bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human DUX4 and porcine DUXC activate similar early embryonic programs in pig muscle cells: implications for preclinical models of FSHD
Authors: Nip Yee , Bennett Sean R , Smith Andrew A , Jones Takako I , Jones Peter L , Tapscott Stephen J 
Published: February 2023

Abstract
Human DUX4 and its mouse ortholog Dux are normally expressed in the early embryo—the 4-cell or 2-cell cleavage stage embryo, respectively—and activate a portion of the first wave of zygotic gene expression. DUX4 is epigenetically suppressed in nearly all somatic tissue, whereas facioscapulohumeral dystrophy (FSHD)-causing mutations result in its aberrant expression in skeletal muscle, transcriptional activation of the early embryonic program and subsequent muscle pathology. Although DUX4 and Dux both activate an early totipotent transcriptional program, divergence of their DNA binding domains limits the use of DUX4 expressed in mice as a preclinical model for FSHD. In this study, we identify the porcine DUXC messenger ribonucleic acid expressed in early development and show that both pig DUXC and human DUX4 robustly activate a highly similar early embryonic program in pig muscle cells. These results support further investigation of pig preclinical models for FSHD.
Interaction of methionine sulfoxide reductase B5 with SlMYC2 stimulates the transcription of MeJA-mediated autophagy-related genes in tomato fruit
Authors: Min Dedong , Li Fujun , Ali Maratab , Liu Jiong , Fu Xiaodong , Song Yanan , Ding Jun , Li Xiaoan , Ji Nana , Zhang Xinhua 
Published: February 2023

AbstractMethyl jasmonate (MeJA) has been shown to induce autophagy in various plant stress responses and metabolic pathways. MYC2 is involved in MeJA-mediated postharvest fruit biological metabolism, but it is unclear how it affects MeJA-induced fruit autophagy. In this study, we noticed that silencing SlMYC2 significantly reduced the increase in autophagy-related genes (SlATGs) expression induced by MeJA. SlMYC2 could also bind to the promoters of several SlATGs, including SlATG13a, SlATG13b, SlATG18a, and SlATG18h, and activate their transcript levels. Moreover, SlMsrB5, a methionine sulfoxide reductase, could interact with SlMYC2. Methionine oxidation in SlMYC2 and mimicking sulfoxidation in SlMYC2 by mutation of methionine-542 to glutamine reduced the DNA-binding ability and transcriptional activity of SlMYC2, respectively. SlMsrB5 partially repaired oxidized SlMYC2 and restored its DNA-binding ability. On the other hand, silencing SlMsrB5 inhibited the transcript levels of SlMYC2-targeted genes (SlATG13a, SlATG13b, SlATG18a, and SlATG18h). Similarly, dual-luciferase reporter (DLR) analysis revealed that SlMsrB5–SlMYC2 interaction significantly increased the ability of SlMYC2-mediated transcriptional activation of SlATG13a, SlATG13b, SlATG18a, and SlATG18h. These findings demonstrate that SlMsrB5-mediated cyclic oxidation/reduction of methionine in SlMYC2 influences SlATGs expression. Collectively, these findings reveal the mechanism of SlMYC2 in SlATGs transcriptional regulation, providing insight into the mechanism of MeJA-mediated postharvest fruit quality regulation.
RsERF40contributes to cold stress tolerance and cell expansion of taproot in radish (Raphanus sativusL.)
Authors: Li Cui , Mao Baozhen , Wang Kai , Xu Liang , Fan Lianxue , Wang Yan , Li Ying , Ma Yinbo , Wang Lun , Liu Liwang 
Published: February 2023

