bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo assembling a high-quality genome sequence of Amur grape (Vitis amurensis Rupr.) gives insight into Vitis divergence and sex determination
Authors: Wang Pengfei , Meng Fanbo , Yang Yiming , Ding Tingting , Liu Huiping , Wang Fengxia , Li Ao , Zhang Qingtian , Li Ke , Fan Shutian , Li Bo , Ma Zhiyao , Zhang Tianhao , Zhou Yongfeng , Zhao Hongjun , Wang Xiyin 
Published: April 2024

Abstract
To date, there has been no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding efforts to improve grape cultivars. This study presents ~522 Mb of the Vitis amurensis (Va) genome sequence containing 27 635 coding genes. Phylogenetic analysis indicated that Vitis riparia (Vr) may have first split from the other two species, Va and Vitis vinifera (Vv). Divergent numbers of duplicated genes reserved among grapes suggests that the core eudicot-common hexaploidy (ECH) and the subsequent genome instability still play a non-negligible role in species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in Va, resulting in a more robust network of regulatory cold resistance genes, explaining why it is extremely cold-tolerant compared with Vv and Vr. In contrast, Va has preserved many fewer nucleotide binding site (NBS) disease resistance genes than the other grapes. Notably, multi-omics analysis identified one trans-cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during Va berry development. A selective sweep analysis revealed a hypothetical Va sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related to sex determination in Va. The content and arrangement order of genes in the putative SDR of female Va were similar to those of female Vv. However, the putative SDR of female Va has lost one flavin-containing monooxygenase (FMO) gene and contains one extra protein-coding gene uncharacterized so far. These findings will improve the understanding of Vitis biology and contribute to the improvement of grape breeding.
A Generalization of Operads Based on Subgraph Contractions
Authors: Lyskov Denis 
Published: April 2024

Abstract
We introduce a generalization of the notion of operad that we call a contractad, whose set of operations is indexed by connected graphs and whose composition rules are numbered by contractions of connected subgraphs. We show that many classical operads, such as the operad of commutative algebras, Lie algebras, associative algebras, pre-Lie algebras, the little disks operad, and the operad of moduli spaces of stable curves $\operatorname{\overline{{\mathcal{M}}}}_{0,n+1}$, admit generalizations to contractads. We explain that standard tools like Koszul duality and the machinery of Gröbner bases can be easily generalized to contractads. We verify the Koszul property of the commutative, Lie, associative, and Gerstenhaber contractads.
The Genetic Diversity of Nipah Virus Across Spatial Scales
Authors: Cortes-Azuero Oscar , Lefrancq Noémie , Nikolay Birgit , McKee Clifton , Cappelle Julien , Hul Vibol , Ou Tey Putita , Hoem Thavry , Lemey Philippe , Rahman Mohammed Ziaur , Islam Ausraful , Gurley Emily S , Duong Veasna , Salje Henrik 
Published: April 2024

Abstract

Background
Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity.

Methods
We develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N = 257, 175 from bats, 73 from humans) from 6 countries over 22 years (1999–2020). We divide the 4 major NiV sublineages into 15 genetic clusters. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate the presence and the average size of genetic clusters per area.

Results
We find that, within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1500–2000 km2. We estimate that each genetic cluster occupies an average area of 1.3 million km2 (95% confidence interval [CI], .6–2.3 million km2), with 14 clusters in an area of 100 000 km2 (95% CI, 6–24 km2). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only approximately 15% of overall NiV diversity has been uncovered.

Conclusions
Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales.
Determining the prevalence of Escherichia coli, Salmonella, and shiga toxin-producing Escherichia coli in manure of dairy lagoons
Authors: Pandey Prachi , Gaa Megan Elise , Huo Jiang , Okada Yu , Lee Katie Yen , Giat Sharon , Li Xunde , Zhang Ruihong , Pandey Pramod 
Published: April 2024

Abstract

Aim
The aim of this study was to determine the prevalence of microbial pathogens in manure of dairy lagoons in California.

Methods and results
To determine pathogens in dairy manure stored in anaerobic lagoons of dairy farm, an extensive field study was conducted across California to sample manure from 20 dairy farms. Samples were analyzed to determine the prevalence of indicator Escherichia coli, Shiga toxin producing E. coli (STEC), Salmonella, and E. coli O157: H7. To test the E. coli, STEC, and Salmonella, we used agar culture-based method followed by polymerase chain reaction (PCR) method. In addition, a real- time PCR based method was used to determine the presence of E coli O157: H7. Study demonstrated that the prevalence of Salmonella in manure sample is lower than E. coli. The presence of Salmonella was found in 2.26% of the samples, and both the culture-based and PCR methods yielded comparable outcomes in detecting Salmonella. Moreover, ∼11.30% of the total samples out of the 177 were identified as positive for STEC by qPCR.

