bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of brain metabolism redistribution from neocortex to primitive brain structures in early acute COVID-19 respiratory syndrome
Authors: Souza Stephan P. M. , Colet Nicoli , Fujiwara Mariana , Fernandes Alins P. , Tobar Natalia , Dertkigil Sergio S. J. , Takahashi Maria Emilia S. , Amorim Bárbara J. , Silva Lucas S. , Yasuda Clarissa L. , Cendes Fernando , de Souza Thiago F. , Rodrigues Juliano T. , Zantut-Wittmann Denise E. , Ramos Celso Dario 
Published: March 2024

Abstract
Background
Neuropsychiatric sequelae of COVID-19 have been widely documented in patients with severe neurological symptoms during the chronic or subacute phase of the disease. However, it remains unclear whether subclinical changes in brain metabolism can occur early in the acute phase of the disease. The aim of this study was to identify and quantify changes in brain metabolism in patients hospitalized for acute respiratory syndrome due to COVID-19 with no or mild neurological symptoms.

Results
Twenty-three non-intubated patients (13 women; mean age 55.5 ± 12.1 years) hospitalized with positive nasopharyngeal swab test (RT-PCR) for COVID-19, requiring supplemental oxygen and no or mild neurological symptoms were studied. Serum C-reactive protein measured at admission ranged from 6.43 to 189.0 mg/L (mean: 96.9 ± 54.2 mg/L). The mean supplemental oxygen demand was 2.9 ± 1.4 L/min. [18F]FDG PET/CT images were acquired with a median of 12 (4–20) days of symptoms. After visual interpretation of the images, semiquantitative analysis of [18F]FDG uptake in multiple brain regions was evaluated using dedicated software and the standard deviation (SD) of brain uptake in each region was automatically calculated in comparison with reference values of a normal database. Evolutionarily ancient structures showed positive SD mean values of [18F]FDG uptake. Lenticular nuclei were bilaterally hypermetabolic (> 2 SD) in 21/23 (91.3%) patients, and thalamus in 16/23 (69.6%), bilaterally in 11/23 (47.8%). About half of patients showed hypermetabolism in brainstems, 40% in hippocampi, and 30% in cerebellums. In contrast, neocortical regions (frontal, parietal, temporal and occipital lobes) presented negative SD mean values of [18F]FDG uptake and hypometabolism (< 2 SD) was observed in up to a third of patients. Associations were found between hypoxia, inflammation, coagulation markers, and [18F]FDG uptake in various brain structures.

Conclusions
Brain metabolism is clearly affected during the acute phase of COVID-19 respiratory syndrome in neurologically asymptomatic or oligosymptomatic patients. The most frequent finding is marked hypermetabolism in evolutionary ancient structures such as lenticular nucleus and thalami. Neocortical metabolism was reduced in up to one third of patients, suggesting a redistribution of brain metabolism from the neocortex to evolutionary ancient brain structures in these patients.
Elevation affects both the occurrence of ungulate browsing and its effect on tree seedling growth for four major tree species in European mountain forests
Authors: Bernard Marianne , Barrere Julien , Morin Xavier , Saïd Sonia , Boulanger Vincent , Granda Elena , Benavides Raquel , Jactel Hervé , Heurich Marco , Rabasa Sonia G. , Valladares Fernando , Kunstler Georges 
Published: March 2024

Abstract
Key message
In European mountain forests, the growth of silver fir (Abies alba Mill.), sycamore maple (Acer pseudoplatanus L.), European beech (Fagus sylvatica L.) and Norway spruce (Picea abies (L.) H. Karst.) seedlings is more strongly affected by ungulate browsing than by elevation. But, the constraint exerted by ungulates, in particular the probability for seedlings to be browsed, increases with elevation for most species.

Context
While concerns about mountain forest regeneration rise due to their high vulnerability to climate change, the increase in wild ungulate populations and the expansion of their range in the last decades exert an additional constraint on the survival and growth of young trees. Understanding how this constraint can vary with elevation is thus a key to assess the consequences of this population increase for the regeneration of mountain forests.

Aims
In this study, we investigate the effect of elevation on (i) the occurrence of browsing for seedlings and on (ii) the reduction in seedling growth induced by ungulate browsing.

Methods
We monitored height growth and browsing occurrence on silver fir, sycamore maple, European beech and Norway spruce seedlings across seven elevation gradients (from 400 to 2013 m) located from France to northern Sweden.

