 and H218 of DipR, examined by site-directed mutagenesis, played crucial roles in DipR regulation. Bioinformatics analysis showed that dip clusters including dipR genes are widely distributed in bacteria, are taxon-related, and co-evolved with their hosts. This paper provides new insights into the transcriptional regulatory mechanism of dipicolinic acid degradation by DipR in bacteria.
A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato
Authors: Rosenkranz Remus R E , Vraggalas Stavros , Keller Mario , Sankaranarayanan Srimeenakshi , McNicoll François , Löchli Karin , Bublak Daniela , Benhamed Moussa , Crespi Martin , Berberich Thomas , Bazakos Christos , Feldbrügge Michael , Schleiff Enrico , Müller-McNicoll Michaela , Zarnack Kathi , Fragkostefanakis Sotirios
Published: August 2024

Global warming poses a threat for crops, therefore, the identification of thermotolerance mechanisms is a priority. In plants, the core factors that regulate transcription under heat stress (HS) are well described and include several HS transcription factors (HSFs). Despite the relevance of alternative splicing in HS response and thermotolerance, the core regulators of HS-sensitive alternative splicing have not been identified. In tomato, alternative splicing of HSFA2 is important for acclimation to HS. Here, we show that several members of the serine/arginine-rich family of splicing factors (SRSFs) suppress HSFA2 intron splicing. Individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) combined with RNA-Seq revealed that RS2Z35 and RS2Z36, which make up a plant-specific clade of SR proteins, not only regulate HSFA2 but approximately 50% of RNAs that undergo HS-sensitive alternative splicing, with preferential binding to purine-rich RNA motifs. Single and double CRISPR rs2z mutant lines show a dysregulation of splicing and exhibit lower basal and acquired thermotolerance compared to wild type plants. Our results suggest that RS2Z35 and RS2Z36 have a central role in mitigation of the negative effects of HS on RNA splicing homeostasis, and their emergence might have contributed to the increased capacity of plants to acclimate to high temperatures.
Insights into the Anticancer Mechanisms Modulated by Gamma and Delta Tocotrienols in Colorectal Cancers
Authors: Khalid Ali Qusay , Zaidan Tabarek Najeeb , Bhuvanendran Saatheeyavaane , Magalingam Kasthuri B , Mohamedahmed Shaza M , Ramdas Premdass , Radhakrishnan Ammu K
Published: August 2024

Colorectal cancer (CRC) is a growing concern all over the world. There has been a concerted effort to identify natural bioactive compounds that can be used to prevent or overcome this condition. Tocotrienols (T3s) are a naturally occurring form of vitamin E known for various therapeutic effects, such as anticancer, antioxidant, neuroprotective, and anti-inflammatory activities. The literature evidence suggests that two T3 analogues, ie, gamma (γ)- and delta (δ)-T3, can modulate cancers via several cancer-related signaling pathways. The aim of this review was to compile and analyze the existing literature on the diverse anticancer mechanisms of γT3 and δT3 exhibited in CRC cells, to showcase the anticancer potential of T3s. Medline was searched for research articles on anticancer effects of γT3 and δT3 in CRC published in the past 2 decades. A total of 38 articles (26 cell-based, 9 animal studies, 2 randomized clinical trials, and 1 scoping review) that report anticancer effects of γT3 and δT3 in CRC were identified. The findings reported in those articles indicate that γT3 and δT3 inhibit the proliferation of CRC cells, induce cell cycle arrest and apoptosis, suppress metastasis, and produce synergistic anticancer effects when combined with well-established anticancer agents. There is preliminary evidence that shows that T3s affect telomerase functions and support anticancer immune responses. γT3 and δT3 have the potential for development as anticancer agents.
Advances and future directions in ROS1 fusion-positive lung cancer
Authors: Boulanger Mary C , Schneider Jaime L , Lin Jessica J
Published: August 2024