Conclusion
These findings demonstrate that indicator E. coli are abundantly present in anaerobic lagoons. However, the presence of STEC, and Salmonella is substantially low.
K1 capsule-dependent phage-driven evolution in Escherichia coli leading to phage resistance and biofilm production
Authors: Antoine Céline , Laforêt Fanny , Fall Abdoulaye , Blasdel Bob , Delcenserie Véronique , Thiry Damien 
Published: April 2024

Abstract

Aims
Understanding bacterial phage resistance mechanisms has implications for developing phage-based therapies. This study aimed to explore the development of phage resistance in Escherichia coli K1 isolates’ to K1-ULINTec4, a K1-dependent bacteriophage.

Methods and results
Resistant colonies were isolated from two different strains (APEC 45 and C5), both previously exposed to K1-ULINTec4. Genome analysis and several parameters were assessed, including growth capacity, phage adsorption, phenotypic impact at capsular level, biofilm production, and virulence in the in vivo Galleria mellonella larvae model. One out of the six resistant isolates exhibited a significantly slower growth rate, suggesting the presence of a resistance mechanism altering its fitness. Comparative genomic analysis revealed insertion sequences in the region 2 of the kps gene cluster involved in the capsule biosynthesis. In addition, an immunoassay targeting the K1 capsule showed a very low positive reaction compared to the control. Nevertheless, microscopic images of resistant strains revealed the presence of capsules with a clustered organization of bacterial cells and biofilm assessment showed an increased biofilm production compared to the sensitive strains. In the G. mellonella model, larvae infected with phage-resistant isolates showed better survival rates than larvae infected with phage-sensitive strains.

Conclusions
A phage resistance mechanism was identified at the genomic level and had a negative impact on the K1 capsule production. The resistant isolates showed an increased biofilm production and a decreased virulence in vivo.
Zearalenone exposure differentially affects the ovarian proteome in pre-pubertal gilts during thermal neutral and heat stress conditions
Authors: Roach Crystal M , Mayorga Edith J , Baumgard Lance H , Ross Jason W , Keating Aileen F 
Published: April 2024

Abstract
Zearalenone (ZEN), a nonsteroidal estrogenic mycotoxin, causes endocrine disruption and porcine reproductive dysfunction. Heat stress (HS) occurs when exogenous and metabolic heat accumulation exceeds heat dissipation. Independently, HS and ZEN both compromise swine reproduction; thus, the hypothesis investigated was two-pronged: that ZEN exposure would alter the ovarian proteome and that these effects would differ in thermal neutral (TN) and HS pigs. Pre-pubertal gilts (n = 38) were fed ad libitum and assigned to either (TN: 21.0 ± 0.1 °C) or HS (12 h cyclic temperatures of 35.0 ± 0.2 °C and 32.2 ± 0.1 °C). Within the TN group, a subset of pigs were pair-fed (PF) to the amount of feed that the HS gilts consumed to eliminate the confounding effects of dissimilar nutrient intake. All gilts orally received a vehicle control (CT) or ZEN (40 μg/kg/BW) resulting in six treatment groups: thermoneutral (TN) vehicle control (TC; n = 6); TN ZEN (TZ; n = 6); PF vehicle control (PC; n = 6); PF ZEN (PZ; n = 6); HS vehicle control (HC; n = 7); or HS ZEN (HZ; n = 7) for 7 d. When compared to the TC pigs, TZ pigs had 45 increased and 39 decreased proteins (P ≤ 0.05). In the HZ pigs, 47 proteins were increased and 61 were decreased (P ≤ 0.05). Exposure to ZEN during TN conditions altered sec61 translocon complex (40%), rough endoplasmic reticulum membrane (8.2%), and proteasome complex (5.4%), asparagine metabolic process (0.60%), aspartate family amino acid metabolic process (0.14%), and cellular amide metabolic process (0.02%) pathways. During HS, ZEN affected cellular pathways associated with proteasome core complex alpha subunit complex (0.23%), fibrillar collagen trimer (0.14%), proteasome complex (0.05%), and spliceosomal complex (0.03%). Thus, these data identify ovarian pathways altered by ZEN exposure and suggest that the molecular targets of ZEN differ in TN and HS pigs.
‘Now completely Americanized’: Collecting and transatlantic exchange of the Lansdowne Marbles
Authors: Cochrane Nicole 
Published: April 2024

