bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequencing of
Agrobacterium leguminum
strain EL101 isolated from
Khaya senegalensis
tree bark using nanopore technology
Authors: Toh Wai Keat , Gan Han Ming , Wong Hann Ling 
Published: June 2024

ABSTRACT

We report the complete genome sequence of
Agrobacterium leguminum
strain EL101, isolated from the tree bark of
Khaya senegalensis
in Kampar, Perak, Malaysia, obtained using Q20+ Nanopore Sequencing chemistry. The assembled genome has a total length of 5,324,685 bp, comprising a circular chromosome, a linear chromid, and two non-Ti circular plasmids.
Identification of the global regulatory roles of RraA via the integrative transcriptome and proteome in
Vibrio alginolyticus
Authors: Chen Huizhen , Gao Qian , Liu Bing , Zhang Ying , Fang Jianxiang , Wang Songbiao , Chen Youqi , Chen Chang 
Published: June 2024

ABSTRACT

Bacterial ribonuclease E (RNase E) is vital for posttranscriptional regulation by degrading and processing RNA. The RraA protein inhibits RNase E activity through protein-protein interactions, exerting a global regulatory effect on gene expression. However, the specific role of RraA remains unclear. In this study, we investigated
rraA
expression in
Vibrio alginolyticus
ZJ-T and identified three promoters responsible for its expression, resulting in transcripts with varying 5′-UTR lengths. During the stationary phase,
rraA
was significantly posttranscriptionally inhibited. Deletion of
rraA
had no impact on bacterial growth in rich medium Luria-Bertani broth with salt (LBS) but resulted in decreased biofilm formation and increased resistance to polymyxin B. Transcriptome analysis revealed 350 differentially expressed genes (DEGs) between the wild type and the
rraA
mutant, while proteome analysis identified 267 differentially expressed proteins (DEPs). Integrative analysis identified 55 genes common to both DEGs and DEPs, suggesting that RraA primarily affects gene expression at the posttranscriptional level. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis demonstrated that RraA facilitates the conversion of fatty acids, propionic acid, and branched-chain amino acids to acetyl-CoA while enhancing amino acid and peptide uptake. Notably, RraA positively regulates the expression of virulence-associated genes, including those involved in biofilm formation and the type VI secretion system. This study expands the understanding of the regulatory network of RraA through transcriptome analysis, emphasizing the importance of proteomic analysis in investigating posttranscriptional regulation.

IMPORTANCE

RraA is an inhibitor protein of ribonuclease E that interacts with and suppresses its endonucleolytic activity, thereby playing a widespread regulatory role in the degradation and maturation of diverse mRNAs and noncoding small RNAs. However, the physiological functions and associated regulon of RraA in
Vibrio alginolyticus
have not been fully elucidated. Here, we report that RraA impacts virulence-associated physiological processes, namely, antibiotic resistance and biofilm formation, in
V. alginolyticus
. By conducting an integrative analysis of both the transcriptome and proteome, we revealed the involvement of RraA in carbon metabolism, amino acid catabolism, and transport, as well as in the type VI secretion system. Collectively, these findings elucidate the regulatory influence of RraA on multiple pathways associated with metabolism and pathogenesis in
V. alginolyticus
.
Phase variable colony variants are conserved across
Gardnerella
spp. and exhibit different virulence-associated phenotypes
Authors: Garcia Erin M. , Klimowicz Amy K. , Edupuganti Laahirie , Topf Madeline A. , Bhide Shraddha R. , Slusser Dawson J. , Leib Samantha M. , Coddington Cayden L. , Matveyev Andrey , Buck Gregory A. , Jefferson Kimberly K. , Pepperell Caitlin S. , Dillard Joseph P. 
Published: June 2024

