bluuebunny/crossref_metadata_2025_split huggingface dataset:
The type II secretion system as an underappreciated and understudied mediator of interbacterial antagonism
Authors: Cianciotto Nicholas P. 
Published: July 2024

ABSTRACT

Interbacterial antagonism involves all major phyla, occurs across the full range of ecological niches, and has great significance for the environment, clinical arena, and agricultural and industrial sectors. Though the earliest insight into interbacterial antagonism traces back to the discovery of antibiotics, a paradigm shift happened when it was learned that protein secretion systems (e.g., types VI and IV secretion systems) deliver toxic “effectors” against competitors. However, a link between interbacterial antagonism and the Gram-negative type II secretion system (T2SS), which exists in many pathogens and environmental species, is not evident in prior reviews on bacterial competition or T2SS function. A current examination of the literature revealed four examples of a T2SS or one of its known substrates having a bactericidal activity against a Gram-positive target or another Gram-negative. When further studied, the T2SS effectors proved to be peptidases that target the peptidoglycan of the competitor. There are also reports of various bacteriolytic enzymes occurring in the culture supernatants of some other Gram-negative species, and a link between these bactericidal activities and T2SS is suggested. Thus, a T2SS can be a mediator of interbacterial antagonism, and it is possible that many T2SSs have antibacterial outputs. Yet, at present, the T2SS remains relatively understudied for its role in interbacterial competition. Arguably, there is a need to analyze the T2SSs of a broader range of species for their role in interbacterial antagonism. Such investigation offers, among other things, a possible pathway toward developing new antimicrobials for treating disease.
Deciphering the interplay of gut microbiota and metabolomics in retinal vein occlusion
Authors: Ai Jing , Cao Yunbo , Zhang Cong , Sun Jun-Hui , Dong Feng , Jing Li , Wang Jianyong , Cui Hongguang 
Published: July 2024

ABSTRACT

This study aims to explore the link between retinal vein occlusion (RVO), a blinding ocular condition, and alterations in gut microbiota composition, to offer insights into the pathogenesis of RVO. Fecal samples from 25 RVO patients and 11 non-RVO individuals were analyzed using 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS). Significant differences in the abundance of gut microbial species were noted between RVO and non-RVO groups. At the phylum level, the RVO group showed an elevation in the ratio of Firmicutes to Bacteroidetes. At the genus level, the RVO group showed higher abundance in
Escherichia_Shigella
(
P
< 0.05) and less abundance in
Parabacteroides
(
P
< 0.01) than the non-RVO group. Functional predictions indicated reduced folate synthesis, biotin metabolism, and oxidative phosphorylation, with an increase in butyric acid metabolism in the RVO group. LC-MS analysis showed significant differences in purine metabolism, ABC transporters, and naphthalene degradation pathways, especially purine metabolism. Pearson correlation analysis revealed significant associations between bacterial genera and fecal metabolites. Enrichment analysis highlighted connections between specific metabolites and bacterial genera. The findings showed that the dysregulation of gut microbiota was observed in RVO patients, suggesting the gut microbiota as a potential therapeutic target. Modulating the gut microbiota could be a novel strategy for managing RVO and improving patient outcomes. Furthermore, the study findings suggest the involvement of gut microbial dysbiosis in RVO development, underscoring the significance of understanding its pathogenesis for effective treatment development.

IMPORTANCE
Retinal vein occlusion (RVO) is a blinding ocular condition, and understanding its pathogenesis is crucial for developing effective treatments. This study demonstrates significant differences in gut microbiota composition between RVO patients and non-RVO individuals, implicating the involvement of gut microbial dysbiosis in RVO development. Functional predictions and metabolic profiling provide insights into the underlying mechanisms, highlighting potential pathways for therapeutic intervention. These findings suggest that modulating the gut microbiota might be a promising strategy for managing RVO and improving patient outcomes.
A comparative study of sampling methods in the detection of esophageal cancer-related microbiota
Authors: Xue Xia , Wang Siyu , Li Yi , Liu Zhenzhen , Zhang Jun , Hu Ziqing , Fan Chengcheng , Zhang Xiaojuan , Li Hongle , Li Jun 
Published: July 2024

