bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Legal Fabrique of Global Security Governance
Authors: Mignot-Mahdavi Rebecca 
Published: November 2024

Abstract
This article scrutinizes diverse institutions and processes within the framework of the global security architecture to unveil the intricate legal fabrique of global security governance (GSG). This fabrique encompasses both the processes and outcomes of norm production in these sites of GSG. The legal norms produced—regardless and sometimes because of their formal non-bindingness—interlace to form tight webs of norms. These webs of norms, in turn, stabilize practices that wield significant effects on individuals and societies, spanning domestic and transnational realms. A major implication of this argument is that, while international law ostensibly adheres to a dichotomy between soft and hard law, this demarcation reveals a conceptual framework that might, at best, be illusory and at worst, stand as one of the most misleading constructs within orthodox international legal thought. Recognizing that the norms originating from multiple sites of GSG form and reveal a tight, cohesive legal fabrique opens avenues, not only for refining existing theoretical reflections and international legal vocabularies on global (security) governance but also for recognizing the pivotal significance of this legal fabrique.
Caribbean Court of Justice (CCJ)
Authors: Berry David S. 
Published: November 2024

Abstract
The four judgments issued by the Caribbean Court of Justice in its original jurisdiction over the period 2022–2023 usher in several firsts. Belize v. Trinidad and Tobago was the first state-to-state dispute under Article 211(a) of the Revised Treaty of Chaguaramas (RTC). The Court also first addressed the issue of whether a state could bring a claim on behalf of a national (i.e., diplomatic protection). The case of Ellis Richards et al. v. Trinidad and Tobago was the first to consider Article 30 of the RTC, a provision which excludes activities involving the exercise of governmental authority from the scope of Chapter Three. In the same period, the Court considered issues related to evidence, the relation of CARICOM to the WTO system, and whether potential new claimants can be added to an original jurisdiction case.
Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa
Authors: Albaina Aitor , Garić Rade , Yebra Lidia 
Published: November 2024

Abstract
Eleven years after the publication of the first work applying deoxyribonucleic acid (DNA) metabarcoding to zooplankton communities, the commonly known “miniCOI” barcode is widely used, becoming the marker of choice. However, several primer combinations co-exist for this barcode and a critical evaluation of their performance is needed. This article reviews the misperformance of miniCOI metabarcoding with marine zooplankton communities, comparing them to microscopy and/or other universal markers. In total, misperformances were reported for 26 zooplankton taxa, including 18 copepods and five tunicates. We report a detection failure with Class Appendicularia and contrasting performances for Oithona similis (from good correspondence to detection failure), two worldwide abundant taxa with a crucial role in the marine pelagic realm. A combination of forward primer mismatches, the presence of long poly-T inserts and a low number of reference sequences would explain the failure to detect appendicularians. However, the contrasting performance with O. similis would correspond to distinct numbers of mismatches in the forward primer in different lineages within this cryptic taxon. This is reinforced by the report of similar patterns with other locally abundant zooplankton taxa. Therefore, we strongly call for the use of miniCOI in combination with alternative methods capable of addressing these limitations.
Protective Factors Predict Resilient Outcomes in Clinical High-Risk Youth with the Highest Individualized Psychosis Risk Scores
Authors: Cadenhead Kristin S , Addington Jean , Bearden Carrie E , Cannon Tyrone D , Cornblatt Barbara A , Keshavan Matcheri , Mathalon Daniel H , Perkins Diana O , Stone William , Walker Elaine F , Woods Scott W 
Published: November 2024

Abstract

Background and Hypothesis
Studying individuals at Clinical High Risk (CHR) for psychosis provides an opportunity to examine protective factors that predict resilient outcomes. Here, we present a model for the study of protective factors in CHR participants at the very highest risk for psychotic conversion based on the Psychosis Risk Calculator.

Study Design
CHR participants (N = 572) from NAPLS3 were assessed on the Risk Calculator. Those who scored in the top half of the distribution and had 2 years of follow-up (N = 136) were divided into those who did not convert to psychosis (resilient, N = 90) and those who did (nonresilient, N = 46). Groups were compared based on candidate protective factors that were not part of the Risk Calculator. Better functional outcome was also examined as an outcome measure of resiliency. Study Results: Exploratory analyses suggest that Hispanic heritage, social engagement, desirable life experiences, premorbid functioning and IQ are all potential protective factors that predict resilient outcomes. Reduced startle reactivity, brain area and volume were also associated with greater resilience.

