bluuebunny/crossref_metadata_2025 huggingface dataset:
Spontaneous fast-ultradian dynamics of polymorphic interictal events in drug-resistant focal epilepsy
Authors: Dellavale Damián , Bonini Francesca , Pizzo Francesca , Makhalova Julia , Wendling Fabrice , Badier Jean-Michel , Bartolomei Fabrice , Bénar Christian-George
Published: April 2023

Objective

We studied the rate dynamics of interictal events occurring over fast-ultradian time scales, as commonly examined in clinics to guide surgical planning in epilepsy.

Methods

Stereoelectroencephalography (SEEG) traces of 35 patients with good surgical outcome (Engel I) were analyzed. For this, we developed a general data mining method aimed at clustering the plethora of transient waveform shapes including interictal epileptiform discharges (IEDs), and assessed the temporal fluctuations in the capability to map the epileptogenic zone (EZ) of each type of event.

Results

We found that the fast-ultradian dynamics of the IEDs rate may effectively impair the precision of EZ identification, and appear to occur spontaneously, that is, not triggered by or exclusively associated with a particular cognitive task, wakefulness, sleep, seizure occurrence, post-ictal state or antiepileptic drug withdrawal. Propagation of IEDs from the EZ to the propagation zone (PZ) could explain the observed fast-ultradian fluctuations in a reduced fraction of the analyzed patients, suggesting that other factors like the excitability of the epileptogenic tissue could play a more relevant role. A novel link was found between the fast-ultradian dynamics of the overall rate of polymorphic events and the rate of specific IEDs subtypes. We exploited this feature to estimate in each patient the 5 min interictal epoch for near-optimal EZ and resected zone (RZ) localization, which resulted at the population level better than those obtained using either 1) the whole time series available in each patient (P = 0.084 for EZ, P < 0.001 for RZ, Wilcoxon signed rank test) and 2) 5 min epochs randomly sampled from the interictal recordings of each patient (P < 0.05 for EZ, P < 0.001 for RZ, 105random samplings).

Significance

Our results highlight the relevance of the fast-ultradian IEDs dynamics in mapping the EZ, and show how it can be prospectively estimated to inform surgical planning in epilepsy.

Key Points

The rate of IED observed in SEEG recordings undergoes spontaneous fluctuations over fast-ultradian time scales.

The fast-ultradian dynamics of the IED rate may impair the EZ identification and hence are clinically relevant for surgical planning.

Propagation does not fully explain the fast-ultradian dynamics of the IED rate constraining the precision to localize the EZ.

Interictal epochs, as commonly examined in clinics, producing near-optimal EZ mapping can be inferred based solely on the LFP dynamics.

Fluctuations of the AUPREC based on epileptic and non-epileptic events are linked to scale-free and scale-rich processes, respectively.
Dynamic analysis of the individual patterns of intakes, voids, and bladder sensations reported in bladder diaries collected in the LURN study
Authors: Andreev Victor P. , Helmuth Margaret E. , Smith Abigail R. , Zisman Anna , Cameron Anne P. , DeLancey John O. L. , Bushman Wade A.
Published: April 2023

The goal of this study was to perform an in-depth dynamic analysis of individual bladder diaries to inform which behavioral modifications would best reduce lower urinary tract symptoms, such as frequency and urgency. Three-day bladder diaries containing data on timing, volumes, and types of fluid intake, as well as timing, volumes, and bladder sensation at voids were analyzed for 197 participants with lower urinary tract symptoms. A novel dynamic analytic approach to bladder diary time series data was proposed and developed, including intra-subject correlations between time-varying variables: rates of intake, bladder filling rate, and urge growth rate. Grey-box models of bladder filling rate and multivariable linear regression models of urge growth rate were developed for individual diaries. These models revealed that bladder filling rate, rather than urine volume, was the primary determinant of urinary frequency and urgency growth rate in the majority of participants. Simulations performed with the developed models predicted that the most beneficial behavioral modifications to reduce the number of urgency episodes are those that smooth profiles of bladder filling rate, which might include behaviors such as exclusion of caffeine and alcohol and/or other measures, e.g., increasing number and decreasing volumes of intakes.
The development and validation of multiplex real-time PCRs with fluorescent melting curve analysis for simultaneous detection of six bacterial pathogens of lower respiratory tract infections and antimicrobial resistance genes
Authors: Ngoc Dung Tran Thi , Phat Voong Vinh , Vinh Chau , Huong Lan Nguyen Phu , Nha Phuong Nguyen Luong , Quynh Ngan Le Thi , Thwaites Guy , Thwaites Louise , Rabaa Maia , Kim Anh Nguyen Thi , Duy Pham Thanh
Published: April 2023

Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureusare among the major bacterial causative agents of lower respiratory tract infections (LRTIs), causing substantial morbidity and mortality globally. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for effective antibiotic therapy of LRTIs. In low-resourced settings, the diagnostics of LRTIs relies heavily on microbiological culture and patients are often treated with empirical antibiotics while awaiting several days for culture results. Rapid detection of LRTIs pathogens and AMR genes could prompt early antibiotic switching and inform antibiotic treatment duration. In this study, we developed multiplex quantitative real-time PCRs using EvaGreen dye and melting curve analysis (MCA) to rapidly identify the six major LRTIs pathogens and their AMR genes directly from the tracheal aspirate and sputum samples. The accuracy of RT-PCRs was assessed by comparing its performance against the gold standard, conventional culture method on 50 tracheal aspirate and sputum specimens. Our RT-PCR assays had 100% sensitivity forK. pneumoniae, A. baumannii, P. aeruginosa, E. coliand 63.6% forS. aureusand the specificity ranked from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection (LOD) of target bacteria in multiplex RT-PCRs was 1600 CFU/mL. Compared to the culture results, PCR assays exhibited higher sensitivity in detecting mixed infections andS. pneumoniae. Our findings also demonstrated a high level of concordance between the detection of AMR gene and AMR phenotype in single infections. We conclude that our multiplex quantitative RT-PCRs with fluorescence MCA is simple but sensitive and specific in detecting six major drug resistant bacterial pathogens of LRTIs and should be further evaluated for clinical utility.
Pseudotemporal ordering of spatial lymphoid tissue microenvironment profiles trails Unclassified DLBCL at the periphery of the follicle
Authors: Tripodo Claudio , Bertolazzi Giorgio , Cancila Valeria , Morello Gaia , Iannitto Emilio
Published: April 2023

We have established a pseudotemporal ordering for the transcriptional signatures of distinct microregions within reactive lymphoid tissues, namely germinal center dark zones (DZ), germinal center light zones (LZ), and peri-follicular areas (Peri). By utilizing this pseudotime trajectory derived from the functional microenvironments of DZ, LZ, and Peri, we have ordered the transcriptomes of Diffuse Large B-cell Lymphoma cases. The apex of the resulting pseudotemporal trajectory, which is characterized by enrichment of molecular programs fronted by TNFR signaling and inhibitory immune checkpoint overexpression, intercepts a discrete peri-follicular biology. This observation is associated with DLBCL cases that are enriched in the Unclassified/type-3 COO category, raising questions about the potential extra-GC microenvironment imprint of this peculiar group of cases. This report offers a thought-provoking perspective on the relationship between transcriptional profiling of functional lymphoid tissue microenvironments and the evolving concept of the cell of origin in Diffuse Large B-cell Lymphomas.
The effects of creatine supplementation on cognitive performance - a randomised controlled study
Authors: Sandkühler Julia Fabienne , Kersting Xenia , Faust Annika , Königs Eva Kathrin , Altman George , Ettinger Ulrich , Lux Silke , Philipsen Alexandra , Müller Helge , Brauner Jan
Published: April 2023

Background

Creatine is an organic compound that facilitates the recycling of energy-providing adenosine triphosphate (ATP) in muscle and brain tissue. It is a safe, well-studied supplement for strength training. Previous studies have shown that supplementation increases brain creatine levels, which might increase cognitive performance. The results of studies that have tested cognitive performance differ greatly, possibly due to different populations, supplementation regimens and cognitive tasks. This is the largest study on the effect of creatine supplementation on cognitive performance to date. As part of our study, we replicated Rae et al. (2003).

Methods

Our trial was cross-over, double-blind, placebo-controlled, and randomised, with daily supplementation of 5g for six weeks each. Like Rae et al. (2003), we tested participants on Raven’s Advanced Progressive Matrices (RAPM) and on the Backward Digit Span (BDS). In addition, we included eight exploratory cognitive tests. About half of our 123 participants were vegetarians and half were omnivores.

Results

There was no indication that vegetarians benefited more from creatine than omnivores, so we merged the two groups. Participants’ scores after creatine and after placebo differed to an extent that was not statistically significant (BDS: p = 0.064, η2P= 0.029; RAPM: p = 0.327, η2P= 0.008). Compared to the null hypothesis of no effect, Bayes factors indicate weak evidence in favour of a small beneficial creatine effect and strong evidence against a large creatine effect. There was no indication that creatine improved the performance of our exploratory cognitive tasks. Side effects were reported significantly more often for creatine than for placebo supplementation (p = 0.002, RR = 4.25).

Conclusions

Our results do not support large effects of creatine on the selected measures of cognition. However, our study, in combination with the literature, implies that creatine might have a small beneficial effect. Larger studies are needed to confirm or rule out this effect. Given the safety and broad availability of creatine, this is well worth investigating; a small effect could have large benefits when scaled over time and over many people.
Incidence of Symptoms Associated with Post-Acute Sequelae of SARS-CoV-2 infection in Non-Hospitalized Vaccinated Patients Receiving Nirmatrelvir-Ritonavir
Authors: Patel Rushin , Dani Sourbha , Khadke Sumanth , Ahmad Javaria , Shah Jui , Mehta Neev , Wener Kenneth , McQuillen Daniel P , Abraham George , Faust Jeremy , Maley Jason , Patel Smita , Mullington Janet , Wachter Robert M. , Mosenthal Anne , Sax Paul E. , Ganatra Sarju
Published: April 2023

Background

The role of Nirmatrelvir plus ritonavir (NMV-r) in preventing post-acute sequelae of SARS-CoV-2 infection (PASC) is unknown. The objective of this study is to assess the effect of NMV-r in non-hospitalized, vaccinated patients on the occurrence of PASC.