ABSTRACT

Esophageal cancer (EC) is a multifaceted disease. Our understanding of the involvement of esophageal microbiota in its pathogenesis and progression is limited, which is due to the lack of proper endoscopic sampling methods. Hereby, we conducted a comparative analysis of paired samples obtained through endoscopic brushing and cytosponge, aiming at assessing the feasibility of using cytosponge as a minimally invasive sampling way for studying esophageal microbiota. Our findings suggest that cytosponge sampling yielded significantly superior community richness and diversity compared to endoscopic brushing in both controls (non-cancerous) and EC individuals. The analysis of beta-diversity revealed distinct microbial community pattern in the genus diversity between the two sampling methods, underscoring the importance of selecting appropriate sampling methods to effectively characterize the esophageal microbiota. Specifically,
Lactococcus
and
Serratia
showed higher abundance in the samples collected by endoscopic brushing, while
Alloprevotella
and
Leptotrichia
were more enriched in the samples collected by cytosponge. These differences in dominant microbes were associated with metabolic pathways that particularly were related to host inflammation, such as pyruvate and glucose metabolisms. Notably, the phylogenetic levels of the microbiota indicated varied explanatory power for different detection purposes. This study underscores the substantial impact of sampling method selection on the acquisition of esophageal microbiota associated with the EC development, encompassing considerations of both abundance and diversity. This highlights the significance of selecting an appropriate sampling method for investigating the esophageal microbial status and studying the micro-environment in EC-related individuals.

IMPORTANCE
This study addresses a critical issue in esophageal cancer study by comparing two different sampling methods, endoscopic brushing and cytosponge, for investigating the esophageal microbiota. Our work highlights the suitability of the cytosponge technique as a minimally invasive sampling method for studying the esophageal microbiota and emphasizes the importance of selecting an appropriate sampling method to characterize the microbial community. Our findings have significant implications for advancing the understanding of the role of the esophageal microbiota in cancer development and will inform future research and clinical approaches in this field.
Comparison of
Bordetella
species identification among differing rt-PCR assays in the United States
Authors: Cole Matthew , Simon Ashley K. , Faulkner Amanda , Skoff Tami , Tondella Maria L. , Montero Clemente , Nye Melinda B. , Williams Margaret 
Published: July 2024

ABSTRACT

In the United States, the general laboratory method for diagnosing pertussis, caused by
Bordetella pertussis,
is real-time PCR (rt-PCR) targeting insertion sequence 481 (IS
481
). Other
Bordetella
species (
parapertussis, holmesii
, and
bronchiseptica
) can also cause a pertussis-like syndrome, and some commercial laboratory assays include the insertion sequence 1001 (pIS
1001
) that can detect
B. parapertussis
/
B. bronchiseptica (BppBb
). Because IS
481
exists in
B. pertussis
and
B. holmesii
, current commercial assays cannot differentiate these two species. We used a multiplex rt-PCR assay containing species-specific targets to
Bordetella
to evaluate clinical specimens detected as
B. pertussis
/
B. holmesii
(
BpBh
) or
BppBb
by commercial laboratories. A sample of 3,984 clinical specimens positive for IS
481
or pIS
1001
from two commercial laboratories during 2012–2019 were re-tested at CDC. Agreement of
Bordetella
species between the CDC and commercial laboratory assays, and the proportion of commercial laboratory specimens that were non-
B
.
pertussis
by CDC’s assay was assessed. Overall agreement in
Bordetella
species detection and identification between the CDC and commercial lab assays was 85%. Agreement for identifying
B. pertussis
was 87% for 3,663
BpBh
specimens and 98% for identifying
B. parapertussis
in 310
BppBb
specimens. CDC’s assay detected
B. holmesii
in 55/3,984 (1.4%) specimens. Most discrepant results (410/490, 82%) were
BpBh
specimens interpreted as indeterminate
B. pertussis
at CDC. We found a small portion of
B. holmesii
in a sample of IS
481
-positive clinical specimens originally identified by commercial laboratory rt-PCR assays, suggesting that commercial PCR assays are a reliable diagnostic tool for correctly identifying
Bordetella
species in most patients with suspected pertussis.

