bluuebunny/crossref_metadata_2025_split huggingface dataset:
Misinformation
Authors: Talbott Siobhan 
Published: February 2025

Abstract
While honesty was a desirable quality in business, sometimes information was shared which was—or later became—false. Occasionally this resulted from a deliberate intent to deceive, but false information more commonly arose from genuine misunderstanding or an unexpected change in circumstance. An increase in the availability of information presented as many challenges as benefits for commercial agents, as it led to conflicting data, issues of trust, and the need to deal with what we might now term ‘fake news’. This chapter explores the cause of ‘false’ information and shows how merchants navigated and sought to verify the information available to them. I consider the difference between ‘misinformation’ and ‘disinformation’, and the benefits of secrecy to merchant operations. In some circumstances more was to be gained by controlling and manipulating, rather than sharing, privileged business information.
Kynurenine, a derivative of tryptophan, inhibits progesterone biosynthesis in porcine granulosa luteal cells through AHR-mediated downregulation of GATA4, GATA6, and CEBPB
Authors: Liao Shiying , Cheng Jinhua , Zhao Weimin , Dai Chaohui , Fu Yanfeng , Li Bixia , Deng Yanfei , Li Hui 
Published: February 2025

Abstract
Kynurenine (KYN) is a primary tryptophan derivative found in the human body and fermented foods. Previous studies have shown that KYN is an Aryl hydrocarbon receptor (AHR) agonist and is important in regulating various physiological activities, including female reproduction. Progesterone is a vital steroid hormone that facilitates embryo implantation and maintains pregnancy. However, whether KYN affects its biosynthesis remains unclear. To gain understanding, in vitro luteinized porcine granulosa luteal (pGL) cells were treated with KYN. The results showed that KYN disrupted progesterone biosynthesis by decreasing the expression of STAR and HSD3B in pGL cells. In addition, the expression of three transcription factors of STAR and HSD3B (GATA4, GATA6, and CEBPB) decreased after KYN treatment. Furthermore, the AHR blockade results showed comparable to those of KYN treatment, and subsequent knockdown experiments confirmed these results. These findings suggest that KYN inhibits progesterone biosynthesis in pGL cells by downregulating GATA4, GATA6, and CEBPB expression through AHR. Thus, our results showed for the first time, a previously unknown connection between KYN and progesterone biosynthesis.
Chronic constrictive pericarditis with rheumatic mitral regurgitation
Authors: Tribak Mohammed , Adanho Christ-Marion , Elmourabit Yassine , Leghlimi Lalla Hasna , Soufiani Aida , Agoumy Zineb , El-Mhadi Samah , Marmade Lahcen 
Published: February 2025

Abstract
The case of a 31-year-old woman presenting with chronic constrictive pericarditis and mitral valve regurgitation secondary to rheumatic heart disease is described along with a review of the literature with the aim to highlight this uncommon association.
The maize GSK3-like kinase ZmSK1 negatively regulates drought tolerance by phosphorylating the transcription factor ZmCPP2
Authors: Xiang Yang , Liu Weijuan , Niu Yingxue , Li Qian , Zhao Chongyang , Pan Yitian , Li Guangdong , Bian Xiangli , Miao Yadan , Zhang Aying 
Published: February 2025

Abstract
Glycogen synthase kinase 3 (GSK3)–like kinases play important roles in stress responses in plants. However, the mechanism of GSK3-like kinases in drought-induced antioxidant defense is not clear. In this study, we discovered that the GSK3-like kinase SHAGGY-like kinase 1 (ZmSK1) negatively regulates drought tolerance by inhibiting antioxidant defense in maize (Zea mays). Then, we determined that cysteine-rich polycomb-like protein 2 (ZmCPP2) interacts with ZmSK1 and enhances maize drought tolerance by inducing antioxidant defense. ZmCPP2 is phosphorylated at Ser-250 by ZmSK1, which is dependent on ZmSK1 kinase activity and attenuates maize drought tolerance. Furthermore, ZmCPP2 directly binds to the promoter of the superoxide dismutase (SOD) gene ZmSOD4, encoding an antioxidant defense enzyme, and activates its expression. ZmSK1 phosphorylating ZmCPP2 at Ser-250 represses the binding of ZmCPP2 to the ZmSOD4 promoter. Taken together, our results indicate that the phosphorylation of ZmCPP2 by ZmSK1 results in decreased SOD activity and thus reduces drought tolerance in maize. These findings reveal a mechanism of GSK3-like kinases regulating antioxidant defense in the drought stress response.
South Dakota State University Extension’s two-year beefSD program has high impact on beginning beef cattle producers
Authors: Ehlert Krista A , Blair Amanda D , Hadrick Stacy , Olson Kenneth C 
Published: February 2025

