bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of nasal microbiota between preterm and full-term infants in early life
Authors: Gorlanova Olga , Nissen-Kratzert Annika , Mostacci Nadja , Rüttimann Céline , Künstle Noemi , Marten Andrea , Gisler Amanda , Bacher Katharina , Decrue Fabienne , Salem Yasmin , Usemann Jakob , Korten Insa , Yammine Sophie , Nahum Uri , Schulzke Sven , Latzin Philipp , Röösli Martin , Fuchs Oliver ,   BILD study consortium, Beck Fiona , Bovermann Xenia , Casaulta Carmen , Curdy Marion , Sena Carla Rebeca Da Silva , de Hoogh Kees , Frauchiger Bettina , Frey Urs , Gorlanova Olga , Dac Léa Kim-Mi Ho , Kieninger Elisabeth , Korten Insa , Künstle Noëmi , Latzin Philipp , Marten Andrea , Müller Loretta , Nahum Uri , Oestreich Marc-Alexander , Röösli Martin , Rüttimann Céline , Schulzke Sven , Sinues Pablo , Steinberg Ruth , Stöcklin Benjamin , Streibel Carmen , Usemann Jakob , Wyler Florian , Yammine Sophie , Hilty Markus , Frey Urs 
Published: November 2024

Abstract
Background
The respiratory microbiota influences infant immune system maturation. Little is known about how perinatal, physiological, and environmental exposures impact the nasal microbiota in preterm infants after discharge, or nasal microbiota differences between preterm and healthy full-term infants.

Methods
Nasal swabs (from 136 preterm and 299 full-term infants at mean postmenstrual age of 45 weeks from the prospective Basel-Bern Infant Lung Development cohort) were analyzed by 16S-rRNA gene amplification and sequencing (Illumina MiSeq). Associations were tested with multivariable linear regression and principal coordinate analysis.

Results
Presence of older siblings in preterm infants was associated with β-diversity (PERMANOVA p = 0.001) and an increased abundance of Moraxella and Haemophilus. The nasal microbiota of preterm infants exhibited a distinct composition compared to that of full-term infants (PERMANOVA, R2 = 0.014, p = 0.001), characterized by a reduced abundance of the Moraxella and Dolosigranulum genera (ANCOM-BC, p < 0.05).

Conclusion
Our results indicate that, despite both infant groups having similar nasal microbiota patterns, there are some disparities which suggest that prematurity influences the initial microbiota colonization. In preterm infants the presence of older siblings had an effect on the nasal microbiota, whereas perinatal and early postnatal factors did not show significant effects.

Impact

Presence of older siblings affected the nasal microbiota of preterm infants.

This study demonstrated that microbiota composition differs between full-term and preterm infants, with a lower abundance of Moraxella and Dolosigranulum in preterm infants.

Examining the differences in nasal microbiota between preterm and full-term infants may contribute to understanding the trajectory of the bacterial component of the nasal microbiota of preterm infants.
Oral health-related quality of life in Egyptian children with Molar Incisor Hypomineralisation. An observational study
Authors: Gadallah Lamia Khairy , Korayem Eman , Wahby Reem 
Published: November 2024

Abstract
Aim
The aim of this study was to study the effect of Molar Incisor Hypomineralisation (MIH) on Oral Health-Related Quality of Life (OHRQoL) in children at the mixed dentition stage and correlate it with their caries experience.

Subjects and methods
One hundred two children aged from 8 to 10 years were recruited, 51 with MIH and 51 as control. Caries experience was recorded using DMFT/deft and ICDAS II. MIH-TNI index was used for classifying MIH severity. CPQ8–10 with its Arabic version was used to evaluate OHRQoL. Mann–Whitney U test and Kruskal–Wallis test were used for comparisons (p ≤ 0.05).

Results
The mean value for CPQ8–10 in MIH group was 24.67 (±11.84; median 23; range 6–55) in comparison to 21.04 (±12.3; median 18; range 2–54) for the control group, with no significant difference between groups (p = 0.109). A significantly higher value (p = 0.011) was recorded in patients with MIH-TNI 4 mean 32.16 (±13.9; median 35; range from 7 to 55) in comparison to other categories of MIH.

