bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Evaluation Between Cutting of the Intersphincteric Space vs Cutting Seton in High Anal Fistula: A Randomized Controlled Trial
Authors: Qin Jiawei , Wu Yanlan , Zheng Xueping , Wu Kunlan , Dai Gongjian , Tan Yanyan , Yang Xu , Sun Yuqing
Published: August 2024

BACKGROUND:

This study compared the efficacy of cutting of the intersphincteric space (COIS) with cutting seton (CS) procedure in treating high anal fistula.

STUDY DESIGN:

Patients diagnosed with high anal fistula were allocated into groups, who randomly received COIS and CS procedures. The primary outcome was wound healing time. Secondary outcomes included surgical parameters (operation time, hospital stay, and hospitalization expense), anal sphincter function, wound pain, wound size, clinical efficacy, recurrence after 12 months of follow-up, and complications.

RESULTS:

A total of 72 patients participated (36 in each group). The wound healing time was notably shorter in the COIS group than that in the CS group (35.75 ± 11.15 vs 55.69 ± 13. 42 days; p < 0.001). The COIS group also demonstrated superior basic surgical parameters compared with the CS group (p < 0.001). Postoperatively, the COIS group exhibited significantly higher anal resting pressure and anal maximum contractile pressure than the CS group at 3 months postoperatively (58.39 ± 6.72 vs 51.25 ± 4.33 mmHg; p < 0.001 and 143.72 ± 8.25 vs 126.75 ± 11.49 mmHg; p < 0.001). The Wexner incontinence score at 3 months postoperation in the COIS group was significantly lower than in the CS group (0.50; 0.00, 1.00 vs 3.00; 3.00, 4.00; p < 0.001). The recurrence rate was 2.78% in the COIS group and 8.33% in the CS group without statistically difference (p = 0.607).

CONCLUSIONS:

In comparison to the CS procedure, COIS appears to be an effective treatment option for high anal fistulas, offering quicker wound healing time, enhanced sphincter function, less pain, minimal invasiveness, and cost-efficiency while maintaining a high healing rate and low recurrence rate.
CagA 3′ region polymorphism of Helicobacter pylori and its association with chronic gastritis in the Chinese population
Authors: Zhu Xiaoyan , Ma Chao , Sa Rina , Wang Yaxuan , Zhu Chaohui , Zhao Yajiao , Luo Juan , Liu Xiaochuan
Published: August 2024

Introduction. Cytotoxin-associated gene A (CagA) from Helicobacter pylori is highly related to chronic gastritis. Tyrosine phosphorylation of Glu-Pro-Ile-Tyr-Ala (EPIYA) motifs from CagA determines the pathogenicity of H. pylori.

Gap statement. The precise amino acid variations surrounding the EPIYA motifs and their correlation with clinical outcomes have been poorly explored.

Aim. The purpose of this study was to examine the CagA 3′ region polymorphism of H. pylori and its association with chronic gastritis in the Chinese population.

Method. A total of 86 cagA-positive H. pylori strains were isolated from patients with chronic gastritis in two different hospitals in Beijing, PR China. Genomic DNA was extracted commercial kits, and the cagA 3′ variable region of H. pylori was amplified by polymerase chain reaction (PCR). The PCR products were sequenced and analysed using the CLC Sequence Viewer, BioEdit, and WebLogo 3.

Results. Two hundred and fifty-nine EPIYA motifs were identified from cagA-positive H. pylori strains. Notably, EPIYA-B exhibited a higher frequency of variation in comparison to EPIYA-A, EPIYA-C, and EPIYA-D. The prevalent sequences for East-Asian-type CagA were QVNK and TIDF, while KVNK and TIDD were most commonly observed for Western-type CagA. The CRPIA motifs of East-Asian-type CagA and Western-type CagA varied at positions 4, 6, 7, 8, and 10. CagA-ABD (73.2%) was the most prevalent type, followed by CagA-ABC (18.6%) and CagA-AB (3.4%). The ratio of CagA-ABD was observed to be higher in cases of chronic non-atrophic gastritis with erosive (NAGE) or chronic atrophic gastritis (AG) compared to chronic non-atrophic gastritis (NAG), and the difference was found to be statistically significant (χ2=59.000/64.000, P<0.001).

Conclusions. The EPIYA segments of Western-type CagA and East-Asian-type CagA differ significantly and the presence of CagA-ABD may be associated with severe chronic gastritis from this study.
Distribution of paramagnetic and diamagnetic cortical substrates following mild Traumatic Brain Injury: A depth- and curvature-based quantitative susceptibility mapping study
Authors: Essex Christi A. , Merenstein Jenna L. , Overson Devon K. , Truong Trong-Kha , Madden David J. , Bedggood Mayan J. , Murray Helen , Holdsworth Samantha J. , Stewart Ashley W. , Morgan Catherine , Faull Richard L. M. , Hume Patria , Theadom Alice , Pedersen Mangor
Published: August 2024

