bluuebunny/crossref_metadata_2025_split huggingface dataset:
H i imaging of a Blueberry galaxy suggests a merger origin
Authors: Dutta Saili , Bera Apurba , Bait Omkar , Narayan Chaitra A , Sebastian Biny , Vaddi Sravani 
Published: June 2024

ABSTRACT
Blueberry galaxies (BBs) are fainter, less massive, and lower redshift counterparts of the Green pea galaxies. They are thought to be the nearest analogues of the high redshift Lyman Alpha (Ly $\alpha$) emitters. We report the interferometric imaging of H i 21 cm emission from a Blueberry galaxy, J1509+3731, at redshift, z = 0.03259, using the Giant Metrewave Radio Telescope. We find that this Blueberry galaxy has an H i mass of $M_{\rm{H\,{{\small I}}}} \approx 3\times 10^8 \, {\rm{M}}_{\odot }$ and an H i-to-stellar mass ratio $M_{\rm{H {\small I}}}/M_* \approx$ 2.4. Using SFR estimates from the H $\beta$ emission line, we find that it has a short H i depletion time scale of ${\approx} 0.2$ Gyr, which indicates a significantly higher star formation efficiency compared to typical star-forming galaxies at the present epoch. Interestingly, we find an offset of ${\approx} 2$ kpc between the peak of the H i 21 cm emission and the optical centre which suggests a merger event in the past. Our study highlights the important role of mergers in triggering the starburst in BBs and their role in the possible leakage of Lyman-$\alpha$ and Lyman-continuum photons which is consistent with the previous studies on BB galaxies.
Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes
Authors: Ciezarek Adam G , Mehta Tarang K , Man Angela , Ford Antonia G P , Kavembe Geraldine Dorcas , Kasozi Nasser , Ngatunga Benjamin P , Shechonge Asilatu H , Tamatamah Rashid , Nyingi Dorothy Wanja , Cnaani Avner , Ndiwa Titus C , Di Palma Federica , Turner George F , Genner Martin J , Haerty Wilfried 
Published: June 2024

Abstract
Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.
Transfer learning for cross-context prediction of protein expression from 5’UTR sequence
Authors: Gilliot Pierre-Aurélien , Gorochowski Thomas E 
Published: June 2024

Abstract
Model-guided DNA sequence design can accelerate the reprogramming of living cells. It allows us to engineer more complex biological systems by removing the need to physically assemble and test each potential design. While mechanistic models of gene expression have seen some success in supporting this goal, data-centric, deep learning-based approaches often provide more accurate predictions. This accuracy, however, comes at a cost — a lack of generalization across genetic and experimental contexts that has limited their wider use outside the context in which they were trained. Here, we address this issue by demonstrating how a simple transfer learning procedure can effectively tune a pre-trained deep learning model to predict protein translation rate from 5’ untranslated region (5’UTR) sequence for diverse contexts in Escherichia coli using a small number of new measurements. This allows for important model features learnt from expensive massively parallel reporter assays to be easily transferred to new settings. By releasing our trained deep learning model and complementary calibration procedure, this study acts as a starting point for continually refined model-based sequence design that builds on previous knowledge and future experimental efforts.
Structure-based learning to predict and model protein–DNA interactions and transcription-factor co-operativity in cis-regulatory elements
Authors: Fornes Oriol , Meseguer Alberto , Aguirre-Plans Joachim , Gohl Patrick , Bota Patricia M , Molina-Fernández Ruben , Bonet Jaume , Chinchilla-Hernandez Altair , Pegenaute Ferran , Gallego Oriol , Fernandez-Fuentes Narcis , Oliva Baldo 
Published: June 2024