ABSTRACT

The
Gardnerella
genus, comprising at least 13 species, is associated with the polymicrobial disorder bacterial vaginosis (BV). However, the details of BV pathogenesis are poorly defined, and the contributions made by individual species, including
Gardnerella
spp., are largely unknown. We report here that colony phenotypes characterized by size (large and small) and opacity (opaque and translucent) are phase variable and are conserved among all tested
Gardnerella
strains, representing at least 10 different species. With the hypothesis that these different variants could be an important missing piece to the enigma of how BV develops
in vivo
, we characterized their phenotypic, proteomic, and genomic differences. Beyond increased colony size, large colony variants showed reduced vaginolysin secretion and faster growth rate relative to small colony variants. The ability to inhibit the growth of
Neisseria gonorrhoeae
and commensal
Lactobacillus
species varied by strain and, in some instances, differed between variants. Proteomics analyses indicated that 127–173 proteins were differentially expressed between variants. Proteins with increased expression in large variants of both strains were associated with amino acid and protein synthesis and protein folding, whereas those increased in small variants were related to nucleotide synthesis, phosphate transport, ABC transport, and glycogen breakdown. Furthermore, whole genome sequencing analyses revealed an abundance of genes associated with variable homopolymer tracts, implicating slipped strand mispairing in
Gardnerella
phase variation and illuminating the potential for previously unrecognized heterogeneity within clonal populations. Collectively, these results suggest that phase variants may be primed to serve different roles in BV pathogenesis.

IMPORTANCE

Bacterial vaginosis is the most common gynecological disorder in women of childbearing age.
Gardnerella
species are crucial to the development of this dysbiosis, but the mechanisms involved in the infection are not understood. We discovered that
Gardnerella
species vary between two different forms, reflected in bacterial colony size. A slow-growing form makes large amounts of the toxin vaginolysin and is better able to survive in human cervix tissue. A fast-growing form is likely the one that proliferates to high numbers just prior to symptom onset and forms the biofilm that serves as a scaffold for multiple BV-associated anaerobic bacteria. Identification of the proteins that vary between different forms of the bacteria as well as those that vary randomly provides insight into the factors important for
Gardnerella
infection and immune avoidance.
Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling
Authors: Zhang Han , Wang Xiang , Chen Anqi , Li Shilin , Tao Ruiyang , Chen Kaiqin , Huang Ping , Li Liliang , Huang Jiang , Li Chengtao , Zhang Suhua 
Published: June 2024

ABSTRACT

The skin microbiome plays a pivotal role in human health by providing protective and functional benefits. Furthermore, its inherent stability and individual specificity present novel forensic applications. These aspects have sparked considerable research enthusiasm among scholars across various fields. However, the selection of specific 16S rRNA hypervariable regions for skin microbiome studies is not standardized and should be validated through extensive research tailored to different research objectives and targeted bacterial taxa. Notably, third-generation sequencing (TGS) technology leverages the full discriminatory power of the 16S gene and enables more detailed and accurate microbial community analyses. Here, we conducted full-length 16S sequencing of 141 skin microbiota samples from multiple human anatomical sites using the PacBio platform. Based on this data, we generated derived 16S sub-region data through an
in silico
experiment. Comparisons between the 16S full-length and the derived variable region data revealed that the former can provide superior taxonomic resolution. However, even with full 16S gene sequencing, limitations arise in achieving 100% taxonomic resolution at the species level for skin samples. Additionally, the capability to resolve high-abundance bacteria (TOP30) at the genus level remains generally consistent across different 16S variable regions. Furthermore, the V1-V3 region offers a resolution comparable with that of full-length 16S sequences, in comparison to other hypervariable regions studied. In summary, while acknowledging the benefits of full-length 16S gene analysis, we propose the targeting of specific sub-regions as a practical choice for skin microbial research, especially when balancing the accuracy of taxonomic classification with limited sequencing resources, such as the availability of only short-read sequencing or insufficient DNA.

IMPORTANCE
Skin acts as the primary barrier to human health. Considering the different microenvironments, microbial research should be conducted separately for different skin regions. Third-generation sequencing (TGS) technology can make full use of the discriminatory power of the full-length 16S gene. However, 16S sub-regions are widely used, particularly when faced with limited sequencing resources including the availability of only short-read sequencing and insufficient DNA. Comparing the 16S full-length and the derived variable region data from five different human skin sites, we confirmed the superiority of the V1-V3 region in skin microbiota analysis. We propose the targeting of specific sub-regions as a practical choice for microbial research.
Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake
Authors: Liébana Raquel , Viver Tomeu , Ramos-Barbero María Dolores , Bustos-Caparros Esteban , Urdiain Mercedes , López Cristina , Amoozegar Mohammad Ali , Antón Josefa , Rossello-Mora Ramon 
Published: June 2024

