bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of
Porphyromonas gingivalis
A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems
Authors: Śmiga Michał , Ślęzak Paulina , Olczak Teresa 
Published: January 2024

ABSTRACT

Porphyromonas gingivalis
strains exhibit different phenotypes
in vitro
, different virulence potential in animal models, and different associations with human diseases, with strains classified as virulent/more virulent (e.g., A7436 and W83) or as less virulent/avirulent (e.g., ATCC 33277). In this study, we comparatively analyzed the A7436 and ATCC 33277 strains to better understand their variability. Global gene expression analysis in response to heme and iron limitation revealed more pronounced differences in the A7436 than in the ATCC 33277 strain; however, in both strains, the largest changes were observed in genes encoding hypothetical proteins, genes whose products participate in energy metabolism, and in genes encoding proteins engaged in transport and binding proteins. Our results confirmed that variability between
P. gingivalis
strains is due to differences in the arrangement of their genomes. Analysis of gene expression of heme acquisition systems demonstrated that not only the availability of iron and heme in the external environment but also the ability to store iron intracellularly can influence the
P. gingivalis
phenotype. Therefore, we assume that differences in virulence potential may also be due to differences in the production of systems involved in iron and heme acquisition, mainly the Hmu system. In addition, our study showed that hemoglobin, in a concentration-dependent manner, differentially influences the virulence potential of
P. gingivalis
strains. We conclude that iron and heme homeostasis may add to the variability observed between
P. gingivalis
strains.

IMPORTANCE

Periodontitis belongs to a group of multifactorial diseases, characterized by inflammation and destruction of tooth-supporting tissues.
P. gingivalis
is one of the most important microbial factors involved in the initiation and progression of periodontitis. To survive in the host, the bacterium must acquire heme as a source of iron and protoporphyrin IX.
P. gingivalis
strains respond differently to changing iron and heme concentrations, which may be due to differences in the expression of systems involved in iron and heme acquisition. The ability to accumulate iron intracellularly, being different in more and less virulent
P. gingivalis
strains, may influence their phenotypes, production of virulence factors (including proteins engaged in heme acquisition), and virulence potential of this bacterium.
Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection
Authors: Romani L. , Del Chierico F. , Pane S. , Ristori M. V. , Pirona I. , Guarrasi V. , Cotugno N. , Bernardi S. , Lancella L. , Perno C. F. , Rossi P. , Villani A. , Campana A. , Palma P. , Putignani L. ,   the CACTUS Study Team, Carducci Francesca Calò , Cancrini Caterina , Chiurchiù Sara , degli Atti Marta Ciofi , Cursi Laura , Cutrera Renato , D’Amore Carmen , D’Argenio Patrizia , De Ioris Maria A. , De Luca Maia , Finocchi Andrea , Manno Emma Concetta , Morrocchi Elena , Pansa Paola , Sessa Libera , Zangari Paola 
Published: January 2024

ABSTRACT

The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission (
T
0
), 72 h to 7 days (
T
1
), and at the discharge (
T
2
) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients (
N
= 71) was characterized by reduction of α-diversity compared to CTRLs (
N
= 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in
Streptococcus
,
Haemophilus
,
Staphylococcus
,
Veillonella
,
Enterococcus
,
Neisseria
,
Moraxella
, Enterobacteriaceae,
Gemella
,
Bacillus
, and reduced in
Faecalibacterium
,
Akkermansia
,
Blautia
,
Bifidobacterium
,
Ruminococcus
, and
Bacteroides,
compared to CTRLs (FDR < 0.001). Exploiting ML models,
Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus
, and
Veillonella
resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL.