Conclusion
Children with and without MIH, with similar caries experience showed no difference in OHRQoL. However, the presence of the severe form of MIH including hypersensitivity and enamel disintegration negatively impacted those children’s OHRQoL.
A novel AI-based score for assessing the prognostic value of intra-epithelial lymphocytes in oral epithelial dysplasia
Authors: Shephard Adam J. , Mahmood Hanya , Raza Shan E. Ahmed , Khurram Syed Ali , Rajpoot Nasir M. 
Published: November 2024

Abstract

Background
Oral epithelial dysplasia (OED) poses a significant clinical challenge due to its potential for malignant transformation and the lack of reliable prognostic markers. Current OED grading systems do not reliably predict transformation and suffer from considerable observer variability. Recent studies have highlighted that peri-epithelial lymphocytes may play an important role in OED malignant transformation, with indication that intra-epithelial lymphocytes (IELs) may also be important.

Methods
We propose a novel artificial intelligence (AI) based IEL score from Haematoxylin and Eosin (H&E) stained Whole Slide Images (WSIs) of OED tissue slides. We determine the prognostic value of our IEL score on a digital dataset of 219 OED WSIs (acquired using three different scanners), compared to pathologist-led clinical grading.

Results
Our IEL scores demonstrated significant prognostic value (C-index = 0.67, p < 0.001) and were shown to improve both the binary/WHO grading systems in multivariate analyses (p < 0.001). Nuclear analyses confirmed the positive association between higher IEL scores, more severe OED and malignant transformation (p < 0.05).

Conclusions
This underscores the potential importance of IELs, and by extension our IEL score, as prognostic indicators in OED. Further validation through prospective multi-centric studies is warranted to confirm the clinical utility of IELs.
High iASPP (PPP1R13L) expression is an independent predictor of adverse clinical outcome in acute myeloid leukemia (AML)
Authors: Bajrami Saipi Mihada , Ruiba Alessia , Schittenhelm Marcus Matthias , Blumenstock Gunnar , Győrffy Balázs , Fazio Serena , Hafner Marlon , Ahrens Anna-Lena , Aldinger Lara , Aellig Vanessa , Kavelaars François G. , Nombela-Arrieta César , Fend Falko , Valk Peter J. M. , Christoph Driessen , Kampa-Schittenhelm Kerstin Maria 
Published: November 2024

AbstractApoptosis-stimulating proteins of p53 (ASPPs) are a family of proteins that modulate key tumor suppressor pathways via direct interaction with p53. Deregulation of these proteins promotes cancer development and impairs sensitivity to systemic (chemo)therapy and radiation. In this study, we describe that the inhibitor of ASPP (iASPP) is frequently highly expressed in acute myeloid leukemia (AML) and that overexpression correlates with a poor clinical outcome. Four independent patient cohorts comprising about 1500 patient samples were analysed and consistently confirm an association of high iASPP expression with unfavourable clinical characteristics and shorter survival. Notably, the predictive role of iASPP is independent of, and adds information to, the European LeukemiaNET (ELN) risk classification. iASPP-interference cell models were developed to investigate the underlying functional aspects of iASPP in AML biology. Attenuation of iASPP expression resulted in reduced proliferation rates of leukemic blasts and rendered cells more susceptible towards induction of apoptosis in response to cytotoxic therapy. In line, independent NSG xenograft mouse experiments demonstrate that attenuation of iASPP results in a significant delay of disease onset and tumor burden and this translates to longer overall survival of mice. In conclusion, deregulation of iASPP has direct functional consequences in AML. Determination of iASPP expression levels provides valuable additional information as a predictive marker in AML and may guide treatment decisions.
A N7-methylguanosine modified circular RNA, circIPP2A2, promotes malignant behaviors in hepatocellular carcinoma by serving as a scaffold in modulating the Hornerin/PI3K/AKT/GSK3β axis
Authors: Guo Zeyi , Li Zhongzhe , Guo Jinhao , Gan Luxiang , Mo Haiyu , Zhang Jiajun , Fu Yu , Wang Yi , Jin Meixian , Wu Yanping , Xie Qingyu , Tan Kunjiang , Wang Chunming , Xu Yuyan , He Guolin , Cai Lei , Gao Yi , Pan Mingxin , Fu Shunjun 
Published: November 2024