Abstract
The value of Extension programming is the generation of short (knowledge gain), medium (behavior change), and long (condition improvement) term outcomes or impact for clientele. Evaluating impact is a critical step in Extension programming. Effective evaluation can be used to measure outcomes, adapt and improve curricula of ongoing programs, and document public value gained from Extension funding. Although evaluation tools administered during or at the end of program activities can measure short-term outcomes, they cannot measure subsequent change in behavior and condition as a result of the program. South Dakota State University Extension has conducted a program entitled “beefSD” wherein cohorts of beginning beef cattle producers have been exposed to a two-year curriculum to increase their capacity to successfully manage their beef cattle enterprises. Five cohorts completed the program between 2010 and 2022. To measure the medium- and long-term impacts of this program, an online survey instrument was administered to the alumni of all five cohorts in Fall 2022. Twenty-two percent of alumni completed the survey. Survey results indicated that since completion of the program, most respondents expanded their beef cattle enterprises, implemented goals, financial, marketing, grazing, drought, and business plans, and became more profitable. The majority of respondents found high value from practices, tools, and concepts learned in beefSD that they incorporated into their enterprise management plans. Evaluation results indicated beefSD has positively impacted the beef cattle enterprises and lives of alumni, increasing the likelihood of their improved sustainability going forward. Further, this evaluation survey clearly demonstrated program impact, documenting public value from the program. Similar Extension programs could be developed for other regions or commodities, contributing comparable outcomes with program evaluation documenting further public value.
Neuromuscular Blockade and Antagonism in Patients with Renal Impairment: A Multicenter Retrospective Cross Sectional Study
Authors: Elkhateb Rania , Campbell Davis L. , Zhao Xinyi , Mentz Graciela , El Sharawi Nadir , Kumar Sathish , Mhyre Jill M. , Kheterpal Sachin , Colquhoun Douglas A 
Published: February 2025

Background:
Current practice guidelines do not address the use of neuromuscular blocking and antagonism agents in patients with renal impairment. The FDA label for sugammadex advises against use in patients with severe renal impairment (eGFR < 30 ml/min). Using a multicenter electronic health record registry, we sought to understand the modern use of neuromuscular blockade and antagonism agents in patients with significant renal impairment (eGFR < 60 ml/min).

Methods:
Data was obtained from the Multicenter Perioperative Outcomes Group (MPOG) registry, for adult patients (>18yrs) with an estimated glomerular filtration rate (eGFR) < 60ml/min, based on most recent serum creatinine, receiving general anesthesia for a non-renal transplant procedure with an endotracheal tube between January 1st 2016 and July 31st 2022. Patients were classified into three mutually exclusive blockade and reversal strategies: rocuronium-sugammadex, cisatracurium-neostigmine and rocuronium-neostigmine. Adjusted incidence of each blockade reversal strategy was established by a multinomial mixed effects model. The contribution of institution, anesthesiologist, and patient/case factors to variation to strategy choice was assessed by multilevel mixed effects models.

Results:
In 243,944 cases across 5,133 anesthesiologists and 48 institutions, adjusted use of rocuronium-sugammadex increased from 4.4% to 95.2% and rocuronium-neostigmine decreased from 84.7% to 4.3% and cisatracurium-neostigmine decreased from 10.9% to 0.5%. In patients with an eGFR <15ml/min, rocuronium-sugammadex use increased from 0.5% to 86.9%. 30.1% of the variation in choice of rocuronium-sugammadex vs cisatracurium-neostigmine, was attributed to the institution, 22.7% to the attending anesthesiologist and 47.2% to patient/case factors or was unexplained. The adjusted median odds ratio for this choice was 2.5 for clinicians and 3.1 for institutions.