ABSTRACT

Hypersaline ecosystems display taxonomically similar assemblages with low diversities and highly dense accompanying viromes. The ecological implications of viral infection on natural microbial populations remain poorly understood, especially at finer scales of diversity. Here, we sought to investigate the influence of changes in environmental physicochemical conditions and viral predation pressure by autochthonous and allochthonous viruses on host dynamics. For this purpose, we transplanted two microbiomes coming from distant hypersaline systems (solar salterns of Es Trenc in Spain and the thalassohaline lake of Aran-Bidgol lake in Iran), by exchanging the cellular fractions with the sterile-filtered accompanying brines with and without the free extracellular virus fraction. The midterm exposure (1 month) of the microbiomes to the new conditions showed that at the supraspecific taxonomic range, the assemblies from the solar saltern brine more strongly resisted the environmental changes and viral predation than that of the lake. The metagenome-assembled genomes (MAGs) analysis revealed an intraspecific transition at the ecotype level, mainly driven by changes in viral predation pressure, by both autochthonous and allochthonous viruses.

IMPORTANCE
Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage–host interaction, and their important role in structuring the prokaryote community at an ecotype level.
Supplemental Material: Peri-Gondwanan sediment in the Arkoma Basin derived from the north: The detrital zircon record of a uniquely concentrated non-Laurentian source signal in the late Paleozoic
Authors: Smith Tyson M. , al. et 
Published: June 2024

<p>Data and metadata for new analyses, detrital zircon source modeling results, and auxiliary data to figures and analyses discussed in the paper. </p>
Ulcerative colitis: a diagnostic odyssey through cutaneous polyarteritis nodosa and granulomatous hepatitis
Authors: Soni Jinal , Khosla Pooja , Taneja Vinus , Rao Seema 
Published: June 2024

SummaryUlcerative colitis (UC), a chronic inflammatory bowel disease, can cause extraintestinal manifestations (EIMs) in approximately 40% of individuals. This case report discusses the diagnostic procedure of a woman in her 20s who initially had non-specific symptoms. The patient underwent a thorough evaluation, which initially pointed towards tuberculosis (TB) due to necrotic lymphadenopathy and granulomatous hepatitis. However, no microbiological evidence of TB was found, and her symptoms worsened despite antitubercular therapy. The patient developed painful nodular-ulcerative skin lesions consistent with cutaneous polyarteritis nodosa (cPAN) on biopsy. Eventually, a definitive diagnosis of UC was made, revealing the true nature of her multisystemic manifestations. Cutaneous vasculitis, including leucocytoclastic vasculitis and cPAN, is a rare EIM of UC, with only five reported cases in the literature. This case report highlights the clinical implications of EIMs and contributes to the expanding knowledge of rare EIMs such as cPAN and granulomatous hepatitis.
Tumor cell-released autophagosomes (TRAPs) induce PD-L1-decorated NETs that suppress T-cell function to promote breast cancer pulmonary metastasis
Authors: Zhou Xiaohe , Wu Chengdong , Wang Xuru , Pan Ning , Sun Xiaotong , Chen Bohao , Zheng Shiya , Wei Yiting , Chen Jing , Wu Yuyang , Zhu Fengjiao , Chen Jinpeng , Chen Huabiao , Wang Li-xin 
Published: June 2024