AbstractDespite the advancements in treatment strategies, the long-term survival of hepatocellular carcinoma (HCC) is still pessimistic. Therefore, understanding the mechanisms of hepatocellular carcinoma may offer substantial benefits for patients. Our previous research has revealed that Hornerin promoted HCC progression by regulating the AKT signaling pathway. To investigate the upstream regulatory mechanism, the results from RNA Immunoprecipitation and RNA pull-down indicated that the specific region of circIPP2A2 interacted with Hornerin. Additionally, patients with circIPP2A2 upregulation exhibited a poorer survival outcome following surgery compared to the cases with downregulated circIPP2A2. After the structure verification of circIPP2A2, loss-of-function studies using a lentiviral vector revealed that circIPP2A2 downregulation significantly inhibited HCC tumorigenesis and progression both in vitro and in vivo. Mechanistically, the m7G-MeRIP results demonstrated significant enrichment of circIPP2A2. Subsequent studies validated that METTL1 influenced the stability of circIPP2A2 and its binding affinity with Hornerin. Immunoprecipitation and immunofluorescence indicated that circIPP2A2 served as a molecular scaffold to facilitate Hornerin to interact with PI3K. In conclusion, our findings reveal that circIPP2A2, regulated by N7-methylguanosine modification, promotes malignant behaviors in HCC by serving as a molecular scaffold in modulating the Hornerin/PI3K/AKT/GSK3β axis. Targeting circIPP2A2 may be a promising therapeutic strategy for patients with HCC.
A wide range of chromosome numbers result from unreduced gamete production in Brassica juncea × B. napus (AABC) interspecific hybrids
Authors: Addo Nyarko Charles , Katche Elvis , Báez Mariana , Lv Zhenling , Mason Annaliese S. 
Published: November 2024

Abstract
The establishment of successful interspecies hybrids requires restoration of a stable “2n” chromosome complement which can produce viable “n” gametes. This may occur (rarely) via recombination between non-homologous chromosomes, or more commonly is associated with a doubling of parental chromosome number to produce new homologous pairing partners in the hybrid. The production of unreduced “2n” gametes (gametes with the somatic chromosome number) may therefore be evolutionarily useful by serving as a key pathway for the formation of new polyploid hybrids, as might specific mechanisms permitting recombination between non-homologous chromosomes. Here, we investigated chromosome complements and fertility in third generation interspecific hybrids (AABC) resulting from a cross between allopolyploids Brassica juncea (AABB) × B. napus (AACC) followed by self-pollination for two generations. Chromosome numbers ranged from 2n = 48–74 in the experimental population (35 plants), with 9–16 B genome chromosomes and up to 4 copies of A genome chromosomes. Unreduced gamete production leading to a putative genome structure of approximately AAAABBCC was hence predicted to explain the high chromosome numbers observed. Additionally, the estimation of nuclei number in post-meiotic sporads revealed a higher frequency of unreduced gametes (0.04–5.21%) in the third generation AABC interspecific hybrids compared to the parental Brassica juncea (0.07%) and B. napus (0.13%). Our results suggest that unreduced gamete production in the subsequent generations following interspecific hybridization events may play a critical role in restoration of more stable, fertile chromosome complements.
Approaches to investigate tissue-resident innate lymphocytes metabolism at the single-cell level
Authors: Corkish Carrie , Aguiar Cristhiane Favero , Finlay David K. 
Published: November 2024

AbstractTissue-resident innate immune cells have important functions in both homeostasis and pathological states. Despite advances in the field, analyzing the metabolism of tissue-resident innate lymphocytes is still challenging. The small number of tissue-resident innate lymphocytes such as ILC, NK, iNKT and γδ T cells poses additional obstacles in their metabolic studies. In this review, we summarize the current understanding of innate lymphocyte metabolism and discuss potential pitfalls associated with the current methodology relying predominantly on in vitro cultured cells or bulk-level comparison. Meanwhile, we also summarize and advocate for the development and adoption of single-cell metabolic assays to accurately profile the metabolism of tissue-resident immune cells directly ex vivo.
Origin of competing charge density waves in kagome metal ScV6Sn6
Authors: Wang Kang , Chen Siyu , Kim Sun-Woo , Monserrat Bartomeu 
Published: November 2024

AbstractUnderstanding competing charge density wave (CDW) orders in the bilayer kagome metal ScV6Sn6 remains challenging. Experimentally, upon cooling, short-range order with wave vector $${{{{\bf{q}}}}}_{2}=(\frac{1}{3},\frac{1}{3},\frac{1}{2})$$

q

2

=

(

1

3

,

1

3

,

1

2

)

forms, which is subsequently suppressed by the condensation of long-range $${{{{\bf{q}}}}}_{3}=(\frac{1}{3},\frac{1}{3},\frac{1}{3})$$

q

3

=

(

1

3

,

1

3

,

1

3

)