Abstract
This article examines the sale in 1930 by Christie’s of the collection of ancient marbles formerly belonging to William Petty-Fitzmaurice, 1st Marquess of Lansdowne, and the role that the auction played in the transatlantic trade in antiquities between Britain and the United States in the early twentieth century. It examines how provenance and collecting histories, and the prestige engendered by owning antiquities from a notable collection, became an important marker of taste and desirability for American collectors.
Feasibility and effectiveness of preconception check-ups at workplaces in Japan
Authors: Fujishima Akiko , Maeda Eri , Sato Koki , Saito Hidekazu , Ozeki Chihiro , Terada Yukihiro 
Published: April 2024

Abstract

Objectives
Despite the recent increase in infertility and perinatal complications, preconception care is not commonly available in Japan. Working women are considered to have the greatest need for preconception care, as increasingly they marry and have children later in life. This study aimed to assess the feasibility and effectiveness of preconception check-ups in the workplace.

Methods
We provided 51 female employees aged 18-39 years with free preconception check-ups, including additional blood tests and an online medical questionnaire, during mandatory health check-ups at their workplace. A doctor provided online counseling based on the check-up results. We assessed fertility knowledge using the Cardiff Fertility Knowledge Scale (CFKS-J) and childbearing desire pre- and postintervention.

Results
Preconception check-ups revealed various potential risk factors for future pregnancies, including underweight (12%), obesity (20%), Chlamydia trachomatis IgG antibody positivity (22%), low rubella IgG antibody levels (47%), iron deficiency (12%), and 25-hydroxyvitamin D levels &lt;30 ng/mL (98%). Postintervention, the participants reported high satisfaction with the check-ups and significantly advanced their reproductive plans (P = .008). Furthermore, 95% of the participants indicated an intention to seek medical attention or make lifestyle changes. The postintervention CFKS-J score (mean [SD]) was higher than the preintervention score (71.7 [19.3] vs 63.0 [22.0]; P = .006).

Conclusions
We developed a preconception check-up package that can be integrated into workplace health examinations, complemented by tailored counseling. This novel check-up package is a feasible and effective approach for improving preconception health and fertility awareness.
Quanzhen Yiqi decoction attenuates inflammation in mice with smoking-induced COPD by activating the Nrf2/HO-1 pathway and inhibiting the NLRP3 inflammasome
Authors: Zeng Jiamin , Li Zhenqiu , Li Wanyan , Liang Zhu , Luo Yuewen , Li Caiping , Liao Sida , Wang Kexin , Hu Yuanlong , Li Yuanyuan , Liang Qiuling , Lu Wenju , Li Lu , Wu Zhijuan , Zhang Dapeng , Zhang Zhimin 
Published: April 2024

Abstract

Objective
Quanzhen Yiqi decoction (QZYQ) is a traditional Chinese medicine for treating chronic obstructive pulmonary disease.

Methods
Mice were exposed to cigarette smoke (CS) 6 days/week (40 cigarettes/day) for 24 weeks and then intragastrically administered QZYQ (4.72, 9.45, or 18.89 g/kg) or dexamethasone (DEX, 0.6 mg/kg) for 6 weeks. We examined the lung function and collected bronchoalveolar lavage fluid for inflammatory cell and cytokine quantification. The pathological lung changes, ROS and oxidative biomarkers were measured. We used immunohistochemistry and western blotting to evaluate the levels of Nrf2/HO-1, NLRP3/ASC/Caspase1/IL-1β/IL-18.

Results
The CS group showed significant increases in the forced vital capacity, lung resistance, and chord compliance and a lower FEV50/FVC compared with the control, and QZYQ improved these changes. In addition, QZYQ effectively reduced emphysema, immune cell infiltration, and airway remodeling. QZYQ stimulated HO-1 expression and reduced oxidative stress through the Nrf2 pathway. QZYQ inhibited the production of NLRP3/ASC/Caspase-1 to inhibit IL-1β and IL-18.

