Proposing candidate genes under telomeric control based on cross-species position data

In this paper, we present a comprehensive computational framework aimed at suggesting genes whose transcriptional regulation is likely to be influenced by their chromosomal position. This framework provides a user-friendly web interface, enabling researchers to explore the positional properties of all human genes and their orthologs across species, with a focus on their relation to the telomeres. Our approach involves multiple scoring methods, each adjustable by users, representing different features of the genes' positional variation across species. The resulting rankings can be combined to identify candidate genes that may be subject to position effects. Furthermore, the ranking can be tailored to a specific set of reference genes. We evaluate the method within the context of TPE-OLD, a mechanism where telomeres can exert a direct influence on gene expression across considerable genomic distances, and empower researchers to delve deeper into genes of interest, analyzing their position across species and estimating their susceptibility to position effects like TPE-OLD. We also provide simple enrichment analyses of user-provided gene lists in relation to top-ranking candidate genes.

Orthokeratology effect on the corneoscleral profile: Beyond the bull's eye

PURPOSE

To assess the impact of 3 months of orthokeratology (ortho-k) contact lenses (CLs) for myopia correction on the corneoscleral profile, as changes in scleral geometry could serve as indirect evidence of alteration in the corneal biomechanical properties.

METHODS

Twenty subjects (40 eyes) were recruited to wear ortho-k lenses overnight; however, after discontinuation (two CL fractures, one under-correction and two non-serious adverse events), 16 subjects (31 eyes) finished a 3-month follow-up. Corneoscleral topographies were acquired using the Eye Surface Profiler (ESP) system before and after 3 months of lens wear. Steep (SimKs) and flat (SimKf) simulated keratometry and scleral sagittal height measurements for 13-, 14- and 15-mm chord lengths were automatically calculated by the ESP software. Additionally, sagittal height and slope were calculated in polar format from 21 radii (0-10 mm from the corneal apex) at 12 angles (0-330°). Linear mixed models were fitted to determine the differences between visits.

RESULTS

SimKs and SimKf were increased significantly (p ≤ 0.02). The sagittal height in polar format increased significantly (p = 0.046) at a radius of 2.5 mm for 150°, 180°, 210° and 240° orientations and at a radius of 3.0 mm for 210°. Additionally, the slope in polar format significantly decreased (p ≤ 0.04) at radii ranges of 0.0-0.5, 0.5-1.0 and 1.0-1.5 mm for multiple angles and at a radii range of 5.0-5.5 mm for 90°. It also increased significantly (p ≤ 0.045) at a radii range of 1.5-2.0 mm for 30° and at radii ranges of 2.0-2.5, 2.5-3.0 and 3.0-3.5 mm for multiple angles. No significant changes were found for any parameter measured from the scleral area.

CONCLUSIONS

Three months of overnight ortho-k lens wear changed the central and mid-peripheral corneal geometry as expected, maintaining the peripheral cornea and the surrounding sclera stability.

Interoception as a function of hypnotizability during rest and a heartbeat counting task

The hypnotizability-related differences in morpho-functional characteristics of the insula could at least partially account for the differences in interoceptive accuracy (IA) observed between high and low hypnotizable individuals (highs, lows). Our aim was to investigate interoceptive processing in highs, lows, and medium hypnotizable individuals (mediums), who represent most of the population, during a 10-minute open eyes relaxation condition (Part 1) and three repetitions of consecutive 2-minute open eyes, closed eyes, and heartbeat counting conditions, followed by a 2-minute post-counting condition (Part 2). Electrocardiogram and electroencephalogram were recorded in 14 highs, 14 mediums, and 18 lows, classified according to the Stanford Hypnotic Susceptibility Scale: Form A. Heartbeat-evoked cortical potentials (HEP) were extracted throughout the entire session, and IA index was obtained for the heartbeat counting task (HCT). In Part 1, significant hypnotizability-related differences were observed in the right central region in both early and late HEP components, with lows showing positive amplitudes and highs/mediums showing negative amplitudes. In Part 2, the same group differences were limited to the early component. Moreover, in the left frontal regions, only mediums modified their HEP during the counting task with respect to the open/closed eyes conditions, whereas highs displayed HEP differences between counting and post-counting rest. HCT did not show significant group differences. In conclusion, highs and mediums seem to be more similar than mediums and lows regarding HEP, despite the absence of significant differences in HCT. Nonetheless, a negative correlation between hypnotizability scores and HEP amplitudes was observed in the regions showing group differences.

Tumor-Infiltrating Lymphocytes Refine Outcomes in Triple-Negative Breast Cancer Treated with Anthracycline-Free Neoadjuvant Chemotherapy

PURPOSE

Stromal tumor-infiltrating lymphocytes (sTIL) are associated with pathologic complete response (pCR) and long-term outcomes for triple-negative breast cancer (TNBC) in the setting of anthracycline-based chemotherapy. The impact of sTILs on refining outcomes beyond prognostic information provided by pCR in anthracycline-free neoadjuvant chemotherapy (NAC) is not known.

