bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early regional cerebral grey matter damage predicts long-term cognitive impairment phenotypes in multiple sclerosis: a 20-year study
Authors: Ziccardi Stefano , Crescenzo Francesco , Guandalini Maddalena , Caliskan Gulser , Martinelli Luigi , Tamanti Agnese , Schiavi Gian Marco , Bajrami Albulena , Marastoni Damiano , Calabrese Massimiliano 
Published: October 2024

Abstract
Despite grey matter atrophy in cortical and subcortical regions has been related to cognitive impairment in multiple sclerosis, only a few studies evaluated its predictive value for alterations in the long-term. We aimed to determine early predictors of cognitive status after 20 years of multiple sclerosis. In this longitudinal retrospective study, participants underwent a 1.5 T MRI scanning at diagnosis (T0) and after two years (T2), which included the evaluation of regional grey matter volume loss patterns. All individuals with multiple sclerosis underwent a comprehensive neuropsychological assessment at the end of the study and were classified considering their global and specific cognitive domains status (memory, attention/information processing speed, executive functioning). Clinical and MRI characteristics were assessed as predictors of long-term cognitive impairment. Analysis of covariance, t-test, unadjusted and adjusted (for age, sex, disease duration, volume of white matter lesions, volume of cortical lesions) logistic regression were conducted. One hundred seventy-five people with multiple sclerosis (118 females; mean ± SD age at the end of study = 47.7 ± 9.4 years) clinically followed for 20 years from onset (mean ± SD = 19.9 ± 5.1) were evaluated. At the end of the study, 81 (47%) were classified as cognitively impaired: 38 as mildly impaired (22%), and 43 as severely impaired (25%). In particular, 46 were impaired in memory (27%), 66 were impaired in attention/information processing speed (38%), and 71 were impaired in executive functioning (41%). Regression models identified precuneus (adjusted odds ratio = 3.37; P &lt; 0.001), insula (adjusted odds ratio = 2.33; P = 0.036), parahippocampal gyrus (adjusted odds ratio = 2.07; P &lt; 0.001) and cingulate (adjusted odds ratio = 1.81; P = 0.009) as the most associated regions with global cognitive impairment and domains-specific cognitive alterations after a mean of 20 years of multiple sclerosis, after adjusting for demographic and clinical variables as well as for focal white matter and grey matter damage. Early grey matter volume loss of specific cortical and deep grey matter regions predicts global and domain cognitive alterations after 20 years from multiple sclerosis diagnosis.
Corticocortical and corticomuscular connectivity dynamics in standing posture: electroencephalography study
Authors: Fujio Kimiya , Takeda Kenta , Obata Hiroki , Kawashima Noritaka 
Published: October 2024

Abstract
Cortical mechanism is necessary for human standing control. Previous research has demonstrated that cortical oscillations and corticospinal excitability respond flexibly to postural demands. However, it is unclear how corticocortical and corticomuscular connectivity changes dynamically during standing with spontaneous postural sway and over time. This study investigated the dynamics of sway- and time-varying connectivity using electroencephalography and electromyography. Electroencephalography and electromyography were recorded in sitting position and 3 standing postures with varying base-of-support: normal standing, one-leg standing, and standing on a piece of wood. For sway-varying connectivity, corticomuscular connectivity was calculated based on the timing of peak velocity in anteroposterior sway. For time-varying connectivity, corticocortical connectivity was measured using the sliding-window approach. This study found that corticomuscular connectivity was strengthened at the peak velocity of postural sway in the γ- and β-frequency bands. For time-varying corticocortical connectivity, the θ-connectivity in all time-epoch was classified into 7 clusters including posture-relevant component. In one of the 7 clusters, strong connectivity pairs were concentrated in the mid-central region, and the proportion of epochs under narrow-base standing conditions was significantly higher, indicating a functional role for posture balance. These findings shed light on the connectivity dynamics and cortical oscillation that govern standing balance.
Low-intensity transcranial ultrasound stimulation modulates neurovascular coupling in mouse models of Alzheimer’s disease
Authors: Li Xin , Wang Qiaoxuan , Wang Mengran , Ma Zhenfang , Yuan Yi 
Published: October 2024