Results
Seedlings of the two most palatable species—fir and maple—were more likely to be browsed at high elevation while the opposite effect was observed for spruce. Browsing strongly reduced seedling growth for all species but Norway spruce, while elevation had no direct effect on seedling growth. This browsing-induced growth reduction was stronger at high elevation for fir seedlings.

Conclusions
Browsing is overall a stronger constraint on seedling growth than elevation for four dominant species of European mountain forests. Elevation can, however, affect both browsing probability and the effect of browsing on seedling growth. Our results highlight the importance of taking into account ungulate pressure and its interactive effect with elevation when forecasting the regeneration of mountain forests under a changing climate.
Hypoxia-induced circRNAs encoded by PPARA are highly expressed in human cardiomyocytes and are potential clinical biomarkers of acute myocardial infarction
Authors: Huang Shasha , Wu Zhangying , Zhou Yang 
Published: March 2024

Abstract
Background
Acute myocardial infarction (AMI) is a serious cardiovascular disease that adversely affects human health. Circular RNAs (circRNAs) are involved in the pathological and physiological processes of AMI, but the biological mechanism of their involvement and their clinical significance remain unknown. We aimed to identify circRNAs that are significantly associated with morbidity in the peripheral blood of patients with AMI and evaluate their diagnostic utility.

Methods
High-throughput sequencing was used to screen for differentially expressed circRNAs in peripheral blood samples obtained from five patients with AMI and five sex- and age-matched healthy controls. A series of bioinformatics tools and databases were used to determine the biological functional classification and pathway enrichment of the circRNAs based on data obtained from sequencing. A hypoxia model was established and used to evaluate the effect of hypoxia on circRNA expression in human cardiomyocytes. A cytoplasmic separation assay and enzyme resistance assay were employed to identify the biological characteristics of circRNA. Polymerase chain reaction validity testing and receiver operating characteristic (ROC) curve analysis were used to evaluate the utility of circRNA assessments in the diagnosis of AMI.

Results
A large number of circRNAs were found to be differentially expressed in the peripheral blood of patients with AMI, and significantly more of these circRNAs were highly expressed than lowly expressed. The genes encoding these circRNAs have a wide range of effects on various functions in the body. A hypoxic environment promoted the upregulation of circRNA expression in human cardiomyocytes, and hsa_circ_0116795 encoded by PPARA was highly expressed in the peripheral blood of the patients with AMI. In terms of biological characteristics, under physiological conditions, hsa_circ_0116795 (circ_PPARA) was mainly located in the cytoplasm of cardiomyocytes and found to be resistant to exonuclease. The ROC curve analysis showed that the expression levels of circ_PPARA in the peripheral blood of patients with AMI were significantly different from those in the peripheral blood of healthy controls.

Conclusion
A large number of abnormally expressed circRNAs are detectable in the peripheral blood of patients with AMI. In particular, circ_PPARA is highly expressed in human myocardial cells under hypoxic conditions, and its biological characteristics indicate that it could be employed as a biomarker for the early diagnosis of AMI.
Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases
Authors: d’Humières Camille , Delavy Margot , Alla Laurie , Ichou Farid , Gauliard Emilie , Ghozlane Amine , Levenez Florence , Galleron Nathalie , Quinquis Benoit , Pons Nicolas , Mullaert Jimmy , Bridier-Nahmias Antoine , Condamine Bénédicte , Touchon Marie , Rainteau Dominique , Lamazière Antonin , Lesnik Philippe , Ponnaiah Maharajah , Lhomme Marie , Sertour Natacha , Devente Savannah , Docquier Jean-Denis , Bougnoux Marie-Elisabeth , Tenaillon Olivier , Magnan Mélanie , Ruppé Etienne , Grall Nathalie , Duval Xavier , Ehrlich Dusko , Mentré France , Denamur Erick , Rocha Eduardo P. C. , Le Chatelier Emmanuelle , Burdet Charles ,   for the PrediRes study group
Published: March 2024

Abstract
Background
Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenotypic and genotypic approaches, we studied the changes in the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity of the stools. This allowed assessing their degrees of perturbation and resilience.

Results
While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting important antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, treatment impact was relatively low on the fungal microbiota. At the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state like the initial one, even if the structure of the bacterial microbiota changed and the dynamics of the different components over time were rarely correlated. The observed richness of the antibiotic resistance genes repertoire was significantly reduced up to day 30, while a significant increase in the relative abundance of β-lactamase encoding genes was observed up to day 10, consistent with a concomitant increase in the β-lactamase activity of the microbiota. The level of β-lactamase activity at baseline was positively associated with the resilience of the metabolome content of the stools.

