bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic network analysis of environmental and livestock F-type plasmid populations
Authors: Matlock William , Chau Kevin K , AbuOun Manal , Stubberfield Emma , Barker Leanne , Kavanagh James , Pickford Hayleah , Gilson Daniel , Smith Richard P , Gweon H Soon , Hoosdally Sarah J , Swann Jeremy , Sebra Robert , Bailey Mark J , Peto Timothy E A , Crook Derrick W , Anjum Muna F , Read Daniel S , Walker A Sarah , Stoesser Nicole , Shaw Liam P ,   REHAB consortium, AbuOun Manal , Anjum Muna F , Bailey Mark J , Brett H , Bowes Mike J , Chau Kevin K , Crook Derrick W , de Maio Nicola , Duggett Nicholas , Wilson Daniel J , Gilson Daniel , Gweon H Soon , Hubbard Alasdair , Hoosdally Sarah J , Matlock William , Kavanagh James , Jones Hannah , Peto Timothy E A , Read Daniel S , Sebra Robert , Shaw Liam P , Sheppard Anna E , Smith Richard P , Stubberfield Emma , Stoesser Nicole , Swann Jeremy , Walker A Sarah , Woodford Neil 
Published: March 2021

Abstract
F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.
Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline
Authors: Michoud Grégoire , Ngugi David Kamanda , Barozzi Alan , Merlino Giuseppe , Calleja Maria Ll , Delgado-Huertas Antonio , Morán Xosé Anxelu G , Daffonchio Daniele 
Published: March 2021

Abstract
Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean’s interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine–seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.
Antihypertensive treatment guided by genetics: PEARL-HT, the randomized proof-of-concept trial comparing rostafuroxin with losartan
Authors: Citterio Lorena , Bianchi Giuseppe , Scioli Giuseppe A. , Glorioso Nicola , Bigazzi Roberto , Cusi Daniele , Staessen Jan A. , Cavuto Silvio , Ferrandi Mara , Lanzani Chiara , Li Xiaoyi , Lau Lit-Fui , Chiang Chern-En , Wang Tzung-Dau , Wang Kang-Ling , Ferrari Patrizia , Manunta Paolo 
Published: March 2021

AbstractWe compared a standard antihypertensive losartan treatment with a pharmacogenomics-guided rostafuroxin treatment in never-treated Caucasian and Chinese patients with primary hypertension. Rostafuroxin is a digitoxigenin derivative that selectively disrupts the binding to the cSrc-SH2 domain of mutant α-adducin and of the ouabain-activated Na-K pump at 10–11 M. Of 902 patients screened, 172 were enrolled in Italy and 107 in Taiwan. After stratification for country and genetic background, patients were randomized to rostafuroxin or losartan, being the difference in the fall in office systolic blood pressure (OSBP) after 2-month treatment the primary endpoint. Three pharmacogenomic profiles (P) were examined, considering: P1, adding to the gene variants included in the subsequent P2, the variants detected by post-hoc analysis of a previous trial; P2, variants of genes encoding enzymes for endogenous ouabain (EO) synthesis (LSS and HSD3B1), EO transport (MDR1/ABCB1), adducin (ADD1 and ADD3); P3, variants of the LSS gene only. In Caucasians, the group differences (rostafuroxin 50 μg minus losartan 50 mg in OSBP mmHg) were significant both in P2 adjusted for genetic heterogeneity (P2a) and P3 LSS rs2254524 AA [9.8 (0.6–19.0), P = 0.038 and 13.4 (25.4–2.5), P = 0.031, respectively]. In human H295R cells transfected with LSS A and LSS C variants, the EO production was greater in the former (P = 0.038); this difference was abolished by rostafuroxin at 10–11 M. Chinese patients had a similar drop in OSBP to Caucasians with losartan but no change in OSBP with rostafuroxin. These results show that genetics may guide drug treatment for primary hypertension in Caucasians.
sRNAanno—a database repository of uniformly annotated small RNAs in plants
Authors: Chen Chengjie , Li Jiawei , Feng Junting , Liu Bo , Feng Lei , Yu Xiaoling , Li Guanliang , Zhai Jixian , Meyers Blake C. , Xia Rui 
Published: March 2021