Abstract
Neurovascular coupling plays an important role in the progression of Alzheimer’s disease. However, it is unclear how ultrasound stimulation modulates neurovascular coupling in Alzheimer’s disease. Here, we found that (i) transcranial ultrasound stimulation modulates the time domain and frequency domain characteristics of cerebral blood oxygen metabolism in Alzheimer’s disease mice; (ii) transcranial ultrasound stimulation can significantly modulate the relative power of theta and gamma frequency of local field potential in Alzheimer’s disease mice; and (iii) transcranial ultrasound stimulation can significantly modulate the neurovascular coupling in time domain and frequency domain induced by forepaw electrical stimulation in Alzheimer’s disease mice. It provides a research basis for the clinical application of transcranial ultrasound stimulation in Alzheimer’s disease patients.
Interventions for Adjunctive Care in Patients With Inflammatory Bowel Disease and Permanent Ileostomy: A Systematic Review
Authors: Vuyyuru Sudheer Kumar , Solitano Virginia , Yuan Yuhong , Narula Neeraj , Singh Siddharth , Ma Christopher , Rieder Florian , Jairath Vipul 
Published: October 2024

Abstract

Background
The evidence for the management of patients with Crohn’s disease (CD) and permanent ileostomy (PI) is limited. We aimed to summarize the interventional studies related to the provision of adjunctive ostomy care in this population.

Methods
MEDLINE, Embase, and Cochrane CENTRAL were searched from inception to January 5, 2024. Eligible studies were non-randomized or randomized controlled trials (RCTs), or comparative cohort studies predominantly recruiting participants with CD and/or ulcerative colitis (UC) with PI assessing interventions for the management of high stoma output, disease recurrence, peristomal skin care, pouching systems, behavioral interventions, mental health support, and diet.

Results
Out of 3217 records, 6 were eligible and all were RCTs (n = 95). Out of these, 5 adopted a crossover design, and 1 study was a double-blind parallel-group RCT. All except 1 were published more than 20 years ago (1976-2003). Two studies exclusively included patients with UC, one included CD, and the remaining included both UC and CD. Four studies assessed pharmacological interventions (loperamide, 5-aminosalysilate [5-ASA], azodisal sodium, and budesonide), one assessed oral supplement with different osmolarities, and one assessed dietary intervention (unrefined vs refined carbohydrate). A decrease in ileostomy output was the primary outcome of interest in 4 studies. None of the studies assessed interventions for peristomal skin care, quality of life, stoma pouching systems, behavioral interventions, mental health, or CD recurrence.

Conclusions
This study highlights that the evidence base to inform care for patients with IBD and PI is almost non-existent. There is an urgent need for focused research in this area to inform evidence-based treatment decisions.
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides
Authors: Anwer Farha , Navid Ahmad , Faiz Fiza , Haider Uzair , Nasir Samavi , Farooq Muhammad , Zahra Maryam , Bano Anosh , Bashir Hafiza Hira , Ahmad Madiha , Abbas Syeda Aleena , Room Shah E , Saeed Muhammad Tariq , Ali Amjad 
Published: October 2024

