bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis
Authors: Peters Hayley , Potla Pratibha , Rockel Jason S. , Tockovska Teodora , Pastrello Chiara , Jurisica Igor , Santos Keemo Delos , Vohra Shabana , Lively Starlee , Perry Kim , Looby Nikita , Li Sheng Han , Chandran Vinod , Hueniken Katrina , Kaur Paramvir , Perruccio Anthony V. , Mahomed Nizar N. , Rampersaud Y. Raja , Syed Khalid A. , Gracey Eric , Krawetz Roman , Buechler Matthew B. , Gandhi Rajiv , Kapoor Mohit 
Published: April 2024

AbstractObjectivesIn this study, we employ a multi-omic approach to identify major cell types and subsets, and their transcriptomic profiles within the infrapatellar fat pad (IFP), and to determine differences in the IFP based on knee osteoarthritis (KOA), sex, and obesity status.MethodsSingle-nucleus RNA sequencing of 82,924 nuclei from 21 IFPs (n=6 healthy control and n=15 KOA donors), spatial transcriptomics and bioinformatic analysis were used to identify contributions of the IFP to KOA. We mapped cell subclusters from other white adipose tissues using publicly available literature. The diversity of fibroblasts within the IFP was investigated by bioinformatic analyses, comparing by KOA, sex, and obesity status. Metabolomics was used to further explore differences in fibroblasts by obesity status.ResultsWe identified multiple subclusters of fibroblasts, macrophages, adipocytes, and endothelial cells with unique transcriptomic profiles. Using spatial transcriptomics, we resolved distributions of cell types and their transcriptomic profiles, and computationally identified putative cell-cell communication networks. Furthermore, we identified transcriptomic differences in fibroblasts from KOA versus healthy control donor IFPs, female versus male KOA-IFPs, and obese versus normal body mass index (BMI) KOA-IFPs. Finally, using metabolomics, we defined differences in metabolite levels in supernatants of naïve, profibrotic- and proinflammatory stimuli-treated fibroblasts from obese compared to normal BMI KOA-IFP.ConclusionsOverall, by employing a multi-omic approach, this study provides the first comprehensive map of cellular and transcriptomic diversity of human IFP and identifies IFP fibroblasts as a key cell type contributing to transcriptomic and metabolic differences related to KOA disease, sex, or obesity.
Alleviating cell-free DNA sequencing biases with optimal transport
Authors: Passemiers Antoine , Jatsenko Tatjana , Vanderstichele Adriaan , Busschaert Pieter , Coosemans An , Timmerman Dirk , Lambrechts Diether , Raimondi Daniele , Vermeesch Joris Robert , Moreau Yves 
Published: April 2024

AbstractCell-free DNA (cfDNA) is a rich source of biomarkers for various (patho)physiological conditions. Recent developments have used Machine Learning on large cfDNA data sets to enhance the detection of cancers and immunological diseases. Preanalytical variables, such as the library preparation protocol or sequencing platform, are major confounders that influence such data sets and lead to domain shifts (i.e., shifts in data distribution as those confounders vary across time or space). Here, we present a domain adaptation method that builds on the concept of optimal transport, and explicitly corrects for the effect of such preanalytical variables. Our approach can be used to merge cohorts representative of the same population but separated by technical biases. Moreover, we also demonstrate that it improves cancer detection via Machine Learning by alleviating the sources of variation that are not of biological origin. Our method also improves over the widely used GC-content bias correction, both in terms of bias removal and cancer signal isolation. These results open perspectives for the downstream analysis of larger data sets through the integration of cohorts produced by different sequencing pipelines or collected in different centers. Notably, the approach is rather general with the potential for application to many other genomic data analysis problems.
Ipsilateral or contralateral boosting of mice with mRNA vaccines confers equivalent immunity and protection against a SARS-CoV-2 Omicron strain
Authors: Ying Baoling , Liang Chieh-Yu , Desai Pritesh , Scheaffer Suzanne M. , Elbashir Sayda M. , Edwards Darin K. , Thackray Larissa B. , Diamond Michael S. 
Published: April 2024