Methods

We performed a comparative retrospective cohort study utilizing data from the TriNetX research network, including vaccinated patients ≥18 years old who subsequently developed Covid-19 between December 2021-April 2022. Cohorts were based on NMV-r administration within five days of diagnosis. Based on previously validated broad and narrow definitions, the main outcome was the presence of symptoms associated with PASC. Outcomes were assessed between 30-180 days and 90-180 days after the index Covid-19 infection.

Results

1,004 patients remained in each cohort after propensity-score matching. PASC (broad definition) occurred in 425 patients (42%) in the NMV-r cohort, vs. 480 patients (48%) in the control cohort (OR 0.8 CI 0.67-0.96; p=0.01) from 30-180 days and in 273 patients (27%) in the NMV-r cohort, as compared to 347 patients (35%) in the control cohort (OR 0.707, CI 0.59-0.86; p<0.001) from 90-180 days. Narrowly defined PASC was reported in 337 (34%) patients in the NMV-r and 404 (40%) in the control cohort between 30-180 days (OR=0.75, CI 0.62-0.9, p=0.002) and in 221 (22%) in the NMV-r cohort as compared to in 278 (28%) patients in the control cohort (OR=0.7, CI 0.63-0.9, p=0.003) between 90 -180 days.

Conclusions

NMV-r treatment in non-hospitalized vaccinated patients with Covid-19 was associated with a reduction in the development of symptoms commonly observed with PASC and healthcare utilization.

Key Points

Assessment of Nirmatrelvir plus ritonavir (NMV-r) in preventing post-acute sequelae of SARS-CoV-2 infection (PASC), based on broad and narrow definitions in non-hospitalized, vaccinated patients between 30-180 days and 90-180 days.
Predictors of long-term recreational exercise participation in adolescents and young adults
Authors: Morgan Julie A. , Bednarz Jana M. , Semo Ronnie , Clark Scott R. , Schubert K. Oliver
Published: April 2023

The individual and societal factors influencing long-term recreational exercise participation during the transition from adolescence to young adulthood are not well explored. We modelled latent longitudinal recreational exercise trajectories spanning 8 years from age 16 to 24, and examined demographic, socioeconomic, behavioural, academic, and psychological predictors at age 15 of trajectory-group membership. We also explored whether trajectories were associated with health, mental health, and educational achievement at age 25. Finite mixture modelling was conducted with population-based longitudinal cohort study data collected from 2006-2017 by the Longitudinal Survey of Australian Youth (LSAY). The study sample comprised 9,353 students (49% female) from 356 Australian schools. Self-reported recreational exercise frequency data were collected in 2007, 2008, 2009, 2011, and 2014. Longitudinal latent trajectories of reported recreational exercise participation were estimated using group-based trajectory modelling for two scenarios: daily/guideline-adherent exercise versus non-daily exercise (model 1) and exercise at least once weekly versus exercise less than once weekly (model 2). Four distinct classes of long-term recreational exercise participation were identified for each model. Model 1: guideline-adherent exercisers (17.9% of the sample), never guideline exercisers (27.5%), guideline drop-outs (15.2%) and towards guideline (39.4%). Model 2: regular weekly (69.5% of the sample), decreasing (17.4%), increasing (4.8%), and infrequent (8.3%). In both models, predictors at age 15 for lower long-term exercise participation included female gender, lower self-efficacy, sport participation and parental socioeconomic status, and higher screen-time and academic literacy. At age 25, people in the guideline-adherent exerciser trajectory (model 1) reported better general health, whereas people in the regular weekly trajectory (model 2) had better general health and reduced rates of psychological distress, were happier with life and were more optimistic for the future relative to participants from other trajectory groups. Interventions and health-promotion activities to support sustained engagement in recreational exercise should particularly address the needs of females, people with low self-efficacy, reluctant exercisers, higher academic achievers, and youth experiencing socioeconomic disadvantage.
Second-order Citations in Altmetrics: A Case Study Analyzing the Audiences of COVID-19 Research in the News and on Social Media
Authors: Alperin Juan Pablo , Fleerackers Alice , Riedlinger Michelle , Haustein Stefanie
Published: April 2023

The potential to capture the societal impact of research has been a driving motivation for the use and development of altmetrics. Yet, to date, altmetrics have largely failed to deliver on this potential because the primary audience who cites research on social media has been shown to be academics themselves. In response, our study investigates an extension of traditional altmetric approaches that goes beyond capturing direct mentions of research on social media. Using research articles from the first months of the COVID-19 pandemic as a case study, we demonstrate the value of measuring ‘second-order citations,’ or social media mentions of news coverage of research. We find that a sample of these citations, published by just five media outlets, were shared and engaged with on social media twice as much as the research articles themselves. Moreover, first-order and second-order citations circulated among Twitter accounts and Facebook accounts that were largely distinct from each other. The differences in audiences and engagement patterns found in this case study highlight the importance of news coverage as a public source of science information and provide strong evidence that investigating these second-order citations can be an effective way of observing non-academic audiences that engage with research content.
Assessment of Gut Microbial β-Glucuronidase and β-Glucosidase Activity in Women with Polycystic Ovary Syndrome
Authors: Patel Jalpa , Chaudhary Hiral , Parekh Bhavin , Joshi Rushikesh
Published: April 2023

Objective

To identify Gut microbial β-Glucuronidase and β-Glucosidase activity in polycystic ovary syndrome (PCOS) and reveal a possible correlation between gut bacterial enzyme activities and estrogen.

Design

Case-Control Study.

