bluuebunny/crossref_metadata_2025 huggingface dataset:
Feasibility of trauma video review for the collection of medication-related information for research and quality improvement
Authors: Uttaro Elizabeth , Hopkins Anthony , Kokanovich Kate , Maynard Kaylee , Vella Michael , Jones Courtney M C , Miglani Andrea , Acquisto Nicole M
Published: October 2024

Purpose

Trauma video review (TVR) involves reviewing video recordings of team-based trauma response to evaluate team performance, identify improvement opportunities, and assess procedures, but the feasibility of using TVR to gather medication-related information is unknown. We aimed to assess the feasibility of using TVR for data collection of medication-related variables for research and quality improvement by comparing and describing differences between TVR and electronic medical record (EMR) review.

Methods

This was an observational study of level I/II trauma patients treated between November 2022 and March 2023. Patients with video recording started within 1 minute of arrival, at least 1 medication administered, and with pharmacist participation in care were included. The number of variables able to be collected by TVR or EMR review were compared and reported in the categories of medication administration, indicators of adverse drug events (ADEs), medication errors, and communication. The numbers and types of discrepancies between data collection modalities were quantified and described. Agreement between TVR and EMR review was assessed and reported as an intraclass correlation coefficient (ICC).

Results

Twenty-five patients were included; 758 and 1,011 variables collected by TVR and EMR review, respectively. In total, 689 variables were collected by both methods, and data collection modalities matched exactly in 4 of 25 patients (16%); ICC, 0.677 (moderate level of agreement). There were 46 (6.7%) discrepancies; 84% involved communication related variables. TVR missed more variables than EMR review, mostly medication errors and inability to assess ADEs but captured more communication-related variables.

Conclusion

TVR and EMR review together offer a greater source of medication-related information for data collection compared to either alone. EMR review collected medication administration, ADE, and medication errors variables more often than TVR and TVR was better able to collect communication-related variables. When designing studies/quality improvement efforts related to medication use during trauma resuscitation (e.g., pharmacist impact on time to administration), combined data collection modalities should be used, when available.
Multicenter Validation of the English Version of the Dépistage Cognitif de Québec: a Cognitive Screening Tool for Atypical Dementias
Authors: Meilleur-Durand Synthia , Lévesque Marianne , St-Onge Frederic , Masellis Mario , Hsiung Ging-Yuek Robin , Jarrett Pamela , Villeneuve Sylvia , Léger Gabriel , Salmon David , Galasko Doug , Cunnane Stephen C , Gauthier Serge , Callahan Brandy , Sellami Leila , Hudon Carol , Macoir Joël , Verret Louis , Cassivi-Joncas Alison , Comishen Michael , Laforce Robert
Published: October 2024

Background

Early detection of atypical dementia remains difficult partly because of the absence of specific cognitive screening tools. This creates undue delays in diagnosis and management. The Dépistage Cognitif de Québec (DCQ; dcqtest.org) was developed in French and later validated in participants with atypical syndromes. We report the validation of the English version.

Methods

This multicentre prospective validation study was conducted in 10 centers across Canada and the United States on 260 English-speaking participants aged over 50. We translated and modified the original French DCQ to add targeted stimuli to the Visusopatial Index and social cognition vignettes to the Behavioral Index. A backward translation was performed and equivalence between languages was assessed by administering both tests to 30 bilingual participants.

Results

Mean DCQ total score (out of 100) was 95.0 (SD = 3.6). Spearman’s correlation coefficient showed a strong and significant correlation (r = 0.49, p < .001) with the Montreal Cognitive Assessment. Test–retest reliability was good (Spearman’s coefficient = 0.72, p < .001) and interrater reliability, excellent (intraclass correlation = 0.97, p < .001). Normative data shown in percentiles were stratified by age and education for a population-based sample of 260 English-speaking controls aged between 50 and 87 years old.

Conclusions

Similar to the French version, the English DCQ proved to be a valid cognitive screening test. The original version was very sensitive to detect atypical dementias such as primary progressive aphasias, Alzheimer’s disease’ variants and syndromes along the frontotemporolobar degeneration spectrum. This 20-min test can be administered à la carte and offers an alternative to detailed comprehensive neuropsychological evaluations.
Artificial intelligence and machine learning in dermatological research and healthcare: British Society for Investigative Dermatology Skin Club Report, Southampton, April 2024
Authors: Lai Chester , Fuggle Nicholas R , Matin Rubeta N , Tanaka Reiko J , Banerji Christopher R S , Rajan Neil
Published: October 2024

Lay Summary

The British Society of Investigative Dermatology is the annual meeting of the UK’s skin research community. At this year’s meeting in Southampton, there was a discussion on the history and potential of artificial intelligence (‘AI’) in health care.

