bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel recombinant S-based subunit vaccine induces protective immunity against porcine deltacoronavirus challenge in piglets
Authors: Li Jizong , Zhao Shuqing , Zhang Baotai , Huang Jin , Peng Qi , Xiao Li , Yuan Xuesong , Guo Rongli , Zhou Jinzhu , Fan Baochao , Xue Tao , Zhu Xuejiao , Liu Chuanmin , Zhu Xing , Ren Lili , Li Bin
Published: October 2023

Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, causes diarrhea in piglets and possesses the potential to infect humans. However, there are no commercially available vaccines for PDCoV. In this study, the immune responses to the spike (S) protein and receptor-binding domain (RBD) trimer were examined in mice. Neutralization assays and flow cytometry analysis demonstrated that S protein elicited more robust neutralizing antibodies (NAbs) and cellular immune responses than the RBD trimer. Spike protein and inactivated vaccine were used in the assessment of immunogenicity in piglets and sows. Immunized piglets, sows, and suckling pig showed high NAb titers and S-specific sIgA in colostrum, milk, and serum. The piglets/suckling pig from the immunized group displayed significantly fewer microscopic lesions in the intestinal tissue, with only one or no piglet showing mild diarrhea. However, all piglets/suckling pig showed mild to watery diarrhea and exhibited a high level of viral shedding in the challenged control group. The feces from the piglets/suckling pig in the S protein and inactivated vaccine group exhibited reduced viral load. Of note, vaccine-elicited NAbs last for more than 4 months in immunized piglets. Together, our data demonstrate for the first time the protective efficacy of S-based subunit vaccine, which could be a candidate vaccine against PDCoV.

IMPORTANCE

As an emerging porcine enteropathogenic coronavirus that has the potential to infect humans, porcine deltacoronavirus (PDCoV) is receiving increasing attention. However, no effective commercially available vaccines against this virus are available. In this work, we designed a spike (S) protein and receptor-binding domain (RBD) trimer as a candidate PDCoV subunit vaccine. We demonstrated that S protein induced more robust humoral and cellular immune responses than the RBD trimer in mice. Furthermore, the protective efficacy of the S protein was compared with that of inactivated PDCoV vaccines in piglets and sows. Of note, the immunized piglets and suckling pig showed a high level of NAbs and were associated with reduced virus shedding and mild diarrhea, and the high level of NAbs was maintained for at least 4 months. Importantly, we demonstrated that S protein-based subunit vaccines conferred significant protection against PDCoV infection.
Comparison of
Helicobacter pylori
positive and negative gastric cancer via multi-omics analysis
Authors: Shang Fumei , Cao Yinghao , Wan Lixin , Ren Zhonghai , Wang Xinghao , Huang Mudan , Guo Yingyun
Published: October 2023

Helicobacter pylori
(
H. pylori
) has been regarded as a definite carcinogenic bacterium for gastric cancer (GC). This multi-omics research was designed to investigate the genetic, microbial, and metabolic changes of GC patients when they are infected with
H. pylori
. We first mined The Cancer Genome Atlas Stomach Adenocarcinoma (STAD) data to identify the key genes and critical pathways in
H. pylori
-positive individuals with GC compared to
H. pylori
-negative individuals with GC. Then, fresh stool samples were collected from GC individuals screened for eligibility, and we analyzed the microbial changes and metabolite alterations between
H. pylori
-positive and
H. pylori
-negative GC individuals. Finally, we tried to explore the interaction between key gut flora and metabolite changes in GC patients infected with
H. pylori
. We identified three genes (GCG, APOA1, and IGFBP1) with significant relevance to
H. pylori
infection, and the survival monogram based on the three
H
.
pylori
-related genes showed good predictive ability for overall survival among GC individuals. 16S rRNA sequencing showed that the abundance of
Escherichia-Shigella, Bacteroides, Enterococcus
,
and Lactobacillus
was upregulated in GC cases with
H. pylori
at the level of genus. There exists a great difference in alpha and beta diversity between
H. pylori
group and non-
H
.
pylori
group. The untargeted metabolome analysis identified 295 significant fecal metabolites, and the levels of penitrem E, auberganol, stercobilinogen, and lys thr are upregulated in the
H. pylori
group. Finally, correlation analysis showed that there exists a significant correlation between the fecal metabolites and gut bacterial strains. This is the first clinical research to investigate the difference between GC patients with
H. pylori
and GC patients without
H. pylori
via multi-omics analysis. 16S rRNA sequencing along with untargeted metabolomics demonstrated decreased microbial diversity and metabolic dysregulation in gastric carcinoma individuals with
H. pylori
infection.