AbstractThe growth and development of taproots are inhibited by cold stress in radish (Raphanus sativus L.). Ethylene-responsive element binding factors (ERF) are key participators in the cold stress response and growth regulation of plants. However, the function of ERF genes in cold tolerance and root development in radish remains elusive. Here, we showed that the secondary growth of radish taproots was inhibited by cold stress. Comparative transcriptome analysis demonstrated that the RsERF40 gene is an important regulator of the cold stress response and root growth regulation. The cold tolerance of transgenic Arabidopsis plants overexpressing the RsERF40 gene was significantly improved. Overexpressing RsERF40 in the cold-sensitive radish genotype and silencing RsERF40 in the cold-tolerant radish genotype indicated that RsERF40 was beneficial for alleviating oxidative damage under cold stress in radish. Transgenic Arabidopsis seedlings showed an increase in the elongation and radial growth of dark-grown roots. RT-qPCR analysis showed that the expression of the cold-related genes (CORs) RsCOR78 and RsCOR413PM1 and the cell wall strengthening-related genes RsCESA6 and RsEXPB3 was upregulated in transgenic Arabidopsis seedlings. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays (DLA) revealed that RsERF40 directly regulates RsCOR78, RsCOR413PM1, RsCESA6 and RsEXPB3 expression, illustrating that RsERF40 enhances cold tolerance and taproot growth by modulating osmotic adjustment and cell wall mechanical strength in radish. In this study, the RsERF40-regulon was firstly found to be a new cold response pathway independent of the CBF-COR pathway conferring cold stress tolerance with increasing radish taproot growth. These results provided novel insight into the molecular mechanism underlying cold stress response and would facilitate the genetic improvement of cold tolerance in radish and other root vegetable crops.
Simulation-based educational approach toward improving thermal outdoor comfort for pedestrians in semi-arid climate
Authors: Sayad Bouthaina , Alkama Djamel , Ibrahim Hossam Samir , Hegazy Ibrahim Rizk , Imam Ayman Amin , Abed Ahmed Mohammed , Alhubashi Haytham Hussain 
Published: February 2023

Abstract
The urban cooling is the most effective strategy to fight the urban climate change effects in summertime. Thus, searching urban cool islands can remedy the rise of urban temperatures. This study aims to consider cool urban pathways offering optimal levels of thermal comfort in downtown Guelma during summer overheating. This involves researching the appropriate tree ratio and typology, tree layout and suitable configurations of water bodies of outdoor spaces. The scientific methodology is made through either straightforward step included on-site measurements and calculating the difference of urban temperatures to select five outdoor spaces with maximum heat stress. As our study also aims to improve the outdoor thermal comfort by natural elements, it simulates different scenarios of the selected stations using ENVI-Met model and exploiting the real field measurement of the urban microclimate. The most significant reductions in thermal comfort levels (UTCI) over three thermal phases identify the coolest urban pathways. Consequently, we confirmed that considering cool pathways spanning from station S2 to station S8 is possible with optimal thermal comfort levels over the day; 0.46–6.9°C in the morning phase, 0.94–3.87°C in the hot thermal phase and 1.42–3.54°C in the thermal relief phase. The findings indicate three main effects of microclimatic regulation underlie the improvement of the thermal comfort levels: tree cooling effect with (Ta ≤ 1.1°C), cooling effect of water bodies (Ta ≤ 0.3°C) and cooling effect of trees in combination with water bodies (Ta ≤ 1.9°C).
Identification and characterization of plasmids carrying the mobile colistin resistance gene mcr-1 using optical DNA mapping
Authors: KK Sriram , Wranne Moa S , Sewunet Tsegaye , Ekedahl Elina , Coorens Maarten , Tangkoskul Teerawit , Thamlikitkul Visanu , Giske Christian G , Westerlund Fredrik 
Published: February 2023

Abstract

Objectives
Colistin is a last-resort antibiotic, but there has been a rapid increase in colistin resistance, threatening its use in the treatment of infections with carbapenem-resistant Enterobacterales (CRE). Plasmid-mediated colistin resistance, in particular the mcr-1 gene, has been identified and WGS is the go-to method in identifying plasmids carrying mcr-1 genes. The goal of this study is to demonstrate the use of optical DNA mapping (ODM), a fast, efficient and amplification-free technique, to characterize plasmids carrying mcr-1.

Methods
ODM is a single-molecule technique, which we have demonstrated can be used for identifying plasmids harbouring antibiotic resistance genes. We here applied the technique to plasmids isolated from 12 clinical Enterobacterales isolates from patients at a major hospital in Thailand and verified our results using Nanopore long-read sequencing.

Results
We successfully identified plasmids encoding the mcr-1 gene and, for the first time, demonstrated the ability of ODM to identify resistance gene sites in small (∼30 kb) plasmids. We further identified blaCTX-M genes in different plasmids than the ones encoding mcr-1 in three of the isolates studied. Finally, we propose a cut-and-stretch assay, based on similar principles, but performed using surface-functionalized cover slips for DNA immobilization and an inexpensive microscope with basic functionalities, to identify the mcr-1 gene in a plasmid sample.