ROS1 gene fusions are an established oncogenic driver comprising 1%-2% of non–small cell lung cancer (NSCLC). Successful targeting of ROS1 fusion oncoprotein with oral small-molecule tyrosine kinase inhibitors (TKIs) has revolutionized the treatment landscape of metastatic ROS1 fusion-positive (ROS1+) NSCLC and transformed outcomes for patients. The preferred Food and Drug Administration-approved first-line therapies include crizotinib, entrectinib, and repotrectinib, and currently, selection amongst these options requires consideration of the systemic and CNS efficacy, tolerability, and access to therapy. Of note, resistance to ROS1 TKIs invariably develops, limiting the clinical benefit of these agents and leading to disease relapse. Progress in understanding the molecular mechanisms of resistance has enabled the development of numerous next-generation ROS1 TKIs, which achieve broader coverage of ROS1 resistance mutations and superior CNS penetration than first-generation TKIs, as well as other therapeutic strategies to address TKI resistance. The approach to subsequent therapy depends on the pace and pattern of progressive disease on the initial ROS1 TKI and, if known, the mechanisms of TKI resistance. Herein, we describe a practical approach for the selection of initial and subsequent therapies for metastatic ROS1+ NSCLC based on these clinical considerations. Additionally, we explore the evolving evidence for the optimal treatment of earlier-stage, non–metastatic ROS1+ NSCLC, while, in parallel, highlighting future research directions with the goal of continuing to build on the tremendous progress in the management of ROS1+ NSCLC and ultimately improving the longevity and well-being of people living with this disease.
Next-generation sequencing-based evaluation of the actionable landscape of genomic alterations in solid tumors: the “MOZART” prospective observational study
Authors: Schettini Francesco , Sirico Marianna , Loddo Marco , Williams Gareth H , Hardisty Keeda-Marie , Scorer Paul , Thatcher Robert , Rivera Pablo , Milani Manuela , Strina Carla , Ferrero Giuseppina , Ungari Marco , Bottin Cristina , Zanconati Fabrizio , de Manzini Nicolò , Aguggini Sergio , Tancredi Richard , Fiorio Elena , Fioravanti Antonio , Scaltriti Maurizio , Generali Daniele
Published: August 2024

Background

The identification of the most appropriate targeted therapies for advanced cancers is challenging. We performed a molecular profiling of metastatic solid tumors utilizing a comprehensive next-generation sequencing (NGS) assay to determine genomic alterations’ type, frequency, actionability, and potential correlations with PD-L1 expression.

Methods

A total of 304 adult patients with heavily pretreated metastatic cancers treated between January 2019 and March 2021 were recruited. The CLIA-/UKAS-accredit Oncofocus assay targeting 505 genes was used on newly obtained or archived biopsies. Chi-square, Kruskal-Wallis, and Wilcoxon rank-sum tests were used where appropriate. Results were significant for P < .05.

Results

A total of 237 tumors (78%) harbored potentially actionable genomic alterations. Tumors were positive for PD-L1 in 68.9% of cases. The median number of mutant genes/tumor was 2.0 (IQR: 1.0-3.0). Only 34.5% were actionable ESCAT Tier I-II with different prevalence according to cancer type. The DNA damage repair (14%), the PI3K/AKT/mTOR (14%), and the RAS/RAF/MAPK (12%) pathways were the most frequently altered. No association was found among PD-L1, ESCAT, age, sex, and tumor mutational status. Overall, 62 patients underwent targeted treatment, with 37.1% obtaining objective responses. The same molecular-driven treatment for different cancer types could be associated with opposite clinical outcomes.