ABSTRACTBoosting with mRNA vaccines encoding variant-matched spike proteins has been implemented to mitigate their reduced efficacy against emerging SARS-CoV-2 variants. Nonetheless, in humans, it remains unclear whether boosting in the ipsilateral or contralateral arm with respect to the priming doses impacts immunity and protection. Here, we boosted K18-hACE2 mice with either monovalent mRNA-1273 (Wuhan-1 spike) or bivalent mRNA-1273.214 (Wuhan-1 + BA.1 spike) vaccine in the ipsilateral or contralateral leg relative to a two-dose priming series with mRNA-1273. Boosting in the ipsilateral or contralateral leg elicited equivalent levels of serum IgG and neutralizing antibody responses against Wuhan-1 and BA.1. While contralateral boosting with mRNA vaccines resulted in expansion of spike-specific B and T cells beyond the ipsilateral draining lymph node (DLN) to the contralateral DLN, administration of a third mRNA vaccine dose at either site resulted in similar levels of antigen-specific germinal center B cells, plasmablasts/plasma cells, T follicular helper cells and CD8+T cells in the DLNs and the spleen. Furthermore, ipsilateral and contralateral boosting with mRNA-1273 or mRNA-1273.214 vaccines conferred similar homologous or heterologous immune protection against SARS-CoV-2 BA.1 virus challenge with equivalent reductions in viral RNA and infectious virus in the nasal turbinates and lungs. Collectively, our data show limited differences in B and T cell immune responses after ipsilateral and contralateral site boosting by mRNA vaccines that do not substantively impact protection against an Omicron strain.IMPORTANCESequential boosting with mRNA vaccines has been effective strategy to overcome waning immunity and neutralization escape by emerging SARS-CoV-2 variants. However, it remains unclear how the site of boosting relative to the primary vaccination series shapes optimal immune responses or breadth of protection against variants. In K18-hACE2 transgenic mice, we observed that boosting with historical monovalent or variant-matched bivalent vaccines in the ipsilateral or contralateral limb elicited comparable levels of serum spike specific antibody and antigen-specific B and T cells responses. Moreover, boosting on either side conferred equivalent protection against a SARS-CoV-2 Omicron challenge strain. Our data in mice suggest that the site of boosting with an mRNA vaccine does not substantially impact immunity or protection against SARS-CoV-2 infection.
Stroke-induced slow oscillations in dynamic brain organization
Authors: Tscherpel Caroline , Mustin Maike , Rosjat Nils , Ziemann Ulf , Fink Gereon R. , Daun Silvia , Grefkes Christian 
Published: April 2024

ABSTRACTA focal ischemic lesion is thought to alter neuronal activity beyond the area of structural damage and thereby interfere with the whole network architecture.We used a combination of transcranial magnetic stimulation and electroencephalography (TMS-EEG) together with dynamic connectivity analyses and graph theory to study alterations and reorganization of cortical reactivity and connectivity in a cohort of 42 stroke patients longitudinally after stroke. We found a link between an increase of low-frequency coupling in the delta band and alterations in neural information processing in the first weeks after stroke and their relevance for motor recovery more than three months later. We demonstrate that stroke to the motor system leading to impaired hand motor function induce an enhancement of slow activity and delta coupling between frontocentral and parietal regions. In addition, we could show a loss of the physiological network architecture with a decrease of small-worldness and modularity in the delta frequency, implying that a focal ischemic lesion distant to the cerebral cortex interferes with both cortical information integration as well as functional segregation within the days and weeks after stroke. While we found a link between bifrontal coupling in the alpha spectrum and the degree of the motor deficit in the early post-acute phase, the amount of small worldness disruption early after stroke indicated the motor outcome three months later. In contrast, recovery of motor function and cortical reorganization after more than three months post-stroke were paralleled by a normalization of increased low-frequency coupling and a reinstatement of the complex network structure featuring a small-world and modular topology.
CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment
Authors: Zhang Jie , Hu Gongcheng , Lu Yuli , Ren Huawei , Huang Yin , Wen Yulin , Ji Binrui , Wang Diyang , Wang Haidong , Liu Huisheng , Ma Ning , Pan Guangjin , Qu Yibo , Zhang Wei , Miao Zhichao , Yao Hongjie 
Published: April 2024

AbstractThe three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations inCTCFhave been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explored the regulatory roles of a clinically relevant R567W point mutation, located within the 11thzinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567Wmutation exhibited growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single- cell transcriptome levels. This mutation induced premature stem-like cell exhaustion, accelerated the maturation of GABAergic neurons, and disrupted neurodevelopmental and synaptic pathways. Additionally, it specifically hindered CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrored the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567Wmutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.
Plant Development Drives Dynamic Shifts in the Root Compartment Microbiomes of Wild and Domesticated Finger Millet Cultivars
Authors: Dadi Fantaye Ayele , Muthusamy Saraladevi , Ghosh Samrat , Muleta Diriba , Tesfaye Kassahun , Assefa Fassil , Xu Jie , Ghadamgahi Farideh , Ortiz Rodomiro , Vetukuri Ramesh Raju 
Published: April 2024