Conclusions
Both ODM and the cut-and-stretch assay developed could be very useful in identifying plasmids encoding antibiotic resistance in hospitals and healthcare facilities. The cut-and-stretch assay is particularly useful in low- and middle-income countries, where existing techniques are limited.
Flies (Insecta, Diptera) collected in the environment of dairy farms as carriers of Rotavirus A and betacoronavirus
Authors: Bertolini Amanda Bezerra , Thyssen Patrícia Jacqueline , Brandão Paulo Eduardo , Prado Aline Marrara , Silva Sheila Oliveira de Souza , Mioni Mateus de Souza Ribeiro , de Gouvea Fábio Lucas Rezende , Pantoja José Carlos de Figueiredo , Langoni Helio , Guimarães Felipe Freitas , Joaquim Sâmea Fernandes , Guerra Simony Trevizan , Leite Domingos da Silva , Rall Vera Mores , Hernandes Rodrigo Tavanelli , Lucheis Simone Baldini , Rossi Gabriel Augusto Marques , Ribeiro Márcio Garcia 
Published: February 2023

AbstractAimsWe aimed to investigate the prevalence of rotavirus and coronavirus in dipterans that commonly inhabit the environment of dairy farms.Methods and ResultsWe collected 217 insect specimens from nine dairy farms, which were examined through hemi-nested RT-PCR followed by Sanger sequencing in search of VP1 and N genes for rotavirus and bovine coronavirus-BCoV, respectively. With a predominance of Muscidae (152/217 = 70%) 11 families of Diptera were identified. Rotavirus A (RVA) and betacoronavirus (BCoV) were detected in 14.7% (32/217) and 4.6% (10/217) of the dipterans, respectively. Sequencing of the amplicons was possible for 11.5% (25/217) of RVA and 0.5% (1/217) of BCoV, confirming the presence of these pathogens.ConclusionsOur findings highlight the role of dipterans as carriers of RVA and BCoV of great relevance for public and animal health.
Lacticaseibacillus caseiCNRZ1874 supplementation promotes M1 alveolar macrophage activation and attenuatesMycoplasma pneumoniaepneumonia
Authors: Zhang Naiyu , Zeng Wuwei , Du Tingfeng , Wei Hongjiang , Tian Wei , Meng Yan , He Guiting , Lei Aihua , Zhu Cuiming 
Published: February 2023

AbstractAimsTo evaluate the protective effect of intestinal supplementation with Lacticaseibacillus casei CNRZ1874 on the inflammatory response induced by Mycoplasma pneumoniae in C57BL/6 J mice, and provide a potential strategy for alleviating M. pneumoniae pneumonia.Methods and resultsC57BL/6 J mice were gavaged with L. casei CNRZ1874 or PBS for 7 consecutive days, and then infected with M. pneumoniae on day 8. Treatment with L. casei CNRZ1874 significantly reduced M. pneumoniae loads in the lungs and alleviated the lung inflammation on day 3 and 10 after pathogen infection. Importantly, oral administration with L. casei CNRZ1874 promoted M1 alveolar macrophages activation as evidenced by increased expression of iNOS, TNF-α, and CXCL1, while inhibited M2 alveolar macrophages activation as the expression of Arg1 and Chi3l3 were significantly decreased. In consistent with the M1 alveolar macrophages activation and enhanced mycoplasma clearance, the level of TNF-α was increased while the level of IL-4 was decreased in lung tissue from the L. casei CNRZ1874 group compared with the control group. However, oral administration with L. casei CNRZ1874 may not influence adaptive immunity induced by M. pneumoniae as evaluated by M. pneumoniae specific antibodies and T cells responses in spleen.ConclusionsIntestinal supplementation with L. casei CNRZ1874 can promote M1 alveolar macrophages activation, which contributes to the clearance of M. pneumoniae and attenuation of M.pneumoniae pneumonia.
Plant Gall Diversity in Burned Semi-natural Grasslands in Japan
Authors: Koyama Asuka , Ide Tatsuya 
Published: February 2023