Evidence has linked head trauma to increased risk factors for neuropathology, including acute mechanical deformation of the cortical sulcal fundus and, later, perivascular accumulation of hyperphosphorylated tau (p-tau) adjacent to these spaces related to chronic traumatic encephalopathy (CTE). Despite this, little is known about microstructural abnormalities and cellular dyshomeostasis at the acute stage of mild traumatic brain injury (mTBI) in humans, particularly in the cortex. To address this gap in the literature, we designed the first architectonically-motivated quantitative susceptibility mapping (QSM) study to assess regional patterns of positive (iron-related) and negative (myelin-, calcium-, and protein-related) magnetic susceptibility in cortical regions of interest (ROI) following mTBI. Depth- and curvature-specific positive and negative QSM values were compared between 25 males with acute (< 14 days) sports-related mTBI (sr-mTBI) and 25 age-matched male controls across 34 cortical ROIs. Bilateral between-group analyses were conducted on specific ROI curvature bins (crown, bank, and fundus) as well as a combined curvature measure, across 21 cortical depths, for each ROI. Correlations between positive and negative susceptibility were analysed for age, brain injury severity, and the number of days since injury. We observed significant group differences in magnetic susceptibility for depth, curvature, and ROIs. Our results suggest a trauma-induced pattern of likely iron deposition preferential to superficial, perivascular-adjacent spaces in the sulci of the parahip-pocampal gyrus. Co-localised decreases in diamagnetism in the same region suggest dual pathology of neural substrates, the biological mechanisms behind which remain speculative. Significant correlations were found between magnetic susceptibility and age, both in ROIs and cortical depths distinct from those showing sr-mTBI-related differences. Little to no relationship was observed between magnetic susceptibility and subjective markers of injury or injury latency. The coherence between our findings and pathognomonic patterns of misfolded proteins in trauma-related neurodegeneration is interesting, which may have implications for the role of brain iron in microstructural cortical tissue damage after a mild brain injury. Further longitudinal research is needed to elucidate the long-term implications of our findings.
Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response
Authors: Lee Alpha A. , Amick Isabelle , Aschenbrenner Jasmin C. , Barr Haim M. , Benjamin Jared , Brandis Alexander , Cohen Galit , Diaz-Tapia Randy , Duberstein Shirly , Dixon Jessica , Cousins David , Fairhead Michael , Fearon Daren , Frick James , Gayvert James , Godoy Andre S. , Griffin Ed J. , Huber Kilian , Koekemoer Lizbé , Lahav Noa , Marples Peter G. , McGovern Briana L. , Mehlman Tevie , Robinson Matthew C. , Singh Usha , Szommer Tamas , Tomlinson Charles W.E. , Vargo Thomas , von Delft Frank , Wang SiYi , White Kris , Williams Eleanor , Winokan Max
Published: August 2024

A strategy for pandemic preparedness is the development of antivirals against a wide set of viral targets with complementary mechanisms of action. SARS-CoV-2 nsp3-mac1 is a viral macrodomain with ADP-ribosylhydrolase activity, which counteracts host immune response. Targeting the virus’ immunomodulatory functionality offers a differentiated strategy to inhibit SARS-CoV-2 compared to approved therapeutics, which target viral replication directly. Here we report a fragment-based lead generation campaign guided by computational approaches. We discover tool compounds which inhibit nsp3-mac1 activity at low nanomolar concentrations, and with responsive structure-activity relationships, high selectivity, and drug-like properties. Using our inhibitors, we show that inhibition of nsp3-mac1 increases ADP-ribosylation, but surprisingly does not translate to demonstrable antiviral activity in cell culture and iPSC-derived pneumocyte models. Further, no synergistic activity is observed in combination with interferon gamma, a main protease inhibitor, nor a papain-like protease inhibitor. Our results question the extent to which targeting modulation of innate immunity-driven ADP-ribosylation can influence SARS-CoV-2 replication. Moreover, these findings suggest that nsp3-mac1 might not be a suitable target for antiviral therapeutics development.
Metabolomic and transcriptomic remodeling of bone marrow myeloid cells in response to maternal obesity
Authors: Alharithi Yem J , Phillips Elysse A. , Wilson Tim D. , Couvillion Sneha P. , Nicora Carrie D. , Darakjian Priscila , Rakshe Shauna , Fei Suzanne S. , Counts Brittany , Metz Thomas O. , Searles Robert , Kumar Sushil , Maloyan Alina
Published: August 2024

Maternal obesity puts the offspring at high risk of developing obesity and cardio-metabolic diseases in adulthood. Here, using a mouse model of maternal high-fat diet (HFD)-induced obesity, we show that whole body fat content of the offspring of HFD-fed mothers (Off-HFD) increases significantly from very early age when compared to the offspring regular diet-fed mothers (Off-RD). We have previously shown significant metabolic and immune perturbations in the bone marrow of newly-weaned offspring of obese mothers. Therefore, we hypothesized that lipid metabolism is altered in the bone marrow Off-HFD in newly-weaned offspring of obese mothers when compared to the Off-RD. To test this hypothesis, we investigated the lipidomic profile of bone marrow cells collected from three-week-old offspring of regular and high fat diet-fed mothers. Diacylgycerols (DAGs), triacylglycerols (TAGs), sphingolipids and phospholipids, including plasmalogen, and lysophospholipids were remarkably different between the groups, independent of fetal sex. Levels of cholesteryl esters were significantly decreased in offspring of obese mothers, suggesting reduced delivery of cholesterol to bone marrow cells. This was accompanied by age-dependent progression of mitochondrial dysfunction in bone marrow cells. We subsequently isolated CD11b+ myeloid cells from three-week-old mice and conducted metabolomics, lipidomics, and transcriptomics analyses. The lipidomic profiles of these bone marrow myeloid cells were largely similar to that seen in bone marrow cells and included increases in DAGs and phospholipids alongside decreased TAGs, except for long-chain TAGs, which were significantly increased. Our data also revealed significant sex-dependent changes in amino acids and metabolites related to energy metabolism. Transcriptomic analysis revealed altered expression of genes related to major immune pathways including macrophage alternative activation, B-cell receptor signaling, TGFβ signaling, and communication between the innate and adaptive immune systems. All told, this study revealed lipidomic, metabolomic, and gene expression abnormalities in bone marrow cells broadly, and in bone marrow myeloid cells particularly, in the newly-weaned offspring of obese mothers, which might at least partially explain the progression of metabolic and cardiovascular diseases in their adulthood.
Assessing the combined effects of forest management and climate change on carbon and water fluxes in European beech forests
Authors: Saponaro Vincenzo , De Cáceres Miquel , Dalmonech Daniela , D’Andrea Ettore , Vangi Elia , Collalti Alessio
Published: August 2024