Conclusions
In healthy adults, antibiotics perturb many components of the microbiota, which return close to the baseline state within 30 days. These data suggest an important role of endogenous β-lactamase-producing anaerobes in protecting the functions of the microbiota by de-activating the antibiotics reaching the colon.
Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor
Authors: Suarez Carolina , Rosenqvist Tage , Dimitrova Ivelina , Sedlacek Christopher J. , Modin Oskar , Paul Catherine J. , Hermansson Malte , Persson Frank 
Published: March 2024

Abstract
Background
Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.

Results
We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known ‘oligotrophic’ ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by ‘copiotrophic’ Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.

Conclusions
We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors.
Identifying structural risk factors for overdose following incarceration: a concept mapping study
Authors: Nall Samantha K. , Jurecka Cole , Ammons Anthony , Rodriguez Avel , Craft Betsy , Waleed Craig , Dias Daniel , Henderson Jessie , Boyer Joshua , Yamkovoy Kristina , Swathi Pallavi Aytha , Patil Prasad , Behne Forrest , LeMasters Katherine , Brinkley-Rubinstein Lauren , Barocas Joshua A. 
Published: March 2024

Abstract
Background
Currently, there are more than two million people in prisons or jails, with nearly two-thirds meeting the criteria for a substance use disorder. Following these patterns, overdose is the leading cause of death following release from prison and the third leading cause of death during periods of incarceration in jails. Traditional quantitative methods analyzing the factors associated with overdose following incarceration may fail to capture structural and environmental factors present in specific communities. People with lived experiences in the criminal legal system and with substance use disorder hold unique perspectives and must be involved in the research process.

Objective
To identify perceived factors that impact overdose following release from incarceration among people with direct criminal legal involvement and experience with substance use.

Methods
Within a community-engaged approach to research, we used concept mapping to center the perspectives of people with personal experience with the carceral system. The following prompt guided our study: “What do you think are some of the main things that make people who have been in jail or prison more and less likely to overdose?” Individuals participated in three rounds of focus groups, which included brainstorming, sorting and rating, and community interpretation. We used the Concept Systems Inc. platform groupwisdom for our analyses and constructed cluster maps.

Results
Eight individuals (ages 33 to 53) from four states participated. The brainstorming process resulted in 83 unique factors that impact overdose. The concept mapping process resulted in five clusters: (1) Community-Based Prevention, (2) Drug Use and Incarceration, (3) Resources for Treatment for Substance Use, (4) Carceral Factors, and (5) Stigma and Structural Barriers.

Conclusions
Our study provides critical insight into community-identified factors associated with overdose following incarceration. These factors should be accounted for during resource planning and decision-making.
Experiences and concerns of parents of children with a 16p11.2 deletion or duplication diagnosis: a reflexive thematic analysis
Authors: Butter Charlotte E. , Goldie Caitlin L. , Hall Jessica H. , Leadbitter Kathy , Burkitt Emma M.M. , van den Bree Marianne B.M. , Green Jonathan M. 
Published: March 2024

Abstract
Background
16p11.2 proximal deletion and duplication syndromes (Break points 4–5) (593KB, Chr16; 29.6-30.2mb - HG38) are observed to have highly varied phenotypes, with a known propensity for lifelong psychiatric problems. This study aimed to contribute to a research gap by qualitatively exploring the challenges families with 16p11.2 deletion and duplication face by answering three research questions: (1) What are parents’ perceptions of the ongoing support needs of families with children who have 16p11.2 living in the UK?; (2) What are their experiences in trying to access support?; (3) In these regards, do the experiences of parents of children with duplication converge or vary from those of parents of children with 16p11.2 deletion?

Methods
33 parents with children (aged 7–17 years) with 16p11.2 deletion or duplication participated in structured interviews, including the Autism Diagnostic Interview– Revised (ADI-R). Their answers to the ADI-R question ‘what are your current concerns’ were transcribed and subsequently analysed using Braun and Clarke’s six step reflexive thematic analysis framework.

Results
Three themes were identified: (1) Child is Behind Peers (subthemes: developmentally; academically; socially; emotionally); (2) Metabolism and Eating Patterns and; (3) Support (subthemes: insufficient support available; parent has to fight to access support; COVID-19 was a barrier to accessing support; 16p11.2 diagnosis can be a barrier to support, child is well-supported).