CDW order at lower temperature. Theoretically, however, the q2 CDW is predicted as the ground state, leaving the CDW mechanism elusive. Here, using anharmonic phonon-phonon calculations combined with density functional theory, we predict a temperature-driven structural phase transitions from the high-temperature pristine phase to the q2 CDW, followed by the low-temperature q3 CDW, explaining experimental observations. We demonstrate that semi-core electron states stabilize the q3 CDW over the q2 CDW. Furthermore, we find that the out-of-plane lattice parameter controls the competing CDWs, motivating us to propose compressive bi-axial strain as an experimental protocol to stabilize the q2 CDW. Finally, we suggest Ge or Pb doping at the Sn site as another potential avenue to control CDW instabilities. Our work provides a full theory of CDWs in ScV6Sn6, rationalizing experimental observations and resolving earlier discrepancies between theory and experiment.
SARS-CoV-2 human challenge reveals biomarkers that discriminate early and late phases of respiratory viral infections
Authors: Rosenheim Joshua , Gupta Rishi K. , Thakker Clare , Mann Tiffeney , Bell Lucy C. K. , Broderick Claire M. , Madon Kieran , Papargyris Loukas , Dayananda Pete , Kwok Andrew J. , Greenan-Barrett James , Wagstaffe Helen R. , Conibear Emily , Fenn Joe , Hakki Seran , Lindeboom Rik G. H. , Dratva Lisa M. , Lemetais Briac , Weight Caroline M. , Venturini Cristina , Kaforou Myrsini , Levin Michael , Kalinova Mariya , Mann Alex J. , Catchpole Andrew , Knight Julian C. , Nikolić Marko Z. , Teichmann Sarah A. , Killingley Ben , Barclay Wendy , Chain Benjamin M. , Lalvani Ajit , Heyderman Robert S. , Chiu Christopher , Noursadeghi Mahdad 
Published: November 2024

AbstractBlood transcriptional biomarkers of acute viral infections typically reflect type 1 interferon (IFN) signalling, but it is not known whether there are biological differences in their regulation that can be leveraged for distinct translational applications. We use high frequency sampling in the SARS-CoV-2 human challenge model to show induction of IFN-stimulated gene (ISG) expression with different temporal and cellular profiles. MX1 gene expression correlates with a rapid and transient wave of ISG expression across all cell types, which may precede PCR detection of replicative infection. Another ISG, IFI27, shows a delayed but sustained response restricted to myeloid cells, attributable to gene and cell-specific epigenetic regulation. These findings are reproducible in experimental and naturally acquired infections with influenza, respiratory syncytial virus and rhinovirus. Blood MX1 expression is superior to IFI27 expression for diagnosis of early infection, as a correlate of viral load and for discrimination of virus culture positivity. Therefore, MX1 expression offers potential to stratify patients for antiviral therapy or infection control interventions. Blood IFI27 expression is superior to MX1 expression for diagnostic accuracy across the time course of symptomatic infection and thereby, offers higher diagnostic yield for respiratory virus infections that incur a delay between transmission and testing.
Subtilase SBT5.2 inactivates flagellin immunogenicity in the plant apoplast
Authors: Buscaill Pierre , Sanguankiattichai Nattapong , Kaschani Farnusch , Huang Jie , Mooney Brian C. , Li Yuge , Lyu Joy , Sueldo Daniela , Kaiser Markus , van der Hoorn Renier A. L. 
Published: November 2024

AbstractMost angiosperm plants recognise the 22-residue flagellin (flg22) epitope in bacterial flagellin via homologs of cell surface receptor FLS2 (flagellin sensitive-2) and mount pattern-triggered immune responses. However, flg22 is buried within the flagellin protein indicating that proteases might be required for flg22 release. Here, we demonstrate the extracellular subtilase SBT5.2 not only releases flg22, but also inactivates the immunogenicity of flagellin and flg22 by cleaving within the flg22 epitope, consistent with previous reports that flg22 is unstable in the apoplast. The prolonged lifetime of flg22 in sbt5.2 mutant plants results in increased bacterial immunity in priming assays, indicating that SBT5.2 counterbalances flagellin immunogenicity to provide spatial-temporal control and restrict costly immune responses and that bacteria take advantage of the host proteolytic machinery to avoid detection by flagellin having a protease-sensitive flg22 epitope.
A single nanophotonic platform for producing circularly polarized white light from non-chiral emitters
Authors: Mendoza-Carreño Jose , Bertucci Simone , Garbarino Mauro , Cirignano Matilde , Fiorito Sergio , Lova Paola , Garriga Miquel , Alonso Maria Isabel , Di Stasio Francesco , Mihi Agustín 
Published: November 2024