The consequences of climate change continue to threaten European forests, particularly for species located at the edges of their latitudinal and altitudinal ranges. While extensively studied in Central Europe, European beech forests require further investigation to understand how climate change will affect these ecosystems in Mediterranean areas. Proposed silvicultural options increasingly aim at sustainable management to reduce biotic and abiotic stresses and enhance these forest ecosystems’ resistance and resilience mechanisms. Process-based models (PBMs) can help us to simulate such phenomena and capture early stress signals while considering the effect of different management approaches. In this study, we focus on estimating sensitivity of two state-of-the-art PBMs forest models by simulating carbon and water fluxes at the stand level to assess productivity changes and feedback resulting from different climatic forcings as well as different management regimes. We applied the 3D-CMCC-FEM and MEDFATE forest models for carbon (C) and water (H2O) fluxes in in two sites of the Italian peninsula, Cansiglio in the north and Mongiana in the south, under managed vs. unmanaged scenarios and under current climate and different climatic scenarios (RCP4.5 and RCP8.5). To ensure confidence in the models’ results, we preliminary evaluated their performance in simulating C and H2O flux in three additional beech forests of the FLUXNET network along a latitudinal gradient spanning from Denmark to central Italy. The 3D-CMCC-FEM model achieved R² values of 0.83 and 0.86 with RMSEs of 2.53 and 2.05 for C and H2O fluxes, respectively. MEDFATE showed R² values of 0.76 and 0.69 with RMSEs of 2.54 and 3.01. At the Cansiglio site in northern Italy, both models simulated a general increase in C and H2O fluxes under the RCP8.5 climate scenario compared to the current climate. Still, no benefit in managed plots compared to unmanaged ones, as the site does not have water availability limitations, and thus, competition for water is low. At the Mongiana site in southern Italy, both models predict a decrease in C and H2O fluxes and sensitivity to the different climatic forcing compared to the current climate; and an increase in C and H2O fluxes when considering specific management regimes compared to unmanaged scenarios. Conversely, under unmanaged scenarios plots are simulated to experience first signals of mortality prematurely due to water stress (MEDFATE) and carbon starvation (3D-CMCC-FEM) scenarios. In conclusion, while management interventions may be considered a viable solution for the conservation of beech forests under future climate conditions at moister sites like Cansiglio, in drier sites like Mongiana conservation may not lie in management interventions alone.
High-quality genome assembly of the endemic threatened White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India.
Authors: K L Vinay , Arvind Chiti , Goyal Naman , V.V. Robin
Published: August 2024

The White-bellied Sholakili (Sholicola albiventris) is an endemic, elevational restricted species occurring in the Shola Sky Islands of the Western Ghats of India. This unique understory bird, with a complex vocal repertoire, exhibits impacts of gene flow due to anthropogenic habitat fragmentation. Here, we present the first genome assembly for Sholicola albiventris, which was assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.083 Gbp, consisting of 975 scaffolds with an N50 of 68.64Mbp and L50 of 6. Our genome assembly's completeness is supported by a high number of BUSCOs (99.9%) and a total of 4887 ultraconserved element (UCE) loci retrieved. We also report the complete mitochondrial genome comprising 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. We identified 11.82% of the nuclear genome as repetitive and 36,000 putative genes, with 12017 genes functionally annotated. Our assembly showed a great synteny between Taeniopygia guttata and Gallus gallus chromosome level assemblies. This reference will be pivotal for investigating landscape connectivity, sub-population genetics, local adaptation, and conservation genetics of this high-elevation, range-restricted endemic bird species.
Long-term monitoring of SARS-CoV-2 load and variant composition at a large metropolitan wastewater treatment plant using a simple two-step direct capture RNA extraction, droplet digital PCR, and targeted mutation assays
Authors: Balogh Steven J. , Sprouse George B. , Beckman Kenneth B. , Watson Ray H.B. , Johnson Darrell M. , Pinkerton Lee D. , Nollet Yabing H. , Sealock Adam W. , Atkins Walter S.C. , Selenke Laura M. , Kinney Joseph A. , Grady Patrick J.R. , Vanderbush Brandon , Daniel Jerry J.
Published: August 2024

Wastewater surveillance offers an objective, comprehensive, and cost-effective means of monitoring the prevalence and genomic heterogeneity of pathogens circulating in a community. Here, a novel two-step extraction procedure for the direct capture of SARS-CoV-2 RNA from raw wastewater is presented. Combined with reverse transcription-droplet digital polymerase chain reaction (RT-ddPCR) detection, the method provides a fast and sensitive method for measuring viral RNA concentrations in wastewater. The method was used to measure the concentration of SARS-CoV-2 RNA in daily samples of wastewater entering a major metropolitan wastewater treatment plant over the course of 32 months, from November 2020 through June 2023. In addition, targeted mutation assays were used with RT-ddPCR to characterize the evolving presence and prevalence of specific SARS-CoV-2 variant sub-lineages in the wastewater stream over time. The results demonstrate the utility of these methods to accurately measure the total load of SARS-CoV-2 RNA, and chronicle its evolving variant composition, in wastewater treatment plant influent, providing near-real-time characterization of COVID-19 disease prevalence and trends in the served community.

