bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term changes in the phenotype and cytokine production of monocytes in COVID-19 recovered and vaccinated individuals
Authors: Ostapchuk Yekaterina O. , Lushova Anzhelika V. , Kan Sofia A. , Abdolla Nurshat , Kali Aikyn , Tleulieva Raikhan , Perfilyeva Anastassiya V. , Perfilyeva Yuliya V. 
Published: June 2024

ABSTRACT

Monocytes play a crucial role in the immune response against pathogens. Here, we sought to determine COVID-19 and the vaccine Gam-COVID-Vac induce long-term changes in the phenotype and cytokine production of circulating monocytes. Monocytes were purified from peripheral blood mononuclear cells of healthy donors who had not had COVID-19 or vaccination, who had received two doses of Gam-COVID-Vac, and who had mild/moderate COVID-19 in the last 6 months and evaluated by flow cytometry. To investigate the effect of SARS-CoV-2 proteins, monocytes were cultured for 2 days with or without stimulation with recombinant SARS-CoV-2 S1 and N peptides. Monocytes obtained from vaccinated and recovered individuals showed increased basal expression of HLA-DR, CD63, CXCR2, and TLR7. We also observed an increased frequency of CD63
+
classical monocytes in both groups, as well as an increased frequency of HLA-DR
+
non-classical monocytes in the COVID-19-recovered group compared to the control group. Monocytes from vaccinated and recovered donors produced higher basal levels of IL-6, IL-1β, and TNF-α cytokines.
Ex vivo
stimulation with SARS-CoV-2 antigens induced increased expression of HLA-DR and TLR7 on monocytes obtained from the control group. The challenge with SARS-CoV-2 antigens had no effect on the production of IL-6, IL-1β, and TNF-α cytokines by monocytes. The acquired data offer compelling evidence of enduring alterations in both the phenotype and functional status of circulating monocytes subsequent to vaccination with Gam-COVID-Vac and mild/moderate COVID-19 infection. At least some of these changes appear to be a consequence of exposure to SARS-CoV-2 S1 and N antigens.
Non-interchangeable functions of efflux transporters of
Pseudomonas aeruginosa
in survival under infection-associated stress
Authors: Adamiak Justyna W. , Ajmal Laiba , Zgurskaya Helen I. 
Published: June 2024

ABSTRACT

Pseudomonas aeruginosa
is a challenging opportunistic pathogen due to its intrinsic and acquired mechanisms of antibiotic resistance. A large repertoire of efflux transporters actively expels antibiotics, toxins, and metabolites from cells and enables growth of
P. aeruginosa
in diverse environments. In this study, we analyzed the roles of representative efflux pumps from the Resistance-Nodulation-Division (RND), Major Facilitator Superfamily (MFS), and Small Multidrug Resistance (SMR) families of proteins in the susceptibility of
P. aeruginosa
to antibiotics and bacterial growth under stresses imposed by human hosts during bacterial infections: an elevated temperature, osmotic stress, low iron, bile salts, and acidic pH. We selected five RND pumps MexAB-OprM, MexEF-OprN, MexCD-OprJ, MuxABC-OpmB, and TriABC-OpmH that differ in their substrate specificities and expression profiles, two MFS efflux pumps PA3136-3137 and PA5158-5160 renamed here into MfsAB and MfsCD-OpmG, respectively, and an SMR efflux transporter PA1540-1541 (MdtJI). We found that the most promiscuous RND pumps such as MexEF-OprN and MexAB-OprM are integrated into diverse survival mechanisms and enable
P. aeruginosa
growth under various stresses. MuxABC-OpmB and TriABC-OpmH pumps with narrower substrate spectra are beneficial only in the presence of the iron chelator 2,2′-dipyridyl and bile salts, respectively. MFS pumps do not contribute to antibiotic efflux but play orthogonal roles in acidic pH, low iron, and in the presence of bile salts. In contrast, MdtJI protects against polycationic antibiotics but does not contribute to survival under stress. Thus, efflux pumps play specific, non-interchangeable functions in
P. aeruginosa
cell physiology and bacterial survival under stresses.

