bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beta to theta power ratio in EEG periodic components as a potential biomarker in mild cognitive impairment and Alzheimer’s dementia
Authors: Azami Hamed , Zrenner Christoph , Brooks Heather , Zomorrodi Reza , Blumberger Daniel M. , Fischer Corinne E. , Flint Alastair , Herrmann Nathan , Kumar Sanjeev , Lanctôt Krista , Mah Linda , Mulsant Benoit H. , Pollock Bruce G. , Rajji Tarek K. ,   on behalf of the PACt-MD Study Group
Published: August 2023

Abstract
Background
Alzheimer’s dementia (AD) is associated with electroencephalography (EEG) abnormalities including in the power ratio of beta to theta frequencies. EEG studies in mild cognitive impairment (MCI) have been less consistent in identifying such abnormalities. One potential reason is not excluding the EEG aperiodic components, which are less associated with cognition than the periodic components. Here, we investigate whether aperiodic and periodic EEG components are disrupted differently in AD or MCI vs. healthy control (HC) individuals and whether a periodic based beta/theta ratio differentiates better MCI from AD and HC groups than a ratio based on the full spectrum.

Methods
Data were collected from 44 HC (mean age (SD) = 69.1 (5.3)), 114 MCI (mean age (SD) = 72.2 (7.5)), and 41 AD (mean age (SD) = 75.7 (6.5)) participants. Aperiodic and periodic components and full spectrum EEG were compared among the three groups. Receiver operating characteristic curves obtained via logistic regression classifications were used to distinguish the groups. Last, we explored the relationships between cognitive performance and the beta/theta ratios based on the full or periodic spectrum.

Results
Aperiodic EEG components did not differ among the three groups. In contrast, AD participants showed an increase in full spectrum and periodic relative powers for delta, theta, and gamma and a decrease for beta when compared to HC or MCI participants. As predicted, MCI group differed from HC participants on the periodic based beta/theta ratio (Bonferroni corrected p-value = 0.036) measured over the occipital region. Classifiers based on beta/theta power ratio in EEG periodic components distinguished AD from HC and MCI participants, and outperformed classifiers based on beta/theta power ratio in full spectrum EEG. Beta/theta ratios were comparable in their association with cognition.

Conclusions
In contrast to a full spectrum EEG analysis, a periodic-based analysis shows that MCI individuals are different on beta/theta ratio when compared to healthy individuals. Focusing on periodic components in EEG studies with or without other biological markers of neurodegenerative diseases could result in more reliable findings to separate MCI from healthy aging, which would be valuable for designing preventative interventions.
To charge or not to charge: reducing patient no-show
Authors: Leibner Gideon , Brammli-Greenberg Shuli , Mendlovic Joseph , Israeli Avi 
Published: August 2023

Abstract
Background
In order to reduce patient no-show, the Israeli government is promoting legislation that will allow Health Plans to require a co-payment from patients when reserving an appointment. It is hoped that this will create an incentive for patients to cancel in advance rather than simply not show up. The goal of this policy is to improve patient access to medical care and ensure that healthcare resources are utilized effectively. We explore this phenomenon to support evidence-based decision making on this issue, and to determine whether the proposed legislation is aligned with the findings of previous studies.

Main body
No-show rates vary across countries and healthcare services, with several strategies in place to mitigate the phenomenon. There are three key stakeholders involved: (1) patients, (2) medical staff, and (3) insurers/managed care organizations, each of which is affected differently by no-shows and faces a different set of incentives. The decision whether to impose financial penalties for no-shows should take a number of considerations into account, such as the fine amount, service type, the establishment of an effective fine collection system, the patient’s socioeconomic status, and the potential for exacerbating disparities in healthcare access. The limited research on the impact of fines on no-show rates has produced mixed results. Further investigation is necessary to understand the influence of fine amounts on no-show rates across various healthcare services. Additionally, it is important to evaluate the implications of this proposed legislation on patient behavior, access to healthcare, and potential disparities in access.