Graphical abstract
SARS-CoV-2 Omicron subvariant genomic variation associations with immune evasion in Northern California: A retrospective cohort study
Authors: Nugent Joshua R. , Wood Mariah S. , Liu Liyan , Bullick Teal , Schapiro Jeffrey M. , Arunleung Phacharee , Gautham Gautham , Getabecha Shiffen , Morales Christina , Amsden Laura B. , Hsiao Crystal A. , Wadford Debra A. , Wyman Stacia K. , Skarbinski Jacek
Published: August 2024

Background

The possibility of association between SARS-CoV-2 genomic variation and immune evasion is not known among persons with Omicron variant SARS-CoV-2 infection.

Methods

In a retrospective cohort, using Poisson regression adjusting for sociodemographic variables and month of infection, we examined associations between individual non-lineage defining mutations and SARS-CoV-2 immunity status, defined as a) no prior recorded infection, b) not vaccinated but with at least one prior recorded infection, c) complete primary series vaccination, and/or d) primary series vaccination and ≥ 1 booster. We identified all non-synonymous single nucleotide polymorphisms (SNPs), insertions and deletions in SARS-CoV-2 genomes with ≥5% allelic frequency and population frequency of ≥5% and ≤95%. We also examined correlations between the presence of SNPs with each other, with subvariants, and over time.

Results

Seventy-nine mutations met inclusion criteria. Among 15,566 persons infected with Omicron SARS-CoV-2, 1,825 (12%) were unvaccinated with no prior recorded infection, 360 (2%) were unvaccinated with a recorded prior infection, 13,381 (86%) had a complete primary series vaccination, and 9,172 (58%) had at least one booster. After examining correlation between SNPs, 79 individual non-lineage defining mutations were organized into 38 groups. After correction for multiple testing, no individual SNPs or SNP groups were significantly associated with immunity status levels.

Conclusions

Genomic variation identified within SARS-CoV-2 Omicron specimens was not significantly associated with immunity status, suggesting that contribution of non-lineage defining SNPs to immune evasion is minimal. Larger-scale surveillance of SARS-CoV-2 genomes linked with clinical data can help provide information to inform future vaccine development.
Epidemiology and excess mortality of antimicrobial resistance in bacteraemias among cancer patients: a cohort study using routinely collected health data from regional hospital trusts in Oxford and Oslo, 2008-2018
Authors: Danielsen Anders Skyrud , Lim Cherry , Yoon Chang Ho , Gran Jon Michael , Kacelnik Oliver , Eyre David W , Bjornholt Jorgen Vildershoj
Published: August 2024

Objectives: We investigated the epidemiology and impact on mortality of antimicrobial resistance (AMR) in cancer patients with bacteraemia at Oxford University Hospitals (OxUH), UK, and Oslo University Hospital (OsUH), Norway, during 2008-2018. Design: Historical cohort study. Setting: Regional hospital trusts with multiple sites in OxUH and OsUH. Methods: Patients with cancer and blood cultures positive for one of six pathogen groups during a hospital stay within three years following their first cancer diagnosis were followed for 30 days after their first bacteraemia episode. We determined the number of cases and the proportion of infections with an AMR phenotype. Excess mortality and the population-attributable fraction (PAF) due to AMR were estimated by contrasting observed mortality at the end of follow-up with an estimated counterfactual scenario where AMR was absent from all bacteraemias, using inverse probability weighting. Main outcome measure: 30-day all-cause mortality following the first bacteraemia episode. Main exposure measure: A resistant phenotype of the causative pathogen. Results: The study included 1929 patients at OxUH and 1640 patients at OsUH. The highest resistance proportions were found for vancomycin-resistance in enterococci (85/314, 27.1%) and carbapenem-resistance in Pseudomonas aeruginosa (63/260, 24.2%) at OxUH, and third-generation cephalosporin-resistance in Escherichia coli (62/743, 8.3%) and Klebsiella pneumoniae (14/223, 6.3%) at OsUH. Observed mortality for all infections was 26.4% at OxUH, with an estimated counterfactual mortality without AMR of 24.7%, yielding an excess mortality of 1.7% (95% CI: 0.8-2.5%). The PAF was 6.3% (95% CI: 2.9-9.6%), meaning an estimated 32 of 509 deaths could be attributed to AMR. Limited events at OsUH precluded a similar estimate. Conclusions: Despite modest excess mortality from AMR at OxUH and limited data at OsUH, the considerable mortality attributable to resistance represents a challenge with the potential to escalate, especially in the context of worsening global trends in resistance.
The SQUEEZE pilot trial: a trial to determine whether septic shock reversal is quicker in pediatric patients randomized to an early goal directed fluid-sparing strategy vs. usual care
Authors: Parker Melissa J. , Choong Karen , Fox-Robichaud Alison , Liaw Patricia C. , Thabane Lehana
Published: August 2024

Objective

The overall objective of our research is to determine in children with septic shock whether use of a fluid-sparing strategy results in improved clinical outcomes without an increased risk of adverse events compared to usual care. The specific objective of this pilot randomized controlled trial was to evaluate the feasibility of a definitive multicenter trial to answer our research question.