IMPORTANCE

The role of multidrug efflux pumps in the intrinsic and clinical levels of antibiotic resistance in
Pseudomonas aeruginosa
and other gram-negative bacteria is well-established. Their functions in bacterial physiology, however, remain unclear. The
P. aeruginosa
genome comprises an arsenal of efflux pumps from different protein families, the substrate specificities of which are typically assessed by measuring their impact on susceptibility to antibiotics. In this study, we analyzed how deletions and overproductions of efflux pumps affect
P. aeruginosa
growth under human-infection-induced stresses. Our results show that the physiological functions of multidrug efflux pumps are non-redundant and essential for the survival of this important human pathogen under stress.
Targeted eradication of EBV-positive cancer cells by CRISPR/dCas9-mediated EBV reactivation in combination with ganciclovir
Authors: Sugiokto Febri Gunawan , Li Renfeng 
Published: June 2024

ABSTRACT

Epstein-Barr virus (EBV) is a ubiquitous human tumor virus that establishes lifelong, persistent infections in B cells. The presence of EBV in cancer cells presents an opportunity to target these cells by reactivating the virus from latency. In this study, we developed a novel approach for EBV reactivation termed clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-mediated EBV reactivation (CMER) strategy. Using modified CRISPR-associated protein 9 (dCas9) fused with VP64, we designed 10 single guide RNAs (sgRNAs) to target and activate the EBV immediate-early gene promoter. In Akata Burkitt lymphoma cells, 9 out of 10 CMER sgRNAs effectively reactivated EBV. Among these, CMER sgRNA-5 triggered robust reactivation across various cell types, including lymphoma, gastric cancer, and nasopharyngeal carcinoma cells. Importantly, the combination of CMER and ganciclovir selectively eliminated EBV-positive cells, regardless of their cell origin. These findings indicate that targeted virus reactivation by CMER, combined with nucleoside analog therapy, holds promise for EBV-associated cancer treatment.

IMPORTANCE
This study explores a novel strategy called clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-mediated Epstein-Barr virus (EBV) reactivation (CMER) to reactivate the Epstein-Barr virus in cancer cells. EBV is associated with various cancers, and reactivating EBV from latency offers a potential therapeutic strategy. We utilized an enzymatically inactive CRISPR-associated protein 9 (dCas9) fused with VP64 and designed 10 single guide RNAs to target the EBV immediate-early gene promoter. Nine of these sgRNAs effectively reactivated EBV in Burkitt lymphoma cells, with CMER sgRNA-5 demonstrating strong reactivation across different cancer cell types. Combining CMER with ganciclovir selectively eliminated EBV-positive cells, showing promise for EBV-associated cancer treatment.
Iron limitation induces motility in uropathogenic
E. coli
CFT073 partially through action of LpdA
Authors: Frick-Cheng A. E. , Shea A. E. , Roberts J. R. , Smith S. N. , Ohi M. D. , Mobley H. L. T. 
Published: June 2024

ABSTRACT

More than half of women will experience a urinary tract infection (UTI) with most cases caused by uropathogenic
Escherichia coli
(UPEC). Bacterial swimming motility enhances UPEC pathogenicity, resulting in more severe disease outcomes including kidney infection. Surprisingly, the connection between motility and iron limitation is mostly unexplored despite the lack of free iron available in the host. We sought to investigate a potential connection between iron restriction and regulation of motility in UPEC. We cultured
E. coli
CFT073, a prototypical UPEC strain, under iron limitation and observed that CFT073 had elevated
fliC
(flagella) promoter activity, and this iron-specific response was repressed by the addition of exogenous iron. We confirmed increased flagellar expression in CFT073 by measuring
fliC
transcript, FliC protein, and surface-expressed flagella under iron-limited conditions. Interestingly, known motility regulator
flhDC
did not have altered transcription under these conditions. To define the regulatory mechanism of this response, we constructed single knockouts of eight master regulators and found the iron-regulated response was lost in
crp, arcA,
and
fis
mutants. Thus, we focused on the five genes regulated by all three regulators. Of the five genes knocked out, the iron-regulated motility response was most strongly dysregulated in the
lpdA
mutant, which also resulted in significantly lowered fitness in the murine model of ascending UTI, both against the WT and a non-motile
fliC
mutant. Collectively, we demonstrated that iron-mediated motility in CFT073 is partially regulated by
lpdA
, which contributes to the understanding of how uropathogens differentially regulate motility mechanisms in the iron-restricted host.