Conclusions
Parents of children with either 16p11.2 deletion or duplication shared similar experiences. However, metabolism concerns were specific to parents of children with 16p11.2 deletion. The theme Child is Behind Peers echoed concerns raised in previous Neurodevelopmental Copy Number Variant research. However, there were some key subthemes relating to research question (2) which were specific to this study. This included parents’ descriptions of diagnostic overshadowing and the impact of a lack of eponymous name and scant awareness of 16p11.2.
Endophilin A2 controls touch and mechanical allodynia via kinesin-mediated Piezo2 trafficking
Authors: Xie Man-Xiu , Lai Ren-Chun , Xiao Yi-Bin , Zhang Xi , Cao Xian-Ying , Tian Xiao-Yu , Chen An-Nan , Chen Zi-Yi , Cao Yan , Li Xiao , Zhang Xiao-Long 
Published: March 2024

Abstract
Background
Tactile and mechanical pain are crucial to our interaction with the environment, yet the underpinning molecular mechanism is still elusive. Endophilin A2 (EndoA2) is an evolutionarily conserved protein that is documented in the endocytosis pathway. However, the role of EndoA2 in the regulation of mechanical sensitivity and its underlying mechanisms are currently unclear.

Methods
Male and female C57BL/6 mice (8–12 weeks) and male cynomolgus monkeys (7–10 years old) were used in our experiments. Nerve injury-, inflammatory-, and chemotherapy-induced pathological pain models were established for this study. Behavioral tests of touch, mechanical pain, heat pain, and cold pain were performed in mice and nonhuman primates. Western blotting, immunostaining, co-immunoprecipitation, proximity ligation and patch-clamp recordings were performed to gain insight into the mechanisms.

Results
The results showed that EndoA2 was primarily distributed in neurofilament-200-positive (NF200+) medium-to-large diameter dorsal root ganglion (DRG) neurons of mice and humans. Loss of EndoA2 in mouse NF200+ DRG neurons selectively impaired the tactile and mechanical allodynia. Furthermore, EndoA2 interacted with the mechanically sensitive ion channel Piezo2 and promoted the membrane trafficking of Piezo2 in DRG neurons. Moreover, as an adaptor protein, EndoA2 also bound to kinesin family member 5B (KIF5B), which was involved in the EndoA2-mediated membrane trafficking process of Piezo2. Loss of EndoA2 in mouse DRG neurons damaged Piezo2-mediated rapidly adapting mechanically activated currents, and re-expression of EndoA2 rescued the MA currents. In addition, interference with EndoA2 also suppressed touch sensitivity and mechanical hypersensitivity in nonhuman primates.

Conclusions
Our data reveal that the KIF5B/EndoA2/Piezo2 complex is essential for Piezo2 trafficking and for sustaining transmission of touch and mechanical hypersensitivity signals. EndoA2 regulates touch and mechanical allodynia via kinesin-mediated Piezo2 trafficking in sensory neurons. Our findings identify a potential new target for the treatment of mechanical pain.
Prediction of Cancer Symptom Trajectory Using Longitudinal Electronic Health Record Data and Long Short-Term Memory Neural Network
Authors: Chae Sena , Street W. Nick , Ramaraju Naveenkumar , Gilbertson-White Stephanie 
Published: March 2024

PURPOSE Ability to predict symptom severity and progression across treatment trajectories would allow clinicians to provide timely intervention and treatment planning. However, such predictions are difficult because of sparse and inconsistent assessment, and simplistic measures such as the last observed symptom severity are often used. The purpose of this study is to develop a model for predicting future cancer symptom experiences on the basis of past symptom experiences. PATIENTS AND METHODS We performed a retrospective, longitudinal analysis using records of patients with cancer (n = 208) hospitalized between 2008 and 2014. A long short-term memory (LSTM)–based recurrent neural network, a linear regression, and random forest models were trained on previous symptoms experienced and used to predict future symptom trajectories. RESULTS We found that at least one of three tested models (LSTM, linear regression, and random forest) outperform predictions based solely on the previous clinical observation. LSTM models significantly outperformed linear regression and random forest models in predicting nausea ( P < .1) and psychosocial status ( P < .01). Linear regression outperformed all models when predicting oral health ( P < .01), while random forest outperformed all models when predicting mobility ( P < .01) and nutrition ( P < .01). CONCLUSION We can successfully predict patients' symptom trajectories with a prediction model, built with sparse assessment data, using routinely collected nursing documentation. The results of this project can be applied to better individualize symptom management to support cancer patients' quality of life.