IMPORTANCE
Since the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load.
Traditional Chinese medicine bufalin inhibits infectious hematopoietic necrosis virus infection
in vitro
and
in vivo
Authors: Zhao Jing-Zhuang , Xu Li-Ming , Li Lin-Fang , Ren Guang-Ming , Shao Yi-Zhi , Liu Qi , Lu Tong-Yan 
Published: January 2024

ABSTRACT

Infectious hematopoietic necrosis virus (IHNV) causes infectious hematopoietic necrosis and severe economic losses to salmon and trout aquaculture worldwide. Currently, the only commercial vaccine against IHNV is a DNA vaccine with some biosafety concerns. Hence, more effective vaccines and antiviral drugs are needed to prevent IHNV infection. In this study, 1,483 compounds were screened from a traditional Chinese medicine monomer library, and bufalin showed potential antiviral activity against IHNV. The 50% cytotoxic concentration of bufalin was >20 µM, and the 50% inhibitory concentration was 0.1223 µΜ against IHNV. Bufalin showed the inhibition of diverse IHNV strains
in vitro
, which confirmed that it had an inhibitory effect against all IHNV strains, rather than random activity against a single strain. The bufalin-mediated block of IHNV infection occurred at the viral attachment and RNA replication stages, but not internalization. Bufalin also inhibited IHNV infection
in vivo
and significantly increased the survival of rainbow trout compared with the mock drug-treated group, and this was confirmed by
in vivo
viral load monitoring. Our data showed that the anti-IHNV activity of bufalin was proportional to extracellular Na
+
concentration and inversely proportional to extracellular K
+
concentration, and bufalin may inhibit IHNV infection by targeting Na
+
/K
+
-ATPase. The
in vitro
and
in vivo
studies showed that bufalin significantly inhibited IHNV infection and may be a promising candidate drug against the disease in rainbow trout.

IMPORTANCE

Infectious hematopoietic necrosis virus (IHNV) is the pathogen of infectious hematopoietic necrosis (IHN) which outbreak often causes huge economic losses and hampers the healthy development of salmon and trout farming. Currently, there is only one approved DNA vaccine for IHN worldwide, but it faces some biosafety problems. Hence, more effective vaccines and antiviral drugs are needed to prevent IHNV infection. In this study, we report that bufalin, a traditional Chinese medicine, shows potential antiviral activity against IHNV both
in vitro
and
in vivo
. The bufalin-mediated block of IHNV infection occurred at the viral attachment and RNA replication stages, but not internalization, and bufalin inhibited IHNV infection by targeting Na
+
/K
+
-ATPase. The
in vitro
and
in vivo
studies showed that bufalin significantly inhibited IHNV infection and may be a promising candidate drug against the disease in rainbow trout.
Patient and parent perspectives on paediatric cancer multidisciplinary team working and national advisory panels in the UK: a qualitative research study
Authors: Brown Sarah , Johnson Katie , Gray Juliet , Bate Jessica 
Published: January 2024

ObjectiveThe concept of patient-centred care is central to the role of cancer multidisciplinary teams (MDTs) and particularly pertinent with the recent rise in number of virtual national advisory panels (NAPs) for childhood cancer in the UK. We sought to explore patient and caregiver views regarding MDT working and NAPs.MethodsThree focus groups were undertaken between March 2019 and January 2020.ResultsSixteen participants attended. All regarded MDTs and NAPs highly, while highlighting patient involvement in decision-making should not be diluted by this process. The importance of personalised consultations was stressed, acknowledging that information-sharing preferences may change with circumstance and time. Most participants felt they had not been actively involved in decisions, including those made following MDT or NAP discussions. Group suggestions to improve patient-centred care included a clinician knowing them presenting their case, referral proformas to include family-related factors and an advocate attending meetings to represent the patient/family view.ConclusionSeveral changes have been driven forward by this work, including the modification of NAP referral proformas to include additional information. Patient and parent perspectives are now embedded into a best practice model for the NAPs to promote personalised recommendations at national level.
Communicative development inventory in type 1 and presymptomatic infants with spinal muscular atrophy: a cohort study
Authors: Buchignani Bianca , Cicala Gianpaolo , Cumbo Francesca , Ricci Martina , Capasso Anna , Ticci Chiara , Mazzanti Sara , Brolatti Noemi , Tosi Michele , Dosi Claudia , Antonaci Laura , Coratti Giorgia , Pera Maria Carmela , Leone Daniela , Palermo Concetta , Berti Beatrice , Frongia Anna Lia , Sacchini Michele , Bruno Claudio , Masson Riccardo , D’Amico Adele , Battini Roberta , Pane Marika , Mercuri Eugenio 
Published: January 2024