Abstract
Transcription factor (TF) binding is a key component of genomic regulation. There are numerous high-throughput experimental methods to characterize TF–DNA binding specificities. Their application, however, is both laborious and expensive, which makes profiling all TFs challenging. For instance, the binding preferences of ∼25% human TFs remain unknown; they neither have been determined experimentally nor inferred computationally. We introduce a structure-based learning approach to predict the binding preferences of TFs and the automated modelling of TF regulatory complexes. We show the advantage of using our approach over the classical nearest-neighbor prediction in the limits of remote homology. Starting from a TF sequence or structure, we predict binding preferences in the form of motifs that are then used to scan a DNA sequence for occurrences. The best matches are either profiled with a binding score or collected for their subsequent modeling into a higher-order regulatory complex with DNA. Co-operativity is modelled by: (i) the co-localization of TFs and (ii) the structural modeling of protein–protein interactions between TFs and with co-factors. We have applied our approach to automatically model the interferon-β enhanceosome and the pioneering complexes of OCT4, SOX2 (or SOX11) and KLF4 with a nucleosome, which are compared with the experimentally known structures.
Quitting Smoking With … Smoke? Unauthorized Claims Used by Herbal Cigarette Manufacturers
Authors: Seidenberg Andrew B , Donovan Emily , Azadi Mona , Goyette Rebecca , Ling Pamela M 
Published: June 2024

Abstract

Introduction
Herbal cigarettes are made with non-tobacco plant materials (eg, tea leaves, hemp), are typically sold pre-rolled in packs and with filters, and are combusted and smoked like tobacco cigarettes. Herbal cigarette manufacturers have a history of making misleading health claims and at least one company has previously settled with the U.S. Federal Trade Commission over deceptive advertising. This study examined current claims and product characteristics of herbal cigarettes sold by a popular online retailer.

Aims and Methods
We searched Amazon.com for “herbal cigarettes” and “hemp cigarettes” and identified all herbal cigarette products sold on the first page of search results (n = 51). Two coders independently content analyzed each product’s Amazon page for claims (eg, smoking cessation, health), product characteristics (eg, flavors), and presence of disclaimers and warnings.

Results
Overall, 78.4% of product pages made smoking cessation claims (eg, “A more scientific way to quit smoking,” “…decreases nicotine craving symptom and helps to quit tobacco smoking”). Further, 45.1% of product pages included claims describing lower risk/exposure compared to tobacco products (eg, “…without the addictive nicotine and toxic chemicals found in tobacco cigarettes”). Some herbal products were available in multiple flavors, including menthol (21.6%) and fruit (17.7%). Only 35.3% of products included visible health warnings on product packaging.

Conclusions
Many herbal cigarette products sold on Amazon.com make unauthorized cessation and health claims. Regulatory agencies must act decisively to stop the misleading advertising of these products and develop appropriate warnings to educate the public about the potential harms.

Implications
This content analysis documents the use of unauthorized and misleading claims made in the marketing of herbal cigarettes. These findings highlight the need for enforcement of existing federal regulations, which prohibit deceptive advertising. Research is needed to inform the development of appropriate warning labels that can be used to inform consumers of the potential harms of smoking herbal cigarettes.
How to construct a new global order
Authors: Rodrik Dani , Walt Stephen 
Published: June 2024

Abstract:
We advance principles for the construction of a stable and broadly beneficial world order that does not require significant commonality in interests and values among states. In particular, we propose a ‘meta-regime’ as a device for structuring a conversation around the relevant issues, and facilitating either agreement or accommodation. Participating in this meta-regime would impose few constraints on states, yet in favourable circumstances could facilitate significant cooperation. It could also encourage increased cooperation over time even among adversaries, as participation in the meta-regime builds trust. We apply these ideas to several issue areas, including US–China competition.
How India can reach net zero: a strategy for 2025–35
Authors: Ahluwalia Montek S , Patel Utkarsh 
Published: June 2024