IMPORTANCE

When testing specimens collected from patients with suspected pertussis, large-scale commercial laboratories in the United States employ an IS
481
-based assay that cannot differentiate between
Bordetella pertussis
and
Bordetella holmseii
. The level of
B. holmesii
causing pertussis-like illness in the United States is not well-understood given that only
B. pertussis
is nationally notifiable. After re-testing with a multiplex, species-specific rt-PCR assay, our data show low levels of
B. holmesii
identified in a sample of IS
481
-positive clinical specimens originally identified by commercial laboratory rt-PCR assays. These results reinforce the validity of large-scale commercial rt-PCR testing as a reliable diagnostic tool for pertussis in the United States.
The role of MNK1-mTORC1 pathway in modulating macrophage responses to
Vibrio vulnificus
infection
Authors: Lou Yong-Liang , Xie Dan-Li , Huang Xian-Hui , Zheng Meng-Meng , Chen Na , Xu Ji-Ru 
Published: July 2024

ABSTRACT

Vibrio vulnificus
(
Vv
) is known to cause life-threatening infections, particularly septicemia. These patients often exhibit elevated levels of pro-inflammatory cytokines. While it is established that mitogen-activated protein kinase (MAPK)-interacting kinase (MNK) contributes to the production of pro-inflammatory cytokines, the role of MNK in macrophages during
Vv
infection remains unclear. In this study, we investigate the impact of MNK on macrophages. We demonstrate that the inhibition of MNK in J774A.1 cells, when treated with lipopolysaccharide or
Vv
, resulted in decreased production of tumor necrosis factor alpha and interleukin-6, without affecting their transcription. Interestingly, treatment with MNK inhibitor CGP57380 led to enhanced phosphorylation of MNK1 but decreased phosphorylation of eIF4E. Moreover, MNK1 knockout cells exhibited an increased capacity for phagocytosis and clearance of
Vv
, with more acidic phagosomes than the parental cells. Notably, CGP57380 did not impact phagocytosis, bacterial clearance, or phagosome acidification in
Vv
-infected J774A.1 cells. Considering the reported association between MNK and mammalian target of rapamycin complex 1 (mTORC1) activation, we investigated the mTORC1 signaling in MNK1 knockout cells infected with
Vv
. Our results revealed that attenuation of the mTORC1 signaling in these cells and treatment with the mTORC1 inhibitor rapamycin significantly enhanced bacterial clearance in J774A.1 cells following
Vv
infection. In summary, our findings suggest that MNK promotes the
Vv
-induced cytokine production in J774A.1 cells without affecting their transcription levels. MNK1 appears to impair the phagocytosis, bacterial clearance, and phagosome acidification in
Vv
-infected J774A.1 cells through the MNK1-mTORC1 signaling pathway rather than the MNK1-eIF4E signaling pathway. Our findings highlight the importance of the MNK1-mTORC1 pathway in modulating macrophage responses to
Vv
infection.

IMPORTANCE

Mitogen-activated protein kinase (MAPK)-interacting kinase (MNK) plays a role in promoting the production of tumor necrosis factor alpha and interleukin-6 in macrophages during
Vibrio vulnificus
(
Vv
) infection. Inhibition or knockout of MNK1 in J774A.1 cells resulted in reduced cytokine production without affecting their transcription levels. MNK1 also impairs phagocytosis, bacterial clearance, and phagosome acidification in
Vv
-infected cells through the MNK1-mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. The findings highlight the importance of the MNK1-mTORC1 pathway in modulating macrophage responses to
Vv
infection.
High rates of respiratory illnesses upon arrival: lessons from Team USA at the Santiago 2023 Pan American and Parapan American Games
Authors: Post Eric G , Anderson Travis , Samson Olivia , Triplett Ashley N , Gidley Alexis D , Isono Steven S , Watters Jennifer , Donaldson Amber T , Finnoff Jonathan T , Adams William M 
Published: July 2024

ObjectiveTo describe the incidence and characteristics of injuries and illnesses among Team USA athletes competing at the Santiago 2023 Pan American Games (PAG) and Parapan American Games (PPAG), with a particular focus on the incidence of respiratory illnesses and on injuries for sports new to the Olympic and Paralympic programmes.MethodsIllnesses and injuries occurring among the 870 Team USA athletes competing in the Santiago 2023 PAG or PPAG were documented within Team USA’s Injury and Illness Surveillance system. Illness and injury incidence per 1000 athlete-days (ADs) and incidence ratios (IR) were calculated, both with 95% CIs.ResultsIllness (IR 2.5, 95% CI 1.6, 3.9) and injury (IR 1.8, 95% CI 1.3, 2.5) rates were greater during PPAG compared with PAG. Illness rates were higher in the pre-opening ceremony period compared with the competition period for both PAG (IR 2.7, 95% CI 1.1, 5.9) and PPAG (IR 1.9, 95% CI 0.9, 3.8). Respiratory illness was the most common illness with 3.2% and 8.9% of all Team USA athletes reporting a respiratory illness during the PAG and PPAG, respectively. Sports that are relatively new to the Olympic/Paralympic programmes exhibited the highest injury rates during the Games: breaking (250.0 (91.7, 544.2) per 1000 ADs), Para taekwondo (93.8 (19.3, 274.0) per 1000 ADs) and surfing (88.9 (24.2, 227.6) per 1000 ADs).ConclusionRespiratory illness rates were the most common type of illness during both PAG and PPAG and were more likely to occur prior to competition starting. Our data have identified high injury risk populations (breaking, surfing, Para taekwondo) and timing (pre-opening ceremony period) for further risk factor analysis.
Comparative effectiveness of neuraxial versus general anesthesia in total joint replacement surgery: an updated retrospective analysis using more recent data
Authors: Illescas Alex , Cozowicz Crispiana , Zhong Haoyan , Reisinger Lisa , Liu Jiabin , Poeran Jashvant , Memtsoudis Stavros G 
Published: July 2024