Subjects

Reproductive-aged women with PCOS (n=23) and controls (n =25) from the Health Centre of Gujarat University.

Interventions

Spectrophotometric analysis of β-Glucuronidase and β-Glucosidase activity of fecal samples from patients and clinical parameters (including body mass index, endocrine hormone levels, and hirsutism) collected for correlation analysis.

Primary outcome

Identification of gut bacterial β-Glucuronidase and β-Glucosidase activity differences and clinical parameters.

Results

Compared to the controls, PCOS women had considerably higher levels of β-glucuronidase activity, having statistically significant p-value (0.05 ± 0.1vs. 0.04± 0.1;p=0.006). We observed a higher trend of β-glucosidase activity in PCOS women compared to the control (0.13 ± 0.08 vs. 0.09 ± 0.05;p=0.06).

Conclusion

We observed a strong trend toward increased levels of β-glucuronidase and β-glucosidase activity in PCOS women compared to healthy control women. This inference requires further validation through studies with a larger sample size. However, if validated, we suggest that β-glucosidase levels can be considered a putative biomarker for PCOS women with metabolic disturbances and might help personalize the treatment.

Graphical abstract
Effects of lower tiers of government healthcare facilities on unmet need for contraception and contraception use in Bangladesh
Authors: Khan Md Nuruzzaman , Khanam Shimlin Jahan , Khan Md Mostaured Ali , Islam M Mofizul , Harris Melissa L.
Published: April 2023

Background

In low- and middle-income countries (LMICs), including Bangladesh, modern contraception use remains lower than desired, resulting in a higher unmet need. A potential factor contributing to lower contraceptive use is reduced access to and use of lower tiers of government healthcare facilities, including home visits by family welfare assistants (FWAs), as well as women’s visits to community and satellite clinics. These relationships, however, are still unexplored in Bangladesh and LMICs more broadly. The aim of this study was to explore effects of lower tiers of government healthcare facilities on unmet need for contraception and contraception use in Bangladesh.

Methods

Data from 17,585 sexually active married women were analyzed from the 2017 Bangladesh Demographic and Health Survey. The outcome variables were any contraceptive use, modern contraceptive use, unmet need for contraception, and unmet need for modern contraception. The explanatory variables considered were respondent’s home visits by FWAs, respondent’s visits to a community clinic, and respondent’s visits to a satellite clinic. Multilevel mixed-effect Poisson regression with robust variance was used to determine the association between the outcome and explanatory variables, adjusted for individual-, household-, and community-level factors.

Results

Approximately 18% of respondents were visited by FWAs in the three months prior to the survey date and only 3.4% and 3.1% of women attended community and satellite clinics, respectively. Women who reported being visited by FWAs in the three months prior to the survey were approximately 36% less likely to report an unmet need for modern contraception and 42% more likely to report using modern contraception than women who did not report such a visit. A higher likelihood of unmet need for contraception and a lower likelihood of contraception use was found among women who did not visit these community or satellite clinics or visited these clinics for other reasons than collecting contraception as compared to women who visited these clinics to collect contraception.

Conclusion

FWAs’ visits to respondents’ homes to provide contraception, as well as respondent’s visits to satellite and community clinics play a major role in Bangladesh to ensure contraception use and reduce the unmet need for contraception. However, their coverage is quite low in Bangladesh. The findings suggest an urgent need for greater government initiatives to increase the number of FWAs and engage in proper monitoring them at the field level.
Effects of dietary interventions focused on adding base in the management of metabolic acidosis in adults with chronic kidney disease: A protocol for systematic review and meta-analysis of randomized clinical trials
Authors: Mahboobi Sepideh , Mollard Rebecca , Tangri Navdeep , Askin Nicole , Rabbani Rasheda , Abou-Setta Ahmed M. , Mackay Dylan
Published: April 2023

Background

Metabolic acidosis is a common complication of chronic kidney disease (CKD) which can impair the function of multiple organs and accelerate CKD progression to kidney failure. The condition is usually treated with sodium bicarbonate (NaHCO3), which is an alkali salt. Although effective, alkali therapy has numerous side effects including gastric discomfort and bloating, with many people having difficulty tolerating higher doses. Research has shown that base producing fruit and vegetables may have the ability to increase serum bicarbonate concentrations similar to what is achieved with alkali therapy, but also provides added benefits. This systematic review aims to identify, critically-appraise and meta-analyze findings from randomized clinical trials (RCTs) comparing the effects of dietary interventions, including base producing fruit and vegetables, on serum bicarbonate concentrations as well as other factors related to kidney function in adult patients with CKD.

Methods

RCTs (in adult participants (18 years of age or older), with CKD will be included in the study. Studies will be excluded if participants are undergoing dialysis or have chronic obstructive pulmonary disease (COPD) requiring oxygen therapy. The interventions of interest are any dietary intervention aimed at manipulating dietary acid load, compared with usual care, no treatment or placebo. Our primary outcome measure will be changes in serum bicarbonate concentration, while other parameters related to kidney function will be considered as secondary outcomes. A knowledge synthesis librarian developed a literature search strategy for MEDLINE (Ovid). The search strategy was then adjusted for use in Cochrane Central (Ovid), Embase (Ovid), Web of Science Core Collection (Clarivate) and CINAHL (EBSCO). Two independent reviewers will select studies for eligibility in Covidence and data extraction will be conducted using a custom MS Excel worksheet. We are planning to perform meta-analysis wherever possible using random effects model. Standardized mean difference (95% confidence interval) and risk ratio will be used to present continuous and dichotomous data, respectively. The assessment of publication bias will be performed using funnel plots and Egger’s regression test while I2statistics will be used to assess heterogeneity. We are planning to perform subgroup analysis to deal with potential heterogeneity.