IMPORTANCE

This is the first clinical research to systematically expound the difference between gastric cancer (GC) individuals with
Helicobacter pylori
and GC individuals without
H. pylori
from the perspective of multi-omics. This clinical study identified significant genes, microbes, and fecal metabolites, which exhibited nice power for differentiating GC individuals with
H. pylori
infection from GC individuals without
H. pylori
infection. This study provides a crucial basis for a better understanding of eradication therapy among the GC population.
Brucella
MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid
Authors: Barton Ian S. , Ren Zhongqing , Cribb Connor B. , Pitzer Joshua E. , Baglivo Ilaria , Martin Daniel W. , Wang Xindan , Roop R. Martin
Published: October 2023

Histone-like nucleoid structuring (H-NS) and H-NS-like proteins serve as global gene silencers and work with antagonistic transcriptional activators (counter-silencers) to properly coordinate the expression of virulence genes in pathogenic bacteria. In
Brucella
, MucR has been proposed as a novel H-NS-like gene silencer, but direct experimental evidence is lacking. Here, we show that MucR serves as an H-NS-like silencer of the
Brucella abortus
genes encoding the polar autotransporter adhesins BtaE and BmaC, the c-di-GMP-specific phosphodiesterase BpdB, and the quorum-sensing regulator BabR. We also demonstrate that the MarR-type transcriptional activator MdrA can displace MucR from the
btaE
promoter, supporting the existence of MucR counter-silencers in
Brucella
. Moreover, our chromatin immunoprecipitation (ChIP)-seq analysis identified 546 MucR enrichment peaks along the genome, including in the promoters of the genes encoding the Type IV secretion machinery and effectors and the quorum-sensing regulator VjbR. Importantly, MucR ChIP-seq peaks overlap with the previously described binding sites for the transcriptional activators VjbR, BvrR, and CtrA suggesting that these regulators serve as MucR counter-silencers and work in concert with MucR to coordinate virulence gene expression in
Brucella
. In addition, using chromosome conformation capture (Hi-C), we show that like H-NS in
Escherichia coli
, MucR alters the global structure of the
Brucella
nucleoid. Finally, a copy of the
E. coli hns
rescues the distinctive growth defect and elevated
btaE
expression of a
B. abortus mucR
mutant. Together, these findings solidify the role of MucR as a novel type of H-NS-like protein and suggest that MucR’s gene-silencing properties play a key role in virulence in
Brucella
.

IMPORTANCE

Histone-like nucleoid structuring (H-NS) and H-NS-like proteins coordinate host-associated behaviors in many pathogenic bacteria, often through forming silencer/counter-silencer pairs with signal-responsive transcriptional activators to tightly control gene expression.
Brucella
and related bacteria do not encode H-NS or homologs of known H-NS-like proteins, and it is unclear if they have other proteins that perform analogous functions during pathogenesis. In this work, we provide compelling evidence for the role of MucR as a novel H-NS-like protein in
Brucella
. We show that MucR possesses many of the known functions attributed to H-NS and H-NS-like proteins, including the formation of silencer/counter-silencer pairs to control virulence gene expression and global structuring of the nucleoid. These results uncover a new role for MucR as a nucleoid structuring protein and support the importance of temporal control of gene expression in
Brucella
and related bacteria.
Draft genome sequence of methicillin-resistant
Staphylococcus aureus
strain D1418m22 isolated from human wound pus
Authors: Iram Daraksha , Sansi Manish Singh , Puniya Anil Kumar , Meena Sunita , Vij Shilpa
Published: October 2023

This study reveals the complete genome sequence of methicillin-resistant
Staphylococcus aureus
(MRSA) strain d1418m22, sourced from a Karnal, Haryana, human skin wound. Classified as community-associated MRSA, it features a 2.78-MB genome harboring
Staphylococcus
-specific genetic elements, encompassing 2,625 protein-coding genes and 18 antimicrobial resistance genes.
Complete genome sequence of Koutango virus strain DakAnD5443 isolated from
Tatera kempi
in 1968
Authors: Haila Gabriel J. , Plante Jessica A. , Widen Steven G. , Beasley David W. C.
Published: October 2023

Koutango virus (KOUV), a close relative of West Nile virus, is highly neuroinvasive in animal models and has been associated with human disease. The complete genome of the KOUV prototype strain DakAnD5443 is reported here and may facilitate development of infectious clones for further characterization of this novel flavivirus.
De novo
assembly of
Roseomonas mucosa
isolated from patients with atopic dermatitis
Authors: Barbian Kent , Bruno Daniel , Sykora Lydia , Ricklefs Stacy , Chaudhary Prem Prashant , Beare Paul A. , Myles Ian A. , Martens Craig M.
Published: October 2023

Roseomonas mucosa
is associated with the normal skin microflora. Here, we present
de novo
sequence assemblies from
R. mucosa
isolates obtained from the skin lesions of three atopic dermatitis patients.
Complete genome sequence of
Lacticaseibacillus paracasei
strain VHProbi M56, isolated from yogurt
Authors: Guo Chaoqun , Cui Hongchang , Wang Qian , Duan Zhi
Published: October 2023

Lacticaseibacillus paracasei
strain VHProbi M56 is a probiotic strain that was isolated from yogurt. Here, we report the whole-genome sequence of this bacterium. The whole genome contains a chromosome and a plasmid.
Complete genome sequence of
Proteiniborus
sp. MB09-C3, isolated from the feces of the black soldier fly larvae
Authors: Qiu Wanling , Zhu Junyu , Shih Chao-Jen , Wu Yen-Chi , Lai Shu-Jung , You Yi-Ting , Wu Chih-Hung , Liao Ching-Hua , Lin Haozhe , Li Shilong , Yan Yujia , Luo Xuming , Li Yin , Chen Sheng-Chung
Published: October 2023