IntroductionOver a decade ago, our study group showed improved outcomes among total hip/knee arthroplasty (THA/TKA) patients given neuraxial versus general anesthesia. As the use of neuraxial anesthesia has increased and anesthesia practices evolve, updated analyses are critical to ensure if previously found differences still persist.MethodsThis retrospective cohort study included elective THA/TKAs from 2006 to 2021 as recorded in the all-payor Premier Healthcare Database. Multivariable regression models measured the association between anesthesia type (neuraxial, general, combined) and several adverse outcomes (pulmonary embolism, cerebrovascular events, pulmonary compromise, cardiac complications, acute myocardial infarction, pneumonia, all infections, acute renal failure, gastrointestinal complications, postoperative mechanical ventilation, intensive care unit admissions, and blood transfusions); models were run separately by period (2006–2015 and 2016–2021) and THA/TKA.ResultsWe identified 587,919 and 499,484 THAs for 2006–2015 and 2016–2021, respectively; this was 1,186,483 and 803,324 for TKAs. Among THAs, neuraxial anesthesia use increased from 10.7% in 2006 to 25.7% in 2021; during both time periods, specifically neuraxial versus general anesthesia was associated with lower odds for most adverse outcomes, with sometimes stronger (protective) effect estimates observed for 2016–2021 versus 2006–2015 (eg, acute renal failure OR 0.72 CI 0.65 to 0.80 vs OR 0.56 CI 0.50 to 0.63 and blood transfusion OR 0.91 CI 0.89 to 0.94 vs OR 0.44 CI 0.41 to 0.47, respectively; all p<0.001). Similar patterns existed for TKAs.ConclusionThese findings re-confirm our study group’s decade-old study using more recent data and offer additional evidence toward the sustained benefit of neuraxial anesthesia in major orthopedic surgery.
Analysis of Investment in Equity: Value or Growth Investing?
Authors: Chari Latha , Siddula Narsimhulu 
Published: July 2024

Mr. TVK Vivek Kumar, Managing Partner at Bestpals Research and Advisory LLP, was searching for investment opportunities during the lockdown period following COVID-19. The stock markets witnessed a crash and most stocks were trading at decade-low prices. Mr. Kumar identified this as an opportunity for investment and wealth creation. He started scanning the stocks related to different sectors like Retail, Fast Moving Consumer Goods, E-commerce, and soon discovered the agricultural equipment and machinery sector stocks may offer attractive opportunities. He collected data related to the agricultural machinery sector and details of Indian companies operating in the Agricultural Machinery and Farm equipment sector. After reviewing the company profiles, he concluded that Escorts Ltd. and VST Tillers Tractors Ltd. were less diversified companies that mostly focused on manufacturing agricultural equipment. Upon analyzing the financial performance of the two companies, he was unable to decide which of these two companies for investments had the potential to deliver better returns. The goal was to identify Value or Growth stocks for a short-term investment horizon of 12-18 months, as he had no idea what the long-term outlook might be in the post-COVID-19 era.
Eisenstein's Capital Diaries: An Introduction
Authors: Vogman Elena 
Published: July 2024