AbstractSmall RNAs (sRNAs) are essential regulatory molecules, and there are three major sRNA classes in plants: microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Excluding miRNAs, the other two classes are not well annotated or available in public databases for most sequenced plant genomes. We performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly available. The results are available via an online repository called sRNAanno (www.plantsRNAs.org). Compared with other public plant sRNA databases, we obtained was much more miRNA annotations, which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA annotations. sRNAanno also provides free access to genomic information for >22,721 PHAS loci and >22 million hc-siRNA loci annotated from these 143 plant species. Both miRNA and PHAS loci can be easily browsed to view their main features, and a collection of archetypal trans-acting siRNA 3 (TAS3) genes were annotated separately for quick access. To facilitate the ease of sRNA annotation, sRNAanno provides free service for sRNA annotations to the community. In summary, the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs.
Immunomodulating nano-adaptors potentiate antibody-based cancer immunotherapy
Authors: Jiang Cheng-Tao , Chen Kai-Ge , Liu An , Huang Hua , Fan Ya-Nan , Zhao Dong-Kun , Ye Qian-Ni , Zhang Hou-Bing , Xu Cong-Fei , Shen Song , Xiong Meng-Hua , Du Jin-Zhi , Yang Xian-Zhu , Wang Jun 
Published: March 2021

AbstractModulating effector immune cells via monoclonal antibodies (mAbs) and facilitating the co-engagement of T cells and tumor cells via chimeric antigen receptor- T cells or bispecific T cell-engaging antibodies are two typical cancer immunotherapy approaches. We speculated that immobilizing two types of mAbs against effector cells and tumor cells on a single nanoparticle could integrate the functions of these two approaches, as the engineered formulation (immunomodulating nano-adaptor, imNA) could potentially associate with both cells and bridge them together like an ‘adaptor’ while maintaining the immunomodulatory properties of the parental mAbs. However, existing mAbs-immobilization strategies mainly rely on a chemical reaction, a process that is rough and difficult to control. Here, we build up a versatile antibody immobilization platform by conjugating anti-IgG (Fc specific) antibody (αFc) onto the nanoparticle surface (αFc-NP), and confirm that αFc-NP could conveniently and efficiently immobilize two types of mAbs through Fc-specific noncovalent interactions to form imNAs. Finally, we validate the superiority of imNAs over the mixture of parental mAbs in T cell-, natural killer cell- and macrophage-mediated antitumor immune responses in multiple murine tumor models.
Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm
Authors: Sun Yu H. , Wang Anqi , Song Chi , Shankar Goutham , Srivastava Rajesh K. , Au Kin Fai , Li Xin Zhiguo 
Published: March 2021

AbstractSperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs, has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). We identify 3440 spiRNA species in mice and 4100 in humans. The spiRNA profile consists of both mRNAs and long non-coding RNAs, is evolutionarily conserved between mice and humans, and displays an enrichment in mRNAs encoding for ribosome. In sum, we characterize the landscape of intact long RNAs in sperm, paving the way for future studies on their biogenesis and functions. Our experimental and bioinformatics approaches can be applied to other tissues and organisms to detect intact transcripts.
Rational design of isostructural 2D porphyrin-based covalent organic frameworks for tunable photocatalytic hydrogen evolution
Authors: Chen Rufan , Wang Yang , Ma Yuan , Mal Arindam , Gao Xiao-Ya , Gao Lei , Qiao Lijie , Li Xu-Bing , Wu Li-Zhu , Wang Cheng 
Published: March 2021

AbstractCovalent organic frameworks have recently gained increasing attention in photocatalytic hydrogen generation from water. However, their structure-property-activity relationship, which should be beneficial for the structural design, is still far-away explored. Herein, we report the designed synthesis of four isostructural porphyrinic two-dimensional covalent organic frameworks (MPor-DETH-COF, M = H2, Co, Ni, Zn) and their photocatalytic activity in hydrogen generation. Our results clearly show that all four covalent organic frameworks adopt AA stacking structures, with high crystallinity and large surface area. Interestingly, the incorporation of different transition metals into the porphyrin rings can rationally tune the photocatalytic hydrogen evolution rate of corresponding covalent organic frameworks, with the order of CoPor-DETH-COF < H2Por-DETH-COF < NiPor-DETH-COF < ZnPor-DETH-COF. Based on the detailed experiments and calculations, this tunable performance can be mainly explained by their tailored charge-carrier dynamics via molecular engineering. This study not only represents a simple and effective way for efficient tuning of the photocatalytic hydrogen evolution activities of covalent organic frameworks at molecular level, but also provides valuable insight on the structure design of covalent organic frameworks for better photocatalysis.
Transcription organizes euchromatin via microphase separation
Authors: Hilbert Lennart , Sato Yuko , Kuznetsova Ksenia , Bianucci Tommaso , Kimura Hiroshi , Jülicher Frank , Honigmann Alf , Zaburdaev Vasily , Vastenhouw Nadine L. 
Published: March 2021