Conclusions

We highlight the clinical value of molecular profiling in metastatic solid tumors using comprehensive NGS-based panels to improve treatment algorithms in situations of uncertainty and facilitate clinical trial recruitment. However, interpreting genomic alterations in a tumor type-specific manner is critical.
Arm symptom pattern among breast cancer survivors with and without lymphedema: a contemporaneous network analysis
Authors: Shen Aomei , Zhang Zhongning , Ye Jingming , Wang Yue , Zhao Hongmeng , Li Xin , Wu Peipei , Qiang Wanmin , Lu Qian
Published: August 2024

Background

Arm symptoms commonly endure in post-breast cancer period and persist into long-term survivorship. However, a knowledge gap existed regarding the interactions among these symptoms. This study aimed to construct symptom networks and visualize the interrelationships among arm symptoms in breast cancer survivors (BCS) both with and without lymphedema (LE).

Patients and Methods

We conducted a secondary analysis of 3 cross-sectional studies. All participants underwent arm circumference measurements and symptom assessment. We analyzed 17 symptoms with a prevalence >15%, identifying clusters and covariates through exploratory factor and linear regression analysis. Contemporaneous networks were constructed with centrality indices calculated. Network comparison tests were performed.

Results

1116 cases without missing data were analyzed, revealing a 29.84% prevalence of LE. Axillary lymph node dissection [ALND] (vs sentinel lymph node biopsy [SLNB]), longer post-surgery duration, and radiotherapy significantly impacted overall symptom severity (P < .001). “Lymphatic Stasis,” “Nerve Injury,” and “Movement Limitation” symptom clusters were identified. Core symptoms varied: tightness for total sample network, firmness for non-LE network, and tightness for LE network. LE survivors reported more prevalent and severe arm symptoms with stronger network connections than non-LE group (P = .010). No significant differences were observed among different subgroups of covariates (P > .05). Network structures were significantly different between ALND and SLNB groups.

Conclusion

Our study revealed arm symptoms pattern and interrelationships in BCS. Targeting core symptoms in assessment and intervention might be efficient for arm symptoms management. Future research is warranted to construct dynamic symptom networks in longitudinal data and investigate causal relationships among symptoms.
A cyclical marker system enables indefinite series of oligonucleotide-directed gene editing in Chlamydomonas reinhardtii
Authors: Ross Ian L , Le Hong Phuong , Budiman Sabar , Xiong Dake , Hemker Fritz , Millen Elizabeth A , Oey Melanie , Hankamer Ben
Published: August 2024

CRISPR/Cas9 gene editing in the model green alga Chlamydomonas reinhardtii relies on the use of selective marker genes to enrich for nonselectable target mutations. This becomes challenging when many sequential modifications are required in a single-cell line, as useful markers are limited. Here, we demonstrate a cyclical selection process which only requires a single marker gene to identify an almost infinite sequential series of CRISPR-based target gene modifications. We used the NIA1 (Nit1, NR; nitrate reductase) gene as the selectable marker in this study. In the forward stage of the cycle, a stop codon was engineered into the NIA1 gene at the CRISPR target location. Cells retaining the wild-type NIA1 gene were killed by chlorate, while NIA1 knockout mutants survived. In the reverse phase of the cycle, the stop codon engineered into the NIA1 gene during the forward phase was edited back to the wild-type sequence. Using nitrate as the sole nitrogen source, only the reverted wild-type cells survived. By using CRISPR to specifically deactivate and reactivate the NIA1 gene, a marker system was established that flipped back and forth between chlorate- and auxotrophic (nitrate)-based selection. This provided a scarless cyclical marker system that enabled an indefinite series of CRISPR edits in other, nonselectable genes. We demonstrate that this “Sequential CRISPR via Recycling Endogenous Auxotrophic Markers (SCREAM)” technology enables an essentially limitless series of genetic modifications to be introduced into a single-cell lineage of C. reinhardtii in a fast and efficient manner to complete complex genetic engineering.
Two serial filters control P2X7 cation selectivity, Ser342 in the central pore and lateral acidic residues at the cytoplasmic interface
Authors: Markwardt Fritz , Schön Eike Christian , Raycheva Mihaela , Malisetty Aparna , Hawro Yakoob Sanaria , Berthold Malte , Schmalzing Günther
Published: August 2024