The four experts who spoke at the meeting have summarized their lectures in this paper. There is a piece on Alan Turing, who proposed the ‘Turing Test’ to find out if a machine could think like a human. Concepts like ‘machine learning’ (a key tool in AI) are explained. Next, there is a piece on the challenges of using AI decision-making tools in the skin cancer pathway. We discuss AI/machine learning approaches to grouping patients and choosing the best treatments for people with ‘atopic dermatitis’ (or ‘eczema’). Finally, potential pitfalls in AI are highlighted, including the need to explain how AI makes decisions and approaches to achieving this.

There is much excitement about AI, and this paper captures the discussion from the meeting of the current state of AI in dermatology health care.
The management of atopic dermatitis in women of childbearing age: confused terminology, lack of evidence and resulting clinical inertia
Authors: Kumari Ruchika , Apfelbacher Christian J , Nelson-Piercy Catherine , Flohr Carsten
Published: October 2024

Confusion in definitions, conflicting opinions and limited evidence leave women of childbearing age with eczema, and treating clinicians, vulnerable to restrictive therapeutic practices.
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

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 < 0.001), insula (adjusted odds ratio = 2.33; P = 0.036), parahippocampal gyrus (adjusted odds ratio = 2.07; P < 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.
Considering clinical history as a determinant of human neuron function
Authors: Booker Sam A
Published: October 2024

This scientific commentary refers to ‘Clinical parameters affect the structure and function of superficial pyramidal neurons in the adult human neocortex’, by Lenz et al. (https://doi.org/10.1093/braincomms/fcae351).
Beyond hyperhidrosis: the use of topical glycopyrronium in plantar acuagenic keratoderma
Authors: Mercader-Salvans Júlia , Santos-e-Silva Caldeira-Marques María-Luisa , Quetglas-Valenzuela Miguel , Sánchez-Báez Daniel Javier , Rodríguez-Rodríguez Rosa Nieves , Ramos-Rodríguez Daniel
Published: October 2024

This letter presents a clinical case detailing the efficacy of topical glycopyrronium in the treatment of plantar aquagenic keratoderma. Our report not only highlights a significant improvement in pruritus but also underscores notable clinical and dermatoscopic advancements following treatment.
Corticocortical and corticomuscular connectivity dynamics in standing posture: electroencephalography study
Authors: Fujio Kimiya , Takeda Kenta , Obata Hiroki , Kawashima Noritaka
Published: October 2024

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

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

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

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

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

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 > 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

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

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

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

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

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.
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods
Authors: Branck Tobyn , Hu Zhiji , Nickols William A , Walsh Aaron M , Bhosle Amrisha , Short Meghan I , Nearing Jacob T , Asnicar Francesco , McIver Lauren J , Maharjan Sagun , Rahnavard Ali , Louyakis Artemis S , Badri Dayakar V , Brockel Christoph , Thompson Kelsey N , Huttenhower Curtis
Published: October 2024

The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the “One Health” concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.
Synergistic oral beta-lactam combinations for treating tuberculosis
Authors: Quan Diana H , Wang Trixie , Martinez Elena , Kim Hannah Y , Sintchenko Vitali , Britton Warwick J , Triccas James A , Alffenaar Jan-Willem C
Published: October 2024

Background

The enormous burden of tuberculosis (TB) worldwide is a major challenge to human health, but the costs and risks associated with novel drug discovery have limited treatment options for patients. Repurposing existing antimicrobial drugs offers a promising avenue to expand TB treatment possibilities. This study aimed to explore the activity and synergy of beta-lactams in combination with a beta-lactamase inhibitor, which have been underutilized in TB treatment to date.

Methods

Based on inhibitory concentration, oral bioavailability, and commercial availability, seven beta-lactams (cefadroxil, tebipenem, cephradine, cephalexin, cefdinir, penicillin V, and flucloxacillin), two beta-lactamase inhibitors (avibactam and clavulanate), and three second-line TB drugs (moxifloxacin, levofloxacin, and linezolid) were selected for combination in vitro testing against Mycobacterium tuberculosis H37Rv. Resazurin assays and colony forming unit enumeration were used to quantify drug efficacy, Chou-Talalay calculations were performed to identify drug synergy and Chou-Martin calculations were performed to quantify drug dose reduction index.