Conclusion:
Rocuronium-sugammadex is the primary neuromuscular blockade-antagonism strategy for patients with moderate and severe renal impairment. Variation in choice is significantly impacted by the institution and attending anesthesiologist providing care.
A kinetic model of antigen-dependent IgG oligomerization and complement binding
Authors: Strasser Jürgen , Frischauf Nikolaus , Schustereder Lukas , Karner Andreas , Bosgra Sieto , Labrijn Aran F. , Beurskens Frank J. , Preiner Johannes 
Published: February 2025

ABSTRACTThe classical complement pathway (CCP), an important branch of the mammalian immune system, is initiated through multivalent binding of complement protein C1 to Immunoglobulin G (IgG) antibody oligomers assembled on the surface of pathogens, infected or malignant cells, culminating in the formation of the membrane attack complex (MAC) and subsequent cell lysis. IgG oligomers can further engage immune effector cells through Fcγ receptors or complement receptors, facilitating antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis (ADCP). Detailed knowledge of the factors that drive IgG oligomerization is thus vitally important to establish and improve IgG based therapies. We here focus on the kinetics of antigen-dependent IgG oligomerization and develop a comprehensive model capable of predicting oligomer formation as a function of IgG concentration, antigen density, IgG subclass and Fc point mutants, as well as the presence of Fc-binding and thus oligomerization-inhibiting factors such as staphylococcal protein A (SpA). We characterize the underlying molecular interactions in single molecule force spectroscopy (SMFS) and grating coupled interferometry (GCI) experiments. By fitting experimental data from high-speed atomic force microscopy (HS-AFM) experiments, we further quantify key rate constants and thermodynamic parameters, including free energy changes associated with oligomerization and apply the model to predict complement-mediated lysis in liposomal vesicle-based assays. The presented mechanistic framework may serve as a basis for optimizing antibody engineering and pharmacokinetic/pharmacodynamic modeling in the context of immunotherapies exploiting the CCP.
Testing a general theory for flowering time shift as a function of growing season length
Authors: Park John S. , Jackson John , Bergsten Anna , Ågren Jon 
Published: February 2025

ABSTRACTUnderstanding the effects of climate change on the evolution of phenological timing, such as start of flowering, is of major interest because phenology is critical for fitness of populations, and underpins many ecological dynamics. Much recent research has focused on the correlation between phenological timing and the arrival of spring. However, the evolutionarily optimal seasonal timing should depend also on the duration of the growing season, within which entire annual life cycles must unfold. Optimal energy allocation theory can explicitly address life-history scheduling in a seasonal environment, and be used to predict how scheduling should adaptively respond to seasonality shifts. Here we extend a seminal theoretical framework for perennial plant scheduling by Iwasa & Cohen (1989), and predict a specific nonlinear relationship between growing season length and optimal flowering time expressed as number of days after the start of the growing season. We tested and found strong support for thisa prioriprediction in two independent common-garden experiments with purple loosestrife (Lythrum salicaria) and European goldenrod (Solidago virgaurea) populations sampled along latitudinal gradients in Sweden. Climate warming is commonly associated with changes in both the start and the duration of the growing season. Considering both effects, our findings suggest that as springs start earlier and growing seasons lengthen, shifts in optimal flowering time expressed as calendar date may initially stall before accelerating, potentially explaining observed variation in phenological shifts across systems. More broadly, we show how mechanistic life history theory can advance understanding of phenological change beyond correlative conclusions.SIGNIFICANCE STATEMENTThe optimal timing for a plant to flower depends both on when spring begins and on the total length of the growing season—both shifting with climate change. However, the adaptation of flowering time to changes in growing season length is much less explored than to an advancing spring. Building on existing theory, we predict a nonlinear relationship between growing season length and optimal flowering time. Data on two species (purple loosestrife and European goldenrod) grown in common gardens strongly support this prediction. Our results demonstrate why species can vary in their observed phenological responses to climate change. More broadly, we highlight the power of mechanistic life history theory for explaining and predicting phenological shifts.
AllMetal3D: joint prediction of localization, identity and coordination geometry of common metal ions in proteins
Authors: Dürr Simon L. , Rothlisberger Ursula 
Published: February 2025