BackgroundLung metastasis is the primary cause of breast cancer-related mortality. Neutrophil extracellular traps (NETs) are involved in the progression of breast cancer. However, the mechanism of NET formation is not fully understood. This study posits that tumor cell-released autophagosomes (TRAPs) play a crucial role in this process.MethodsTRAPs were isolated from breast cancer cell lines to analyze their impact on NET formation in both human and mouse neutrophils. The study used both in vitro and in vivo models, including Toll-like receptor 4 (TLR4−/−) mice and engineered breast cancer cell lines. Immunofluorescence, ELISA, Western blotting, RNA sequencing, and flow cytometry were employed to dissect the signaling pathways leading to NET production and to explore their immunosuppressive effects, particularly focusing on the impact of NETs on T-cell function. The therapeutic potential of targeting TRAP-induced NETs and their immunosuppressive functions was evaluated using DNase I and αPD-L1 antibodies. Clinical relevance was assessed by correlating circulating levels of TRAPs and NETs with lung metastasis in patients with breast cancer.ResultsThis study showed that TRAPs induced the formation of NETs in both human and mouse neutrophils by using the high mobility group box 1 and activating the TLR4-Myd88-ERK/p38 signaling axis. More importantly, PD-L1 carried by TRAP-induced NETs inhibited T-cell function in vitro and in vivo, thereby contributing to the formation of lung premetastatic niche (PMN) immunosuppression. In contrast,Becn1KD-4T1 breast tumors with decreased circulating TRAPs in vivo reduced the formation of NETs, which in turn attenuated the immunosuppressive effects in PMN and resulted in a reduction of breast cancer pulmonary metastasis in murine models. Moreover, treatment with αPD-L1 in combination with DNase I that degraded NETs restored T-cell function and significantly reduced tumor metastasis. TRAP levels in the peripheral blood positively correlated with NET levels and lung metastasis in patients with breast cancer.ConclusionsOur results demonstrate a novel role of TRAPs in the formation of PD-L1-decorated NETs, which may provide a new strategy for early detection and treatment of pulmonary metastasis in patients with breast cancer.
Constraints on quasinormal modes from black hole shadows in regular non-minimal Einstein Yang–Mills gravity
Authors: Gogoi Dhruba Jyoti , Ponglertsakul Supakchai 
Published: June 2024

AbstractThis work deals with scalar quasinormal modes using the higher-order WKB method and black hole shadow in non-minimal Einstein–Yang–Mills theory. To validate the results of quasinormal modes, time domain profiles are also investigated. We find that with an increase in the magnetic charge of the black hole, the ringdown gravitational wave increases non-linearly and the damping rate decreases non-linearly. The presence of a magnetic charge also results in a non-linear decrease in the black hole shadow. For large values of the coupling parameter, the black hole becomes a soliton solution and the corresponding ringdown gravitational wave frequency increases slowly with a decrease in the damping rate. For the soliton solutions, the shadow is also smaller. The constraints on the model parameters calculated using shadow observations of M87* and Sgr A* and an approximate analytical relation between quasinormal modes and shadows at the eikonal limit are discussed.
Quantum entanglement and classical correlation have the same form
Authors: Annila Arto , Wikström Mårten 
Published: June 2024

AbstractIn agreement with the data, the quantum correlation between spins violates Bell’s inequality by following a cosine curve when one analyzer is rotated relative to the other. In contrast, the linear correlation attributed to hidden variables has never been observed. Besides these well-established facts, we show here that classical covariance, Pearson correlation, between spins projected as up or down on the analyzer axes also follows the cosine form hitherto uniquely ascribed to the quantum mechanical expectation value. The common cause for the classical correlation is the conservation of intrinsic angular momentum that aligns the two spins antiparallel at the breakup. Thus, as long as the spins retain their orientations relative to each other, the measurement of one spin in a chosen frame of reference also discloses the opposite orientation of the other in that frame. Realizing that classical correlation has the same functional form as quantum entanglement sheds light on the foundations of modern physics and quantum computing.
Hydrogen Permeation in PFSA Membranes with Different Side Chains and ePTFE Fiber Fraction
Authors: Yandrasits Michael A. , Condon Jeremy , Steinbach Andrew J. , Novy Melissa , Patel Kirit 
Published: June 2024

Hydrogen permeation was measured at 80 °C and four humidities for a series of membranes fabricated from the three most common perfluorosulfonic acid (PFSA) ionomers. In addition, membranes were made with different thicknesses and types of expanded PTFE (ePTFE) reinforcements. A picture has emerged where the permeation constant is lowest for the shortest side chain and decreases with decreasing ion exchange capacity (IEC). A relationship quantifying the impact of ePTFE on reducing hydrogen permeation was developed showing lower cross over with higher fiber content. For both the IEC study and the reinforcement study, the permeability is trending towards the published value for pure poly(tetrafluoroethylene) when the ionomer CF2 content or fiber fraction of the membrane increases. In all cases, the hydrogen permeation was greatest at the highest humidities.
Investigation of Zn Doped Li1.5Al0.5−xZnxGe1.5(PO4)3 (x = 0, 0.1 & 0.2) as a Solid Electrolyte for Li Ion Batteries
Authors: Subash Sruthy , Faizal Abu , Mercy T. D. , Bharathi K. Kamala 
Published: June 2024