Discussion

The results of this systematic review and meta-analysis will be useful in designing effective dietary strategies for the management of CKD-related metabolic acidosis.

Systematic review registration

The present systematic review is registered in International Prospective Register of Systematic Reviews (PROSPERO) (https://www.crd.york.ac.uk/, registration ID: CRD42022342612).
Integrated Metabolomics and Transcriptomics Analysis Identifies Molecular Subtypes within the Early and Late Mild Cognitive Impairment Stages of Alzheimer’s Disease
Authors: Yadev Shashank , Zhou Shu , Karas Zachary , Zhang Yueyang , Garmire Lana X ,   Alzheimer’s Disease Neuroimaging Initiative
Published: April 2023

Alzheimer’s disease (AD) is a highly heterogeneous neurodegenerative condition. The current study identified clinically relevant molecular subtypes of the early and late mild cognitive impairment (EMCI and LMCI) stages of AD using 401 patients’ data from the ADNI consortium. We integrated patients’ metabolomics data with the PBMC transcriptomics data using an unsupervised clustering method called Similarity Network Fusion (SNF), and identified two subtypes in early and late MCI patients, respectively. The differences between these subtypes’ metabolite concentrations and gene expression well correlate with physio-pathogenesis for AD, based on cognitive measurements, pseudo-trajectory analysis, and longitudinal analysis of dementia diagnosis. We detected many dysregulated processes between subtypes, such as aminoacyl-tRNA biosynthesis, immune system activity, zinc imbalances. While immune-related pathways are commonly dysregulated pathways in EMCI and LMCI stages, oxidative stress is prevalent in EMCI, whereas metabolic abnormality is enriched in LMCI. Refined subtypes within EMCI and LMCI are a step-forward toward more personalized treatment strategies for progressing patients before AD diagnosis.
Low-dose cytokine immunotherapy of solid cancers enabled by phagocytic-competent protein co-crystals
Authors: Jones Michael H , Quispe Calla Nirk E , Smith Robert , Talbot-Cooper Callum , Rudge Simon , Kusano Hiroyuki , Shiomi Takayuki , Ishikawa Yuichi , Zeng Hong , Best Jonathan
Published: April 2023

Protein therapeutics are often compromised by sub-optimal biodistribution contributing to poor efficacy and adverse events. Drug delivery mechanisms better able to target protein drugs to the disease site and provide localized, sustained release have the potential to transform therapeutic standards. PODS®crystals (PODS) are natural-mimetic, micron-scale protein co-crystals engineered to incorporate a protein cargo that can be sustainably released under the action of resident proteases. PODS are efficiently taken up by phagocytic cells with the cargo protein subsequently released in a bioactive form. Since blood-circulating phagocytic cells, including monocytes, are actively recruited into diseased and inflamed tissue, such as the tumour microenvironment, we postulated that monocyte/macrophage-mediated PODS delivery could be used as a molecular “Trojan horse” to efficiently deliver therapeutic proteins to target cells. This could improve the pharmacodynamics and pharmacokinetics of protein drug delivery to treat systemic and disseminated diseases. Interleukin-2 (IL-2) is notoriously toxic at the high doses required for therapeutic efficacy. Here, we demonstrate the therapeutic efficacy and tolerability of low doses of PODS containing IL-2 cargo (PODS-IL-2) administered intravenously in a mouse model of melanoma. We further demonstrate the therapeutic benefit of PODS delivering IL-2, interleukin-15 (IL-15) and interferon gamma (IFN-γ) in a mouse model of renal cell carcinoma at two doses. Efficacy was seen in both doses with the higher dose generating rapid and complete rejection of the tumour in some of the mice treated with each cytokine. This study provides proof-of-concept for the utility of intravenously administered PODS to provide a generalised and widely applicable mechanism to effectively deliver protein drugs for the therapy of cancer and potentially other diseases.
Latent evolution of biofilm formation depends on life-history and genetic background
Authors: Nucci Amandine , Rocha Eduardo P.C. , Rendueles Olaya
Published: April 2023

Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival ratesin vivoupon exposure to stresses, like the host’s immune system or antibiotic therapy. However, how the generic process of adaptation impacts the ability to form biofilm and how it may change through time has seldomly been studied. To do so, we used a previous evolution experiment with three strains of theKlebsiella pneumoniaespecies complex, in which we did not specifically select for biofilm formation. We observed that changes in the ability to form biofilm happened very fast at first and afterwards reverted to ancestral levels in many populations. Biofilm changes were associated to phenotypic changes in population yield and surface polysaccharide production. Genotypically, mutational targets in the tip adhesin of type III fimbriae (mrkD) or thefimswitch of type I fimbriae were driven by nutrient availability during evolution, and their impact on biofilm formation was dependent on capsule production. Analyses of natural isolates revealed similar mutations inmrkD, suggesting that they also play an important role in adaptation outside the laboratory. Our work reveals that the latent evolution of biofilm formation, and its evolutionary dynamics, depend on nutrient availability, the genetic background and other intertwined phenotypic and genotypic changes. Ultimately, it suggests that small differences in the environment can alter an organism’s fate in more complex niches like the host.
Coding Sequence Insertions in Fungal Genomes are Intrinsically Disordered and can Impart Functionally-Important Properties on the Host Protein
Authors: Lemire Bernard D. , Uppuluri Priya
Published: April 2023