Abstract
Acinetobacter baumannii has emerged as a prominent nosocomial pathogen, exhibiting a progressive rise in resistance to therapeutic interventions. This rise in resistance calls for alternative strategies. Here, we propose an alternative yet specialized resource on antimicrobial peptides (AMPs) against A. baumannii. Database ‘AbAMPdb’ is the manually curated collection of 300 entries containing the 250 experimental AMP sequences and 50 corresponding synthetic or mutated AMP sequences. The mutated sequences were modified with reported amino acid substitutions intended for decreasing the toxicity and increasing the antimicrobial potency. AbAMPdb also provides 3D models of all 300 AMPs, comprising 250 natural and 50 synthetic or mutated AMPs. Moreover, the database offers docked complexes comprising 5000 AMPs and their corresponding A. baumannii target proteins. These complexes, accessible in Protein Data Bank format, enable the 2D visualization of the interacting amino acid residues. We are confident that this comprehensive resource furnishes vital information concerning AMPs, encompassing their docking interactions with virulence factors and antibiotic resistance proteins of A. baumannii. To enhance clinical relevance, the characterized AMPs could undergo further investigation both in vitro and in vivo.
Database URL: https://abampdb.mgbio.tech/
Low-dose aspirin and risk of anaemia in older adults: insights from a Danish register-based cohort study
Authors: Barbieri Maria Antonietta , Peker Dilsad Simay , Askar Mohsen Gamal Saad , Battini Vera , Abate Andrea , Carnovale Carla , Clementi Emilio , Ofori-Asenso Richard , Spina Edoardo , Pareek Manan , Kragholm Kristian , Torp-Pedersen Christian , Sessa Maurizio 
Published: October 2024

Abstract

Aims
To assess the risk of anaemia among low-dose aspirin (LDA) exposure in Danish older individuals in a real-world setting.

Methods and results
Population based-cohort study conducted using Danish registers. The study population included older individuals (≥65 years) exposed to LDA between 2008 and 2013 for primary or secondary prevention of cardiovascular events. Over a 5-year follow-up, outcomes included anaemia incidence based on haemoglobin values and hematinic deficiency incidence based on antianaemic prescriptions. Among the 313 508 individuals included in the study population, those exposed to LDA (n = 59 869, 19.1%) had an incidence of hematinic deficiency determined by the use of antianaemic treatment of 9.6%, with an incidence rate ratio of 9.11 (95% confidence interval, CI: 8.81–9.41) when compared to non-users of LDA (n = 253 639, 80.9%), who had an incidence of 3.7%. Anaemia determined by haemoglobin value measurements was observed in 5.9% of those exposed to LDA, with an incidence rate ratio of 7.89 (95% CI: 7.58–8.21) when compared to non-users of LDA. Approximately, one in five individuals (n = 2 422, 21.5%) who experienced anaemia also experienced bleeding. Severe anaemia was observed in 1.3% of those exposed to LDA compared to 0.6% of those not exposed. Among the exposed, the reduction in haemoglobin and ferritin levels was associated with the severity of anaemia.

Conclusion
These findings indicate that in a real-world setting, anaemia with LDA can occur in 6–10 older individuals out of every 100 LDA users during the first 5 years of treatment.
Association Between Mobility Limitations and Cognitive Decline in Community-Dwelling Older Adults: The English Longitudinal Study of Ageing
Authors: Cao Bi-Fei , Zhou Rui , Chen Hao-Wen , Liang Yong-Qi , Liu Kuan , Fan Wei-Dong , Huang Rui-Dian , Huang Yi-Ning , Zhong Qi , Wu Xian-Bo 
Published: October 2024

Abstract

Background and Objectives
Mobility limitations have been linked to cognition. However, little is known about the relationship between mobility decline and cognitive decline. This study investigated the effect of mobility limitations and decline on cognitive decline in a population-based cohort of older adults.

Research Design and Methods
A population-based cohort of 9,695 cognitively intact participants (mean age = 65.4 years, standard deviation [SD] = 10.4) was assessed. Mobility limitation scores ranging from 0 to 10 were assessed at baseline (Wave 4) by using self-reporting difficulty in a set of 10 activities, and a higher score indicated worse mobility. A subset of 9,250 participants underwent 2 mobility assessments at Waves 3 and 4, and were categorized into normal mobility or mobility decline (defined as Wave 4 − Wave 3 &gt; 1 SD of Wave 3). Linear mixed models were used to assess the longitudinal contribution of mobility limitations and decline to cognitive decline.