Design

Pragmatic, 2-arm, parallel group, open label, prospective pilot randomized controlled trial including a nested biosample-based translational study.

Setting

Pediatric tertiary care centre

Patients

Children aged 29 days to <18 years of age presenting to the Emergency Department or admitted to an in-patient ward (including the PICU) with suspected or confirmed septic shock and a need for ongoing resuscitation.

Interventions

Fluid-sparing vs. usual care resuscitation strategy continued until shock reversal. The fluid-sparing intervention comprised instructions to restrict fluid bolus therapy in conjunction with early initiation and/or preferential use of vasoactive medication support as a strategy to spare fluid while targeting the hemodynamic goals specified in the American College of Critical Care Medicine Surviving Sepsis Guidelines. The usual care strategy did not limit use of fluid bolus therapy.

Measurements and Main Results

53 were randomized to usual care (n=27) or fluid-sparing (n=26). Fifty-one participants were available for primary outcome analysis. Primary feasibility outcomes related to participant enrolment and protocol adherence. Enrolment rate was 1.8 (51/29); 95% confidence interval [CI]: 1.3-2.3 participants/month. Study procedures were implemented in 49/51 (96.1%), 95% CI: 86.5-99.5% participants within 1 hour of randomization in a median (quartile range [IQR]) of 8 (5, 15) minutes. The protocol required use of an exception to consent process and consent for ongoing participation was 48/51 (94.1%), 95% CI: 83.8-98.8%. There were no serious adverse events.

Conclusions

We concluded the large multicenter SQUEEZE Trial feasible to conduct. Trial Registration: ClinicalTrials.gov [NCT01973907]
Safety and efficacy of rapamycin on healthspan metrics after one year: PEARL Trial Results
Authors: Harinath Girish , Lee Virginia , Nyquist Andy , Moel Mauricio , Morgan Stefanie L. , Isman Anar , Zalzala Sajad
Published: August 2024

Background

Low-dose rapamycin promotes longevity in mice, but clinical safety and longevity data effects in humans remain limited.

Objectives

Evaluate the long-term safety of intermittent low-dose rapamycin in a healthy, normative-aging human cohort.

Design

This decentralized double-blinded, randomized, placebo-controlled trial (NCT04488601, registered 2020-07-28) was performed over 48 weeks. Participants received placebo, 5mg or 10mg compounded rapamycin (equivalent to 1.43mg or 2.86mg of generic formulations) weekly. The primary outcome measure was visceral adiposity (by DXA scan), secondary outcomes were blood biomarkers, and lean tissue and bone mineral content (by DXA scan). Established surveys were utilized to evaluate health and well-being. Safety was assessed through adverse events and blood biomarker monitoring.

Results

Adverse and serious adverse events were similar across all groups. Visceral adiposity did not change significantly (ηp2=0.001,p=0.942), and changes in blood biomarkers remained within normal ranges. Lean tissue mass (ε2=0.202,p=0.013) and self-reported pain (ε2=0.168,p=0.015) improved significantly for women using 10mg rapamycin. Trends of improvement in bone mineral density were observed in males using 10mg rapamycin (ε2=0.221,p=0.061), but no other significant effects were observed.

Conclusions

Low-dose, intermittent rapamycin administration over 48 weeks is relatively safe in healthy, normative-aging adults, and was associated with significant improvements in lean tissue mass and pain in women. Future work will evaluate benefits of a broader range of rapamycin doses on healthspan metrics for longevity, and will aim to more comprehensively establish efficacy.
Epigenetic age acceleration and mortality risk prediction in U.S. adults
Authors: Mendy Angelico , Mersha Tesfaye B.
Published: August 2024

Background

Epigenetic clocks have emerged as novel measures of biological age and potential predictors of mortality. We aimed to test whether epigenetic age acceleration (EAA) estimated using different epigenetic clocks predict long-term overall, cardiovascular or cancer mortality.

Methods

We analyzed data from 2,105 participants to the 1999-2002 National Health and Nutrition Examination Survey aged ≥50 years old who were followed for mortality through 2019. EAAs was calculated from the residuals of Horvath, Hannum, SkinBlood, Pheno, Zhang, Lin, Weidner, Vidal-Bralo and Grim epigenetic clocks regressed on chronological age. Using cox proportional hazards regression, we estimated the hazard ratio (HR) and 95% confidence interval (CI) for the association of EAA (per 5-year) and the DunedinPoAm pace of aging (per 10% increase) with overall, cardiovascular and cancer mortality, adjusting for covariates and white blood cell composition.

Results

During a median follow-up of 17.5 years, 998 deaths occurred, including 272 from cardiovascular disease and 209 from cancer. Overall mortality was most significantly predicted by Grim EAA (P< 0.0001; HR: 1.50, 95% CI: 1.32-1.71) followed by Hannum (P= 0.001; HR: 1.16, 95% CI: 1.07-1.27), Pheno (P= 0.001; HR: 1.13, 95% CI: 1.05-1.21), Horvath (P= 0.007; HR: 1.13, 95% CI: 1.04-1.22) and Vidal-Bralo (P= 0.008; HR: 1.13, 95% CI: 1.03-1.23) EAAs. Grim EAA predicted cardiovascular mortality (P< 0.0001; HR: 1.55, 95% CI: 1.29-1.86), whereas Hannum (P= 0.006; HR: 1.24, 95% CI: 1.07-1.44), Horvath (P= 0.02; HR: 1.18, 95% CI: 1.02-1.35) and Grim (P= 0.049; HR: 1.37, 95% CI: 1.00-1.87) EAAs predicted cancer mortality. DunedinPoAm pace of aging was associated with overall (P= 0.003; HR: 1.23, 95% CI: 1.08-1.38) and cardiovascular (P= 0.04; HR: 1.25, 95% CI: 1.01-1.55) mortality.