Conclusions
The primary focus of CHR research has been the risk and prediction of psychosis, while less is known about protective factors. Clearly, a supportive childhood environment, positive experiences, and educational enrichment may contribute to better premorbid functioning and brain development, which in turn contribute to more resilient outcomes. Therapies focused on enhancing protective factors in the CHR population are logical preventive interventions that may benefit this vulnerable population. Future CHR research might use similar models to develop a “protective index” to predict resilient outcomes.
Second generation multiple channeling using platelet-rich plasma enhances cartilage repair through recruitment of endogenous MSCs in bone marrow
Authors: Lee Min Ji , Jiang Jian , Kim Soo Hyun , Jo Chris Hyunchul 
Published: November 2024

Abstract
In the treatment of cartilage defects, a key factor is the adequate and specific recruitment of endogenous stem cells to the site of injury. However, the limited quantity and capability of endogenous bone marrow stem cells (BM MSCs) often result in the formation of fibrocartilage when using bone marrow stimulation (BMS) procedures. We engineered second-generation platelet-rich plasma (2G PRP) with defibrinogenating and antifibrinolytic agents for injection into the condyle of the right femur, followed by multiple channeling (MCh) 5 days later. This approach aims to enhance repair by promoting the local proliferation and migration of BM MSCs to the full-thickness knee cartilage defect (ftKD). In our in vitro study, 2G PRP increased the number of endogenous BM MSCs and their ability to migrate toward an IL-1β-induced inflammatory condition. This significance was further confirmed by in vivo proliferation results after injection of 2G PRP into the condyle of rats. Fifty-four healthy male Sprague-Dawley rats were divided into 3 groups (ftKD, MCh, 2G MCh) for 3 time points (2 weeks, 4 weeks, 8 weeks). The 2G MCh (2G PRP injection + MCh) groups significantly improved cartilage formation at 4 and 8 weeks compared to the ftKD and MCh groups. The 2G MCh initiated cartilage repair earlier than MCh and significantly enhanced up to 8 weeks. This study demonstrated that 2G PRP increased the number of BM MSCs through the enhancement of proliferation and recruitment into the injured site, thereby improving articular cartilage repair.
Nondestructive Seed Genotyping via Microneedle-Based DNA Extraction
Authors: Li Mingzhuo , Poonam Aditi Dey , Cui Qirui , Hsieh Tzungfu , Jagadeesan Sumeetha , Bruce Wes , Vogel Jonathan T. , Sessions Allen , Cabrera Antonio , Saville Amanda C. , Ristaino Jean , Paul Rajesh , Wei Qingshan 
Published: November 2024

AbstractCrop breeding plays an essential role in addressing food security by enhancing crop yield, disease resistance, and nutritional value. However, the current crop breeding process faces multiple challenges and limitations, especially in genotypic evaluations. Traditional methods for seed genotyping remain labor-intensive, time-consuming, and cost-prohibitive outside of large-scale breeding programs. Here, we present a handheld microneedle (MN)-based seed DNA extraction platform for rapid, nondestructive, and in-field DNA isolation from crop seeds for instant marker analysis. Using soybean seeds as a case study, we demonstrated the use of polyvinyl alcohol (PVA) MN patches for the successful extraction of DNA from softened soybean seeds. This extraction technology maintained high seed viability, showing germination rates of 82% and 79%, respectively, before and after MN sampling. The quality of MN-extracted DNA was sufficient for various genomic analyses, including PCR, LAMP, and whole genome sequencing. Importantly, this MN patch method also allowed for the identification of specific genetic differences between soybean varieties. Additionally, we designed a 3D-printed extraction device, which enabled multiplexed seed DNA extraction in a microplate format. In the future, this method could be applied at scale and in-field for crop seed DNA extraction and genotyping analysis.
Detection of airborneCoccidioidesspores using lightweight portable air samplers affixed to uncrewed aircraft systems in California’s Central Valley
Authors: Radosevich Molly T. , Dobson Sarah , Weaver Amanda K. , Lampman Phinehas , Kollath Daniel , Couper Lisa , Campbell Grace , Taylor John W. , Remais Justin V. , Kobziar Leda , Markwiese James , Head Jennifer R. 
Published: November 2024