Results
During a median follow-up period of 9.4 years (SD 1.8), the participants in the highest quartile of mobility scores displayed an accelerated cognitive decline (−0.191 SD/year, 95% confidence interval [CI] = −0.223, −0.159) compared with those in the lowest quartile. Notably, individuals experiencing mobility decline exhibited a marked cognitive decline (−0.179 SD/year, 95% CI = −0.220, −0.139), potentially influenced by factors such as physical activity and depression.

Discussion and Implications
Mobility limitations and decline significantly correlate with cognitive decline in older adults, highlighting that mobility focused interventions in healthcare strategies preserve cognition.
Modelling uncertainty in P-wave arrival-times retrieved from DAS data: case-studies from 15 fibre optic cables
Authors: Bozzi E , Agostinetti N Piana , Fichtner A , Klaasen S , Ugalde A , Biondi B , Yuan S , Dahm T , Isken M , Paitz P , Walter F , Baird A F , Becerril C , Nishimura T , Shen J , Zhu T , Saccorotti G 
Published: October 2024

SUMMARY
Distributed acoustic sensing (DAS) technology enables the detection of waves generated by seismic events, generally as uniaxial strain/strain rate time-series observed for dense, subsequent, portions of a Fibre Optic Cable (FOC). Despite the advantages in measurement density, data quality is often affected by uniaxial signal polarization, site effects and cable coupling, beyond the physical energy decay with distance. To better understand the relative importance of these factors for data inversion, we attempt a first modelling of noise patterns affecting DAS arrival times for a set of seismic events. The focus is on assessing the impact of noise statistics, together with the geometry of the problem, on epicentral location uncertainties. For this goal, we consider 15 ‘real-world’ cases of DAS arrays with different geometry, each associated with a seismic event of known location. We compute synthetic P-wave arrival times and contaminate them with four statistical distributions of the noise. We also estimate P-wave arrival times on real waveforms using a standard seismological picker. Eventually, these five data sets are inverted using a Markov chain Monte Carlo method, which offers the evaluation of the relative event location differences in terms of posterior probability density (PPD). Results highlight how cable geometry influences the shape, extent and directionality of the PPDs. However, synthetic tests demonstrate how noise assumptions on arrival times often have important effects on location uncertainties. Moreover, for half of the analysed case studies, the observed and synthetic locations are more similar when considering noise sources that are independent of the geometrical characteristics of the arrays. Thus, the results indicate that axial polarization, site conditions and cable coupling, beyond other intrinsic features (e.g. optical noise), are likely responsible for the complex distribution of DAS arrival times. Overall, the noise sensitivity of DAS suggests caution when applying geometry-only-based approaches for the a priori evaluation of novel monitoring systems.
R&D investments, ownership and local firm growth
Authors: Wang Yifei , Henning Martin 
Published: October 2024

Abstract
How do research and development (R&D) investments stimulate the local economy? Our paper complements and extends the voluminous literature on the externalities of R&D investments by looking at internal firm growth across regions and the “spillovers” from R&D workers on other workers within the same firm. More specifically, we examine how R&D investments affect the change in employment and productivity in the same firm over time. We also investigate the differences that come with domestic or foreign ownership. Combining data from the Swedish biennial survey series on R&D with firm and establishment registers, we find that R&D-stimulated growth is a localized phenomenon: firms tend to grow in the same regions where they invest in R&D activities. This link is particularly strong for employment effects. While we find that the positive association between R&D and labor productivity holds for all firms, growth effects on local employment are limited to domestically owned firms, especially in manufacturing. The results strengthen our understanding of the correlation between R&D and firm growth on a local level, and contribute to both the academic and policy debate on the effects of globalization on local economic growth.
ICESp1109, a Novel Hybrid Integrative Conjugative Element of Macrolide-Resistant Streptococcus pyogenes Serotype M77 Collected Between 2003 and 2017 in Poland
Authors: Gawor Jan , Żuchniewicz Karolina , Ojeda Saavedra Matthew , Beres Stephen B , Kiedrowska Marlena , Wróbel-Pawelczyk Izabela , Kozińska Aleksandra , Gromadka Robert , Musser James M , Sitkiewicz Izabela , Kern-Zdanowicz Izabela 
Published: October 2024