Conclusions

In a U.S. representative sample, Horvath, Hannum, Pheno, Vidal-Bralo and Grim EAA all predicted overall mortality but only Grim EAA predicted cardiovascular mortality and Horvath, Hannum or Grim EAA predicted cancer mortality. Pace of aging predicted overall and cardiovascular mortality.
Ventral-to-dorsal electrocyte development in electric organs of electric eel (Electrophorus)
Authors: Senarat Sinlapachai , Matsumoto Ayako , Sakaki Shintaro , Tsuzuki Daichi , Uchida Kazuko , Kuwahara Makoto , Hondo Eiichi , Iida Atsuo
Published: August 2024

Electric eels (Electrophorus) are renowned for their ability to generate electric discharge, which is used for prey capture and defense. Their electric organs (EOs) are located along the lateral– ventral region of the tail and contain electrocytes, which are multinucleated syncytium cells. Two major hypotheses for the electrocyte origin are proposed: (1) muscle fibers or their precursors, and (2) mesodermal cells not via muscle lineage. In this study, we demonstrate the likely molecular mechanisms and processes involved in this differentiation, supporting the second hypothesis. We report the regional differences in cell morphology within the main EO (mEO) ofElectrophorus. The cell morphology and distribution from the ventral terminal to the dorsal region of the mEO suggest the segregation of progenitors from the ventral cluster and their gradual transformation into mature multinucleated electrocytes via the layering and proliferation stages along the dorsal axis. Myosin-positive muscle cells were not included in the mEO differentiation process. Immunohistochemistry revealed strong expression of sodium-potassium adenosine triphosphatase (Na+/K+-ATPase), a key component in generating electric discharge in the mEO, across most mEO regions, except in the ventral cluster cells. Based on these observations, we propose that electrocyte progenitors develop from ventral cluster cells in the mEO and differentiate into mature multinucleated cells as they migrate dorsally. This is the first report to approach the developmental process ofElectrophoruselectrocytes from cell morphology and genetic profiles. Our findings represent a breakthrough in understanding the differentiation of electrocytes during the growth stages ofElectrophorus.
Platelets as key cells in endometriosis patients: insights from small extracellular vesicles in peritoneal fluid and endometriotic lesions analysis
Authors: Bortot Barbara , Di Florio Roberta , Merighi Simona , Peacock Ben , Lees Rebecca , Valle Francesco , Brucale Marco , Mangogna Alessandro , Di Lorenzo Giovanni , Romano Federico , Zito Gabriella , Zanconati Fabrizio , Ricci Giuseppe , Cancila Valeria , Belmonte Beatrice , Biffi Stefania
Published: August 2024

Endometriosis is a chronic inflammatory condition characterized by the presence of endometrium-like tissue outside the uterus, primarily affecting pelvic organs and tissues. In this study, we explored platelet activation in endometriosis. We utilized the STRING database to analyze the functional interactions among proteins previously identified in small extracellular vesicles (EVs) isolated from the peritoneal fluid of endometriosis patients and controls. The bioinformatic analysis indicated enriched signaling pathways related to platelet activation, hemostasis, and neutrophil degranulation. Double immunohistochemistry analysis for CD61 and MPO revealed a significant presence of neutrophils and platelets infiltrating endometriotic lesions, suggesting potential cell-cell interactions. Subsequently, we isolated small EVs from the peritoneal fluid of women diagnosed with endometriosis and from women without endometriosis who underwent surgery for non-inflammatory benign diseases. We performed single-particle phenotyping analysis based on platelet biomarkers GPIIb/IIIa and PF4 using nanoflow cytometry, as well as single-particle morphological and nanomechanical characterization through atomic force microscopy. The study demonstrated that patients with endometriosis had a notably higher proportion of particles testing positive for platelet biomarkers compared to the total number of EVs. This finding implies a potential role for platelets in the pathogenesis of endometriosis. Further research is necessary to delve into the mechanisms underlying this phenomenon and its implications for disease progression.
WHIX is a T6SS secretion domain found in polymorphic double-edged sword effectors
Authors: Fridman Chaya Mushka , Keppel Kinga , Rudenko Vladislav , Altuna-Alvarez Jon , Albesa-Jové David , Bosis Eran , Salomon Dor
Published: August 2024

Gram-negative bacteria employ the type VI secretion system (T6SS) to deliver toxic effectors into neighboring cells and outcompete rivals. Although many effectors have been identified, their secretion mechanism often remains unknown. Here, we describe WHIX, a domain that is sufficient to mediate the secretion of effectors via the T6SS. Remarkably, we find WHIX in T6SS effectors that contain a single toxic domain, as well as in effectors that contain two distinct toxic domains fused to either side of WHIX. We demonstrate that the latter, which we name double-edged sword effectors, require two cognate immunity proteins to antagonize their toxicity. Furthermore, we show that WHIX can be used as a chassis for T6SS-mediated secretion of multiple domains. Our findings reveal a new class of polymorphic T6SS cargo effectors with a unique secretion domain that can deploy two toxic domains in one shot, possibly reducing recipients’ ability to defend themselves.
Distinct checkpoint and homolog biorientation pathways regulate meiosis I inDrosophilaoocytes
Authors: Shapiro Joanatta G. , Changela Neha , Jang Janet K. , Joshi Jay N. , McKim Kim S.
Published: August 2024