AbstractNature uses a variety of metal ions as cofactors for specific tasks. The three main classes of metals in biological systems are alkali ions (e.g. sodium and potassium), alkaline earth ions (e.g. magnesium and calcium) as well as transition metal ions (e.g. zinc or iron and many others). To date no selective predictor to localize each of these metals in a given protein structure exists. Current methods require either preselecting a specific ion (e.g MIB2 (Lu et al., 2022), ESMBind (Dai et al., 2024) or AlphaFold3 (Abramson et al., 2024) or a location (MICShub et al. (2024)). In this work, we describe an extension of the recently introduced Metal3D framework (Dürr et al., 2023) that was originally trained on zinc sites to predict the location of all biologically relevant classes of metal ions as well as to classify their coordination geometry. Our model is the first of its kind and even outperforms Metal3D for the prediction of the location of Zn2+and generalizes well to the other metals in terms of location prediction as well as identity classification. Comparing the model to several other available tools such as MetalSiteHunter, AlphaFold3, MIC, MIB2 and MetalHawk highlights important shortcomings in these tools with respect to data bias, prediction of negative sites and selectivity. However, concerning coordination geometry prediction, similar to other work, we find that our method cannot accurately make correct classifications beyond the most common classes in natural proteins i.e. tetrahedral and octahedral arrangements. AllMetal3D is available as ChimeraX extension, standalone web app as well as python package:https://github.com/lcbc-epfl/allmetal3d
Increased contact between lipid droplets and mitochondria in skeletal muscles of male elite endurance athletes
Authors: Nielsen Joachim , Petersen Kristine Grøsfjeld , de Almeida Martin Eisemann , Shepherd Sam O. , Christensen Britt , Petersen Maria Houborg , Højlund Kurt , Ørtenblad Niels , Gejl Kasper Degn 
Published: February 2025

AbstractEndurance athletes exhibit higher skeletal muscle mitochondrial and lipid droplet (LD) content compared to recreationally active individuals, along with greater whole-body oxygen uptake and maximal fat oxidation rates. In this study, we investigated if these differences manifest in a greater LD-mitochondria contact and how this may relate to the organelles’ size, shape, and numerical densities. We obtained skeletal muscle biopsies from 17 male elite triathletes and road cyclists and 7 recreationally active men. Using quantitative transmission electron microscopy, we found that the endurance athletes had 2-3-fold greater LD-mitochondria contact length than the recreationally active individuals. This was related to higher numerical densities of both mitochondria and LDs in the intermyofibrillar space. Adding data from untrained individuals with equally high intermyofibrillar LD density as the endurance athletes revealed a 24% greater LD-mitochondria contact length in the endurance athletes. We observed small trivial differences in the shape of both organelles between populations. However, large mitochondrial profiles were more elongated and irregular in shape compared to small mitochondrial profiles, while large LD profiles were more circular and less irregular than small LD profiles. Within the group of athletes, large intermyofibrillar LD profiles correlated with a high fraction of PLIN5-positive LDs and their maximal fat oxidation rate was positively associated with an interaction between the profile size of both intermyofibrillar LDs and mitochondria. In conclusion, male endurance athletes have a greater LD-mitochondria contact than recreationally active and untrained individuals. This muscular phenotype is restricted to the intermyofibrillar space and to fibres rich in mitochondria.
Lipopolysaccharides nanodiscs, a biomimetic platform to study bacterial surface
Authors: Massilia Abbas , Samantha Micciulla , Jean-Marie Teulon , Meriem Maalej , Macha Trembley , Roberta Marchetti , Antonio Molinaro , Michel Thépaut , Franck Fieschi , Jean-Luc Pellequer , Cédric Laguri 
Published: February 2025

ABSTRACTLipopolysaccharides (LPS) are essential components of the outer membranes of Gram-negative bacteria, playing a crucial role in antimicrobial resistance, virulence, and the host’s immune response. Self-assembled particles displaying LPS are essential for biophysical studies addressing the behavior of bacterial surfaces under specific biomimetic conditions. Styrene-maleic acid (SMA) copolymers were employed to form LPS nanodiscs, either from extracted LPS or directly from purified outer membranes. These nanodiscs, derived from pathogenic O157:H7 or laboratoryE. colistrains, are well-defined in size and yield high-resolution nuclear magnetic resonance (NMR) spectra. They have been successfully used to investigate molecular recognition by a human C-type Lectin Receptor (CLR) of the immune system and interaction with polymyxin antibiotics using various biophysical methods. This study high-lights the significance of LPS nanodiscs as bacterial surface mimetics and opens promising avenues for further research into LPS structure and interactions. The ability to generate well-defined LPS nanodiscs offers a powerful tool for studying the molecular mechanisms underlying bacterial pathogenesis and immune response.
Binding Affinity Ranking at the Molecular Initiating Event (BARMIE): An open- source computational pipeline for ecological hazard ranking of endocrine disrupting chemicals
Authors: Calahorro Fernando , Fouladi Parsa , Pandini Alessandro , Khushi Matloob , Gaihre Yogendra , Bury Nic 
Published: February 2025