Abstract
This paper assesses the feasibility of India achieving its stated objective of getting to net zero carbon emissions by 2070 and outlines a possible strategy for the next 10 years consistent with this goal. It recommends a combination of price-based measures and several sector-specific interventions. The ideal price-based measure would be a carbon tax. This may not be feasible for various reasons, but in its absence a well-designed emissions trading system, as described in the paper, could make a major contribution in reducing emissions. On sectoral interventions, the critical areas over the next 10 years would be (i) accelerated expansion of various forms of renewable energy capacity, which will require several policy changes, (ii) electrification of transport, and (iii) a shift from private to public transport in urban areas and from road to rail for freight. Action will also be necessary in other sectors such as industry, agriculture, and buildings, but a detailed strategy for these may take more time to put in place. Since responsibility for action in all these areas is spread across different ministries in the central government and, in many cases, state governments, evolving an internally consistent and cost-effective strategy will present a major challenge. There is a case for setting up a high-level commission chaired by the Prime Minister to approve a national strategy. The paper estimates that the additional investment needed to make this transition will be about 2 per cent of India’s GDP by 2030, much of which will have to come from additional public and private savings. In this context, some form of carbon pricing would help generate additional revenue.
Three Arabidopsis UMP kinases have different roles in pyrimidine nucleotide biosynthesis and (deoxy)CMP salvage
Authors: Rinne Jannis , Niehaus Markus , Medina-Escobar Nieves , Straube Henryk , Schaarschmidt Frank , Rugen Nils , Braun Hans-Peter , Herde Marco , Witte Claus-Peter 
Published: June 2024

Abstract
Pyrimidine nucleotide monophosphate biosynthesis ends in the cytosol with uridine monophosphate (UMP). UMP phosphorylation to uridine diphosphate (UDP) by UMP KINASEs (UMKs) is required for the generation of all pyrimidine (deoxy)nucleoside triphosphates as building blocks for nucleic acids and central metabolites like UDP-glucose. The Arabidopsis (Arabidopsis thaliana) genome encodes five UMKs and three belong to the AMP KINASE (AMK)-like UMKs, which were characterized to elucidate their contribution to pyrimidine metabolism. Mitochondrial UMK2 and cytosolic UMK3 are evolutionarily conserved, whereas cytosolic UMK1 is specific to the Brassicaceae. In vitro, all UMKs can phosphorylate UMP, cytidine monophosphate (CMP) and deoxycytidine monophosphate (dCMP), but with different efficiencies. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-induced null mutants were generated for UMK1 and UMK2, but not for UMK3, since frameshift alleles were lethal for germline cells. However, a mutant with diminished UMK3 activity showing reduced growth was obtained. Metabolome analyses of germinating seeds and adult plants of single- and higher-order mutants revealed that UMK3 plays an indispensable role in the biosynthesis of all pyrimidine (deoxy)nucleotides and UDP-sugars, while UMK2 is important for dCMP recycling that contributes to mitochondrial DNA stability. UMK1 is primarily involved in CMP recycling. We discuss the specific roles of these UMKs referring also to the regulation of pyrimidine nucleoside triphosphate synthesis.
Epigenetic control during root development and symbiosis
Authors: Zanetti María Eugenia , Blanco Flavio , Ferrari Milagros , Ariel Federico , Benoit Matthias , Niebel Andreas , Crespi Martin 
Published: June 2024

Abstract
The roots of plants play multiple functions that are essential for growth and development, including anchoring to the soil as well as water and nutrient acquisition. These underground organs exhibit the plasticity to modify their root system architecture in response to environmental cues, allowing adaptation to change in water and nutrient availability. In addition, roots enter in mutualistic interactions with soil microorganisms, for example, the root nodule symbiosis (RNS) established between a limited group of plants and nitrogen-fixing soil bacteria and the arbuscular mycorrhiza symbiosis involving most land plants and fungi of the Glomeromycetes phylum. In the past 20 years, genetic approaches allowed the identification and functional characterization of genes required for the specific programs of root development, root nodule, and arbuscular mycorrhiza symbioses. These genetic studies provided evidence that the program of the RNS recruited components of the arbuscular mycorrhiza symbiosis and the root developmental programs. The execution of these programs is strongly influenced by epigenetic changes—DNA methylation and histone post-translational modifications—that alter chromatin conformation modifying the expression of key genes. In this review, we summarize recent advances that highlight how DNA methylation and histone post-translational modifications, as well as chromatin remodeling factors and long noncoding RNAs, shape the root system architecture and allow the successful establishment of both root nodule and arbuscular mycorrhiza symbioses. We anticipate that the analysis of dynamic epigenetic changes and chromatin 3D structure in specific single cells or tissue types of root organs will illuminate our understanding of how root developmental and symbiotic programs are orchestrated, opening exciting questions and new perspectives to modulate agronomical and ecological traits linked to nutrient acquisition.
Monetary Policy and Heterogeneity: An Analytical Framework
Authors: Bilbiie Florin O 
Published: June 2024