Mitosis and meiosis have two mechanisms for regulating the accuracy of chromosome segregation: error correction and the spindle assembly checkpoint (SAC). We have investigated the function of several checkpoint proteins in meiosis I ofDrosophilaoocytes. Evidence of a SAC response by several of these proteins is found upon depolymerization of microtubules by colchicine. However, unattached kinetochores or errors in biorientation of homologous chromosomes does not induce a SAC response. Furthermore, the metaphase I arrest does not depend on SAC genes, suggesting the APC is inhibited even if the SAC is silenced. Two SAC proteins, ROD of the ROD-ZW10-Zwilch (RZZ) complex and MPS1, are also required for the biorientation of homologous chromosomes during meiosis I, suggesting an error correction function. Both proteins aid in preventing or correcting erroneous attachments and depend on SPC105R for localization to the kinetochore. We have defined a region of SPC105R, amino acids 123-473, that is required for ROD localization and biorientation of homologous chromosomes at meiosis I. Surprisingly, ROD removal, or “streaming”, is independent of the dynein adaptor Spindly and is not linked to the stabilization of end-on attachments. Instead, meiotic RZZ streaming appears to depend on cell cycle stage and may be regulated independently of kinetochore attachment or biorientation status. We also show that dynein adaptor Spindly is also required for biorientation at meiosis I, and surprisingly, the direction of RZZ streaming.

Author Summary

The Spindle Assembly Checkpoint (SAC) is known to delay cell cycle progression until chromosomes are properly attached to microtubules. Meiotic cells often have modified cell cycle phases, and natural arrest points such as metaphase I inDrosophila. We show that inDrosophilaoocytes, the SAC is sensitive to loss of microtubules, but not sensitive to a variety of kinetochore attachment errors. Thus, the function of the SAC appears to be limited to monitoring oocyte spindle assembly, and not required for accurate chromosome segregation. However, two of the SAC genes,rodandMps1, are required for the biorientation of homologous chromosomes during meiosis I, suggesting an error correction function. Rod is part of the RZZ complex and is notable for its property of streaming off the kinetochores. However, our results show that streaming off the kinetochore may not contribute to RZZ regulation of microtubule attachments, and only be associated with SAC function. Instead, the establishment of stable end-on attachments may occur while RZZ is still present at kinetochore. We suggest that RZZ interacts with multiple motors to promote bidirectional movement of kinetochores along microtubules, which allows chromosomes to find and attach to the correct pole.
Learning reshapes the hippocampal representation hierarchy
Authors: Chiossi Heloisa S. C. , Nardin Michele , Tkačik Gašper , Csicsvari Jozsef L.
Published: August 2024

A key feature of biological and artificial neural networks is the progressive refinement of their neural representations with experience. In neuroscience, this fact has inspired several recent studies in sensory and motor systems. However, less is known about how higher associational cortical areas, such as the hippocampus, modify representations throughout the learning of complex tasks. Here we focus on associative learning, a process that requires forming a connection between the representations of different variables for appropriate behavioral response. We trained rats in a spatial-context associative task and monitored hippocampal neural activity throughout the entire learning period, over several days. This allowed us to assess changes in the representations of context, movement direction and position, as well as their relationship to behavior. We identified a hierarchical representational structure in the encoding of these three task variables that was preserved throughout learning. Nevertheless, we also observed changes at the lower levels of the hierarchy where context was encoded. These changes were local in neural activity space and restricted to physical positions where context identification was necessary for correct decision making, supporting better context decoding and contextual code compression. Our results demonstrate that the hippocampal code not only accommodates hierarchical relationships between different variables but also enables efficient learning through minimal changes in neural activity space. Beyond the hippocampus, our work reveals a representation learning mechanism that might be implemented in other biological and artificial networks performing similar tasks.
Magnetic Activation of Spherical Nucleic Acids for the Remote Control of Synthetic Cells
Authors: Parkes Ellen , Al Samad Assala , Mazzotti Giacomo , Newell Charlie , Ng Brian , Radford Amy , Booth Michael J.
Published: August 2024

The advancement of synthetic cells as drug delivery devices hinges on the development of targeting strategies, in particular the controlled synthesis of biomolecules in-situ using a deeply penetrative stimulus. To address this, we have designed spherical nucleic acids comprising DNA promoter sequences decorating magnetic nanoparticle cores. By harnessing the heat dissipated from magnetic hyperthermia (a clinically-approved anticancer therapy) we tightly controlled cell-free protein synthesis. We then deployed a tissue phantom that is impenetrable by current activation methods to demonstrate the potential of this technology for the remote control of synthetic cells using deeply tissue-penetrating magnetic fields. This paves the way for targeting and controlling the in-situ synthesis of biomolecules deep within the body.