IMPORTANCE

Urinary tract infections (UTIs) are ubiquitous and responsible for over five billion dollars in associated health care costs annually. Both iron acquisition and motility are highly studied virulence factors associated with uropathogenic
Escherichia coli
(UPEC), the main causative agent of uncomplicated UTI. This work is innovative by providing mechanistic insight into the synergistic relationship between these two critical virulence properties. Here, we demonstrate that iron limitation has pleiotropic effects with consequences that extend beyond metabolism and impact other virulence mechanisms. Indeed, targeting iron acquisition as a therapy may lead to an undesirable enhancement of UPEC pathogenesis through increased motility. It is vital to understand the full breadth of UPEC pathogenesis to adequately respond to this common infection, especially with the increase of antibiotic-resistant pathogens.
Cellular endosomal potassium ion flux regulates arenavirus uncoating during virus entry
Authors: Shaw Amelia B. , Tse Hiu Nam , Byford Owen , Plahe Grace , Moon-Walker Alex , Hover Samantha E. , Saphire Erica Ollmann , Whelan Sean P. J. , Mankouri Jamel , Fontana Juan , Barr John N. 
Published: June 2024

ABSTRACT

Lymphocytic choriomeningitis virus (LCMV) is an enveloped and segmented negative-sense RNA virus classified within the
Arenaviridae
family of the
Bunyavirales
order. LCMV is associated with fatal disease in immunocompromised populations and, as the prototypical arenavirus member, acts as a model for the many highly pathogenic members of the
Arenaviridae
family, such as Junín, Lassa, and Lujo viruses, all of which are associated with devastating hemorrhagic fevers. To enter cells, the LCMV envelope fuses with late endosomal membranes, for which two established requirements are low pH and interaction between the LCMV glycoprotein (GP) spike and secondary receptor CD164. LCMV subsequently uncoats, where the RNA genome-associated nucleoprotein (NP) separates from the Z protein matrix layer, releasing the viral genome into the cytosol. To further examine LCMV endosome escape, we performed an siRNA screen which identified host cell potassium ion (K

+

) channels as important for LCMV infection, with pharmacological inhibition confirming K
+
channel involvement during the LCMV entry phase completely abrogating productive infection. To better understand the K
+
-mediated block in infection, we tracked incoming virions along their entry pathway under physiological conditions, where uncoating was signified by separation of NP and Z proteins. In contrast, K
+
channel blockade prevented uncoating, trapping virions within Rab7 and CD164-positive endosomes, identifying K
+
as a third LCMV entry requirement. K
+
did not increase GP-CD164 binding or alter GP-CD164-dependent fusion. Thus, we propose that K
+
mediates uncoating by modulating NP-Z interactions within the virion interior. These results suggest K
+
channels represent a potential anti-arenaviral target.

IMPORTANCE

Arenaviruses can cause fatal human disease for which approved preventative or therapeutic options are not available. Here, using the prototypical LCMV, we identified K

+

channels as critical for arenavirus infection, playing a vital role during the entry phase of the infection cycle. We showed that blocking K

+

channel function resulted in entrapment of LCMV particles within late endosomal compartments, thus preventing productive replication. Our data suggest K

+

is required for LCMV uncoating and genome release by modulating interactions between the viral nucleoprotein and the matrix protein layer inside the virus particle.
Novel biomarker profiles to improve individual diagnosis and prognosis in patients with suspected inflammatory bowel disease: protocol for the Nordic inception cohort study (NORDTREAT)
Authors: Fejrskov Anja , Füchtbauer Johannes David , Davíðsdóttir Lóa G , Halfvarson Jonas , Høivik Marte Lie , Jensen Michael Dam , Mortensen Joachim Høg , Nielsen Lene Nyholm , Rejler Martin , Repsilber Dirk , Söderholm Johan D , Aalykke Claus , Andersen Vibeke , Christensen Robin , Kjeldsen Jens 
Published: June 2024

IntroductionInflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease, can be challenging to diagnose, and treatment outcomes are difficult to predict. In the NORDTREAT cohort study, a Nordic prospective multicentre study, we aim to identify novel molecular biomarkers of diagnostic value by assessing the diagnostic test accuracy (cross-sectionally), as well as the prognostic utility when used as prognostic markers in the long-term (cohort study). In the diagnostic test accuracy study, the primary outcome is a successful diagnosis using one or more novel index tests at baseline compared with the ECCO criteria as the reference standard. The composite outcome of the prognostic utility study is ‘severe IBD’ within 52 weeks from inclusion, defined as one or more of the following three events: IBD-related surgery, IBD-related hospitalisation or IBD-related death.Methods and analysisWe aim to recruit 800 patients referred on suspicion of IBD to this longitudinal observational study, a collaboration between 11 inclusion sites in Denmark, Iceland, Norway and Sweden. Inclusion will occur from February 2022 until December 2023 with screening and baseline visits for all participants and three outcome visits at weeks 12, 26 and 52 after baseline for IBD-diagnosed patients. Biological material (blood, faeces, biopsies, urine and hair), clinical data and lifestyle information will be collected during these scheduled visits.Ethics and disseminationThis study will explore novel biomarkers to improve diagnostic accuracy and prediction of disease progression, thereby improving medical therapy and the quality of life for patients with IBD.The study is approved by the Ethics Committee (DK: S-20200051, v1.4, 16.10.2021; IS: VSNb2021070006/03.01, NO: 193064; SE: DNR 2021-05090) and the Danish Data Protecting Agency (20/54594). Results will be disseminated through peer-reviewed journals, patient associations and presentations at international conferences.Clinical trial registration numberNCT05414578.
Transcutaneous auricular vagal nerve stimulation for consciousness recovery in patients with prolonged disorders of consciousness (TAVREC): study protocol for a multicenter, triple-blind, randomized controlled trial in China
Authors: Zhou Long-yun , Peng Li-jun , Liu Ya-feng , Wang Shu-wei , Qiu Yue , Chen Si-jing , Feng Ming-ming , Liu Jin , Wu Shan-shan , Luo Ting , Liu Zhen-yu , Wu Hui-juan , Ge Jiang-ping , Reinhardt Jan D , Lu Xiao 
Published: June 2024

IntroductionProlonged disorders of consciousness (pDoC) are a catastrophic condition following brain injury with few therapeutic options. Transcutaneous auricular vagal nerve stimulation (taVNS), a safe, non-invasive intervention modulating thalamo-cortical connectivity and brain function, is a possible treatment option of pDoC. We developed a protocol for a randomised controlled study to evaluate the effectiveness of taVNS on consciousness recovery in patients with pDoC (TAVREC).Methods and analysisThe TAVREC programme is a multicentre, triple-blind, randomised controlled trial with 4 weeks intervention followed by 4 weeks follow-up period. A minimum number of 116 eligible pDoC patients will be recruited and randomly receive either: (1) conventional therapy plus taVNS (30 s monophasic square current of pulse width 300 μs, frequency of 25 Hz and intensity of 1 mA followed by 30 s rest, 60 min, two times per day, for 4 weeks); or (2) conventional therapy plus taVNS placebo. Primary outcome of TAVREC is the rate of improved consciousness level based on the Coma Recovery Scale-Revised (CRS-R) at week 4. Secondary outcomes are CRS-R total and subscale scores, Glasgow Coma Scale score, Full Outline of UnResponsiveness score, ECG parameters, brainstem auditory evoked potential, upper somatosensory evoked potential, neuroimaging parameters from positron emission tomography/functional MRI, serum biomarkers associated with consciousness level and adverse events.Ethics and disseminationThis study was reviewed and approved by the Research Ethics Committee of the First Affiliated Hospital of Nanjing Medical University (Reference number: 2023-SR-392). Findings will be disseminated in a peer-reviewed journal and presented at relevant conferences.Trial registration numberChiCTR2300073950.
Ultrasound-based comparative analysis and nomogram development for predicting triple-negative and non-triple-negative breast cancer: a 4-year institutional study in Quanzhou First Hospital
Authors: Su Liyang , Xie Qiaojie , Chen Jiaohong , Zhang Qingquan , Li Nian , Hong Chuntian 
Published: June 2024