Here, we report the complete genome sequence of
Proteiniborus
sp. MB09-C3 (= BCRC 81405), isolated from the feces of black soldier fly (
Hermetia illucens
) larvae. The genome of strain MB09-C3 was selected for further species delineation and comparative genomic analysis.
Draft genome sequence of
Staphylococcus gallinarum
MTR_B001 strain isolated from breast muscle of a chicken in Bangladesh
Authors: Islam Md. Saiful , Ballah Fatimah Muhammad , Hoque M. Nazmul , Rahman A. M. M. Taufiquer , Rahman Md. Tanvir
Published: October 2023

We announce the genome sequence of the
Staphylococcus gallinarum
MTR_B001 strain isolated from the breast muscle of a chicken in 2022 in Bangladesh. This assembled genome had an estimated length of 2,889,393 bp (with 50× genome coverage), 15 contigs, 36 predicted antibiotic resistance genes, and 27 predicted virulence factor genes.
The complete genome sequence of
Pantoea agglomerans
NBBC-01, isolated from rot potato tubers
Authors: Wang Yueying , Chen Ling , Liu Fang , Zhang Zhigang , Zhang Fei , Wang Kaimei , Fang Wei
Published: October 2023

The Gram-negative bacterium
Pantoea agglomerans
has been isolated from various habitats including disease plants. Here, we present the genome of
P. agglomerans
strain NBBC-01 obtained from rotten potatoes that were infected by
Ditylenchus desstructor
. The genome information will prove advantageous in elucidating its ecological role.
Whole-genome sequence of a genotype VIII infectious bronchitis virus isolated from California layer chickens in 2021
Authors: Jude Rachel , da Silva Ana P. , Rejmanek Daniel , Crossley Beate , Jerry Carmen , Stoute Simone , Gallardo Rodrigo
Published: October 2023

Herein, we report the complete genome for an avian infectious bronchitis virus isolated from cecal tonsils of California layers in 2021. This whole-genome sequence belongings to genotype GVIII, previously classified as a unique variant.
Morphodynamics of non-canonical autophagic structures in
Neurospora crassa
Authors: Rivetta Alberto , Allen Kenneth , Graham Morven , Potapova Tatiana , Slayman Clifford , Liu Xinran
Published: October 2023

Autophagy is a major pathway for unspooling cytoplasmic constituents and recycling them. Here, we investigate autophagy in
Neurospora crassa,
a close ascomycete relative to the model yeast
Saccharomyces cerevisiae
. High-pressure-freeze and freeze-substitution techniques proved keys to preservation of the surprising autophagic structures observed in
Neurospora
by transmission electron microscopy and electron tomography. Depriving
Neurospora
of carbon triggers two parallel processes at the plasma membrane: formation of vacuoles, initially along the plasma membrane but stuffing 70%–80% of cytoplasmic volume after several hours. The vacuoles contain material left over from digested proteins, disrupted ribosomes or glycogen clumps, plus other discrete organelle-like objects. Also, they accumulate the canonical autophagy marker Atg8, appear to be lytic from the start, and probably grow from lysosomes. Formation of diverse phagophores and autophagosomes,
multi-membrane
organelles manufactured
de novo
by the plasma membrane—a feature so far unique to
Neurospora
. These autophagic structures can be observed attached either to the cell membrane, to the cell wall, or free in the cytoplasm, viz. as mature organelles after detachment from the cell membrane. Although phagophores are clearly observed in carbon-replete cells, their production increases with carbon starvation—and these, too, often appear lytic.
ATG1
, the canonical initiator of phagophore formation in yeast, is not required for the formation of phagophores in
Neurospora
. This work provides clear structural and functional evidence that
Neurospora
’s autophagic organelles differ from those observed by others in yeast.

IMPORTANCE

Neurospora
is a quintessential tip-growing organism, which is well known for packaging and longitudinal transport of tip-building blocks. Thus far, however, little attention has been paid to the co-essential process of reclamation, that is—taking apart of upstream, older structural elements, otherwise known as “autophagy”. We are not yet prepared to set out the chemistry of that elaborate process, but its morphological start alone is worthy of attention. Carbon starvation triggers significant autophagic changes, beginning with prolific vacuolation along the plasma membrane, and eventual filling of 70% (or more) of cytoplasmic volume. Additionally, the
Neurospora
plasma membrane elaborates a variety of phagophores which themselves often look lytic. These have either dual enclosing membranes, like the familiar autophagosomes, can be doubled and have four wrapping membranes, or can be compounded with multiple membrane layers. These reclamation processes must be accommodated by the mechanism of tip growth.
Prevalence and genetic characterization of
Campylobacter
from clinical poultry cases in China
Authors: Li Xiaofei , Xu Xiangxiang , Chen Xinyi , Li Yunlu , Guo Jiale , Gao Jie , Jiao Xinan , Tang Yuanyue , Huang Jinlin
Published: October 2023