Abstract Figure
Fc-independent SARS-CoV-2 infection-enhancing antibodies decouple N-terminal and receptor-binding domains by cross-linking neighboring spikes
Authors: van Eerden Floris J. , Li Songling , Lusiany Tina , Ismanto Hendra S. , Terada Tohru , Gerle Christoph , Akamatsu Kanako , Hirose Mika , Sugihara Fuminori , Chen David Virya , Kishikawa Jun-ichi , Kato Takayuki , Liu Yafei , Okada Masato , Arase Hisashi , Standley Daron M.
Published: August 2024

Antibody dependent enhancement (ADE) is a serious concern in vaccine development. The canonical ADE pathways are dependent on the fragment crystallizable (Fc) region of the antibody. In SARS-CoV-2 several antibodies have been discovered that inflict ADE in vitro. These antibodies target the N-terminal domain (NTD) of the SARS-CoV-2 spike protein. We previously proposed that these NTD-targeting infection-enhancing antibodies (NIEAs) cross-link neighboring spike proteins via their NTDs, and that this results in a decoupling between the NTD and receptor binding domain (RBD), facilitating the “RBD down” to “up” transition. In this study we present a combination of molecular dynamics simulations and cryogenic electron microscopy data that, together, demonstrate that NIEAs are indeed able to cross-link neighboring SARS-CoV-2 spike proteins, and that this cross-linking results in a decoupling of the NTD and RBD domains. These findings provide support for an Fc region independent ADE pathway that is not only relevant for SARS-CoV-2 but also for other viruses of which the spike proteins undergo a conformational change upon host cell entry.
Cortical Excitability is Affected by Light Exposure – Distinct Effects in Adolescents and Young Adults
Authors: Sharifpour Roya , Balda Aizpurua Fermin , Paparella Ilenia , Read John , Leysens Zoé , Letot Sara , Campbell Islay , Beckers Elise , Collette Fabienne , Phillips Christophe , Zubkov Mikhail , Vandewalle Gilles
Published: August 2024

Light, particularly blue-wavelength light, exerts a broad range of non-image forming (NIF) effects including the stimulation of cognition and alertness and the regulation of mood, sleep and circadian rhythms. However, its underlying brain mechanisms are not fully elucidated. Likewise, whether adolescents show a different NIF sensitivity to light compared to adults is not established. Here, we investigated whether cortical excitability, a basic aspect of brain function that depends on sleep-wake regulation, is affected by blue light and whether the effect is similar in young adults and adolescents. To do so, we used transcranial magnetic stimulation coupled to high-density electroencephalography (TMS–EEG) in healthy young adults (N=13, 24.2y ±3.4) and in adolescents (N=15, 16.9y ±1.1). Our results showed that, in young adults, blue light affected cortical excitability following an apparent inverted-U relationship, while adolescents’ cortical excitability was not significantly impacted by blue light. In addition, although light did not affect performance on a visuomotor vigilance task completed during the TMS-EEG recordings, cortical excitability was positively correlated to task performance in both age groups. This study provides valuable insights into the complex interplay between light, cortical excitability, and behavior. Our findings highlight the role of age in NIF effects of light, suggesting that brain responses to light differ during developmental periods.
A diagnostic gap to fill: Development of molecular tools to distinguish the plant-parasitic nematode speciesHeterodera carotaeandHeterodera cruciferae
Authors: Fouville Didier , Biget Marine , Montarry Josselin , Fournet Sylvain , Grenier Eric
Published: August 2024

The carrot-parasitic nematode,Heterodera carotae, is an important pest causing qualitative and quantitative production losses across several countries worldwide and must be carefully identified and monitored. Indeed, in culture crops,Heterodera carotaeandHeterodera cruciferae, two genetically closely related species from the Goettingiana group, can be found in mixture and are virtually morphologically non-recognizable. However, onlyH. carotaeis able to develop on carrot. To monitor carrot production and set up suitableH. carotaecontrol plans, simple and reliable diagnostic methods to detect and identify these two species are needed. In this study, we developed and successfully tested two real-time PCR protocols (SYBR Green singleplex and TaqMan multiplex real-time PCRs) against both sister species:H. carotaeandH. cruciferae. Using two specific sets of primers targeting the two species, which were designed from sequences containing microsatellite loci, we managed, whatever the methods, to distinguish the two species. Moreover, we showed a higher specificity using the TaqMan assays (test on cysts) but a better sensitivity (tests on J2 juvenile larvae) with the SYBR Green assays. In this study, we thus proposed two useful and reliable diagnostic tools to enable farmers and scientists to rapidly detect two plant-parasitic nematodes and supervise agricultural management.
Graph models of brain state in deep anaesthesia reveal sink state dynamics of reduced spatiotemporal complexity
Authors: Wilsenach James , Deane Charlotte M. , Reinert Gesine , Warnaby Katie
Published: August 2024

Anaesthetisia is an important surgical and explorative tool in the study of consciousness. Much work has been done to connect the deeply anaesthetised condition with decreased complexity. However, anaesthesia-induced unconsciousness is also a dynamic condition in which functional activity and complexity may fluctuate, being perturbed by internal or external (e.g. noxious) stimuli. We use fMRI data from a cohort undergoing deep propofol anaesthesia to investigate resting state dynamics using dynamic brain state models and spatiotemporal network analysis. We focus our analysis on group-level dynamics of brain state temporal complexity, functional activity, connectivity and spatiotemporal modularization in deep anaesthesia and wakefulness. We find that in contrast to dynamics in the wakeful condition, anaesthesia dynamics are dominated by a handful of sink states that act as low-complexity attractors to which subjects repeatedly return. On a subject-level, our analysis provides tentative evidence that these low complexity attractor states appear to depend on subject-specific age and anaesthesia susceptibility factors. Finally, our spatiotemporal analysis, including a novel spatiotemporal clustering of graphs representing hidden Markov models, suggests that dynamic functional organisation in anaesthesia can be characterised by mostly unchanging, isolated regional subnetworks that share some similarities with the brain's underlying structural connectivity, as determined from normative tractography data.