AbstractDirect manipulation of light spin-angular momentum is desired in optoelectronic applications such as, displays, telecommunications, or imaging. Generating polarized light from luminophores avoids using optical components that cause brightness losses and hamper on-chip integration of light sources. Endowing chirality to achiral emitters for direct generation of polarized light benefits from existing materials and can be achieved by chiral nanophotonics. However, most chiral nanostructures operate in narrow wavelength ranges and involve nanofabrication processes incompatible with high-throughput production. Here, a single nanophotonic architecture is designed to sustain chiroptical resonances along the visible spectrum. This platform, fabricated with scalable soft-nanoimprint lithography transfers its chirality to conventional emitters (CdSe/CdS nanoplatelets, CdSe/CdS quantum dots, CsPbBr3, CsPbI3 perovskite nanocrystals and F8BT) placed atop, achieving a high dissymmetry emission factor (glum > 1). The dynamics study suggests enhanced out-coupling efficiency for one helicity by the photonic structure. Finally, a white light-emitting blend containing different emitters shows simultaneous dissymmetric emission values along the visible spectrum with this chiral nanophotonic platform.
Immune digital twins for complex human pathologies: applications, limitations, and challenges
Authors: Niarakis Anna , Laubenbacher Reinhard , An Gary , Ilan Yaron , Fisher Jasmin , Flobak Åsmund , Reiche Kristin , Rodríguez Martínez María , Geris Liesbet , Ladeira Luiz , Veschini Lorenzo , Blinov Michael L. , Messina Francesco , Fonseca Luis L. , Ferreira Sandra , Montagud Arnau , Noël Vincent , Marku Malvina , Tsirvouli Eirini , Torres Marcella M. , Harris Leonard A. , Sego T. J. , Cockrell Chase , Shick Amanda E. , Balci Hasan , Salazar Albin , Rian Kinza , Hemedan Ahmed Abdelmonem , Esteban-Medina Marina , Staumont Bernard , Hernandez-Vargas Esteban , Martis B Shiny , Madrid-Valiente Alejandro , Karampelesis Panagiotis , Sordo Vieira Luis , Harlapur Pradyumna , Kulesza Alexander , Nikaein Niloofar , Garira Winston , Malik Sheriff Rahuman S. , Thakar Juilee , Tran Van Du T. , Carbonell-Caballero Jose , Safaei Soroush , Valencia Alfonso , Zinovyev Andrei , Glazier James A. 
Published: November 2024

AbstractDigital twins represent a key technology for precision health. Medical digital twins consist of computational models that represent the health state of individual patients over time, enabling optimal therapeutics and forecasting patient prognosis. Many health conditions involve the immune system, so it is crucial to include its key features when designing medical digital twins. The immune response is complex and varies across diseases and patients, and its modelling requires the collective expertise of the clinical, immunology, and computational modelling communities. This review outlines the initial progress on immune digital twins and the various initiatives to facilitate communication between interdisciplinary communities. We also outline the crucial aspects of an immune digital twin design and the prerequisites for its implementation in the clinic. We propose some initial use cases that could serve as “proof of concept” regarding the utility of immune digital technology, focusing on diseases with a very different immune response across spatial and temporal scales (minutes, days, months, years). Lastly, we discuss the use of digital twins in drug discovery and point out emerging challenges that the scientific community needs to collectively overcome to make immune digital twins a reality.
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology
Authors: Juwayria  , Shrivastava Priyansh , Yadav Kaustar , Das Sourabh , Mittal Shubham , Kumar Sunil , Jain Deepali , Malik Prabhat Singh , Gupta Ishaan 
Published: November 2024

Abstract10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D printing to enhance slide throughput. Our design facilitates independent replication and customization in individual labs to suit specific experimental needs. We provide a step-by-step guide from designing TMAs to the library preparation step. We demonstrate MIST’s cost-effectiveness and technical benefits over Visium and GeoMx Nanostring. We also introduce ‘AnnotateMap’, a novel computational tool for efficient analysis of multiple ROIs processed through MIST.