All solid lithium-ion batteries (ASLB) have gained a lot of attention as it could deliver high energy and power density. In order to completely establish ASLB, proper understanding of solid electrolyte is very vital and the research from diverse point is still undergoing. Among them, NASICON-type phosphate based solid electrolytes are one of the promising materials due to good ionic conductivity and atmospheric stability. Addition of proper dopants into the parent material could cause an increment in their ionic conductivity as well as stability, thus fitting the material apt as solid electrolyte. This study aims in understanding the effect of ionic conductivity and stability of Lithium Aluminium Germanium Phosphate (LAGP) material upon adding Zinc as dopant material. We explored the effect of structural, ionic conductivity, stability against Li and Ac conductivity properties of Li1.5Al0.5−xZnxGe1.5(PO4)3 solid electrolyte with x = 0, 0.1 and 0.2. Our study showed that doping of aluminium with slightly bigger Zn ion could enhance the stability and conductivity of the material without changing the crystal structure. When x = 0.1 the ionic conductivity of the material attained is 1 × 10−5 S cm−1 at RT, which reaches 2.57 × 10−5 S cm−1 at 60 °C. Such a change in conductivity arises due to the expansion of ionic pathways which can be further tuned by exploring the limiting concentration 0 ≤ x < 0.1. Moreover, the sample also showed good stability at 0.03 and 0.05 mA cm−2 current densities against Li metal. Present study shows that Zn doping can improve the ionic conductivity of LAGP moderately and it can be used as a solid electrolyte for fabricating all-solid-state batteries.
Impact of Weight Gain on Cardiovascular Outcomes in Patients With Atrial Fibrillation
Authors: Bhonsale Aditya , Zhu Jianhui , Thoma Floyd , Kancharla Krishna , Voigt Andrew , Estes Nathan A. , Shalaby Alaa A. , Saba Samir , Mulukutla Suresh , Jain Sandeep 
Published: June 2024

Background
The long‐term impact of weight gain (WG) on cardiovascular outcomes among patients with atrial fibrillation (AF) is unclear.

Methods and Results

We studied 62 871 (mean age, 72±12, 43% women) adult patients with AF evaluated at the University of Pittsburgh Medical Center between January 1, 2010, and May 13, 2021. Serial body mass index, risk factors, comorbidities, and subsequent death and hospitalization were ascertained and stratified according to percentage WG (≥0% to <5%, ≥5% to <10%, and ≥10%). Over 4.9±3.19 years of follow‐up, 27 114 (43%) patients gained weight (61%, ≥0% to <5%; 23%, ≥5% to <10%; 16%, ≥10%). Patients with progressive WG were incrementally younger (
P
<0.001) women (40%, 42%, and 47%) with lower median household income (
P
=0.002) and active smoking (8%, 13% and 13%), and they were less likely to be on a non–vitamin K oral anticoagulant (39%, 37%, and 32%). WG was incrementally associated with a significant increase in risk of hospitalization for AF (≥10% WG; hazard ratio [HR], 1.2 [95% CI, 1.2–1.3];
P
<0.0001), heart failure (≥10% WG; HR, 1.44 [95% CI, 1.3–1.6];
P
<0.001; ≥5% to <10% WG; HR, 1.17 [95% CI, 1.1–1.2];
P
<0.001), myocardial infarction (≥10% WG; HR, 1.2 [95% CI, 1.3–1.6];
P
<0.001) and all‐cause stroke (4.2%, 4.3%, and 5.6%) despite significantly lower mean CHADS
2
Vasc score (2.9±1.7, 2.7±1.6, and 2.7±1.7). Patients with more WG were significantly more likely to receive cardiac and electrophysiologic interventions.

Conclusions
Among patients with AF, WG is incrementally associated with increased hospitalization for cardiovascular causes, particularly heart failure, stroke, myocardial infarction, and AF.