AbstractIn eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. Euchromatin, which is permissive for transcription, is spatially organized into transcriptionally inactive domains interspersed with pockets of transcriptional activity. While transcription and RNA have been implicated in euchromatin organization, it remains unclear how their interplay forms and maintains transcription pockets. Here we combine theory and experiment to analyze the dynamics of euchromatin organization as pluripotent zebrafish cells exit mitosis and begin transcription. We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. We propose that the accumulating RNA recruits RNA-binding proteins that together tend to separate from transcriptionally inactive euchromatin. Full phase separation is prevented because RNA remains tethered to transcribed euchromatin through RNA polymerases. Instead, smaller scale microphases emerge that do not grow further and form the typical pattern of euchromatin organization.
Structure of mammalian Mediator complex reveals Tail module architecture and interaction with a conserved core
Authors: Zhao Haiyan , Young Natalie , Kalchschmidt Jens , Lieberman Jenna , El Khattabi Laila , Casellas Rafael , Asturias Francisco J. 
Published: March 2021

AbstractThe Mediator complex plays an essential and multi-faceted role in regulation of RNA polymerase II transcription in all eukaryotes. Structural analysis of yeast Mediator has provided an understanding of the conserved core of the complex and its interaction with RNA polymerase II but failed to reveal the structure of the Tail module that contains most subunits targeted by activators and repressors. Here we present a molecular model of mammalian (Mus musculus) Mediator, derived from a 4.0 Å resolution cryo-EM map of the complex. The mammalian Mediator structure reveals that the previously unresolved Tail module, which includes a number of metazoan specific subunits, interacts extensively with core Mediator and has the potential to influence its conformation and interactions.
Photoresponsive supramolecular coordination polyelectrolyte as smart anticounterfeiting inks
Authors: Li Zhiqiang , Liu Xiao , Wang Guannan , Li Bin , Chen Hongzhong , Li Huanrong , Zhao Yanli 
Published: March 2021

AbstractWhile photoluminescence printing is a widely applied anticounterfeiting technique, there are still challenges in developing new generation anticounterfeiting materials with high security. Here we report the construction of a photoresponsive supramolecular coordination polyelectrolyte (SCP) through hierarchical self-assembly of lanthanide ion, bis-ligand and diarylethene unit, driven by metal-ligand coordination and ionic interaction. Owing to the conformation-dependent photochromic fluorescence resonance energy transfer between the lanthanide donor and diarylethene acceptor, the ring-closure/ring-opening isomerization of the diarylethene unit leads to a photoreversible luminescence on/off switch in the SCP. The SCP is then utilized as security ink to print various patterns, through which photoreversible multiple information patterns with visible/invisible transformations are realized by simply alternating the irradiation with UV and visible light. This work demonstrates the possibility of developing a new class of smart anticounterfeiting materials, which could be operated in a noninvasive manner with a higher level of security.
Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes
Authors: Ansai Satoshi , Mochida Koji , Fujimoto Shingo , Mokodongan Daniel F. , Sumarto Bayu Kreshna Adhitya , Masengi Kawilarang W. A. , Hadiaty Renny K. , Nagano Atsushi J. , Toyoda Atsushi , Naruse Kiyoshi , Yamahira Kazunori , Kitano Jun 
Published: March 2021

AbstractSexual selection drives rapid phenotypic diversification of mating traits. However, we know little about the causative genes underlying divergence in sexually selected traits. Here, we investigate the genetic basis of male mating trait diversification in the medaka fishes (genusOryzias) from Sulawesi, Indonesia. Using linkage mapping, transcriptome analysis, and genome editing, we identifycsf1as a causative gene for red pectoral fins that are unique to maleOryzias woworae. Acis-regulatory mutation enables androgen-induced expression ofcsf1in male fins.csf1-knockout males have reduced red coloration and require longer for mating, suggesting that coloration can contribute to male reproductive success. Contrary to expectations, non-red males are more attractive to a predatory fish than are red males. Our results demonstrate that integrating genomics with genome editing enables us to identify causative genes underlying sexually selected traits and provides a new avenue for testing theories of sexual selection.
Effects of obesity on breast aromatase expression and systemic metabo-inflammation in women with BRCA1 or BRCA2 mutations
Authors: Iyengar Neil M. , Zhou Xi Kathy , Mendieta Hillary , El-Hely Omar , Giri Dilip D. , Winston Lisle , Falcone Domenick J. , Wang Hanhan , Meng Lingsong , Ha Taehoon , Pollak Michael , Morrow Monica , Dannenberg Andrew J. 
Published: March 2021