ObjectiveThe aim of this study was to assess early language acquisitions in treated individuals with spinal muscular atrophy (SMA) type 1 and in infants identified by newborn screening (NBS).MethodsParents of SMA individuals aged between 8 and 36 months were asked to fill in the MacArthur-Bates Communicative Development Inventory (MB-CDI) that assesses comprehension, gesture and expressive skills. A follow-up assessment was performed in 21 of the 36.ResultsThe MB-CDI was completed by parents of 24 type 1 and 12 infants identified by NBS. Comprehension skills were preserved in 81% of the type 1 SMA and in 87% infants identified by NBS. Gesture abilities were <5th centile in 55% of the type 1 SMA and in none of those identified by NBS. Lexical expressions were <5th centile in more than 80% type 1 SMA and in 50% of infants identified by NBS. At follow-up, despite an increase in lexical expression skills, the scores remained below the fifth centile in 43% type 1 SMA and in 86% of infants identified by NBS.ConclusionsThese results suggest that language and communication development may follow a similar pattern to that observed in motor function with the possibility to develop skills (eg, ability to say clear words) that are not usually present in untreated infants but with a level of performance that does not reach that of their typically developing peers.
Predictors of 24-month onset of macular fibrosis in type 3 macular neovascularisation
Authors: Forte Paolo , Fontana Vincenzo , Muzio Julia , Di Cello Luca , Corazza Paolo , Rosa Raffaella , Musetti Donatella , Vagge Aldo , Traverso Carlo Enrico , Nicolò Massimo 
Published: January 2024

AimsTo explore prognostic multimarker models for progression to macular fibrosis (MF) over 24 months specific to type 3 macular neovascularisation (T3 MNV).MethodsThis retrospective, exploratory, single-centre, cohort study comprised 65 eyes of 43 Caucasian patients with treatment naive T3 MNV, all with a 24-month follow-up post anti-VEGF therapy using a strict pro-re-nata (PRN) regimen. Data on demographic features, clinical findings, frequency of intravitreal treatments and optical coherence tomography biomarkers were collected at baseline and after 12 and 24 months of follow-up. Logistic regression models (LRM) and receiver-operating curve (C-index) analyses were performed to evaluate the prognostic ability of the studied biomarkers in discriminating between MF affected and unaffected patients.ResultsAt final follow-up, MF was present in 46.2% of eyes. Subretinal hyper-reflective material (SHRM) and subretinal pigment epithelium multilaminar hyper-reflectivity (multilaminae) emerged as significant predictors for MF, with adjusted odds ratios (OR) of 18.0 (95% CL 13.4 to 24.1) and 11.8 (95% CL 8.66 to 16.0), respectively. Additionally, the presence of multifocal lesions (OR 0.04, 95% CL 0.01 to 0.30) appeared to decrease the likelihood of MF. C-indexes for the selected LRMs ranged between 0.92 and 0.88, indicating a comparably high discriminant ability. Despite consistent treatment schedules between the two groups (MF: median intravitreal treatment (IVT) number=10.5, IQR=7; non-MF: median IVT=10, IQR=6), a decline in best-corrected visual acuity was noted in the group with MF onset over the 24-month follow-up (−13.0 ETDRS letters; 95% CL –22.1 to –3.9; p=0.006).ConclusionOur study identifies SHRM and multilaminae as relevant predictors of 24-month onset of MF in patients with T3 MNV. These findings enrich our understanding of the development of MF in T3 MNV and can guide improved risk prognostication. Future research should consider larger samples and prospective designs to validate these predictors.
High-risk factors for zonular complications during cataract surgery in eyes with pseudoexfoliation syndrome
Authors: Hayashi Ken , Yoshida Motoaki , Manabe Shin-ichi , Hirata Akira 
Published: January 2024