Abstract
We surveyed woody plants, including oaks and chestnuts (Quercus L. and Castanea Mill.), and recorded the inhabiting galls induced by oak gall wasps (Hymenoptera: Cynipidae: Cynipini) at seven Japanese semi-natural grassland sites maintained by traditional regular burning with two of the seven abandoned grassland areas. Woody plants were established in all burned and abandoned grasslands. Oak species were found at four of the seven sites. In total, 15 types of cynipid galls were recorded at all four sites where oak species were found. However, the occurrence of species was site-specific for host trees and cynipid galls. Although a few ecological studies of oak gall wasps inhabiting grassland environments, which have rapidly decreased in recent decades, have been conducted, this study suggests that semi-natural grasslands may be potential habitats for oak gall wasps and their host trees, and we provide a checklist of oak gall wasps with host oak records in semi-natural grasslands throughout Japan.
KAT7 promotes radioresistance through upregulating PI3K/AKT signaling in breast cancer
Authors: Ma Yan , Chen Xiaohua , Ding Ting , Zhang Hanqun , Zhang Qiuning , Dai Huanyu , Zhang Haibo , Tang Jianming , Wang Xiaohu 
Published: February 2023

AbstractChromatin-modifying enzymes are commonly altered in cancers, but the molecular mechanism by which they regulate cancers remains poorly understood. Herein, we demonstrated that Lysine acetyltransferase 7 (KAT7) was upregulated in breast cancer. KAT7 expression negatively correlated with the survival of breast cancer patients, and KAT7 silencing suppressed breast cancer radioresistance in vitro. Mechanistically, KAT7 activated Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) transcription, leading to enhanced PI3K/AKT signaling and radioresistance. Overexpression of AKT or PIK3CA restored radioresistance suppression induced by KAT7 inhibition. Moreover, overexpression of KAT7, but not KAT7 acetyltransferase activity-deficient mutants promoted AKT phosphorylation at the Ser473 site, PIK3CA expression and radioresistance suppression due to KAT7 inhibition. In conclusion, KAT7 has huge prospects for clinical application as a new target for predicting radioresistance in breast cancer patients.
Group- and individual-based approaches to health inequality: towards an integration
Authors: Permanyer Iñaki , Sasson Isaac , Villavicencio Francisco 
Published: February 2023

Abstract
When assessing health inequalities, should one compare health outcomes across predetermined groups (e.g., race, ethnicity, socioeconomic status), or across individuals? Group-based approaches comparing group-specific means do not account for intra-group heterogeneity. Yet, traditional approaches based on additive decompositions splitting total inequality in its within- and between-group components fail to elucidate the groups’ relative performance. Here, we develop a third approach based on pairwise comparisons to evaluatenot only the variability that might exist across individuals within and between groups, but also the relative performance of the different groups vis-a-vis each other—thus integrating both perspectives into a coherent framework.
Experimental evaluation of algorithm-assisted human decision-making: application to pretrial public safety assessment*
Authors: Imai Kosuke , Jiang Zhichao , Greiner D James , Halen Ryan , Shin Sooahn 
Published: February 2023

Abstract
Despite an increasing reliance on fully-automated algorithmic decision-making in our day-to-day lives, humans still make consequential decisions. While the existing literature focuses on the bias and fairness of algorithmic recommendations, an overlooked question is whether they improve human decisions. We develop a general statistical methodology for experimentally evaluating the causal impacts of algorithmic recommendations on human decisions. We also examine whether algorithmic recommendations improve the fairness of human decisions and derive the optimal decision rules under various settings. We apply the proposed methodology to the first-ever randomized controlled trial that evaluates the pretrial Public Safety Assessment in the United States criminal justice system. Our analysis of the preliminary data shows that providing the PSA to the judge has little overall impact on the judge’s decisions and subsequent arrestee behaviour.
Haemorrhagic mesenteric abscess in infective endocarditis: a unique cause of spontaneous haemoperitoneum
Authors: Read Phillipa , Walker Patrick , Menon Tulsi 
Published: February 2023