Campylobacter
is one of the leading causes of bacterial foodborne diseases globally. Poultry is considered a major reservoir for the transmission of
Campylobacter
to humans. The occurrence and epidemiology of
Campylobacter
in healthy poultry have been extensively studied, but the prevalence in diseased poultry has rarely been reported. In this study, a total of 1,563 intestinal samples, 547 gallbladder samples, and 3,729 parenchyma organ samples were collected from diseased chickens, ducks, and geese in Yangzhou Veterinary Hospital between December 2016 and September 2017. The bacterial isolates were analyzed for genotype, resistance, and virulence genes. The overall prevalence of
Campylobacter
was 17.9%, and a significantly higher prevalence was observed in the diseased chickens (21.8%) than in the diseased ducks (12.1%) and geese (11.9%).
Campylobacter
was significantly more prevalent in the intestinal tract (39.6%), followed by the gallbladder (11.7%) and parenchyma organ (9.7%). Among 84 whole-genome sequenced
Campylobacter
isolates, we identified 47 multi-locus sequence typing types, of which ST-51 and ST-825 were the most predominant sequence types (STs) for
Campylobacter jejuni
and
Campylobacter coli
, respectively. Phylogenetic analysis showed that
Campylobacter
isolates from different tissues from the same host tended to cluster together with the same STs, which indicated
Campylobacter
infection in different tissues
in vivo
. The antimicrobial resistance genes most frequently identified were
gyrA
(T86I) (97.6%) and
tet (O)
(65.5%). Our results revealed the high prevalence of
Campylobacter
in diseased poultry in China, which will help the farms take the necessary action to develop effective mitigation strategies for reducing
Campylobacter
infection in poultry.

IMPORTANCE

Campylobacter
is a major cause of campylobacteriosis worldwide, and poultry is the main reservoir for its transmission.
Campylobacter
was generally considered to be a harmless commensal organism in poultry without pathogenic properties. However, it was proposed that a
Campylobacter
-like organism may be the cause of vibrionic hepatitis, which poses a significant public health risk. The occurrence and epidemiology of
Campylobacter
in healthy poultry have been studied systematically, but little is known about the epidemiology of
Campylobacter
isolates from diseased poultry in China. Therefore, this study determined the prevalence and molecular characterization of
Campylobacter
from diseased chickens, ducks, and geese in Yangzhou Veterinary Hospital between December 2016 and September 2017, which was critical for improving the diagnosis and prevention of
Campylobacter
infections.
Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation
Authors: Jiang Hubiao , Luo Jinyan , Liu Quanhong , Ogunyemi Solabomi Olaitan , Ahmed Temoor , Li Bing , Yu Shanhong , Wang Xiao , Yan Chenqi , Chen Jianping , Li Bin
Published: October 2023

Rice bacterial leaf blight (BLB) is the most destructive phyllosphere bacterial disease caused by
Xanthomonas oryzae
pv.
oryzae
. The effect of soil-borne diseases on the rhizosphere microbiome has been extensively investigated. However, the regulatory role of the phyllosphere disease BLB on the rhizosphere microbiome remains unclear. Here, we observed that BLB significantly altered the composition of the bacterial-fungal community in the rhizosphere, decreasing bacterial diversity but not fungal diversity. The scale of inter-kingdom networks in the rhizosphere microbiome of BLB-infected plants was more complex and broader than in healthy plants, while the bacterial community was more vulnerable to BLB than the fungal community. Indeed, the relative abundance of
Streptomyces
,
Chitinophaga
,
Sphingomonas
, and
Bacillus
was higher in the BLB rhizosphere, which can be explained by their keystone hub taxa status in the rhizosphere co-occurrence network. Null model analysis showed that the deterministic assembly of bacterial communities increased while that of fungi decreased. Additionally, the assembly of bacterial and fungal communities was significantly related to variations in BLB and soil nutrients, especially pH and available phosphorus. Random forest model results showed that the bacterial community in the rhizosphere had a strong potential for predicting BLB. Metagenomic analysis revealed that BLB had a considerable impact on the functional adaptation of the rhizosphere microbiome. Interestingly, the abundance of some functional genes involved in carbon, phosphorus, and methane metabolism increased drastically.

IMPORTANCE

Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera
Streptomyces
,
Chitinophaga
,
Sphingomonas
, and
Bacillus
increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.
Community structure and niche differentiation of endosphere bacterial microbiome in
Camellia oleifera
Authors: Zhang Yan , Ding Chu Ting , Jiang Taoya , Liu Yu Hua , Wu Yang , Zhou Hui Wen , Zhang Li Sha , Chen Ye
Published: October 2023