AimsTo predict high-risk factors for zonular complications during cataract surgery due to pre-existing severe zonular dehiscence in eyes with pseudoexfoliation (PXF) syndrome.Methods315 eyes of 315 consecutive patients with PXF scheduled for phacoemulsification surgery underwent preoperative examination of various ocular parameters using an anterior segment-optical coherence tomography and other devices. When zonular complications occurred during surgery due to zonular dehiscence, scleral fixation of the intraocular lens (IOL) or implantation of a capsular tension ring (CTR) was performed. High-risk factors for these intraoperative zonular complications were examined using classification-tree and logistic regression analyses.ResultsOf the 315 eyes, 31 (9.84%) underwent scleral IOL fixation or CTR implantation. High-risk factors identified by classification-tree analysis were a small pupillary diameter after mydriasis <6.30 mm, a shallow anterior chamber depth <2.074 mm and lens decentration >0.260 mm. Based on exact logistic regression analysis, the OR was 4.81-fold higher for eyes with poor mydriasis than for eyes without poor mydriasis (p=0.006, 95% CI 1.49 to 18.23), 23.99-fold higher for eyes with poor mydriasis and a shallow anterior chamber (p<0.001, 5.92 to 109.02) and 287.39-fold higher for eyes with poor mydriasis, a shallow chamber and great lens decentration (p<0.001, 50.46 to infinity).ConclusionIn eyes with PXF, high-risk factors for zonular complications during cataract surgery due to pre-existing severe zonular dehiscence were poor mydriasis, shallow anterior chamber and large lens decentration, suggesting the importance of evaluating these conditions preoperatively.
Lack of consistency in measurement methods and semantics used for network measures in adolescent health behaviour studies using social network analysis: a systematic review
Authors: Collonnaz Magali , Minary Laetitia , Riglea Teodora , Kalubi Jodi , O'Loughlin Jennifer , Kestens Yan , Agrinier Nelly 
Published: January 2024

BackgroundSocial network analysis (SNA) is often used to examine how social relationships influence adolescent health behaviours, but no study has documented the range of network measures used to do so. We aimed to identify network measures used in studies on adolescent health behaviours.MethodsWe conducted a systematic review to identify network measures in studies investigating adolescent health behaviours with SNA. Measures were grouped into eight categories based on network concepts commonly described in the literature: popularity, position within the network, network density, similarity, nature of relationships, peer behaviours, social norms, and selection and influence mechanisms. Different subcategories were further identified. We detailed all distinct measures and the labels used to name them in included articles.ResultsOut of 6686 articles screened, 201 were included. The categories most frequently investigated were peer behaviours (n=201, 100%), position within the network (n=144, 71.6%) and popularity (n=110, 54.7%). The number of measurement methods varied from 1 for ‘similarity on popularity’ (within the ‘similarity’ category) to 28 for the ‘characterisation of the relationship between the respondent and nominated peers’ (within the ‘nature of the relationships’ category). Using the examples of ‘social isolation’, ‘group membership’, ‘individuals in a central position’ (within the ‘position within the network’ category) and ‘nominations of influential peers’ (sub within the ‘popularity’ category), we illustrated the inconsistent reporting and heterogeneity in measurement methods and semantics.ConclusionRobust methodological recommendations are needed to harmonise network measures in order to facilitate comparison across studies and optimise public health intervention based on SNA.
Prognostic model for unresectable hepatocellular carcinoma treated with dual PD-1 and angiogenesis blockade therapy
Authors: Mo Zhiqiang , Lv Ling , Mai Qicong , Li Qiao , He Jian , Zhang Tao , Xu Jingwu , Fang Jiayan , Shi Ning , Gou Qing , Chen Xiaoming , Zhang Jing , Zhuang Wenhang , Jin Haosheng 
Published: January 2024