The human P2X7 receptor (hP2X7R) is a homotrimeric cell surface receptor gated by extracellular ATP4− with two transmembrane helices per subunit, TM1 and TM2. A ring of three S342 residues, one from each pore-forming TM2 helix, located halfway across the membrane bilayer, functions to close and open the gate in the apo and ATP4−-bound open states, respectively. The hP2X7R is selective for small inorganic cations, but can also conduct larger organic cations such as Tris+. Here, we show by voltage-clamp electrophysiology in Xenopus laevis oocytes that mutation of S342 residues to positively charged lysines decreases the selectivity for Na+ over Tris+, but maintains cation selectivity. Deep in the membrane, laterally below the S342 ring are nine acidic residues arranged as an isosceles triangle consisting of residues E14, D352, and D356 on each side, which do not move significantly during gating. When the E14K mutation is combined with lysine substitutions of D352 and/or D356, cation selectivity is lost and permeation of the small anion Cl− is allowed. Lysine substitutions of S342 together with D352 or E14 plus D356 in the acidic triangle convert the hP2X7R mutant to a fully Cl−-selective ATP4−-gated receptor. We conclude that the ion selectivity of wild-type hP2X7R is determined by two sequential filters in one single pathway: (i) a primary size filter, S342, in the membrane center and (ii) three cation filters lateral to the channel axis, one per subunit interface, consisting of a total of nine acidic residues at the cytoplasmic interface.
Associations of physical activity levels with fatigue in people with inflammatory rheumatic diseases in the LIFT trial
Authors: Gray Stuart R , Montoye Alexander H K , Vondrasek Joseph D , Neph Sylvia , Siebert Stefan , Paul Lorna , Bachmair Eva M , Basu Neil
Published: August 2024

Objectives

The overall aim of the current study was to quantify physical activity levels in inflammatory rheumatic diseases (IRDs) and to explore their role in fatigue.

Methods

We conducted a secondary analysis of data from the Lessening the Impact of Fatigue in IRDs (LIFT) trial of the personalized exercise program (PEP) intervention for fatigue. Participants with IRDs were recruited from 2017 to 2019 and the current analysis used fatigue, measured by the Chalder Fatigue Scale (CFS) and the Fatigue Severity Scale (FSS), and accelerometer measured physical activity data collected at baseline and at the 6-month follow-up. Physical activity levels were quantified and associations with fatigue and effects of PEP investigated.

Results

Of the 337 included participants, 195 (68.4%) did not meet the current recommendations for moderate–vigorous physical activity (MVPA). In baseline cross-sectional analysis, many dimensions of physical activity were associated with fatigue. After mutual adjustment, overall physical activity (vector magnitude) was associated with CFS [−0.88 (95% CI −0.12, −1.64)] and distribution of time spent at different activity intensities was associated with FSS [−1.16 (95% CI −2.01, −0.31)]. Relative to usual care, PEP resulted in an increase in upright time, with trends for increases in step count and overall physical activity. People who increased overall physical activity (vector magnitude) more had greater improvements in CFS and FSS, while those who increased step count and MVPA more had greater improvements in FSS.

Conclusion

Increasing physical activity is important for fatigue management in people with IRDs and further work is needed to optimize PEPs to target the symptoms and impact of fatigue.