Abstract

Background
The antibiotic resistance determinants and associated mobile genetic elements (MGEs) were detected among Streptococcus pyogenes (group A streptococci [GAS]) clinical isolates of an M77 serotype collected in Poland between 2003 and 2017.

Methods
The genomes of 136 M77 GAS isolates were sequenced using short- and selected with long-read approach; whole genome sequences were analyzed to determine the genetic context of macrolide resistance determinants.

Results
The analysed strains were collected from in- and outpatients. Sequencing data analysis revealed that all strains carried the tet(O) gene. They were classified as a single sequence type, ST63. The unique erythromycin-resistance determinant, the erm(TR), was detected in 76.5% (n = 104) of isolates. It was found predominantly (n = 74) within a novel hybrid integrative conjugative element composed of the ICESp1108-like sequence and ICESp2906 variant, which was then named ICESp1109. However, in strains isolated before 2008, erm(TR) was located within ICESp2905 (n = 27) and in 3 strains - within stand-alone ICESp1108-like sequences.

Conclusions
Based on phylogenetic analysis results, the clonal dissemination of the macrolide-resistant S. pyogenes M77/ST63 strain with hybrid ICESp1109 was observed between 2008 and 2017. ICESp1109 is the novel hybrid ICE in gram-positive bacteria.
Rhizospheric miRNAs affect the plant microbiota
Authors: Middleton Harriet , Dozois Jessica Ann , Monard Cécile , Daburon Virginie , Clostres Emmanuel , Tremblay Julien , Combier Jean-Philippe , Yergeau Étienne , El Amrani Abdelhak 
Published: October 2024

Abstract
Small ribonucleic acids (RNAs) have been shown to play important roles in cross-kingdom communication, notably in plant–pathogen relationships. Plant micro RNAs (miRNAs)—one class of small RNAs—were even shown to regulate gene expression in the gut microbiota. Plant miRNAs could also affect the rhizosphere microbiota. Here we looked for plant miRNAs in the rhizosphere of model plants, and if these miRNAs could affect the rhizosphere microbiota. We first show that plant miRNAs were present in the rhizosphere of Arabidopsis thaliana and Brachypodium distachyon. These plant miRNAs were also found in or on bacteria extracted from the rhizosphere. We then looked at the effect these plants miRNAs could have on two typical rhizosphere bacteria, Variovorax paradoxus and Bacillus mycoides. The two bacteria took up a fluorescent synthetic miRNA but only V. paradoxus shifted its transcriptome when confronted to a mixture of six plant miRNAs. V. paradoxus also changed its transcriptome when it was grown in the rhizosphere of Arabidopsis that overexpressed a miRNA in its roots. As there were differences in the response of the two isolates used, we looked for shifts in the larger microbial community. We observed shifts in the rhizosphere bacterial communities of Arabidopsis mutants that were impaired in their small RNA pathways, or overexpressed specific miRNAs. We also found differences in the growth and community composition of a simplified soil microbial community when exposed in vitro to a mixture of plant miRNAs. Our results support the addition of miRNAs to the plant tools shaping rhizosphere microbial assembly.
NovoLign: metaproteomics by sequence alignment
Authors: Kleikamp Hugo B C , van der Zwaan Ramon , van Valderen Ramon , van Ede Jitske M , Pronk Mario , Schaasberg Pim , Allaart Maximilienne T , van Loosdrecht Mark C M , Pabst Martin 
Published: October 2024

Abstract
Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.