ObjectiveThe objective of this study was to compare ultrasound features and establish a predictive nomogram for distinguishing between triple-negative breast cancer (TNBC) and non-TNBC.DesignA retrospective cohort study.SettingThis study was conducted at Quanzhou First Hospital, a grade A tertiary hospital in Quanzhou, China, with the research data set covering the period from September 2019 to August 2023.ParticipantsThe study included a total of 205 female patients with confirmed TNBC and 574 female patients with non-TNBC, who were randomly divided into a training set and a validation set at a ratio of 7:3.Main outcome measuresAll patients underwent ultrasound examination and received a confirmatory pathological diagnosis. Nodules were classified according to the Breast Imaging-Reporting and Data System standard. Subsequently, the study conducted a comparative analysis of clinical characteristics and ultrasonic features.ResultsA statistically significant difference was observed in multiple clinical and ultrasonic features between TNBC and non-TNBC. Specifically, in the logistic regression analysis conducted on the training set, indicators such as posterior echo, lesion size, presence of clinical symptoms, margin characteristics, internal blood flow signals, halo and microcalcification were found to be statistically significant (p<0.05). These significant indicators were then effectively incorporated into a static and dynamic nomogram model, demonstrating high predictive performance in distinguishing TNBC from non-TNBC.ConclusionThe results of our study demonstrated that ultrasound features can be valuable in distinguishing between TNBC and non-TNBC. The presence of posterior echo, size, clinical symptoms, margin, internal flow, halo and microcalcification was identified as predictive factors for this differentiation. Microcalcification, hyperechoic halo, internal flow and clinical symptoms emerged as the strongest predictive factors, indicating their potential as reliable indicators for identifying TNBC and non-TNBC.
Realist Approach to Social Policies (RASP) study to reduce socioeconomic health inequalities through systems change: protocol for a research project combining mixed-methods realist research with institutional action research
Authors: Van Berkel Jantien , de Bruijn Ernst-Jan , Waardenburg Maikel , la Grouw Yvonne , van Bennekom Eline , van der Horst Hilje , Tonnon Susanne , Haggenburg- Mohammed Milou , Haveman-Nies Annemien , Madern Tamara , Knoef Marike , de Vet Emely 
Published: June 2024

IntroductionHealth inequalities are rooted in inequality in vital resources for health, including financial resources, a supportive informal network, a stable living situation, work or daytime activities or education and literacy. About 25% of Dutch citizens experience deprivation of such resources. Social policy consists of crucial instruments for improving resources in those groups but can also have adverse effects and lead to additional burdens. This project aims to contribute to the reduction of health inequalities through (1) a better understanding of how social policy interventions can contribute to reducing health inequality through the redistribution of burdens and resources and (2) developing anticipatory governance strategies to implement those insights, contributing to a change in social policy systems.Methods and analysisTwo systems approaches are combined for establishing a systems change in the Netherlands. First, a realist approach enables insights into what in social policy interventions may impact health outcomes, for whom and under what circumstances. Second, an institutional approach enables scaling up these insights, by acknowledging the crucial role of institutional actors for accomplishing a systems change. Together with stakeholders, we perform a realist review of the literature and identify existing promising social policy interventions. Next, we execute mixed-methods realist evaluations of selected social policy interventions in seven municipalities, ranging from small, mid-size to large, and in both urban and rural settings. Simultaneously, through action research with (national) institutional actors, we facilitate development of anticipatory governance strategies.Ethics and disseminationThis study is not liable to the Medical Research Involving Subjects Act (WMO). Informed consent to participate in the study is obtained from participants for the use of all forms of personally identifiable data. Dissemination will be codeveloped with target populations and includes communication materials for citizens, education materials for students, workshops, infographics and decision tools for policy-makers and publications for professionals.