Insertion and deletion mutations (indels) are important mechanisms of generating protein diversity. Indels in coding sequences are under considerable selective pressure to maintain reading frames and to preserve protein function, but once generated, indels provide raw material for the acquisition of new protein properties and functions. We reported recently that coding sequence insertions in theCandida albicansNDU1 protein, a mitochondrial protein involved in the assembly of the NADH:ubiquinone oxidoreductase are imperative for respiration, biofilm formation and pathogenesis. NDU1 inserts are specific to CTG-clade fungi, absent in human ortholog and successfully harnessed as drug targets. Here, we present the first comprehensive report investigating indels and clade-defining insertions (CDIs) in fungal proteomes. We investigated 80 ascomycete proteomes encompassing CTG clade species, the Saccharomycetaceae family, the Aspergillaceae family and the Herpotrichiellaceae (black yeasts) family. We identified over 30,000 insertions, 4,000 CDIs and 2,500 clade-defining deletions (CDDs). Insert sizes range from 1 to over 1,000 residues in length, while maximum deletion length is 19 residues. Inserts are strikingly over-represented in protein kinases, and excluded from structural domains and transmembrane segments. Inserts are predicted to be highly disordered. The amino acid compositions of the inserts are highly depleted in hydrophobic residues and enriched in polar residues. An indel in theSaccharomyces cerevisiaeSth1 protein, the catalytic subunit of the RSC (Remodel the Structure of Chromatin) complex is predicted to be disordered until it forms a ß-strand upon interaction. This interaction performs a vital role in RSC-mediated transcriptional regulation, thereby expanding protein function.
Therapeutic strategy for spinal muscular atrophy by combining gene supplementation and genome editing
Authors: Hatanaka Fumiyuki , Suzuki Keiichiro , Shojima Kensaku , Yu Jingting , Takahashi Yuta , Sakamoto Akihisa , Prieto Javier , Shokhirev Maxim , Esteban Concepcion Rodriguez , Nuñez-Delicado Estrella , Belmonte Juan Carlos Izpisua
Published: April 2023

Defect in theSMN1gene causes spinal muscular atrophy (SMA), which shows loss of motor nerve cells, muscle weakness and atrophy. While current treatment strategies, including small molecules or viral vectors, have been reported to improve motor function and survival, an ultimate and long-term treatment to correct SMA endogenous mutations and improve its phenotypes is still highly challenging. We have previously developed a CRISPR-Cas9 based homology-independent targeted integration (HITI) strategy, which allowed for unidirectional DNA knock-in in both dividing and non-dividing cellsin vivo. Here, we demonstrated its utility by correcting a SMA mutation in mice, and when combined withSmn1cDNA supplementation show SMA long-term therapeutic benefits in mice. Our observations may provide new avenues for long term and efficient treatment of inherited diseases.

The Gene-DUET strategy by combining cDNA supplementation and genome editing was sufficient to ameliorate SMA phenotypes in mouse modelin vivo.
Butyrate prevents visceral adipose tissue inflammation and metabolic alterations in a mouse model of Friedreich’s ataxia
Authors: Turchi Riccardo , Sciarretta Francesca , Tiberi Marta , Audano Matteo , Pedretti Silvia , Panebianco Concetta , Nesci Valentina , Pazienza Valerio , Ferri Alberto , Carotti Simone , Chiurchiù Valerio , Mitro Nico , Lettieri-Barbato Daniele , Aquilano Katia
Published: April 2023

Friedreich’s ataxia (FA) is a genetic neurodegenerative disease caused by mutation inFXNgene encoding for the mitochondrial protein frataxin (FXN). Patients with FA display an increased risk of developing diabetes that may aggravate disease prognosis. Recent studies have indicated that in addition to increased visceral adiposity, FA patients undergo a low-grade inflammatory state. The expansion of white adipose tissue (WAT) plays a fundamental role in the development of type 2 diabetes as it becomes insulin-resistant and a source of inflammatory molecules (adipokines). In this work, we have characterized visceral WAT (vWAT) at metabolic and immunological level in a murine FA model (KIKO) to test whether dysfunction of vWAT could be involved in FA metabolic complications. Through RNAseq analyses we found an alteration of inflammatory, angiogenesis and fibrosis genes in vWAT of KIKO mice. We also found other diabetes-related hallmarks such as increased lipid droplet size, immune cell infiltration and increased expression of pro-inflammatory cytokines. In addition, by targeted metabolomics we disclosed a raise in lactate production, an event usually associated with obesity and diabetes and that triggers activation of vWAT resident macrophages. To reproduce anin vitromodel of FA, we downregulated FXN protein in cultured white adipocytes and recapitulated the diabetes-like features observed in vWAT. Real time monitoring of adipocyte metabolism evidenced metabolic rewiring towards glycolysis according to increased lactate production. Analysis of fecal samples revealed a reduction of some butyrate-producing bacteria in KIKO mice. As this microbiota derived short-chain fatty was demonstrated to exert anti-diabetic function, we fed KIKO mice with a butyrate-enriched diet for 16 weeks. This dietary approach limited vWAT alterations and mitigated other diabetes-like signatures both inin vitroandin vivomodels.