Trial registration

ClinicalTrials.gov (http://clinicaltrials.gov), NCT03248518.
Computational forms for binary particle interactions at different levels of anisotropy
Authors: Everett Christopher N , Cotter Garret
Published: August 2024

Particle interactions are key elements of many dynamical systems. In the context of systems described by a Boltzmann equation, such interactions may be described by a collision integral, a multidimensional integral over the momentum-phase space of the interaction. This integral is often simplified by assuming isotropic particle distributions; however, such an assumption places constraints on the dynamics of the system. This paper presents computational forms of the collision integral for relativistic, binary interactions at three levels of anisotropy, including a novel form in the isotropic case. All these forms are split into two parts, an absorption and an emission spectrum, which may be pre-calculated via numerical integration for simulation purposes. We demonstrate the use of these forms by comparison with the analytically integrated, isotropic emission spectrum of electron–positron annihilation, which are shown to agree to numerical precision. The emission spectrum is then further extended to axisymmetric particle distributions, where two-dimensional spectral maps can be generated to provide new insight.
Techno-nationalism to collaborative technology sovereignty
Authors: Lee Jeong-Dong , Kim Hanbin , Si Saerom , Lee Saangkeub
Published: August 2024

The current geopolitical instability has driven global policy frameworks to prioritize economic security. This shift has intensified the debate on technology sovereignty among developed countries, due to concerns over supply chain disruptions and competition for future technologies. However, equating technology sovereignty with techno-nationalism should be avoided. Techno-nationalism can lead to unrealistic goals of domestically possessing all necessary technologies, resulting in protectionism. Given the complex and interconnected nature of technological development, no single country can control all component technologies. This study proposes a concept of collaborative technology sovereignty, promoting openness in technology development and acquisition. Policies should focus on creating systems for sharing technologies with like-minded countries while securing critical technologies. Lessons from existing policies are essential for expanding this collaborative approach and establishing strategies for collaborative technology sovereignty.
State Complicity: Settler Colonialism, Multisided Violence, and Missing and Murdered Indigenous Women and Girls in Canada
Authors: García-Del Moral Paulina
Published: August 2024

This article theorizes and analyzes the Canadian state’s complicity in the crisis of missing and murdered Indigenous women and girls (MMIWG) in terms of the acts of omission (inaction) and commission (action) of the police and courts. Building on the intersectional perspective of Indigenous and antiracist feminist scholarship on MMIWG, I argue that these acts of omission and commission are rooted in a context of “multisided violence” that is colonial in nature: state action and inaction reproduce and normalize the conditions in which Indigenous women and girls can be murdered with impunity. I analyze reports by Indigenous and feminist civil society organizations as part of their transnational advocacy to compel the Canadian state to address MMIWG. I show that state acts of omission and commission are intertwined and reinforce each other through a pattern of inconsistent, deficient, and contradictory institutional responses to violence against Indigenous women and girls.
Building a future for phage-based technologies—a thought leadership approach to accelerating progress in the UK
Authors: Hodges Francesca E , Smith Darren L
Published: August 2024

Antimicrobial resistance is a global issue that threatens our ability to effectively manage and treat bacteria in the context of human health, animal health, and the environment. Bacteriophages provide a viable and necessary alternative to existing antimicrobials. Recognizing the extensive expertise and existing infrastructure that can support phage development in the UK, the Phage Innovation Network (PIN) was established with the aim of catalysing progress in this area. Through comprehensive consultation with the phage community and wider stakeholders, the PIN has carried out a variety of activities to address key issues that are considered to be preventative for the development and use of phage-based technologies in the UK. The successful outcomes of these activities demonstrate how this thought leadership approach has been effective in increasing engagement, delivering solutions, and supporting progress of the phage sector in the UK.
Live and carcass production traits for progeny of an F1 USDA Prime—Yield Grade 1 carcass clone sire compared to progeny of popular beef terminal sires
Authors: Francis Forest L , Grimes Becca B , Hawkins Dean E , Lust David G , McEvers Trent J , Tennant Travis C , Veneklasen Gregg O , Abraham Jason M , Gleghorn Justin F , Lawrence Ty E
Published: August 2024