Background and aimsDual programmed death 1 (PD-1) and angiogenesis blockade therapy is a frontline treatment for hepatocellular carcinoma (HCC). An accepted model for survival prediction and risk stratification in individual patients receiving this treatment is lacking. Aimed to develop a simple prognostic model specific to these patients.Approach and resultsPatients with unresectable HCC undergoing dual PD-1 and angiogenesis blockade therapy were included in training cohort (n=168) and validation cohort (n=72). We investigated the prognostic value of clinical variables on overall survival using a Cox model in the training set. A prognostic score model was then developed and validated. Predictive performance and discrimination were also evaluated.Largest tumor size andAlpha-fetoprotein concentration at baseline andNeutrophil count andSpleen volume change after 6 weeks of treatment were identiﬁed as independent predictors of overall survival in multivariable analysis and used to develop LANS score. Time-dependent receiver operating characteristic analysis, calibration curves, and C-index showed LANS score had favorable performance in survival prediction. Patients were divided into three risk categories based on LANS score. Median survival for patients with low, intermediate, and high LANS scores was 31.7, 23.5, and 11.5 months, respectively (p<0.0001). The disease control rates were 96.4%, 64.3%, and 32.1%, respectively (p<0.0001). The predictive performance and risk stratification ability of the LANS score were confirmed in validation and entire cohorts.ConclusionThe LANS score model can provide individualized survival prediction and risk stratification in patients with unresectable HCC undergoing dual PD-1 and angiogenesis blockade therapy.
The MOG antibody non-P42 epitope is predictive of a relapsing course in MOG antibody-associated disease
Authors: Liyanage Ganesha , Trewin Benjamin P , Lopez Joseph A , Andersen Jane , Tea Fiona , Merheb Vera , Nguyen Kristy , Lee Fiona X Z , Fabis-Pedrini Marzena J , Zou Alicia , Buckland Ali , Fok Anthony , Barnett Michael H , Reddel Stephen W , Marignier Romain , El Hajj Aseel , Monif Mastura , van der Walt Anneke , Lechner-Scott Jeannette , Kermode Allan G , Kalincik Tomas , Broadley Simon A , Dale Russell C , Ramanathan Sudarshini , Brilot Fabienne 
Published: January 2024

BackgroundMyelin oligodendrocyte glycoprotein (MOG) IgG seropositivity is a prerequisite for MOG antibody-associated disease (MOGAD) diagnosis. While a significant proportion of patients experience a relapsing disease, there is currently no biomarker predictive of disease course. We aim to determine whether MOG-IgG epitopes can predict a relapsing course in MOGAD patients.MethodsMOG-IgG-seropositive confirmed adult MOGAD patients were included (n=202). Serum MOG-IgG and epitope binding were determined by validated flow cytometry live cell-based assays. Associations between epitopes, disease course, clinical phenotype, Expanded Disability Status Scale and Visual Functional System Score at onset and last review were evaluated.ResultsOf 202 MOGAD patients, 150 (74%) patients had MOG-IgG that recognised the immunodominant proline42 (P42) epitope and 115 (57%) recognised histidine103/serine104 (H103/S104). Fifty-two (26%) patients had non-P42 MOG-IgG and showed an increased risk of a relapsing course (HR 1.7; 95% CI 1.15 to 2.60, p=0.009). Relapse-freedom was shorter in patients with non-P42 MOG-IgG (p=0.0079). Non-P42 MOG-IgG epitope status remained unchanged from onset throughout the disease course and was a strong predictor of a relapsing course in patients with unilateral optic neuritis (HR 2.7, 95% CI 1.06 to 6.98, p=0.038), with high specificity (95%, 95% CI 77% to 100%) and positive predictive value (85%, 95% CI 45% to 98%).ConclusionsNon-P42 MOG-IgG predicts a relapsing course in a significant subgroup of MOGAD patients. Patients with unilateral optic neuritis, the most frequent MOGAD phenotype, can reliably be tested at onset, regardless of age and sex. Early detection and specialised management in these patients could minimise disability and improve long-term outcomes.