In conclusion, this study identified vWAT as an important player in the onset of metabolic complications typical of FA and suggests butyrate as safe and promising adjuvant tool to treat metabolic complications in FA.
Strain-specific changes in nucleus accumbens transcriptome and motivation for food reward in mice exposed to maternal separation
Authors: Benoit Simon , Henry Mathilde , Fneich Sara , Mathou Alexia , Xia Lin , Foury Aline , Jouin Mélanie , Junien Claudine , Capuron Lucile , Jouneau Luc , Moisan Marie-Pierre , Delpierre Cyrille , Gabory Anne , Darnaudery Muriel
Published: April 2023

Adversity in childhood exerts enduring effects on brain and increases the vulnerability to psychiatric diseases. It also leads to a higher risk for eating disorders and obesity. We hypothesised that neonatal stress in mice affects motivation to obtain palatable food in adulthood and changes gene expression in reward system. Male and female pups from C57Bl/6J and C3H/HeN mice strains were subjected to a daily maternal separation (MS) protocol from PND2 to PND14. In adulthood, their motivation for palatable food reward was assessed in operant cages. Compared to control mice, male and female C3H/Hen mice exposed to MS significantly did more lever presses to obtain palatable food especially when the effort required to obtain the reward is high. Transcriptional analysis reveals 375 genes differentially expressed in the nucleus accumbens of male MS C3H/HeN mice compared to the control group, some of these being associated with the regulation of the reward system (e.g.Gnas, Pnoc). Interestingly, C57Bl/6J mice exposed to MS did not show any alteration in their motivation to obtain a palatable reward nor significant changes in gene expression in the nucleus accumbens. In conclusion, neonatal stress produces lasting changes in motivation for palatable food in C3H/HeN offspring but has no impact in C57Bl/6J offspring. These behavioural alterations are accompanied by drastic changes in gene expression specifically within the nucleus accumbens, a key structure in the regulation of motivational processes.
Virological characteristics of the SARS-CoV-2 Omicron XBB.1.16 variant
Authors: Yamasoba Daichi , Uriu Keiya , Plianchaisuk Arnon , Kosugi Yusuke , Pan Lin , Zahradnik Jiri ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito Jumpei , Sato Kei
Published: April 2023

At the end of March 2023, XBB.1.16, a SARS-CoV-2 omicron XBB subvariant, emerged and was detected in various countries. Compared to XBB.1.5, XBB.1.16 has two substitutions in the S protein: E180V is in the N-terminal domain, and T478R in the receptor-binding domain (RBD). We first show that XBB.1.16 had an effective reproductive number (Re) that was 1.27- and 1.17-fold higher than the parental XBB.1 and XBB.1.5, respectively, suggesting that XBB.1.16 will spread worldwide in the near future. In fact, the WHO classified XBB.1.16 as a variant under monitoring on March 30, 2023. Neutralization assays demonstrated the robust resistance of XBB.1.16 to breakthrough infection sera of BA.2 (18-fold versus B.1.1) and BA.5 (37-fold versus B.1.1). We then used six clinically-available monoclonal antibodies and showed that only sotrovimab exhibits antiviral activity against XBB subvariants, including XBB.1.16. Our results suggest that, similar to XBB.1 and XBB.1.5, XBB.1.16 is robustly resistant to a variety of anti-SARS-CoV-2 antibodies. Our multiscale investigations suggest that XBB.1.16 that XBB.1.16 has a greater growth advantage in the human population compared to XBB.1 and XBB.1.5, while the ability of XBB.1.16 to exhibit profound immune evasion is comparable to XBB.1 and XBB.1.5. The increased fitness of XBB.1.16 may be due to (1) different antigenicity than XBB.1.5; and/or (2) the mutations in the non-S viral protein(s) that may contribute to increased viral growth efficiency.
Correcting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules
Authors: Sun Jianfeng , Philpott Martin , Loi Danson , Li Shuang , Monteagudo-Mesas Pablo , Hoffman Gabriela , Robson Jonathan , Mehta Neelam , Gamble Vicki , Brown Tom , Sr Tom Brown , Canzar Stefan , Oppermann Udo , Cribbs Adam P
Published: April 2023

Unique Molecular Identifiers (UMIs) are random oligonucleotide sequences that remove PCR amplification biases. However, the impact that PCR associated sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We show that PCR errors are the main source of inaccuracy in both bulk and single-cell sequencing data, and synthesizing UMIs using homotrimeric nucleotide blocks provides an error correcting solution, that allows absolute counting of sequenced molecules.
Data driven and cell specific determination of nuclei-associated actin structure
Authors: Nikitina Nina , Bursa Nurbanu , Goelzer Matthew , Goldfeldt Madison , Crandall Chase , Howard Sean , Rubin Janet , Satici Aykut , Uzer Gunes
Published: April 2023