Understanding the changes in bacterial community structure in different microenvironments of
Camellia oleifera
is essential to better explore the benign interaction between beneficial microorganisms and plants. Using
Camellia oleifera
trees, a Chinese wooden oil plant as a model ecosystem, we characterized the archaeal and bacterial microbiome across five different tissue-level niches using 16S rRNA gene analyses. Our research indicates that the diversity of
Camellia oleifera
endophytic bacterial communities is highly dependent on the plant compartment. The species replacement process (69.90%) is the dominant factor in the differences in bacterial community structure. The dominant bacteria phyla (
Proteobacteria
,
Acidobacteria
,
Actinobacteria
,
Bacteroidetes
,
Firmicutes
,
Chloroflexi
, and
Verrucomicrobia
) of
Camellia oleifera
show a significant plant compartment (roots, stems, leaves, fruits) enrichment effects. A variety of bacteria (
Hymenobacter
,
Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium
,
Mesorhizobium
,
Bradyrhizobium
,
Bacillus
,
Ochrobactrum
,
Pantoea
,
Pseudomonas
, etc.) with nitrogen-fixed potentials are enriched in
Camellia oleifera
tissue. In addition, the hub bacterial groups of
Camellia oleifera
are
Nitrospira
,
Haemophilus
,
Staphylococcus
,
Ruminiclostridium
, and
Ochrobactrum
. They are widespread colonization in various tissues with a low relative abundance and may play an important role in the nitrogen cycle, host life promotion, and plant defense. This study provides a holistic understanding of the endosphere bacterial community structure, which is one of the most complete ecological niche-level analyses of
Camellia oleifera
. These results provide a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.

IMPORTANCE

Microorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of
Camellia oleifera
endophytic bacterial communities is highly dependent on the plant compartment.
Proteobacteria
,
Acidobacteria
,
Actinobacteria
,
Bacteroidetes
,
Firmicutes
,
Chloroflexi
, and
Verrucomicrobia
are dominant bacteria phyla. The tissues of
Camellia oleifera
contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.
Maternal transmission of bacterial microbiota during embryonic development in a viviparous lizard
Authors: Montoya-Ciriaco Nina , Hereira-Pacheco Stephanie , Estrada-Torres Arturo , Dendooven Luc , Méndez de la Cruz Fausto R. , Gómez-Acata Elizabeth Selene , Díaz de la Vega-Pérez Aníbal H. , Navarro-Noya Yendi E.
Published: October 2023

The maternal transmission of microbiota during embryonic development of vertebrates is still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA bacterial genes to determine the bacterial communities in the gastrointestinal tract and amniotic environment, i.e., the amniotic fluid, amniotic membrane and extraembryonic yolk, of embryos at the last stage of development of the viviparous lizard
Sceloporus grammicus
Wiegmann, 1828. We compared these communities to those found in the maternal intestine, mouth, cloaca, and the aseptic ventral skin as a control of the aseptic technique. Our results showed that bacterial 16S rRNA genes were present in the embryos of
S. grammicus
. Their diversity was lower and more similar in composition between individuals than those found in the maternal tissues. This suggests that a strong control exists on the transmission of bacteria from the mother to the embryos. We found 78% of the embryonic amplicon sequence variants (ASVs) in the maternal bacterial microbiota, suggesting that the transmission of bacteria from the mother to the embryos is a continuous process and some bacteria may have been transferred during early embryonic stages. The embryonic bacteria were found to overlap mostly with those found in the mouth and aseptic ventral skin of the mother, although it is difficult to conclude that the shared ASVs originated from these maternal tissues. Our study provides evidence of microbiota vertical transfer during embryonic development in the animal kingdom. It also highlights that this maternal transmission could be included in the maternal effects that impact the offspring.

IMPORTANCE

We investigated the presence and diversity of bacteria in the embryos of the viviparous lizard
Sceloporus grammicus
and their amniotic environment. We compared this diversity to that found in the maternal intestine, mouth, and cloaca. We detected bacterial DNA in the embryos, albeit with a lower bacterial species diversity than found in maternal tissues. Most of the bacterial species detected in the embryos were also found in the mother, although not all of them. Interestingly, we detected a high similarity in the composition of bacterial species among embryos from different mothers. These findings suggest that there may be a mechanism controlling the transmission of bacteria from the mother to the embryo. Our results highlight the possibility that the interaction between maternal bacteria and the embryo may affect the development of the lizards.
The formation of lithium-rich pegmatites through multi-stage melting
Authors: Koopmans Lot , Martins Tania , Linnen Robert , Gardiner Nicholas J. , Breasley Catriona M. , Palin Richard M. , Groat Lee A. , Silva David , Robb Laurence J.
Published: October 2023

Lithium-cesium-tantalum–type pegmatites (the primary source of lithium) crystallize from highly evolved, volatile felsic melts that incorporated crustal material in their source. Pegmatites are classically thought to form either from extreme fractionation of a parental granite body or via low-degree partial melting of a metamorphic rock (anatectic origin). However, the processes that lead to the formation of economic lithium pegmatite deposits remain enigmatic, because precipitation of lithium ore minerals requires melt lithium concentrations in excess of 5000 ppm—~500 times upper crustal abundances. We use petrological modeling to quantify lithium enrichment in an anatectic-origin scenario and show that it is primarily driven by the relative stability of residual biotite and muscovite at medium to high pressures (~8 kbar), and biotite and cordierite at low pressures (~3 kbar). We show anatexis of an average lithium-enriched metasedimentary source cannot sufficiently elevate the lithium content of the ensuing melt to form economic deposits; however, if this first-generation melt—now crystallized as granitic crust—is re-melted, the second-generation melt will be sufficiently concentrated in lithium to crystallize lithium ore minerals. We propose a petrogenetic model for anatectic-origin lithium pegmatites, in which a region experiences at least two stages of partial melting, ultimately generating lithium-rich melts without invoking extensive fractional crystallization. This mechanism can both account for the occurrence of unzoned lithium pegmatites and explain why economic pegmatites in many terranes are younger than their inferred source granites.
Characterisation of a novel missense mutation in theERCC5gene leading to group G xeroderma pigmentosum/Cockayne syndrome overlap
Authors: Stehnach William Christopher , Cantor Aaron , Bongiorno Michelle
Published: October 2023