Conclusion
It is anticipated that the proposed legislation will have minimal impact on attendance rates. To achieve meaningful change, efforts should focus on enhancing medical service availability and improving the ease with which appointments can be cancelled or alternatively substantial fines should be imposed. Further research is imperative for determining the most effective way to address the issue of patient no-show and to enhance healthcare system efficiency.
Dimensionality and invariance of ADL, IADL, BI-M2/WG-SS, and GALI in large surveys in France (2008–2014) and implications for measuring disability in epidemiology
Authors: Coste Joël , Pérès Karine , Robine Jean-Marie , Carcaillon-Bentata Laure 
Published: August 2023

Abstract
Background
The epidemiological investigation and surveillance of disability requires well-constructed, invariant, and, if possible, exchangeable measures. However, the current or recommended measures have not been thoroughly investigated with respect to these issues. Here we examined the dimensional structure and invariance of four measures across sociodemographic groups: Activities of Daily Living (ADL), Instrumental Activities of Daily Living (IADL), Budapest Initiative Mark 2 (BI-M2) and Washington Group on Disability Statistics Short Set (WG-SS), and Global Activity Limitation Indicator (GALI).

Methods
We used data from three large nationwide representative surveys conducted in France between 2008 and 2014. The surveys included these four measures and classical and modern approaches (correlations, principal component analysis, Rasch modeling) were used to assess their dimensional structure as well as their invariance through differential item functioning (DIF) for sociodemographic characteristics. Polytomous logistic regression models were used to assess gradients in health inequalities associated with these measures.

Results
For many items of ADL, IADL, and BI-M2/WG-SS, we consistently observed disordered response thresholds, rejection of unidimensionality, and DIF evidence for sociodemographic characteristics across the survey samples. Health inequality gradients were erratic. In addition, it was impossible to identify a common continuum for GALI, ADL, IADL, and BI-M2/WG-SS or their constituent items.

Conclusion
This study warns against the current practice of investigating disability in epidemiology using measures that are unsuitable for epidemiological use, incommensurable, and inadequate regarding the basic requisites of dimensionality and invariance. Developing invariant measures and equating them along a common continuum to enlarge the common bases of measurement should therefore be a priority.
Causal relationships between delirium and Alzheimer's disease: a bidirectional two-sample Mendelian randomization study
Authors: Zheng Jiang , Du Xiaohui , Yang Liu , Fu Hong 
Published: August 2023

Abstract
Background
Previous observational studies have reported that delirium has an association with an increased risk of Alzheimer's disease (AD), and that patients with AD have a higher risk of developing delirium. However, due to the limitations of observational study, it is challenging to confirm whether delirium has a causal effect on AD or reverse causation exists.

Methods
A bidirectional two-sample Mendelian randomization (MR) was performed to investigate the relationship between delirium and AD. Summary statistics from genome-wide association studies of delirium and AD phenotypes were utilized. Inverse-variance weighted (IVW) method was used as the main analysis approach, and additional analyses were performed using MR Egger, weighted median, simple mode and weighted mode to ensure result accuracy. Heterogeneity and horizontal pleiotropy were assessed using Cochran's Q statistics and MR Egger intercept, separately.

Results
The MR analyses showed that genetically predicted delirium was not associated with AD (IVW: odds ratio [OR] 0.98, 95% CI 0.91–1.05, P = 0.544; MR Egger: OR 0.98, 95% CI 0.83–1.15, P = 0.780; weighted median: OR 0.96, 95% CI 0.88–1.05, P = 0.323; simple mode: OR 0.91, 95% CI 0.80–1.04, P = 0.212; weighted mode: OR 0.93, 95% CI 0.83–1.05, P = 0.277). However, in the reverse direction, AD was associated with delirium (IVW: OR 1.32, 95% CI 1.13–1.54, P = 3.91E-04; MR Egger: OR 1.42, 95% CI 1.02–1.98, P = 5.60E-02; Weighted median: OR 1.39, 95% CI 1.18–1.63, P = 8.22E-05; Simple mode: OR 1.41, 95% CI 1.10–1.80, P = 1.41E−02; Weighted mode: OR 1.39, 95% CI 1.16–1.67, P = 3.23E-03).