Abstract
THANK is a tractable heterogeneous-agent New-Keynesian model that captures analytically core micro-heterogeneity channels of quantitative-HANK: cyclical inequality and risk; self-insurance, precautionary saving, and realistic intertemporal marginal propensities to consume. I use it to elucidate key transmission mechanisms and dynamic properties of HANK models. Countercyclical inequality yields aggregate-demand amplification and makes determinacy with Taylor rules more stringent; but solving the forward guidance puzzle requires procyclical inequality: a Catch-22. Solutions include combining inequality with a distinct risk channel, with compensating cyclicalities; I provide evidence that disposable income inequality was procyclical in the last two, Great and COVID recessions, while risk is countercyclical. Alternative policy rules also solve the Catch-22, e.g. price-level-targeting or, in the model version with liquidity, setting nominal public debt. Optimal policy with heterogeneity features a novel inequality-stabilization motive generating higher inflation volatility—but is unaffected by risk, insofar as the target efficient equilibrium entails no inequality.
Effects of peer victimization on cortical processing of social-evaluative stress in patients with major depressive disorder
Authors: Iffland Benjamin , Kley Hanna , Neuner Frank 
Published: June 2024

Abstract
Peer victimization contributes to the development of major depressive disorders (MDDs). While previous studies reported differentiated peripheral physiological responses in peer-victimized individuals with depression, little is known about potential alterations of cortical event-related potentials (ERPs) in response to social stimuli in depressive patients with a history of peer victimization. Using a social condition paradigm, the present study examined whether peer victimization alters conditioned cortical responses to potentially threatening social stimuli in MDD patients and healthy controls. In the task, we studied ERPs to conditioned stimuli (CSs), i.e. still images of faces, that were coupled to unconditioned socially negative and neutral evaluative video statements. Peer victimization was related to more pronounced P100 amplitudes in reaction to negative and neutral CSs. Attenuated P200 amplitudes in peer-victimized individuals were found in response to negative CSs. Cortical responses to CSs were not influenced by a diagnosis of MDD. The results suggest altered responsiveness to interpersonal information in peer-victimized individuals. Facilitated early processing of social threat indicators may prevent peer-victimized individuals from adaptive responses to social cues, increasing their vulnerability for depression.
Phylogenomic analyses in the complex Neotropical subfamily Corydoradinae (Siluriformes: Callichthyidae) with a new classification based on morphological and molecular data
Authors: Dias Angelica C , Tencatt Luiz F C , Roxo Fabio F , Silva Gabriel de Souza da Costa , Santos Sérgio A , Britto Marcelo R , Taylor Martin I , Oliveira Claudio 
Published: June 2024