Xeroderma pigmentosum–Cockayne syndrome complex (XP–CS) is exceedingly rare, with 43 cases described over the past five decades; 21 of these cases exhibited mutations in the ERCC5 endonuclease associated with xeroderma pigmentosum, group G.

We report the first known phenotypic characterisation of the homozygous chromosome 13ERCC5, Exon 11, c.2413G>A (p.Gly805Arg) missense mutation in a female toddler presenting with findings of both XP and CS.

Her severe presentation also questions previous hypotheses that only truncating mutations and early missense mutations of XPG are capable of producing the dire findings of XP–CS.
Locally advanced solitary fibrous tumour of the prostate
Authors: Wahlstedt Eric , Zhou Christopher , Strup Sydney , Kyung Kim Joon , Strup Stephen E , Yenwong Leonard , Allison Derek B , Hensley Patrick J
Published: October 2023

Solitary fibrous tumours (SFTs) are rare mesenchymal neoplasms composed of spindle cells, most often occurring in the pleura. SFTs arising from the prostate are exceptionally rare, with only around 40 cases reported in literature to date. We report a man in his 60s who was referred to our clinic for elevated prostate-specific antigen and presented with mild obstructive lower urinary tract and defecatory symptoms. Prostate needle-core biopsy revealed neoplastic spindle cells that strongly expressed CD34. Cross-sectional imaging demonstrated a 12 cm locally advanced heterogeneous prostate mass with intravesical extension and mass effect on the anterior rectum. Radical cystoprostatectomy with orthotopic neobladder reconstruction was performed, and the diagnosis of primary prostatic SFT was made based on histological characteristics and immunophenotyping. We present diagnostic, clinical management and prognostic considerations in patients with primary prostatic SFT.
Authorship equity in global health research: who gets the credit at University of California, San Francisco?
Authors: Kaufman Rebekah , Fair Elizabeth , Reid Michael , Mirzazadeh Ali
Published: October 2023

Authorship inequity exists in global health research and can be representative of unequal partnerships. Previous studies showed that low-income and middle-income country (LMIC) authors are under-represented in publications from global collaborative research between LMIC and high-income countries (HIC). However, there are little data on trends for how specific HIC institutions are performing concerning equitable authorship. We used Web of Science to find published articles affiliated with the University of California, San Francisco (UCSF), where an LMIC was referred to in the title, abstract or keywords from 2008 to 2021. The country affiliation of each author for all included articles was grouped based on World Bank data. A total of 5805 articles were included. On average, 53.6% (n=3109) of UCSF affiliated articles had at least one low-income country (LIC) or LMIC author; however, this number increased from 43.2% (n=63) in 2008 to 63.3% (n=421) in 2021. Overall, 16.3% (n=948) of UCSF affiliated articles had an LIC or LMIC researcher as the first author, 18.8% (n=1,059) had an LIC or LMIC researcher as second author, and 14.2% (n=820) had an LIC or LMIC researcher as last author. As long as manuscripts produced by UCSF have no LIC or LMIC authors included the university’s commitment to authentic equity is undermined. Global health partnerships cannot be equitable without changing authorship trends between HIC and LMIC institutions.
Circumstances that promote social connectedness in older adults participating in intergenerational programmes with adolescents: a realist review
Authors: Simionato Jessica , Vally Hassan , Archibald Daryll
Published: October 2023

Objectives

Limited social connectedness in older adults is a risk factor for poor physical and mental health. Older adults who are socially isolated, lonely and disconnected have a higher risk of chronic illness, depression and premature death. Current literature suggests that improved social connectedness reduces these risks. Intergenerational programmes are an effective way to improve health outcomes. Despite this, there is yet to be a review using realist review methods that seeks to identify the circumstances that promote social connectedness in older adults participating in intergenerational programmes with adolescents.

Design

A realist review methodology was chosen to account for the complexity of intergenerational interventions. Nine studies were included. In line with realist review methodology, iterative data extraction and analysis was conducted to identify the specific contexts, mechanisms and outcomes of the programmes. Specific circumstances were identified to develop theories relating to improved social connectedness in older adults.

Data sources

MEDLINE, PsycINFO, CINAHL were searched using English language limitation.

Eligibility criteria

Included participants were aged 65 and over (older adults) and between 13 and 19 years (adolescents) participating in intergenerational programmes from non-familial generations. Studies had to be published in English between 2000 and 2020 and could be quantitative, qualitative or mixed-methods primary research studies.