Results

The order of activity of beta-lactams was cefadroxil > tebipenem > cephradine > cephalexin > cefdinir > penicillin V > flucloxacillin. The addition of clavulanate improved beta-lactam activity to a greater degree than the addition of avibactam. As a result, avibactam was excluded from further investigations, which focused on clavulanate. Synergy was demonstrated for cefdinir/cephradine, cefadroxil/tebipenem, cefadroxil/penicillin V, cefadroxil/cefdinir, cephalexin/tebipenem, cephalexin/penicillin V, cephalexin/cefdinir, cephalexin/cephradine, and cefadroxil/cephalexin, all with clavulanate. However, combining beta-lactams with moxifloxacin, levofloxacin, or linezolid resulted in antagonistic effects, except for the combinations of penicillin V/levofloxacin, penicillin V/moxifloxacin, and cefdinir/moxifloxacin.

Conclusions

Beta-lactam synergy may provide viable combination therapies for the treatment of TB.
Nisin-loaded chitosan/sodium alginate microspheres enhance the antimicrobial efficacy of nisin against Staphylococcus aureus
Authors: Tang Taya , Chen Yinzhu , Zhao Zhongling , Bai Qianyu , Leisner Jørgen J , Liu Tianlong
Published: October 2024

Aims

To develop and evaluate nisin-loaded chitosan/sodium alginate (CS/SA) microspheres as an improved antimicrobial delivery system targeting Staphylococcus aureus strains.

Methods and results

The microspheres were prepared using a modified water-in-oil emulsion cross-linking method, resulting in spherical particles sized 1–8 µm with a surface charge of −7.92 ± 5.09 mV, confirmed by scanning electron microscopy (SEM) and Zetasizer analysis. Encapsulation efficiency (EE) and loading capacity (LC) of nisin were 87.60% ± 0.43% and 1.99% ± 0.01%, respectively. In vitro release studies over 48 h indicated a controlled release pattern of nisin, described by the Korsmeyer–Peppas model, with higher release rates at 37°C and alkaline pH. Antimicrobial assays showed an enhanced efficacy of nisin-loaded CS/SA microspheres compared to free nisin, with minimum inhibitory concentration values reduced by 50%. Confocal laser scanning microscopy (CLSM), SEM, and transmission electron microscopy showed significant bacterial membrane damage and cellular disruption induced by the microspheres.

Conclusions

This study highlights the potential of nisin-loaded CS/SA microspheres as an innovative antimicrobial delivery system with improved stability and antimicrobial efficacy against S. aureus, addressing limitations associated with nisin applied alone.
Application of a digital quality measure for cancer diagnosis in Epic Cosmos
Authors: Zimolzak Andrew J , Khan Sundas P , Singh Hardeep , Davila Jessica A
Published: October 2024

Objectives

Missed and delayed cancer diagnoses are common, harmful, and often preventable. We previously validated a digital quality measure (dQM) of emergency presentation (EP) of lung cancer in 2 US health systems. This study aimed to apply the dQM to a new national electronic health record (EHR) database and examine demographic associations.

Materials and Methods

We applied the dQM (emergency encounter followed by new lung cancer diagnosis within 30 days) to Epic Cosmos, a deidentified database covering 184 million US patients. We examined dQM associations with sociodemographic factors.

Results

The overall EP rate was 19.6%. EP rate was higher in Black vs White patients (24% vs 19%, P < .001) and patients with younger age, higher social vulnerability, lower-income ZIP code, and self-reported transport difficulties.

Discussion

We successfully applied a dQM based on cancer EP to the largest US EHR database.

Conclusion

This dQM could be a marker for sociodemographic vulnerabilities in cancer diagnosis.
Taurine enhances growth performance by improving intestinal integrity and antioxidant capacity of weaned piglets
Authors: Chen Jianjun , Zhang Xiaofeng , Zhang Yuhui , Jiang Shouchuan , Han Yu , Zhang Lei , Zhang Yuanyuan , Du Huahua
Published: October 2024