Quantitative and volumetric assessment of filamentous actin fibers (F-actin) remains challenging due to their interconnected nature, leading researchers to utilize threshold based or qualitative measurement methods with poor reproducibility. Here we introduce a novel machine learning based methodology for accurate quantification and reconstruction of nuclei-associated F-actin. Utilizing a Convolutional Neural Network (CNN), we segment actin filaments and nuclei from 3D confocal microscopy images and then reconstruct each fiber by connecting intersecting contours on cross-sectional slices. This allowed measurement of the total number of actin filaments and individual actin filament length and volume in a reproducible fashion. Focusing on the role of F-actin in supporting nucleocytoskeletal connectivity, we quantified apical F-actin, basal F-actin, and nuclear architecture in mesenchymal stem cells (MSCs) following the disruption of the Linker of Nucleoskeleton and Cytoskeleton (LINC) Complexes. Disabling LINC in mesenchymal stem cells (MSCs) generated F-actin disorganization at the nuclear envelope characterized by shorter length and volume of actin fibers contributing a less elongated nuclear shape. Our findings not only present a new tool for mechanobiology but introduce a novel pipeline for developing realistic computational models based on quantitative measures of F- actin.
Fine particulate air pollution and neuropathology markers of Alzheimer’s disease in donors with and without APOE ε4 alleles – results from an autopsy cohort
Authors: Christensen Grace M. , Li Zhenjiang , Liang Donghai , Ebelt Stefanie , Gearing Marla , Levey Allan I. , Lah James J. , Wingo Aliza P. , Wingo Thomas S. , Huels Anke
Published: April 2023

Introduction

Higher fine particulate matter (PM2.5) exposure has been found to be associated with Alzheimer’s disease (AD). PM2.5has been hypothesized to cause inflammation and oxidative stress in the brain, contributing to neuropathology. A major genetic risk factor of AD, the apolipoprotein E (APOE) gene, has also been hypothesized to modify the association between PM2.5and AD. However, little prior research exisits to support these hypotheses. Therefore, this paper aims to investigate the association between traffic-related PM2.5and AD hallmark pathology, including effect modification byAPOEgenotype, in an autopsy cohort.

Methods

Brain tissue donors enrolled in the Emory Goizueta Alzheimer’s Disease Research Center (ADRC) who died before 2020 (n=224) were assessed for AD pathology including Braak Stage, Consortium to Establish a Registry for AD (CERAD) score, and the combined AD neuropathologic change (ABC score). Traffic-related PM2.5concentrations were modeled for the metro-Atlanta area during 2002-2019 with a spatial resolution of 200-250m. One-, 3-, and 5-year average PM2.5concentrations prior to death were matched to participants home address. We assessed the association between traffic-related PM2.5and AD hallmark pathology, as well as effect modification byAPOEgenotype, using adjusted ordinal logistic regression models.

Results

Traffic-related PM2.5was significantly associated with CERAD score for the 1-year exposure window (OR: 1.92; 95% CI: 1.12, 3.30), and the 3-year exposure window (OR: 1.87; 95%-CI: 1.01, 3.17). PM2.5had harmful, but non-significant associations on Braak Stage and ABC score. The strongest associations between PM2.5and neuropathology markers were among those withoutAPOEε4alleles (e.g., for CERAD and 1-year exposure window, OR: 2.31; 95% CI: 1.36, 3.94), though interaction between PM2.5andAPOEgenotype was not statistically significant.

Conclusions

Our study found traffic-related PM2.5exposure was associated with CERAD score in an autopsy cohort, contributing to epidemiologic evidence that PM2.5affects Aβ deposition in the brain. This association was particularly strong among donors withoutAPOEε4alleles. Future studies should further investigate the biological mechanisms behind this assocation.
A scoping literature review of global dengue age-stratified seroprevalence data: estimating dengue force of infection in endemic countries
Authors: Vicco Anna , McCormack Clare , Pedrique Belen , Ribeiro Isabela , Malavige Gathsaurie Neelika , Dorigatti Ilaria
Published: April 2023

Dengue poses a significant burden worldwide, and a more comprehensive understanding of the heterogeneity in the intensity of dengue transmission within endemic countries is necessary to evaluate the potential impact of public health interventions.

This scoping literature review aimed to update a previous study of dengue transmission intensity by collating global age-stratified dengue seroprevalence data published in the Medline and Embase databases from 2014 to 2022. These data were then utilized to calibrate catalytic models and estimate the force of infection (FOI), which is the yearly per-capita risk of infection for a typical susceptible individual.

We found a total of 44 new publications containing 47 relevant datasets across 20 endemic countries. Together with the previously available average FOI estimates, there are now 280 dengue average FOI estimates obtained from seroprevalence data and 149 estimates obtained from case-notification data available across the world.

The results showed large heterogeneities in average dengue FOI both across and within countries. These new estimates can be used to inform ongoing modelling efforts to improve our understanding of the drivers of heterogeneity in dengue transmission globally, which in turn can help inform the optimal implementation of public health interventions.

Author summary

In this work, we conducted a scoping literature review to collate global dengue age-specific seroprevalence data from dengue endemic areas published between 2014 and 2022. These data were used to calibrate mathematical models and estimate the average yearly force of infection (FOI), which is a fundamental measure of transmission intensity. FOI estimates can be used to quantify the risk of infection, disease burden and the potential impact of new interventions, such as vaccination.

In addition, the FOI estimates generated in this study contribute to ongoing efforts to better characterise and map dengue transmission intensity worldwide.