Conclusion
Our study suggested that QZYQ can improve the function and histology of the lungs and reduce inflammatory cell recruitment. QZYQ inhibits ROS production and NLRP3 inflammasome activation by upregulating Nrf2 to reduce lung injury. The anti-inflammatory effects of QZYQ are similar to those of DEX.
Redox regulation of meristem quiescence: outside/in
Authors: Considine Michael J , Foyer Christine H 
Published: April 2024

Abstract
Quiescence is an essential property of meristematic cells, which restrains the cell cycle while retaining the capacity to divide. This crucial process not only facilitates life-long tissue homeostasis and regenerative capacity but also provides protection against adverse environmental conditions, enabling cells to conserve the proliferative potency while minimizing DNA damage. As a survival attribute, quiescence is inherently regulated by the products of aerobic life, in particular reactive oxygen species (ROS) and the redox (reduction/oxidation) mechanisms that plant have evolved to channel these into pervasive signals. Adaptive responses allow quiescent cells to compensate for reduced oxygen tension (hypoxia) in a reversible manner, while the regulated production of the superoxide anion (O2·−) facilitates cell division and the maintenance of stem cells. Here we discuss the role of ROS and redox reactions in the control of the quiescent state in plant meristems, and how this process is integrated with cellular energy and hormone biochemistry. We consider the pathways that sense and transmit redox signals with a focus on the central significance of redox regulation in the mitochondria and nucleus, which is a major regulator of quiescence in meristems. We discuss recent studies that suggest that ROS are a critical component of the feedback loops that control stem cell identity and fate, and suggest that the ROS/hypoxia interface is an important ‘outside/in’ positional cue for plant cells, particularly in meristems.
Mitochondrial transplantation for the treatment of cardiac and noncardiac diseases: mechanisms, prospective, and challenges
Authors: Wang Xinyi , Liu Zhiyuan , Zhang Ling , Hu Guangyu , Tao Ling , Zhang Fuyang 
Published: April 2024

Abstract
Mitochondrial transplantation (MT) is a promising therapeutic strategy that involves introducing healthy mitochondria into damaged tissues to restore cellular function. This approach has shown promise in treating cardiac diseases, such as ischemia-reperfusion injury, myocardial infarction, and heart failure, where mitochondrial dysfunction plays a crucial role. Transplanting healthy mitochondria into affected cardiac tissue has resulted in improved cardiac function, reduced infract size, and enhanced cell survival in preclinical studies. Beyond cardiac applications, MT is also being explored for its potential to address various noncardiac diseases, including stroke, infertility, and genetic mitochondrial disorders. Ongoing research focused on refining techniques for mitochondrial isolation, preservation, and targeted delivery is bolstering the prospects of MT as a clinical therapy. As the scientific community gains a deeper understanding of mitochondrial dynamics and pathology, the development of MT as a clinical therapy holds significant promise. This review provides an overview of recent research on MT and discusses the methodologies involved, including sources, isolation, delivery, internalization, and distribution of mitochondria. Additionally, it explores the effects of MT and potential mechanisms in cardiac diseases, as well as non-cardiac diseases. Future prospects for MT are also discussed.
‘Formalistic Freaks in Music’: ‘Ilya Golovin’, Shostakovich, and Zhdanovshchina for the Masses
Authors: Elphick Daniel 
Published: April 2024

ABSTRACT
Amidst all the art, literature, music, and theatre of the ‘Zhdanovshchina’ (the post-war Soviet intervention in arts policy), one play stands out: Sergei Mikhalkov’s Ilya Golovin. In this play, a leading Soviet composer is chastised for his formalism but sees the error of his ways and again writes music of sufficiently socialist character. Ilya Golovin is noteworthy not just because it presents a crude parody of Shostakovich and his music, but because it reveals the wider context of the ideological campaign against artists and shows us something of how different artists responded. In this article, I argue that Ilya Golovin is not simply a bizarre example of multiple artists toeing the ideological line: instead it reveals the uglier side of late Stalinism in the form of vehement anti-Semitism, as well as demonstrating the xenophobic Cold War patriotism that served as the ultimate motivation behind the Zhdanovshchina itself.
Cosmological prediction of the CSST Ultra Deep Field Type Ia supernova photometric survey
Authors: Wang Minglin , Gong Yan , Deng Furen , Miao Haitao , Chen Xuelei , Zhan Hu 
Published: April 2024