Taurine is an amino acid that has been considered by animal husbandry as a feed additive due to its abundant biological functions. However, the effective dose of taurine added to feed is unknown. The aim of the current study was to determine the optimal taurine supplementation level by investigating its effects on growth performance, diarrhea index, intestinal health, and antioxidant capacity of weaned piglets. A total of 160 crossbred piglets (Landrace × Yorkshire, initially 8.39 ± 0.11 kg) were assigned to 4 groups (10 pigs/pen and 4 replicates/group). Basal diets containing 0 (control, CON), 0.1%, 0.3%, and 0.5% taurine were respectively provided to the piglets for a duration of 28 d. Six piglets from each group were selected for euthanasia and subsequent sample collection on day 29. The results showed that dietary 0.3% or 0.5% taurine supplementation increased average daily gain (P < 0.05), feed-to-gain ratio (P < 0.01), and serum albumin (P < 0.05), and decreased diarrhea index (P < 0.01) and diamine oxidase (DAO) level in the serum (P < 0.05). The greater expression of tight junction-related genes, including ZO-1 (P < 0.05) and Claudin-1 (P < 0.01), were observed in the duodenum after supplementation with 0.5% taurine. The supplementation of 0.3% or 0.5% taurine resulted in a significant reduction of crypt depth (P < 0.01) and an increase of villus height-to-crypt depth ratio (P < 0.01) in the duodenum. A greater abundance of goblet cells was detected in the duodenum and jejunum of piglets fed 0.5% taurine (P < 0.05). In addition, serum superoxide dismutase (SOD) level, liver catalase (CAT) level, and liver total antioxidant capacity level were all significantly (P < 0.05) increased with 0.1%, 0.3% or 0.5% dietary taurine supplementation. On the whole, dietary supplementation with 0.3% or 0.5% taurine has the potential to significantly enhance the growth performance of piglets by improving the integrity of the intestinal barrier and boosting their antioxidant capacity.
Dietary fiber and weaning age affect stress and immune markers in saliva of sows and their offspring
Authors: Grześkowiak Łukasz , Cerón José Joaquín , Lopez-Arjona Marina , Martínez-Vallespín Beatriz , Holthausen Johannes Schulze , Krüsselmann Philip , Metges Cornelia C , Kuhla Björn , Vahjen Wilfried , Zentek Jürgen , Saliu Eva-Maria
Published: October 2024

Diet, especially the intake of dietary fiber, and weaning practices may influence pig wellbeing. This study assessed changes in salivary stress and immune markers in sows and their offspring fed either hay (HAY) or sugar beet pulp (SBP), either fine (F) or coarse (C), during gestation and lactation. The effect of weaning age (conventional—CW, late—LW) on these markers was also evaluated. Saliva was analyzed for chromogranin A (CgA), cortisol, alpha-amylase, oxytocin, immunoglobulin A (IgA), and adenosine deaminase (ADA). CgA was higher at CW versus LW in sows fed SBP-F (P = 0.038). Alpha-amylase was higher in sows fed HAY-C at CW versus LW (P = 0.005) and in sows fed SBP-C at LW versus CW (P = 0.096). CgA and oxytocin were higher in sows fed SBP-F at CW versus LW (P = 0.038 and P = 0.017, respectively). ADA was higher in sows fed SBP-C versus HAY-C (P = 0.035) at LW and at LW versus CW in sows fed SBP-C (P = 0.002). Piglet salivary CgA was higher at CW versus LW in HAY-F (P = 0.002) and SBP-F (P = 0.031). Oxytocin was higher at CW versus LW in piglets fed HAY-F (P = 0.006). Piglet salivary IgA was higher in HAY-C versus HAY-F at CW (P = 0.010) and at LW versus CW in piglets fed HAY-F (P = 0.021). ADA was higher in piglets fed SBP-F versus HAY-F (P = 0.053) at CW and SBP-F versus SBP-C (P = 0.042) at LW. Dietary fiber type, weaning age, and to a lesser extent grinding degree affect stress and immune markers in pigs. These findings highlight the impact of diet and weaning practice on pig welfare.
Data Protection Considerations in Competition Law Assessments: A Qualitative Document Analysis of EU Decision Texts
Authors: Vandendriessche Robin , Buts Caroline
Published: October 2024