The cloning of beef carcasses that grade United States Department of Agriculture (USDA) Prime—yield grade (YG) 1 (P1) has produced a sire that ranked well against high-performing bulls from multiple breeds. An F1 (P1 × P1 - first generation offspring) sire would ideally outperform its high-performing parents. A terminal sire study was conducted comparing progeny of an F1 (P1 × P1) sire (AxG1) against progeny (heifers and steers) of four high-performing sires of varying breeds {P1 (ALPHA); Angus; Simmental; Angus × Simmental}. Production traits included morbidity and mortality frequencies, weaning weight, feedlot arrival weight, and days on feed; carcass traits included frequency of abscessed liver and lung health, quality grade and YG parameters, total carcass value (US$), and carcass value per hundredweight (CWT [45.4 kg]; US$). A completely randomized experimental design was used; data were analyzed using a mixed model with a fixed effect of sire and random effects of harvest date, sex, and pen. AxG1 sired heifers had the highest (P < 0.01) marbling score, the highest (P < 0.01) carcass value per CWT, and numerically had the lowest calculated YG and highest frequency of YG one carcass. Steers sired by AxG1 had the least (P = 0.05) backfat, lowest (P < 0.01) calculated YG, highest (P < 0.01) marbling score, highest (P < 0.01) frequency of USDA Prime carcasses, the greatest (P < 0.03) total carcass value, and greatest (P < 0.01) carcass value per CWT. Collectively, AxG1 steer and heifer carcasses exhibited the least 12th rib fat thickness and lowest USDA YG in addition to the largest longissimus muscle area, highest marbling score, and greatest frequency of USDA Prime. These data suggest that AxG1 performed comparably to other high-performing industry terminal sires in carcass quality and YG outcomes.
Modulation of Metabolomic Profile in Sepsis According to the State of Immune Activation
Authors: Kranidioti Eleftheria , Ricaño-Ponce Isis , Antonakos Nikolaos , Kyriazopoulou Evdoxia , Kotsaki Antigone , Tsangaris Iraklis , Markopoulou Dimitra , Rovina Nikoleta , Antoniadou Eleni , Koutsodimitropoulos Ioannis , Dalekos George N. , Vlachogianni Glykeria , Akinosoglou Karolina , Koulouras Vasilios , Komnos Apostolos , Kontopoulou Theano , Dimopoulos George , Netea Mihai G. , Kumar Vinod , Giamarellos-Bourboulis Evangelos J.
Published: August 2024

OBJECTIVE:

To investigate the metabolomic profiles associated with different immune activation states in sepsis patients.

DESIGN:

Subgroup analysis of the PROVIDE (a Personalized Randomized trial of Validation and restoration of Immune Dysfunction in severe infections and Sepsis) prospective clinical study.

SETTING:

Results of the PROVIDE study showed that patients with sepsis may be classified into three states of immune activation: 1) macrophage-activation-like syndrome (MALS) characterized by hyperinflammation, sepsis-induced immunoparalysis, and 3) unclassified or intermediate patients without severe immune dysregulation.

PATIENTS OR SUBJECTS:

Two hundred ten patients from 14 clinical sites in Greece meeting the Sepsis-3 definitions with lung infection, acute cholangitis, or primary bacteremia.

INTERVENTIONS:

During our comparison, we did not perform any intervention.

MEASUREMENTS AND MAIN RESULTS:

Untargeted metabolomics analysis was performed on plasma samples from 210 patients (a total of 1394 products). Differential abundance analysis identified 221 significantly different metabolites across the immune states. Metabolites were enriched in pathways related to ubiquinone biosynthesis, tyrosine metabolism, and tryptophan metabolism when comparing MALS to immunoparalysis and unclassified patients. When comparing MALS to unclassified, 312 significantly different metabolites were found, and pathway analysis indicated enrichment in multiple pathways. Comparing immunoparalysis to unclassified patients revealed only two differentially regulated metabolites.