Data extraction and synthesis

Two independent reviewers used a bespoke data extraction form. All authors were involved in the synthesis process which used the extracted data to illuminate the contexts, mechanisms and outcomes that underpinned reviewed programmes.

Results

The nine included studies were set in different contexts, including community organisations, schools and aged care facilities. They used an array of interventions including reminiscence therapy, craft or space for conversation. Despite study heterogeneity, the parallels in psychosocial development between older adults and adolescents were shown to be a likely driver for improved social health outcomes. Programmes most likely to improve social health outcomes were those that acknowledged psychosocial development, were delivered in community settings, leveraged pedagogical frameworks, used trained facilitators and supported participants to build relationships through shared purpose.

Conclusions

This review contributes a logic model to support the design and development of intergenerational programmes involving adolescents to improve social connectedness in older adults. Future research to test the logic model in practice is needed.
Exploring the postoperative pain experiences of individuals with opioid use disorder and the nurses providing care in the USA: A qualitative descriptive study protocol
Authors: Pavone Kara , Gorgol Hilary , Rust Victoria , Bronski Mary , Labelle Colleen , Compton Peggy
Published: October 2023

Introduction

The goal of this study is to gain firsthand insights from individuals with a history of opioid use disorder (OUD) using medication for OUD on their experiences with postoperative pain care. This study also seeks to describe the experiences of nurses caring for individuals with OUD, and the challenges they may face managing complaints of pain in this population. Research suggests that hospitals can significantly enhance the quality of the care they deliver by investigating an individual’s experience in the care setting. These insights will allow for the development of strategies for nurses to deepen their understanding of and, therefore, advocate and improve care for, this vulnerable and often stigmatised population.

Methods and analysis

A qualitative descriptive study will be conducted consisting of a prescreening and demographics questionnaire, and individual semistructured interviews with approximately 10–15 individuals with OUD having recently undergone surgery and 10–15 nurses providing care for this population for a total of 20–30 interviews. This approach involves the collection of separate but complementary data (ie, perceptions of individuals with OUD and nurses) concerning the phenomena of postoperative pain management. Sampling will continue until data saturation is reached. Descriptive statistics and thematic analysis will then be used. Reporting will adhere to the Standards for Reporting Qualitative Research checklist.

Ethics and dissemination

This study received approval from the Institutional Review Board at Northeastern University. Alongside peer-reviewed journal publications, the findings will be presented at relevant conferences, and a plain language summary will be distributed to the study participants.
Volume-outcome relationship in balloon aortic valvuloplasty: results of a consecutive, patient-level data analysis from a Japanese nationwide multicentre registry (J-SHD)
Authors: Iwasaki Masamichi , Konishi Akihide , Takahara Mitsuyoshi , Kohsaka Shun , Okuda Masanori , Hayashi Takatoshi , Takamisawa Itaru , Ishii Hideki , Amano Tetsuya , Shinke Toshiro , Ikari Yuji
Published: October 2023

Objective

Transcatheter balloon aortic valvuloplasty (BAV) remains an important alternative treatment for severe, symptomatic aortic stenosis. With increasing numbers of BAVs being performed, the need for large-scale volume-outcome relationship assessments has become evident. Here, we aimed to explain such relationships by analysing consecutive, patient-level BAV data recorded in a prospective Japanese nationwide multicentre registry.

Design

Prospective study.

Setting

Data of 1920 BAVs performed in 200 Japanese hospitals from January 2015 to December 2019.

Participants

The mean patient age was 85 years, and 36.9% of procedures involved male patients.

Methods

The efficacy of BAV was assessed by reducing the mean transaortic valve gradient after the procedure. We also assessed in-hospital complication rates, including in-hospital death, bleeding, urgent surgery, distal embolism, vessel rupture and contrast-induced nephropathy. Based on the distribution of case volume (median 20, IQR 10–46), we divided the patients into high-volume (≥20) and low-volume (<20) groups. In-hospital complication risk was assessed with adjustment by logistic regression modelling.

Results

Indications for BAV included palliative/destination (44.2%), bridge to transcatheter aortic valve replacement (34.5%), bridge to surgical aortic valve replacement (7.4%) and salvage (9.7%). Reduction of the mean transaortic valve gradient was similar between the high-volume and low-volume groups (20 mm Hg vs 20 mm Hg, p=0.12). The proportion of in-hospital complications during BAV was 4.2%, and the incidence of complications showed no difference between the high-volume and low-volume groups (4.2% vs 4.1%, p=1.00). Rather than hospital volume, salvage procedure was an independent predictor of in-hospital complications (OR, 4.04; 95% CI, 2.03 to 8.06; p<0.001).

Conclusion

The current study demonstrated that procedural outcomes of BAV were largely independent of its institutional volume.
Evaluation of US oncology electronic health record real-world data to reduce uncertainty in health technology appraisals: a retrospective cohort study
Authors: Mpofu Philani , Kent Seamus , Jónsson Páll , Pittell Harlan , Groves Brad , Altomare Ivy , Copeland Amanda , Baxi Shrujal , Bargo Danielle , Sujenthiran Arun , Adamson Blythe
Published: October 2023

Objectives

Examine whether data from early access to medicines in the USA can be used to inform National Institute for Health and Care Excellence (NICE) health technology assessments (HTA) in oncology.