Abstract
The family Callichthyidae, which comprises the subfamilies Corydoradinae and Callichthyinae, represents one of the largest families within the Siluriformes. Corydoradinae, the largest subfamily of Callichthyidae, alone accounts for &gt;200 valid species, with new species being described frequently. This subfamily holds significant popularity among catfish enthusiasts worldwide, mainly because Corydoras are small, peaceful, and colourful fishes. Recognizing the existence of polyphyletic groups within Corydoradinae, the aim of this study was to construct a new phylogenetic hypothesis using genomic data (ultraconserved elements) and to re-evaluate the synonymized genera using the most recent morphological data. Our results supported the monophyly of Corydoradinae and identified seven distinct groups of species, each one with an associated pre-available generic name. These genera, namely Corydoras, Aspidoras, Scleromystax, Gastrodermus (resurrected), Osteogaster (resurrected), Brochis (resurrected), and Hoplisoma (resurrected), were all validated based on evidence derived from molecular and morphological analyses. A taxonomic key for the Corydoradinae genera is provided.
Multiomics analysis reveals serine catabolism as a potential therapeutic target for MELAS
Authors: Liufu Tongling , Zhao Xutong , Yu Meng , Xie Zhiying , Meng Lingchao , Lv He , Zhang Wei , Yuan Yun , Xing Guogang , Deng Jianwen , Wang Zhaoxia 
Published: June 2024

AbstractMitochondrial disease is a devastating genetic disorder, with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke‐like episodes (MELAS) and m.3243A>G being the most common phenotype and genotype, respectively. The treatment for MELAS patients is still less effective. Here, we performed transcriptomic and proteomic analysis in muscle tissue of MELAS patients, and discovered that the expression of molecules involved in serine catabolism were significantly upregulated, and serine hydroxymethyltransferase 2 (SHMT2) increased significantly in both the mRNA and protein levels. The SHMT2 protein level was also increased in myoblasts with m.3243A>G mutation, which was transdifferentiated from patients derived fibroblasts, accompanying with the decreased nicotinamide adenine dinucleotide (NAD+)/reduced NAD+ (NADH) ratio and cell viability. After treating with SHMT2 inhibitor (SHIN1), the NAD+/NADH ratio and cell viability in MELAS myoblasts increased significantly. Taken together, our study indicates that enhanced serine catabolism plays an important role in the pathogenesis of MELAS and that SHIN1 can be a potential small molecule for the treatment of this disease.
HDAC1/2/3‐mediated downregulation of neurogranin is involved in cognitive impairment in offspring exposed to maternal subclinical hypothyroidism
Authors: Yu Xi , Guo Jun , Song Yueyang , Wei Bin , Shi Yajun , Zhao Yan , Zhao Zejun , Gao Qinqin , Wang Bin , Sun Miao 
Published: June 2024

AbstractSubclinical hypothyroidism (SCH) in pregnancy is the most common form of thyroid dysfunction in pregnancy, which can affect fetal nervous system development and increase the risk of neurodevelopmental disorders after birth. However, the mechanism of the effect of maternal subclinical hypothyroidism on fetal brain development and behavioral phenotypes is still unclear and requires further study. In this study, we constructed a mouse model of maternal subclinical hypothyroidism by exposing dams to drinking water containing 50 ppm propylthiouracil (PTU) during pregnancy and found that its offspring were accompanied by severe cognitive deficits by behavioral testing. Mechanistically, gestational SCH resulted in the upregulation of protein expression and activity of HDAC1/2/3 in the hippocampus of the offspring. ChIP analysis revealed that H3K9ac on the neurogranin (Ng) promoter was reduced in the hippocampus of the offspring of SCH, with a significant reduction in Ng protein, leading to reduced expression levels of synaptic plasticity markers PSD95 (a membrane‐associated protein in the postsynaptic density) and SYN (synaptophysin, a specific marker for presynaptic terminals), and impaired synaptic plasticity. In addition, administration of MS‐275 (an HDAC1/2/3‐specific inhibitor) to SCH offspring alleviated impaired synaptic plasticity and cognitive dysfunction in offspring. Thus, our study suggests that maternal subclinical hypothyroidism may mediate offspring cognitive dysfunction through the HDAC1/2/3‐H3K9ac‐Ng pathway. Our study contributes to the understanding of the signaling mechanisms underlying maternal subclinical hypothyroidism‐mediated cognitive impairment in the offspring.