ABSTRACTCoccidioidomycosis is an emerging fungal infection caused by inhalation ofCoccidioidesspp. spores. While airborne dispersal is critical toCoccidioidestransmission, limited recovery of the pathogen from air has hindered understanding of the aerosolization and transport of spores. Here, we examine uncrewed aircraft systems (UAS) with portable, active air samplers as a novel means of capturing aerosolizedCoccidioidesand characterizing emissions and exposure risk. We sampled in September 2023 in eastern San Luis Obispo County, California, in an area with confirmedCoccidioides immitisin soils. We completed 41 20-minute flights across 14 sites using UAS equipped with an 8 L/min bioaerosol sampler and a low-cost particulate matter sensor. We sampled source soils and air under ambient conditions using one UAS at 1-10 m above ground level, and under a simulated high-dust event using two UAS, one at <2 m height and one at 5-12 m. We detectedCoccidioidesDNA in two of 41 air samples (4.9%), both under ambient conditions at 8 m above ground level, representing the highest known height of airborneCoccidioidesdetection. Spatially explicit UAS-based sampling could enhance understanding ofCoccidioidesaerobiology and enable detection in hard-to-reach or hazardous air masses, including dust storms and wildfire smoke.SynopsisUAS-based air sampling for bioaerosols, including pathogenicCoccidioidesspp., opens new possibilities for characterizing the aerosolization and transport of fungal spores and other airborne pathogens.
Switch of TIR signaling by a Ca2+sensor activates ADR1 recognition of pRib-AMP-EDS1-PAD4 for stomatal immunity
Authors: Wang Hanling , Tan Jiaxin , Cui Xiulin , Bai Yuhan , Gao Shang , Staskawicz Brian , Song Susheng , Yan Chuangye , Qi Tiancong 
Published: November 2024

AbstractPlants swiftly close stomata upon detecting pathogen entry, a crucial defense termed stomatal immunity. The process is initiated by cell-surface pattern recognition receptors (PRRs) that perceive pathogen-associated molecular patterns (PAMPs) and evoke a series of early cellular responses including calcium ions (Ca2+) influx, and is conducted by the intracellular nucleotide-binding leucine-rich-repeat receptors (NLRs) ADR1s within an EDS1-PAD4-ADR1 module. However, the underlying mechanisms linking PRR signaling to the NLRs ADR1s remain unclear. Here, we show that theNicotiana benthamianaToll/interleukin-1 receptor (TIR)-only protein Stomatal TIR1 (STIR1) produces the immune molecule pRib-AMP, induces formation of EDS1-PAD4-ADR1 complexes, and mediates stomatal immunity. The Inhibitor of Stomatal Immunity C2-domain protein 1 (ISIC1) interacts with and constrains STIR1 function at basal condition, whereas upon pathogen infection, ISIC1 senses Ca2+signals and de-represses STIR1 signaling. Cryo-electron microscopy structure of pathogen infection-elicitedArabidopsisAtEDS1-AtPAD4-AtADR1-L2 complex reveals the pRib-AMP binding to AtEDS1-AtPAD4 receptor and the AtADR1-L2 recognition of pRib-AMP-AtPAD4-AtEDS1 for stomatal immunity. Collectively, this study uncovers a repression/de-repression mechanism linking PRR signaling to NLRs by a Ca2+sensor/TIR-only node, and elucidates an NLR recognition mechanism of the pRib-AMP-EDS1-PAD4 complex in governing innate immunity.SynopsisAt basal condition, the Ca2+sensor ISIC1 interacts with and inhibits the TIR-only protein STIR1; upon pathogen infection, ISIC1 perceives Ca2+signal and releases STIR1 to produce pRib-AMP; the EDS1-PAD4 receptor binds pRib-AMP and is recognized by the NLR ADR1-L2, thereby activating stomatal immunity.
Targeted disruption of linkage-specific ubiquitylation reveals a key role of K29-linked ubiquitylation in epigenome integrity
Authors: Arroyo-Gomez Javier , Wang Juanjuan , Guérillon Claire , Isaakova Ekaterina , Reverón-Gómez Nazaret , Koutrouli Mikaela , Rahmanto Aldwin Suryo , Mitrofanov Katrine , Ingham Andreas , Schovsbo Sofie , Weischenfeldt Katrine , Coscia Fabian , Typas Dimitris , Völker-Albert Moritz , Solis Victor , Jensen Lars Juhl , Groth Anja , Mund Andreas , Beli Petra , Shearer Robert F , Mailand Niels 
Published: November 2024