Conclusion
Based on the results of our MR study, there is no bidirectional causality between delirium and AD, delirium is not associated with an increased risk of AD, while genetically predicted AD is a potential causal risk factor for delirium.
Analysis of the efficacy of a single subumbilical stoma for bilateral cutaneous ureterostomy after radical cystectomy
Authors: Fu Zhenyu , Tian Zhen , Chen Yongchang , Jia Zongming , Wang Chengyu , Zhang Xuefeng , Zhang Weijie , Li Gang , Wei Xuedong , Huang Yuhua 
Published: August 2023

Abstract
Background
Radical cystectomy and urinary diversion are the standard surgical treatments for patients with muscle-invasive or high-risk, or recurrent non-muscle-invasive bladder cancer. Although this approach significantly prolongs patient survival, it can lead to postoperative complications. This study aims to compare the efficacy and complications of bilateral cutaneous ureterostomy with a single subumbilical stoma to those of cutaneous ureterostomy with two stomas and an ileal conduit as a means of urinary diversion after radical cystectomy. The findings of this study will provide valuable information for healthcare providers in selecting the appropriate urinary diversion method for their patients.

Methods
The clinical data for 108 patients who received bilateral cutaneous ureterostomy with a single subumbilical stoma (ureterostomy with a single stoma group), cutaneous ureterostomy with two stomas (ureterostomy with two stomas group), or an ileal conduit (ileal conduit group) after radical cystectomy were retrospectively analysed. The operative time, pathological stage, survival status, perioperative complication rate, rate of successful first extubation, rehospitalization rate at 6 months after surgery,ostomy-related medical costs,and postoperative quality of life were compared between the three groups of patients.

Results
A significant difference in the operative time was found between the three groups (P = 0.001). No significant differences in pathological stage, survival status, perioperative complication rate, rehospitalization rate at 6 months after surgery, or bladder cancer index (BCI) score were identified among the three groups. The difference in the successful first extubation rate between the three groups of patients was significant (P = 0.001). Significant differences in ostomy-related medical costs were observed among the three groups of patients (P = 0.006).

Conclusion
A single subumbilical stoma for bilateral cutaneous ureterostomy after radical cystectomy may result in shorter surgery time, increased success rates for initial catheter removal, and lower medical expenses. However, to confirm these findings, further prospective randomized clinical trials are necessary.
metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering
Authors: Hao Chunlin , Elias Joshua E. , Lee Patrick K. H. , Lam Henry 
Published: August 2023

Abstract
Background
The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely on accurate identification of the MS/MS spectra to their corresponding short peptides in the digested samples, followed by protein inference and subsequent taxonomic and functional analysis of the detected proteins. These approaches are dependent on the availability of protein sequence databases derived either from sample-specific metagenomic data or from public repositories. Due to the incompleteness and imperfections of these protein sequence databases, and the preponderance of homologous proteins expressed by different bacterial species in the community, this computational process of peptide identification and protein inference is challenging and error-prone, which hinders the comparison of metaproteomes across multiple samples.

Results
We developed metaSpectraST, an unsupervised and database-independent metaproteomics workflow, which quantitatively profiles and compares metaproteomics samples by clustering experimentally observed MS/MS spectra based on their spectral similarity. We applied metaSpectraST to fecal samples collected from littermates of two different mother mice right after weaning. Quantitative proteome profiles of the microbial communities of different mice were obtained without any peptide-spectrum identification and used to evaluate the overall similarity between samples and highlight any differentiating markers. Compared to the conventional database-dependent metaproteomics analysis, metaSpectraST is more successful in classifying the samples and detecting the subtle microbiome changes of mouse gut microbiomes post-weaning. metaSpectraST could also be used as a tool to select the suitable biological replicates from samples with wide inter-individual variation.

Conclusions
metaSpectraST enables rapid profiling of metaproteomic samples quantitatively, without the need for constructing the protein sequence database or identification of the MS/MS spectra. It maximally preserves information contained in the experimental MS/MS spectra by clustering all of them first and thus is able to better profile the complex microbial communities and highlight their functional changes, as compared with conventional approaches. tag the videobyte in this section as ESM4
Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems
Authors: Zhu Xiao-Yu , Li Yang , Xue Chun-Xu , Lidbury Ian D. E. A. , Todd Jonathan D. , Lea-Smith David J. , Tian Jiwei , Zhang Xiao-Hua , Liu Jiwen 
Published: August 2023

Abstract
Background
Hadal trenches (>6000 m) are the deepest oceanic regions on Earth and depocenters for organic materials. However, how these enigmatic microbial ecosystems are fueled is largely unknown, particularly the proportional importance of complex polysaccharides introduced through deposition from the photic surface waters above. In surface waters, Bacteroidetes are keystone taxa for the cycling of various algal-derived polysaccharides and the flux of carbon through the photic zone. However, their role in the hadal microbial loop is almost unknown.