AbstractOne of the key challenges in ecological risk assessment lies in identifying the chemicals that pose the greatest threat and determining the species that are most vulnerable to their effects. Computational prediction of protein binding affinity can help in assessing the risk of chemicals to species. In this study we developed and validated an open-source tool called BARMIE (Binding Affinity Ranking at the Molecular Initiating Event) to rank chemical hazards and identify species that are most susceptible based on the binding affinity of the chemical to steroid receptor proteins. As an exemplar of BARMIE’s output we focus on 163 teleost fish glucocorticoid receptors (GRs) and the natural ligand cortisol and 10 synthetic glucocorticoid (GCs) drugs and five other potential chemical GR agonists. The hazard ranking is based on the likelihood that the chemicals with the highest binding affinity are likely to outcompete cortisol at the receptor binding site. In this analysis, halcinonide, a GC, was predicted to be the most hazardous based on its binding affinity and the superorder Protacanthopterygii species, including the Esociformes and Salmoniformes, were identified as the most vulnerable. This computational pipeline can be expanded to evaluate more chemicals, species, and proteins as part of an in silico chemical hazard assessment tool.
Condensin IDChas a Functional ATPase That is Required for X-Chromosome Dosage Compensation inC. elegans
Authors: Chawla Bahaar , Jatia Suchi , Sloan Dillon E. , Csankovszki Gyorgyi 
Published: February 2025

AbstractDosage compensation (DC) inC. elegansutilizes a condensin complex that resembles mitotic condensins, but differs by one subunit, DPY-27. DPY-27 replaces SMC-4, one of the Structural Maintenance of Chromosome (SMC) proteins that is responsible for hydrolyzing ATP, required for condensation of DNA and other mitotic condensin functions. To understand if the ATPase function is required in DC, we first demonstrated that DPY-27 is capable of hydrolyzing ATPin vitro. Then, we used CRISPR/Cas9-mediated genome editing to generate an ATPase mutation indpy-27and demonstrated that this mutation results in a loss of DC. Specifically, we found that without ATPase function, DPY-27 containing condensin IDChas reduced capacity to bind DNA, condense the X chromosomes, and facilitate H4K20me1 enrichment on the X-chromosomes. Our results suggest that condensin IDC, like mitotic condensins, uses ATP hydrolysis to perform its functions, makingC. elegansDC a model for how activities attributed to mitotic condensins can be used to regulate gene expression.
Poly-L-Ornithine Coated Plant Scaffolds Support Motor Recovery in Rats after Traumatic Spinal Cord Injury
Authors: Couvrette Lauren J. , Walker Krystal L. A. , Bayat Arman , Modulevsky Daniel J. , Laliberté Alex , Cuerrier Charles M. , Leblanc-Latour Maxime , Hickey Ryan J. , Boudria Rose , Monty Ruthie , Obhi Ras-Jeevan K. , Shore Isabel , Galuta Ahmad , Tsai Eve C. , Bui Tuan , Pelling Andrew E. 
Published: February 2025

ABSTRACTSpinal cord injury (SCI) is a debilitating neurological condition with far-reaching consequences for patients, including loss of motor function and significant limitations to quality of life. Implantable biomaterials have emerged as a therapeutic strategy to modulate the SCI microenvironment and facilitate regeneration of axons. In this study, plant-derived cellulose scaffolds coated with poly-L-ornithine (PLO) are shown to support locomotor recovery and neural tissue repair in a rat model of spinal cord injury. Upon complete transection of the spinal cord, animals were implanted with a plant-derived scaffold coated in poly-L-ornithine, a positively charged amino acid chain that is known to promote neural stem cell differentiation into neurons and enhance myelin regeneration. Recovery of motor function was evaluated by the Basso, Beattie and Bresnahan (BBB) locomotor scale as well as the Karolinska Institutet Swim Assessment Tool (KSAT). Retrograde tracing of ascending sensory tracts revealed enhanced regeneration in animals that received the PLO-coated scaffold. Numerous β-III tubulin and neurofilament 200 positive fibers may indicate axonal sprouting within the cellulose scaffold and LFB staining highlights myelination around the PLO-coated scaffold. These results demonstrate the potential of plant-based biomaterials in a rat model of acute spinal cord injury and highlight their enhancement after PLO functionalization.