AbstractObesity is associated with an increased risk of breast cancer in post-menopausal women and decreased risk in pre-menopausal women. Conversely, in BRCA1/2 mutation carriers, pre-menopausal obesity is associated with early-onset breast cancer. Here we show that obese, pre-menopausal BRCA1/2 mutation carriers have increased levels of aromatase and inflammation in the breast, as occurs in post-menopausal women. In a prospective cohort study of 141 women with germline BRCA1 (n = 74) or BRCA2 (n = 67) mutations, leptin, and aromatase expression were higher in the breast tissue of obese versus lean individuals (P < 0.05). Obesity was associated with breast white adipose tissue inflammation, which correlated with breast aromatase levels (P < 0.01). Circulating C-reactive protein, interleukin-6, and leptin positively correlated with body mass index and breast aromatase levels, whereas negative correlations were observed for adiponectin and sex hormone-binding globulin (P < 0.05). These findings could help explain the increased risk of early-onset breast cancer in obese BRCA1/2 mutation carriers.
Lymphovascular invasion, race, and the 21-gene recurrence score in early estrogen receptor-positive breast cancer
Authors: Makower Della , Lin Juan , Xue Xiaonan , Sparano Joseph A. 
Published: March 2021

AbstractLymphovascular invasion (LVI) and Black race are associated with poorer prognosis in early breast cancer (EBC). We evaluated the association between LVI and race, and whether LVI adds prognostic benefit to the 21-gene recurrence score (RS) in EBC. Women with ER+ HER2− EBC measuring up to 5 cm, with 0–3 involved axillary nodes, diagnosed between 1 January 2010 and 1 January 2014, who underwent surgery as first treatment and had available RS, were identified in the NCDB database. Bivariate associations between two categorical variables were examined using chi-square test. Multivariate Cox proportional hazards model were used to assess the association of LVI, race, and other covariates with overall survival (OS). 77,425 women, 65,018 node-negative (N0), and 12,407 with 1–3 positive (N+) nodes, were included. LVI was present in 12.7%, and associated with poor grade, RS 26–100, and N+ (all p < 0.0001), but not Black race. In multivariate analysis, LVI was associated with worse OS in N0 [HR 1.37 (95% CI 1.27, 1.57], but not N+ EBC. LVI was associated with worse OS in N0 patients with RS 11–25 [HR 1.31 (95% CI 1.09, 1.57)] and ≥26 [HR 1.58 (95% CI 1.30, 1.93)], but not RS 0–10. No interaction between LVI and chemotherapy benefit was seen. Black race was associated with worse OS in N0 (HR 1.21, p = 0.009) and N+ (HR 1.37, p = 0.015) disease. LVI adds prognostic information in ER+, HER2−, N0 BCA with RS 11–100, but does not predict chemotherapy benefit. Black race is associated with worse OS, but not LVI.
High-power amplified spontaneous emission pulses with tunable coherence for efficient non-linear processes
Authors: Valero Nicolas , Marion Denis , Lhermite Jerome , Delagnes Jean-Christophe , Renard William , Royon Romain , Cormier Eric 
Published: March 2021

AbstractWe report on a detailed study of an amplified spontaneous emission source operated in a pulsed regime with particular attention paid to the influence of high-intensity chaotic temporal events on the generation of nonlinear processes. To this aim, we have developed a monolithic high-power fiber system delivering partially coherent pulses of adjustable coherence. We also have demonstrated a non-linear method to characterize the stochastic properties of the source mitigating the bandwidth limitation of linear techniques. Measured parameters of the source for various configurations are presented. An enhanced classical model has been established to reproduce the statistical properties of the source and predict the behaviour when exciting non-linear processes. Finally, a non-linear process (second harmonic generation) is investigated comparing the efficiency when the process is pumped by a pulsed beam with maximal and low coherence.
Gas chromatography techniques to evaluate the hydrogen permeation characteristics in rubber: ethylene propylene diene monomer
Authors: Jung Jae Kap , Kim In Gyoo , Chung Ki Soo , Baek Un Bong 
Published: March 2021

AbstractWe established an ex-situ technique for evaluating hydrogen gas permeability by thermal desorption analysis (TDA) gas chromatography (GC) and by self-developed diffusion analysis software. Absorbed hydrogen mass in rubber, related to the GC-peak area, is recorded as a function of elapsed time after decompressing the hydrogen under high-pressure. From the charging amount (CH0) and diffusivity (D) obtained by the developed diffusion analysis program, the solubility(S) and permeability(P) is evaluated via Henry’s law and P = SD, respectively. The techniques were applied to ethylene propylene diene monomer (EPDM) rubber, sealing material candidates in hydrogen infrastructures. EPDM sample mixed with carbon black fillers showed dual hydrogen diffusion behaviors, whereas EPDM sample without carbon black showed a single hydrogen diffusion behavior. There was no appreciable pressure or size dependence on D, S and P. P are consistent with that measured by different researcher within the expanded uncertainty.