Personal data are both protected by a fundamental right and serves as a source of market power. As such, a complex interplay between data protection and competition law arises, sparking debate among policymakers and scholars on whether to incorporate data protection considerations (DPCs) in competition law assessments. Proponents argue that competition cases involving such an interplay require a normative contribution from data protection law, while opponents emphasize the practical challenges of considering data protection as a non-economic public policy objective. We identify nine ways in which data protection might ultimately surface in competition law assessments, categorized into five areas: (i) competition enforcement actions, (ii) existing legal and regulatory framework, (iii) personal data collection, (iv) exclusionary abuses, and (v) alleviation of competition concerns. Using a multiple-step approach for qualitative document analysis, we explore how these considerations have surfaced in the European Commission’s decisional practice through a dataset of 2.041 EU competition decision texts based on articles 101 TFEU and 102 TFEU and the EU Merger Regulation. We identify 53 decisions where DPCs have surfaced, especially in the information and communication industry, where they are more frequently subjected to commitments. In line with the evolving literature, we observe an increasingly integrationist trend as these considerations surface more frequently, particularly since the adoption of the General Data Protection Regulation in 2016 and the Digital Markets Act proposal in 2020. We also find a pattern where data protection provisions are included in commitments as a ‘tick-the-box’ exercise. Several influential alleviations of competition concerns suggest that the Commission is more comfortable using data protection to approve transactions unconditionally rather than as a substantive argument for commitments. We conclude by making a case for a more collaborative approach based on the European Court of Justice’s recent Meta Platforms (2023) judgment. Data protection should be considered in competition law assessments if its normative contribution is required. Such a stance would simply align with the internal logic of competition law without unlawfully expanding its material scope.
The 1996 Hague convention on international child protection in the UK post-Brexit: focus on jurisdiction and recognition and enforcement
Authors: Trimmings Katarina , Le Xuan Tung , Kalaitsoglou Konstantina
Published: October 2024

This article discusses the strength and weakness of the 1996 Hague Convention vis-à-vis the Brussels IIbis Regulation and its successor the Brussels IIter Regulation. It engages with relevant UK case-law to assess the application of the Convention in the UK, with the aim of encouraging uniformity in the application of the Convention across Contracting States. The focus of the article is on the topics of jurisdiction and recognition and enforcement. The article concludes that, overall, the Convention mechanism is fully capable of securing adequate cross-border child protection post-Brexit. Nevertheless, it might be too early to declare conclusively whether the disapplication of the Brussels regime in the area of parental responsibility and its replacement with the 1996 Hague Child Protection Convention in the UK has strengthened or weakened the protection of international families with links to the European Union post-Brexit, in particular with respect to recognition and enforcement. Regarding jurisdiction, the article expresses anticipation that the emerging UK case-law on Chapter II of the Convention will provide valuable guidance for the courts of other Contracting States, including UK’s former EU partners, with the view of harmonizing the application of the Convention across Contracting States. To facilitate exchange of good practice in a systematic manner, the article proposes that the Hague Conference establishes a database of case-law on the 1996 Convention.
COVID-19 Personal Experiences and Posttraumatic Stress in National Guard Service Members
Authors: Mash Holly B Herberman , Fullerton Carol S , Adler Amy B , Morganstein Joshua C , Blumhorst Alexandra , LaCroix Christina L , Biggs Quinn M , Ursano Robert J
Published: October 2024

Introduction

The National Guard (NG) was an important component of the U.S. emergency response for the coronavirus (COVID-19) pandemic. Understanding how the personal COVID-19 experiences of NG members may be associated with posttraumatic stress symptoms (PTSS) and disorder (PTSD) can inform approaches to identifying and sustaining service members’ mental health.

Materials and Methods

We surveyed 3,993 NG service members (75% Army; 79% enlisted; 33% 30-39 years old; 81% male) during the pandemic. Forty-six percent of participants were activated in response to COVID-19. Surveys were administered between August and December 2020. We defined personal COVID-19 experiences as having COVID-19, a family member(s) having COVID-19, and/or having a close relationship with someone who died from COVID-19. In addition, using a 4-item form of the PTSD Checklist for DSM-5 (PCL-5), current posttraumatic stress symptoms (PTSS) and probable PTSD were assessed. Linear and logistic regression analyses were conducted to examine the relationship of COVID-19 experiences to PTSS and probable PTSD, respectively.

Results

Approximately 32% of participants reported at least one personal COVID-19 experience. Univariable linear regression analyses indicated that NG service members who had a personal COVID-19 experience reported more PTSS than those with no personal experience (B = 0.53, SE = 0.12, P < .001). After adjusting for demographics and service-related characteristics, having a personal COVID-19 experience continued to be associated with higher PTSS (B = 0.48, SE = 0.12, P < .001). When examining the relationships of distinct types of personal COVID-19 experiences to PTSS and PTSD together in multivariable models, those who had a close relationship with someone who died from COVID-19 had higher levels of PTSS (B = 1.31, SE = 0.22, P < .001) and were almost 3 times more likely to have PTSD (OR = 2.94[95%CI = 1.93-4.47], P < .001).

Conclusions

Personal COVID-19 experiences are associated with increased PTSS and PTSD risk in NG service members. Such knowledge may aid in selection of service members for activation and identifying those in need of care.