ABSTRACT
Type Ia supernova (SN Ia) as a standard candle is an ideal tool to measure cosmic distance and expansion history of the Universe. Here, we investigate the SN Ia photometric measurement in the China Space Station Telescope Ultra Deep Field (CSST-UDF) survey, and study the constraint power on the cosmological parameters, such as the equation of state of dark energy. The CSST-UDF survey is expected to cover a 9 deg2 sky area in 2 yr with 250 s × 60 exposures for each band. The magnitude limit can reach i ≃ 26 AB mag for 5σ point source detection with a single exposure. We generate light-curve mock data for SNe Ia and different types of core-collapse SNe (CCSNe). sncosmo is chosen as the framework by utilizing the salt3 model to simulate SN Ia data. After selecting high-quality data and fitting the light curves, we derive the light-curve parameters and identify CCSNe as contamination, resulting in ∼2200 SNe with an $\sim\!\! 7{{\ \rm per\, cent}}$ CCSN contamination rate. We adopt a calibration method similar to Chauvenet’s criterion, and apply it to the distance modulus data to further reduce the contamination. We find that this method is effective and can suppress the contamination fraction to $\sim\!\! 3.5{{\ \rm per\, cent}}$ with 2012 SNe Ia and 73 CCSNe. In the cosmological fitting stage, we did not distinguish between SNe Ia and CCSNe. We find that the constraint accuracies on ΩM, ΩΛ, and w are about two times better than the current SN surveys, and they could be further improved by a factor of ∼1.4 if including the baryon acoustic oscillation data from the CSST spectroscopic wide-field galaxy survey.
Constraints on cosmological models from quasars calibrated with type Ia supernova by a Gaussian process
Authors: Zhang Haixiang , Liu Yang , Yu Hongwei , Nong Xiaodong , Liang Nan , Wu Puxun 
Published: April 2024

ABSTRACT
In this paper, we use quasars calibrated from type Ia supernova (SN Ia) to constrain cosmological models. We consider three different X-ray luminosity (LX)–ultraviolet luminosity (LUV) relations of quasars, i.e. the standard LX–LUV relation and two redshift–evolutionary relations (Type I and Type II), respectively, constructed from copula and considering a redshift correction to the luminosity of quasars. Only in the case of the Type I relation, quasars can always provide effective constraints on the ΛCDM (cosmological constant Λ plus cold dark matter) model. Furthermore, we show that, when the observational Hubble data (OHD) are added, the constraints on the absolute magnitude M of SN Ia and the Hubble constant H0 can be obtained. In the ΛCDM model, the OHD measurements plus quasars with the Type I relation yields M = $-19.321^{+0.085}_{-0.076}$, which is in good agreement with the measurement from SH0ES (M = −19.253 ± 0.027), and H0 = $70.80\pm 3.6~\mathrm{km~s^{-1}\, Mpc^{-1}}$, falling between the measurements from SH0ES and the Planck cosmic microwave background radiation data.
Mapper of the IGM spin temperature: instrument overview
Authors: Monsalve R A , Altamirano C , Bidula V , Bustos R , Bye C H , Chiang H C , Díaz M , Fernández B , Guo X , Hendricksen I , Hornecker E , Lucero F , Mani H , McGee F , Mena F P , Pessôa M , Prabhakar G , Restrepo O , Sievers J L , Thyagarajan N 
Published: April 2024

ABSTRACT
The observation of the global 21 cm signal produced by neutral hydrogen gas in the intergalactic medium (IGM) during the Dark Ages, Cosmic Dawn, and Epoch of Reionization requires measurements with extremely well-calibrated wideband radiometers. We describe the design and characterization of the Mapper of the IGM Spin Temperature (MIST), which is a new ground-based, single-antenna, global 21 cm experiment. The design of MIST was guided by the objectives of avoiding systematics from an antenna ground plane and cables around the antenna, as well as maximizing the instrument’s on-sky efficiency and portability for operations at remote sites. We have built two MIST instruments, which observe in the range 25–105 MHz. For the 21 cm signal, this frequency range approximately corresponds to redshifts 55.5 &gt; z &gt; 12.5, encompassing the Dark Ages and Cosmic Dawn. The MIST antenna is a horizontal blade dipole of 2.42 m in length, 60 cm in width, and 52 cm in height above the ground. This antenna operates without a metal ground plane. The instruments run on 12 V batteries and have a maximum power consumption of 17 W. The batteries and electronics are contained in a single receiver box located under the antenna. We present the characterization of the instruments using electromagnetic simulations and lab measurements. We also show sample sky measurements from recent observations at remote sites in California, Nevada, and the Canadian High Arctic. These measurements indicate that the instruments perform as expected. Detailed analyses of the sky measurements are left for future work.