Results
Here, culture-dependent and culture-independent methods were used to study the potential of Bacteroidetes to catabolize diverse polysaccharides in Mariana Trench waters. Compared to surface waters, the bathypelagic (1000–4000 m) and hadal (6000–10,500 m) waters harbored distinct Bacteroidetes communities, with Mesoflavibacter being enriched at ≥ 4000 m and Bacteroides and Provotella being enriched at 10,400–10,500 m. Moreover, these deep-sea communities possessed distinct gene pools encoding for carbohydrate active enzymes (CAZymes), suggesting different polysaccharide sources are utilised in these two zones. Compared to surface counterparts, deep-sea Bacteroidetes showed significant enrichment of CAZyme genes frequently organized into polysaccharide utilization loci (PULs) targeting algal/plant cell wall polysaccharides (i.e., hemicellulose and pectin), that were previously considered an ecological trait associated with terrestrial Bacteroidetes only. Using a hadal Mesoflavibacter isolate (MTRN7), functional validation of this unique genetic potential was demonstrated. MTRN7 could utilize pectic arabinans, typically associated with land plants and phototrophic algae, as the carbon source under simulated deep-sea conditions. Interestingly, a PUL we demonstrate is likely horizontally acquired from coastal/land Bacteroidetes was activated during growth on arabinan and experimentally shown to encode enzymes that hydrolyze arabinan at depth.

Conclusions
Our study implies that hadal Bacteroidetes exploit polysaccharides poorly utilized by surface populations via an expanded CAZyme gene pool. We propose that sinking cell wall debris produced in the photic zone can serve as an important carbon source for hadal heterotrophs and play a role in shaping their communities and metabolism.
Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines
Authors: Zhong Zhi-Ping , Vik Dean , Rapp Josephine Z. , Zablocki Olivier , Maughan Heather , Temperton Ben , Deming Jody W. , Sullivan Matthew B. 
Published: August 2023

Abstract
Background
Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions.

Results
We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races.

Conclusions
Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.
Optimisation of the DNA dipstick as a rapid extraction method for Schistosoma japonicum in infected mice samples and spiked human clinical samples
Authors: Aula Oyime P. , McManus Donald P. , Jones Malcolm K. , You Hong , Cai Pengfei , Gordon Catherine A. 
Published: August 2023

Abstract
Background
Schistosomiasis remains a public health issue and the need for accurate and affordable diagnostics is crucial in the elimination of the disease. While molecular diagnostics are highly effective, they are expensive, with the main costs been associated with DNA extraction. The DNA dipstick is a rapid, affordable and simple purification method that allows DNA to be extracted from diagnostic samples within 30 s. We aimed to optimise the DNA dipstick method for samples from mice and egg-spiked human samples.

Methods
Urine, blood and faeces were collected from mice exposed to Schistosoma japonicum infection at weekly intervals from Day 0 to Day 42. Urine and faecal samples were also collected from volunteer, uninfected humans and spiked with S. japonicum eggs. All samples were subject to several optimisation procedures and DNA extracted with the DNA dipstick. Amplification of the target DNA was carried out using LAMP and visualised using agarose gel electrophoresis and flocculation.

Results
The DNA dipstick successfully identified S. japonicum from infected mice and human clinical samples spiked with cracked eggs or genomic DNA from S. japonicum. Amplification was observed from week 4 post infection in infected mice. For human samples, amplification was observed in sieved faecal samples, filtered urine samples heated at 95 °C for 30 min, and sera samples heated at 95 °C for 30 min.

Conclusions
The DNA dipstick combined with LAMP has huge potential in providing cost-effective, simple and accurate detection of schistosomiasis infection in endemic regions. This will allow for rapid treatment, tracking outbreaks—such as occur after typhoons, leading to better health outcomes and contributing to control and eventual elimination of schistosomiasis.