AbstractLinkage-specific ubiquitin chains dictate the functional outcome of numerous critical ubiquitin-dependent signaling processes. However, the functions and targets of several poly-ubiquitin topologies remain poorly defined due to a paucity of tools for their specific detection and manipulation. To remedy this knowledge gap, we applied a cell-based ubiquitin replacement strategy enabling targeted conditional abrogation of each of the seven lysine-based ubiquitin chain types in human cells to profile system-wide impacts of disabling formation of individual chain types. Focusing on K29-linked ubiquitylation, we reveal a strong association of this linkage type with chromatin-associated proteins and show that the H3K9me3 methyltransferase SUV39H1 is a prominent cellular target of this modification. We demonstrate that K29-linked ubiquitylation is essential for proteasomal degradation of SUV39H1 despite its extensive modification by K48-linked ubiquitylation, and that K29-linked ubiquitylation of SUV39H1 is catalyzed and reversed by TRIP12 and TRABID, respectively. Preventing K29-linked ubiquitylation-mediated control of SUV39H1 stability deregulates the H3K9me3 landscape, but not other histone marks. Collectively, our ubiquitin replacement cell line panel and datasets provide valuable resources for illuminating cellular functions of linkage-specific ubiquitin chains and establish a key role of K29-linked ubiquitylation in epigenome integrity.
Evolutionary strategies ofKlebsiellaphages in a host-diverse environment
Authors: Ferriol-González Celia , Domingo-Calap Pilar 
Published: November 2024

AbstractPhage-host interactions have been studied using one or a few phages and hosts in simple, controlled systems. Here, we implemented an experimental design to evolve a 12-phage cocktail in a highly diverse environment, including a combination of 39Klebsiellaspp. capsular types. Our results showed how phages modulate their host range through different strategies, adopting a more generalist lifestyle or maintaining their host specificity, depending on the versatility of receptor binding proteins. Some of these proteins were mutational hotspots during the evolution experiment, mainly due to their intrinsic versatility, allowing a broader or narrower host range, and host diversity in the environment. Other mutations found in evolved phages were associated with evading bacterial defense systems or improving fitness on current hosts. Ecological dynamics between phages and hosts, including prophage activation and recombination events, also determined the fate of phage populations. In addition, single phage evolution experiments were performed to validate the results, allowing a model of receptor binding protein evolution and host range modulation to be proposed. This work is a step forward in the understanding of phage-host interactions and the appropriate implementation of phages as biomedical tools, providing insights into their impact in complex environments such as the human microbiota.
Efficient Sampling of PROTAC-Induced Ternary Complexes
Authors: Zhao Hongtao , Schiesser Stefan , Tyrchan Christian , Czechtizky Werngard 
Published: November 2024

AbstractProteolysis targeting chimeras (PROTACs) are bifunctional small molecules that recruit an E3 ligase to a target protein, leading to ubiquitin transfer and subsequent proteasomal degradation. The formation of ternary complexes is a crucial step in PROTAC-induced protein degradation, and gaining structural insights is essential for rational PROTAC design. In this study, we present a novel approach for efficiently sampling PROTAC-induced ternary complexes, which has been validated using 40 co-crystallized ternary complex structures. In comparison to protein-protein docking-based integrative approaches, our method achieved an impressive success rate of 97% and 50% retrospectively, measured by Cα-RMSD to the crystal structure within 10 and 4 Å, respectively, with an average CPU time of 4 hours. Notably, utilizing unbound protein structures, the Cα-RMSD values between the predicted and experimental structures were consistently within 7 Å across six WDR5-PROTAC-VHL ternary structures. Our open-source software enables the modeling of ternary structures in a single step and holds promise for enhancing PROTAC design efforts.TOC
Characterizing the Responses of Camelina and Sorghum to Environmental Stress through a Multi-Modal Approach
Authors: Seitz Kati A. , Morales Demosthenes P. , Bristow Steven T. , Pauer Erica G. , Ryan Duncan P. , Newell Raymond T. , Hanson David T. , Werner James H. 
Published: November 2024