CONCLUSIONS:

Findings suggest distinct metabolic dysregulation patterns associated with different immune dysfunctions in sepsis: the strongest metabolic dysregulation is associated with MALS.
Evaluation of the Implementation of a Day-Treatment Program for Executive Functioning for Individuals With Traumatic Brain Injury in Rehabilitation Settings Using the Consolidated Framework for Implementation Research
Authors: Kajankova Maria , Tsaousides Theodore , Dudek Emily , Ashman Teresa
Published: August 2024

Objective:

To identify barriers and facilitators to implementation of a cognitive rehabilitation intervention (Short-Term Executive Plus [STEP]) into routine clinical practice using the Consolidated Framework for Implementation Research (CFIR) by comparing high (HI) and low implementation (LI) sites.

Setting:

Qualitative interviews conducted with professionals who work with people who have sustained brain injuries at various rehabilitations sites across the United States.

Participants:

Seven sites completed training, consultation, and agreed to implement STEP.

Design:

Retrospective qualitative study.

Main Measure(s):

Qualitative interview developed for the purposes of this study and the CFIR for evaluation of implementation efforts and identification of barriers and facilitators.

Results:

Out of 7 sites, 6 completed interviews. Out of the 39 CFIR constructs, 4 distinguished between HI and LI sites. Four distinguishing factors included evidence strength and quality, needs and resources of those served by the organization, leadership engagement, and engaging champions. Five common factors were identified (4 positive and 1 negative) across HI and LI sites, which may reflect aspects of implementation that could inform future implementation efforts. Ten inconclusive factors were identified, having both a positive and a negative influence on implementation.

Conclusions:

While there were several factors that were viewed positively by all sites, only 4 factors made a difference in implementation outcomes. These distinguishing factors can help inform future implementation efforts, highlighting a need for strong evidence supporting an intervention, a match between the intervention and the needs of the population served, engaging those in leadership and decision-making roles and ensuring their buy-in, and having a strong champion directly involved in implementation. In addition, taking a closer look at common and inconclusive factors may enable us to identify areas in which the implementation efforts could be strengthened.
Brief Report: A Scoping Review of Caregiver Coaching Strategies Within Caregiver-Mediated Interventions for Autism
Authors: Pellecchia Melanie , Maye Melissa , Tomczuk Liza , Zhong Nicole , Mandell David S. , Stahmer Aubyn C.
Published: August 2024

Caregiver-mediated interventions for young autistic children are increasingly considered standard of care. These interventions share two sets of components: strategies to improve children’s communication, behavior, and development; and procedures to coach caregivers to implement those strategies. To date, no review has examined how caregiver coaching is described in caregiver-mediated intervention manuals. We assessed how caregiver coaching is described in caregiver-mediated intervention manuals for young autistic children. We conducted a scoping review to identify publicly available manuals that are designed to support providers in their practice; target core or co-occurring symptoms that affect young autistic children; and were tested as caregiver-mediated interventions in randomized controlled trials. We identified 11 publicly available manuals that met inclusion criteria. Manuals were coded using a summative content analysis to identify the presence and frequency of descriptions of caregiver coaching. The content analysis highlighted a wide range in the descriptions of caregiver coaching. Many intervention manuals did not include specific descriptions of caregiver coaching. Intervention developers should include explicit information about how to coach caregivers. Implementation strategies that specifically target caregiver coaching can serve as critical supports to increase the use of coaching in early intervention.
“It Is Natural for Children With and Without Disabilities to Get Along Together”
Authors: Kim Sunyoung , Kim Namhee , Kim Kyoung-Mi , Kang Veronica Y.
Published: August 2024

Policies for early childhood inclusion in South Korea have been enacted and implemented over 3 decades. However, early childhood educators’ experiences and perceptions toward inclusion in early childhood education settings have been understudied. In this qualitative study, we interviewed 11 early childhood educators with inclusive teaching experiences using a semi-structured format. The teachers conceptualized the definition of and suggestions for inclusion in early childhood education settings and discussed the benefits of and challenges for inclusion in current South Korean education settings. We use their suggestions to provide implications for research and practice.