AbstractBackgroundPlant-microbe interactions in two root compartments - the rhizosphere and endosphere - play vital roles in maintaining plant health and ecosystem dynamics. The microbial communities in these niches are shaped in complex ways by factors including the plant’s developmental stage and cultivar, and the compartment where the interactions occur. Different plant cultivars provide distinct nutritional and ecological niches and may selectively enrich specific microbial populations through the secretion of root exudates. This gives rise to complex and dynamic plant-microbe interactions; some cultivars promote the recruitment of beneficial symbionts while others may deter pathogens. To clarify these processes, this work investigated the structure of the endosphere and rhizosphere microbial communities of wild type finger millet and five domesticated cultivars across two plant developmental stages.ResultsOur results showed that the plant developmental stage, compartment, and cultivar have varying degrees of impact on root-associated microbiomes. The dominant bacterial phyla in all samples wereProteobacteria,Actinobacteria, andBacteroidetes, while the dominant fungal phyla wereAscomycotaandBasidiomycota. All of these phyla exhibited pronounced variations in abundance. In general, an increased abundance ofActinobacteriain the endosphere was accompanied by a reduced abundance ofProteobacteria. The most pronounced changes in microbial community structure were observed in the rhizosphere during the flowering stage. Changes in the microbiome patterns of the rhizosphere were driven predominantly by the genusPseudomonas.Moreover, the host plant’s developmental stage strongly influenced the microbial communities, suggesting that plants can recruit specific taxa based on their need for particular soil consortia.ConclusionsOur results show that both host developmental stage and domestication strongly affect the assembly and structure of the plant microbiome. Moreover, plant root compartments can selectively recruit specific taxa from associated core microbial communities to fulfill their needs in a manner that depends on both the plant’s developmental stage and the specific root compartment that is involved. These findings show that deterministic selection pressures exerted by plants during their growth and development can significantly affect their microbial communities and have important implications for efforts to create tools for manipulating the microbiome to sustainably improve primary productivity.
Leptonic signatures of color-sextet scalars. II. Exploiting unique large-
ETmiss
signals at the LHC
Authors: Carpenter Linda M. , Schwind Katherine , Murphy Taylor 
Published: April 2024

The diverse and distinct collider phenomenology of color-sextet scalars motivates a thorough investigation of their effective couplings to the Standard Model at the LHC. Some of the more unique sextet signals involve not only jets but also leptons. In previous work, we proposed an LHC search for color-sextet scalars in a channel with jets and a hard opposite-sign lepton pair, which results from a dimension-six coupling. In this sequel we study the counterpart processes with neutrinos, which produce jets in association with missing transverse energy (ETmiss) in addition to possible leptons. We consider multiple search channels, including both single and pair sextet production, all characterized by significant missing energy and some featuring distinctive kinematic features. Our multifaceted study consists of three reinterpreted existing searches and a joint-likelihood analysis designed by us to maximize HL-LHC sensitivity to single sextet production. We show that our dedicated strategy in the jets+lepton+ETmiss channel can supersede today’s limits from reinterpreted searches, and we make sensitivity projections for the HL-LHC. Altogether, our analysis can exclude sextet scalars lighter than 4.4 TeV or probe effective cutoffs as high as 16.8 TeV.

Published by the American Physical Society
2024
On-Chip Quantum Information Processing with Distinguishable Photons
Authors: Yard Patrick , Jones Alex E. , Paesani Stefano , Maïnos Alexandre , Bulmer Jacob F. F. , Laing Anthony 
Published: April 2024

Multiphoton interference is at the heart of photonic quantum technologies. Arrays of integrated cavities can support bright sources of single photons with high purity and small footprint, but the inevitable spectral distinguishability between photons generated from nonidentical cavities is an obstacle to scaling. In principle, this problem can be alleviated by measuring photons with high timing resolution, which erases spectral information through the time-energy uncertainty relation. Here, we experimentally demonstrate that detection can be implemented with a temporal resolution sufficient to interfere photons detuned on the scales necessary for cavity-based integrated photon sources. By increasing the effective timing resolution of the system from 200 to 20 ps, we observe a 20% increase in the visibility of quantum interference between independent photons from integrated microring resonator sources that are detuned by 6.8 GHz. We go on to show how time-resolved detection of nonideal photons can be used to improve the fidelity of an entangling operation and to mitigate the reduction of computational complexity in boson sampling experiments. These results pave the way for photonic quantum information processing with many photon sources without the need for active alignment.