Design

Retrospective cohort study.

Setting

Oncology-based community and academic treatment centres in the USA.

Participants

Patients present in a nationwide electronic health record (EHR)-derived deidentified database.

Interventions

Cancer drugs that underwent NICE technology appraisal (TA) between 2014 and 2019.

Primary and secondary outcome measures

The count and follow-up time of US patients, available in the EHR, who were exposed to cancer drugs of interest in the period between Food and Drug Administration (FDA) approval and dates relevant to the NICE appraisal process.

Results

In 59 of 60 TAs analysed, the cancer therapy was approved in the USA before the final appraisal by NICE. The median time from FDA approval to the publication of NICE recommendations was 18.5 months, at which time the US EHR-derived database had, on average, 269 patients (SD=356) exposed to the new therapy, with a median of 75.3 person-years (IQR: 13.1–173) in time-at-risk. A case study generated evidence on real-world overall survival and treatment duration.

Conclusions

Across different cancer therapies, there was substantial variability in US real-world data accumulated between FDA approval and NICE decision milestones. The applicability of these data to generate evidence for HTA decision-making should be assessed on a case-by-case basis depending on the intended HTA use case.
Health locus of control and self-management behaviours among individuals with ischaemic heart disease: protocol for a scoping review
Authors: Wang Run , Zhou Chunlan , Parry Monica
Published: October 2023

Introduction

Ischaemic heart disease is a significant cause of morbidity and mortality worldwide. Self-management is a way to reduce the risk associated with ischaemic heart disease; however, some individuals may not have the ability or willingness to engage in self-management behaviours. One approach to identify an individual’s readiness and capacity to engage in self-management behaviours is to assess their health locus of control. Based on the Individual and Family Self-Management Theory, this review’s objectives are to describe: (1) how health locus of control affects the process of engaging in self-management behaviours, (2) impacts of health locus of control on outcomes associated with self-management behaviours and (3) potential contextual variations in the relationship between health locus of control and self-management behaviours.

Methods and analysis

The scoping review will be guided by the Joanna Briggs Institute methodological framework. A comprehensive search will encompass seven electronic databases (Ovid Medline, CINAHL, EMBASE, APA PsycINFO, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Scopus) and grey literature sources (ProQuest Dissertations, ClinicalTrials.gov). Collaborative efforts with library experts will inform our search strategies, building on insights from previous reviews centred on self-management and ischaemic heart disease. Two review authors will independently conduct the screening and data extraction processes; discrepancies will be resolved through consensus or discussion with a third review author. The review will include English studies from database inception, focusing on the health locus of control among adults with ischaemic heart disease. Findings will be presented graphically and tabularly, together with a narrative description.

Ethics and dissemination

We will collect data from published and grey literature, meaning ethical approval is not necessary. Findings will be published in peer-reviewed journals and presented at academic conferences.

Registration details

Open Science Framework (https://doi.org/10.17605/OSF.IO/B4A6F).
Comparisons of procedural characteristics and clinical outcomes between SMARTTOUCH SURROUNDFLOW catheter and other catheters for atrial fibrillation radiofrequency catheter ablation: a systematic literature review
Authors: Li Jianyong , Zhou Guifang , Li Xinzhong , Huang Senlin , Lin Hairuo , Lin Shaopeng , Tan Liang , Chen Wendong , Huang Xiaobo , Wang Yuegang
Published: October 2023

Background

SMARTTOUCH SURROUNDFLOW (STSF) catheter is the new generation of SMARTTOUCH (ST) catheter with an upgraded irrigation system for radiofrequency catheter ablation (RFCA) in patients with atrial fibrillation (AF).

Methods

This systematic literature review searched the major English and Chinese bibliographic databases from 2016 to 2022 for any original clinical studies assessing the STSF catheter for RFCA in AF patients. Meta-analysis with a random effects model was used for evidence synthesis.

Results

Pooled outcomes from 19 included studies indicated that STSF catheter was associated with a significantly shorter procedure time (weighted mean difference (WMD): −17.4 min, p<0.001), shorter ablation time (WMD: −6.6 min, p<0.001) and lower catheter irrigation fluid volume (WMD: −492.7 mL, p<0.001) than ST catheter. Pooled outcomes from four included studies with paroxysmal AF patients reported that using the STSF catheter for RFCA was associated with a significantly shorter ablation time (WMD: −5.7 min, p<0.001) and a lower risk of 1-year postablation arrhythmia recurrence (rate ratio: 0.504, p<0.001) than the SURROUNDFLOW (SF) catheter. Significant reductions in procedure time and ablation time associated with the STSF catheter were also reported in the other four studies using non-ST/SF catheters as the control. Overall complications of STSF catheter and control catheters were comparable.

Conclusions

Using the STSF catheter was superior to using the ST catheter to conduct RFCA for AF by significantly reducing procedure time, ablation time, fluoroscopy time and irrigation fluid volume. The superiority of the STSF catheter over the SF catheter and other non-ST/SF catheters for RFCA needs further confirmation.