Abstract
Spontaneous haemoperitoneum (SH) is a rare but life-threatening condition with several well-recognized causes. SH often occurs in anticoagulated patients and requires urgent treatment to prevent mortality. SH is rarely associated with infective endocarditis (IE). To date, there are no reported cases of a haemorrhagic mesenteric abscess causing haemoperitoneum. We present the case of a warfarinized 30-year-old intravenous drug user with IE 2 weeks post-revision of a metallic valve who reported abdominal pain and subsequently suffered haemodynamic collapse. Abdominal computed tomography and damage-control laparotomy revealed haemoperitoneum secondary to an actively bleeding mesenteric nodule which was resected. Histopathology confirmed a haemorrhagic mesenteric abscess representing a rare sequela of IE and a novel cause of SH. Given that the incidence of IE appears to be increasing in people who inject drugs in Australia, the general surgeon should be aware of this clinical entity and the need for urgent intervention to prevent catastrophic sequelae.
A novel soybean malectin-like receptor kinase-encoding gene, GmMLRK1, provides resistance to soybean mosaic virus
Authors: Che Zhijun , Zhang Shuyu , Pu Yixiang , Yang Yuming , Liu Hailun , Yang Hui , Wang Li , Zhang Yuhang , Liu Baohui , Zhang Hengyou , Wang Hui , Cheng Hao , Yu Deyue 
Published: February 2023

Abstract
Soybean mosaic virus (SMV) severely damages soybean [Glycine max (L.) Merr.] yield and seed quality. Moreover, the underlying genetic determinants of resistance to SMV remain largely unknown. Here, we performed a genome-wide association study (GWAS) of SMV resistance in a panel of 219 diverse soybean accessions across four environments and identified a new resistance-related gene, GmMLRK1, at the major resistance locus Rsv4 on chromosome 2. GmMLRK1 encodes a malectin-like receptor kinase (RK) that was induced earlier and to a greater degree in leaves of the SMV-resistant cultivar Kefeng No. 1 than in those of the susceptible cultivar Nannong 1138-2 after inoculation. We demonstrated that soybean plants overexpressing GmMLRK1 show broad-spectrum resistance to both strains SC7 and SC3 on the basis of reduced viral accumulation, increased reactive oxygen species production, and local cell death associated with the hypersensitive response. In contrast, GmMLRK1 knockout mutants were more susceptible to both pathotypes. Haplotype analysis revealed the presence of five haplotypes (H1–H5) within the soybean population, and only H1 provided SMV resistance, which was independent of its tightly linked SMV resistance gene RNase-H at the same locus. These results report a novel gene that adds new understanding of SMV resistance and can be used for breeding resistant soybean accessions.
Tetracycline resistance of Escherichia coli isolated from water, human stool, and fish gills from the Lake Sevan basin
Authors: Pepoyan A Z , Manvelyan A M , Balayan M H , Harutyunyan N A , Tsaturyan V V , Batikyan H , Bren A B , Chistyakov V , Weeks R , Chikindas M L 
Published: February 2023

Abstract
The ecological state of Lake Sevan, the largest drinking water reservoir for the South Caucasus, formed under the influence of climatic and social changes. This study assesses the bacteriological quality of water in the rivers of the Lake Sevan basin and tetracycline-resistant bacteria isolated from fish and people living near the rivers of the Lake Sevan basin in Armenia in autumn 2019 and spring 2020.
No differences have been shown for the tetracycline resistance of the investigated E. coli isolated from the human gut and the Masrik, Argichi, and Gavaraget Rivers. Horizontal gel electrophoresis revealed the same plasmid bands in most of the investigated E. coli with the same tetracycline resistance from the different sources of the Argichi River (obtained from people/fish/water sources where the fish were caught). The results also showed that most of the waters carried Edwardsiella spp., Erwinia spp., Morganella spp., and Proteus spp. in addition to E. coli; the coliform index did not exceed the standard level of 5 × 104 CFU mL-1 there.
These findings highlight the importance of multidisciplinary studies of bacteria from “interacting” ecosystems, which might serve as a basis for the suggestion of microbial antibiotic resistance as another indicator of water pollution.
Qualitative uncertainty and dynamics of argumentation through dynamic logic
Authors: Yuste-Ginel Antonio , Herzig Andreas 
Published: February 2023

AbstractDynamics and uncertainty are essential features of real-life argumentation, and many recent studies have focused on integrating both aspects into Dung’s well-known abstract argumentation frameworks (AFs). This paper proposes a combination of the two lines of research through a well-behaved logical tool: dynamic logic of propositional assignments (DL-PA). Our results show that the main reasoning tasks of virtually all existing formalisms qualitatively representing uncertainty about AFs are encodable in DL-PA. Moreover, the same tool is also useful for capturing dynamic structures, such as control AFs, as well as for developing more refined forms of argumentative communication under uncertainty.