Abstract
This text serves as an introduction to the first publication of an extensive new selection from Sergei Eisenstein's notebooks for a film of Capital (made “according to the script of K. Marx”): the Capital Diaries. While these texts have haunted the imaginations of historians, artists, and writers (from Guy Debord to Milica Tomic and Alexander Kluge) ever since short excerpts were first published in Russian in 1973 and English in October in 1976, this introduction presents a different and much broader selection, situating the experimental dimension of the notes between their main sources, Karl Marx's Das Kapital and James Joyce's Ulysses, as well as in the discursive framework of Viktor Shklovsky's theory of “defamilarization,” Nikolai Marr's “palaeontology of speech,” Mikhail Bakhtin's notion of “polyphony,” and Eisenstein's own conceptual and cinematic propositions, such as “intellectual attraction,” “typage,” and “inner monologue.” Furthermore, it traces the use value of images and collages in Eisenstein's diaries according to their potential to recirculate Marx's concepts and reveal cinema's participation in the entangled regimes of fascism and capitalism.
Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert
Authors: Han Zhi-peng , Yang Rui-zhi , Zhou Wen , Zhang Lu-lu , Wang Jie-ru , Liu Chun-jie , Liu Shu-dong 
Published: July 2024

AbstractAnalyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental adaptability, enhancing breeding efficiency, and achieving effective conservation and rational utilization of genetic resources. In this study, we utilized Illumina Ovine SNP 50 K BeadChip data from four indigenous sheep breeds from the southern margin of the Taklamakan Desert (Duolang sheep: n = 36, Hetian sheep: n = 74, Kunlun sheep: n = 27, Qira black sheep: n = 178) and three foreign meat sheep breeds (Poll Dorset sheep: n = 105, Suffolk sheep: n = 153, Texel sheep: n = 150) to investigate the population structure, genetic diversity, and genomic signals of positive selection within the indigenous sheep. According to the Principal component analysis (PCA), the Neighbor-Joining tree (NJ tree), and Admixture, we revealed distinct clustering patterns of these seven sheep breeds based on their geographical distribution. Then used Cross Population Extended Haplotype Homozygosity (XP-EHH), Fixation Index (FST), and Integrated Haplotype Score (iHS), we identified a collective set of 32 overlapping genes under positive selection across four indigenous sheep breeds. These genes are associated with wool follicle development and wool traits, desert environmental adaptability, disease resistance, reproduction, and high-altitude adaptability. This study reveals the population structure and genomic selection characteristics in the extreme desert environments of native sheep breeds from the southern edge of the Taklimakan Desert, providing new insights into the conservation and sustainable use of indigenous sheep genetic resources in extreme environments. Additionally, these findings offer valuable genetic resources for sheep and other mammals to adapt to global climate change.
Biocontrol potential and growth-promoting effect of endophytic fungus Talaromyces muroii SD1-4 against potato leaf spot disease caused by Alternaria alternata
Authors: Zhang Lihua , Xu Wei , Zhao Zhibo , Long Youhua , Fan Rong 
Published: July 2024

Abstract
Background
Alternaria alternata is the primary pathogen of potato leaf spot disease, resulting in significant potato yield losses globally. Endophytic microorganism-based biological control, especially using microorganisms from host plants, has emerged as a promising and eco-friendly approach for managing plant diseases. Therefore, this study aimed to isolate, identify and characterize the endophytic fungi from healthy potato leaves which had great antifungal activity to the potato leaf spot pathogen of A. alternata in vitro and in vivo.

Results
An endophytic fungal strain SD1-4 was isolated from healthy potato leaves and was identified as Talaromyces muroii through morphological and sequencing analysis. The strain SD1-4 exhibited potent antifungal activity against the potato leaf spot pathogen A. alternata Lill, with a hyphal inhibition rate of 69.19%. Microscopic and scanning electron microscope observations revealed that the strain SD1-4 grew parallel to, coiled around, shrunk and deformed the mycelia of A. alternata Lill. Additionally, the enzyme activities of chitinase and β-1, 3-glucanase significantly increased in the hyphae of A. alternata Lill when co-cultured with the strain SD1-4, indicating severe impairment of the cell wall function of A. alternata Lill. Furthermore, the mycelial growth and conidial germination of A. alternata Lill were significantly suppressed by the aseptic filtrate of the strain SD1-4, with inhibition rates of 79.00% and 80.67%, respectively. Decrease of leaf spot disease index from 78.36 to 37.03 was also observed in potato plants treated with the strain SD1-4, along with the significantly increased plant growth characters including plant height, root length, fresh weight, dry weight, chlorophyll content and photosynthetic rate of potato seedlings.

Conclusion
The endophyte fungus of T. muroii SD1-4 isolated from healthy potato leaves in the present study showed high biocontrol potential against potato leaf spot disease caused by A. alternata via direct parasitism or antifungal metabolites, and had positive roles in promoting potato plant growth.