Published by the American Physical Society
2024
Assessing interprofessional and integrated care in providing sexual and reproductive health services to adolescents at primary healthcare level in Nigeria
Authors: Agwu Prince , Agu Ifunanya , Ezumah Nkoli , Mbachu Chinyere , Onwujekwe Obinna 
Published: April 2024

PurposeSexual and reproductive health (SRH) interventions demand diverse services, encompassing medical, social and psychological care to ensure the overall wellbeing of service users. In the absence of multidisciplinary response to SRH interventions, service users could be deprived of crucial SRH services, which could undermine their safety and wellbeing. Based on this knowledge, our study was designed to map the interprofessional space in primary healthcare (PHC) facilities in Ebonyi State, Nigeria that deliver SRH services.Design/methodology/approachInterviews with 20 health workers and group discussions with 72 young people aged 15–24 years provided the data for the study. We analyzed data deductively, focusing on the assessments of the presence or absence of specific professionals that are typically expected to provide different aspects of SRH services.FindingsWe found conspicuous absence of laboratory diagnostic, social care, psycho-cognitive and some medical services expected of primary care. These absences necessitated unnecessary referrals, encouraged breaches in confidentiality, undermined social care and justice, increased cost of care and discouraged young clients from utilizing SRH services provided in PHCs. Our study, therefore, emphasizes the need for integrated care in the delivery of SRH services, which would involve relevant diverse professionals contributing their expertise toward comprehensive care for SRH service users.Originality/valueThe study provides human resource insights toward strengthening primary healthcare in Nigeria vis-à-vis efficient delivery of SRH services to guarantee the health security of service users.
The effect of the road rationing policy on housing prices: evidence from the odd-even policy in Jakarta
Authors: Kusumawardani Amanda Dian Widyasti , Yudhistira Muhammad Halley 
Published: April 2024

Purpose
The purpose of this study is to examine the effects of the Odd-Even Road Rationing Policy (RRP) on housing prices in Jakarta, Indonesia. It aims to evaluate the net effect of the RRP on housing prices.

Design/methodology/approach
The study uses the monocentric model and employs the difference-in-differences (DD) method. Annual neighborhood-level housing price data is analyzed to assess the impact of the RRP on housing prices. Additionally, propensity score matching is used to address potential biases resulting from non-random policy assignments.

Findings
The results demonstrate that houses located within the RRP-restricted area experience a decrease in price that is relative to those in the control group. The findings indicate a decrease in housing prices ranging from 7.59% to 14.7% within the RRP-restricted area. This suggests that the positive impacts resulting from the RRP have not fully compensated for the restricted accessibility experienced by individuals who have limited behavioral changes. The study also confirms the significance of commuting costs in individuals' location decisions, aligning with predictions from urban economics models.

Originality/value
This study contributes to the literature by providing insights into the effects of a RRP on housing prices. It expands understanding beyond the immediate effects on traffic conditions and air pollution, which previous studies have primarily focused on. Furthermore, to the best of the authors’ knowledge, this research will be the first conducted to identify the impacts of RRP on housing prices in Indonesia.
Guardians of the vault: unmasking online threats and fortifying e-banking security, a systematic review
Authors: Ahmad Iftikhar , Khan Salim , Iqbal Shahid 
Published: April 2024

Purpose
The purpose of this paper is to investigate and analyze the adoption of digital technologies in the banking industry and its impact on the rise of digital fraudulent activities, specifically focusing on online banking frauds. This paper aims to provide insights into the current technologies implemented by banks to secure their online banking systems and explores the methods used by cybercriminals to exploit security vulnerabilities in these systems.

Design/methodology/approach
In order to understand how digital technologies in banking can be secured against online fraud, this research conducted a systematic literature review (SLR) on digital banking, online banking fraud, and security measurements. The review encompasses a variety of sources from online databases such as Emerald Insight, Google Scholar, IEEE, JSTOR, Springer and Science Direct.

Findings
The key finding of the paper is that the adoption of digital technologies in the banking industry has led to a significant increase in digital fraudulent activities, particularly in the form of online banking frauds. This paper emphasizes that these frauds have become a global concern and have evolved into an industry where cybercriminals use sophisticated tools such as phishing attacks, denial-of-service attacks, Trojan horses, malware infections, identity theft and computer viruses.

Research limitations/implications
This study relies solely on a literature review without incorporating primary data or case studies; therefore, it might miss out on the firsthand experiences and perspectives of banks and cybersecurity professionals.

Practical implications
This study emphasizes the need for banks to adopt advanced security measures to safeguard their online banking systems.

Social implications
This study underscores the importance of ongoing training and awareness programs for both bank employees and customers.

Originality/value
This study specifically addresses the adoption of digital technologies in the banking industry and its correlation with the increase in digital fraudulent activities. This focus on the intersection of technology and fraud in the banking sector is a distinctive aspect. This study conducts a SLR to examine the current technologies implemented by banks to safeguard their online banking systems. This comprehensive approach provides insights into the diverse security measures used by banks to protect against various types of cyber threats.