ABSTRACTDue to their sessile nature, plants are unable to escape environmental factors that negatively impact health, resulting in losses to agricultural productivity. Rapid, non-invasive tools to detect plant stress response are essential for optimizing resource efficiency and mitigating the effects of extreme environmental pressures. However, many existing methods are either invasive, incompatible with other measurement techniques, or have not been applied to a wide range of varying environmental factors. In this study, we assess the physiological responses of four week old camelina (Camelina sativa) and sorghum (Sorghum bicolor) to chitosan, cold, drought, and both acute and chronic salt stress. Several plant characteristics were measured in parallel during stress exposure, including fluorescence and gas exchange parameters (MultispeQ and LI-6800), tissue electrical impedance with wearable biosensors (Multi-PIP), and biochemical properties via Fourier-transform infrared (FTIR) spectroscopy. We compiled unique profiles for whole plant physiological changes in response to environmental stress, demonstrating that certain aspects of plant health and makeup underwent alterations on differing temporal scales. This finding emphasizes the need for a comprehensive multi-modal approach to rapidly and accurately perform remote sensing of plant health in the field. Physiological parameters such as leaf impedance were also observed to rapidly change in response to treatment and can be leveraged to detect very early signs of plant perturbation. This research establishes the utility of a holistic phenotyping approach to inform agricultural strategies aimed at enhancing crop resilience under changing environmental conditions.
Genetic architecture of a light-temperature coincidence detector
Authors: Seluzicki Adam , Chory Joanne 
Published: November 2024

ABSTRACTLight and temperature variations are inescapable in nature. These signals provide daily and seasonal information, guiding life history determinations across many taxa. Here we show that signals from the PHOTOTROPIN2 (PHOT2) blue photoreceptor combine with low temperature information to control flowering. Plants lacking PHOT2 flower later than controls when grown in low ambient temperature. This phenotype is blocked by removal of NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) and recapitulated by reducing blue light intensity or removing the transcription factor CAMTA2. PHOT2 and CAMTA2 show non-additive genetic interactions in phenotype and gene expression. Network-based co-expression analysis indicates system-level control of key growth modules by PHOT2 and CAMTA2. CAMTA2 is required for low temperature up-regulation ofEHB1, a known NPH3-interacting protein, providing a mechanism of temperature information input to the PHOT-NPH3 blue light signaling system. Together these data describe the genetic architecture of environmental signal integration in this blue light-low temperature coincidence detection module.
Impact of sample size and tissue relevance on T2D gene identification
Authors: Davtian D , Dupuis T , Aly D Mansour , Atabaki-Pasdar N , Walker M , Franks P W , Rutters F , Im HK , Pearson E R , van de Bunt M , Viñuela A , Brown AA 
Published: November 2024

AbstractIdentification of genes and proteins mediating the activity of GWAS variants requires molecular data from disease relevant tissues, but these may be difficult to collect. Using multiple gene expression reference datasets and GWAS summary statistics for T2D we identified 1,818 unique genes associated with T2D. Comparing the performance of different reference datasets, we found that sample size, and not the relevance of the tissue to the disease, was the critical factor in identifying relevant genes. Genes implicated using a well powered expression dataset were also more likely to have multiple lines of genetic evidence. A targeted proteomics reference dataset from plasma samples showed similar power to identify T2D related proteins as gene expression with the same sample size. Accounting for BMI reduces power across all tissues and phenotypes by ∼30%, suggesting that many GWAS links to T2D are mediated by BMI, potentially implicating insulin resistance related effects. Finally, using data from smaller GWAS studies with precisely defined T2D subtypes uncovers genes directly relevant to that subtype, such asLST1, an immune response gene for Severe Autoimmune Diabetes andTRMT2A, involved in beta-cell apoptosis, for Severe Insulin Deficient Diabetes. Our work demonstrates the benefits of well powered reference datasets in accessible tissues and well-defined disease subtypes when studying complex diseases involving multiple tissues.