EXPERIMENTAL DESIGN

This is a pooled analysis of two studies where patients with stage I (T>1 cm)-III TNBC received carboplatin (AUC 6) plus docetaxel (75 mg/m2; CbD) NAC. sTILs were evaluated centrally on pre-treatment hematoxylin and eosin slides using standard criteria. Cox regression analysis was used to examine the effect of variables on event-free survival (EFS) and overall survival (OS).

RESULTS

Among 474 patients, 44% had node-positive disease. Median sTILs were 5% (range, 1%-95%), and 32% of patients had ≥30% sTILs. pCR rate was 51%. On multivariable analysis, T stage (OR, 2.08; P = 0.007), nodal status (OR, 1.64; P = 0.035), and sTILs (OR, 1.10; P = 0.011) were associated with pCR. On multivariate analysis, nodal status (HR, 0.46; P = 0.008), pCR (HR, 0.20; P < 0.001), and sTILs (HR, 0.95; P = 0.049) were associated with OS. At 30% cut-point, sTILs stratified outcomes in stage III disease, with 5-year OS 86% versus 57% in ≥30% versus <30% sTILs (HR, 0.29; P = 0.014), and numeric trend in stage II, with 5-year OS 93% versus 89% in ≥30% versus <30% sTILs (HR, 0.55; P = 0.179). Among stage II-III patients with pCR, EFS was better in those with ≥30% sTILs (HR, 0.16; P, 0.047).

CONCLUSIONS

sTILs density was an independent predictor of OS beyond clinicopathologic features and pathologic response in patients with TNBC treated with anthracycline-free CbD chemotherapy. Notably, sTILs density stratified outcomes beyond tumor-node-metastasis (TNM) stage and pathologic response. These findings highlight the role of sTILs in patient selection and stratification for neo/adjuvant escalation and de-escalation strategies.

A Systematic Review of Potential Biomarkers for Bacterial Burden and Treatment Efficacy Assessment in Tuberculosis Platform-Based Clinical Trials

Adaptive platform trials can be more efficient than classic trials for developing new treatments. Moving from culture-based to simpler- or faster-to-measure biomarkers as efficacy surrogates may enhance this advantage. We performed a systematic review of treatment efficacy biomarkers in adults with tuberculosis. Platform trials can span different development phases. We grouped biomarkers as: α, bacterial load estimates used in phase 2a trials; β, early and end-of treatment end points, phase 2b-c trials; γ, posttreatment or trial-level estimates, phase 2c-3 trials. We considered as analysis unit (biomarker entry) each combination of biomarker, predicted outcome, and their respective measurement times or intervals. Performance metrics included: sensitivity, specificity, area under the receiver-operator curve (AUC), and correlation measures, and classified as poor, promising, or good. Eighty-six studies included 22 864 participants. From 1356 biomarker entries, 318 were reported with the performance metrics of interest, with 103 promising and 41 good predictors. Group results were: α, mycobacterial RNA and lipoarabinomannan (LAM) in sputum, and host metabolites in urine; β, mycobacterial RNA and host transcriptomic or cytokine signatures for early treatment response; and γ, host transcriptomics for recurrence. A combination of biomarkers from different categories could help in designing more efficient platform trials. Efforts to develop efficacy surrogates should be better coordinated.

Pharmacokinetics and Safety of Twice-daily Ritonavir-boosted Atazanavir With Rifampicin

BACKGROUND

Critical drug-drug interactions (DDI) and hepatotoxicity complicate concurrent use of rifampicin and protease inhibitors. We investigated whether dose escalation of atazanavir/ritonavir could safely overcome the DDI with rifampicin.

METHODS

DERIVE (NCT04121195, EDCTP) was a dose-escalation trial in people with human immunodeficiency virus (HIV) on atazanavir/ritonavir-based antiretroviral therapy (ART) in Uganda. Four intensive pharmacokinetic (PK) visits were performed: PK1 300/100 mg OD (baseline); PK2 300/100 mg OD with rifampicin 600 mg; PK3 300/100 mg twice a day (BID) with rifampicin 600 mg OD; PK4 300/100 mg BID with rifampicin 1200 mg OD. Dolutegravir 50 mg BID throughout the study period ensured participants remained protected from subtherapeutic atazanavir concentrations. The data were interpreted with noncompartmental analysis. The target minimum concentration was atazanavir's protein-adjusted IC90 (PA-IC90), 0.014 mg/L.

RESULTS

We enrolled 26 participants (23 female) with median (range) age 44 (28-61) years and weight 67 (50-75) kg. Compared with PK1, atazanavir Ctau, and AUC were significantly reduced at PK2 by 96% and 85%, respectively. The escalation to BID dosing (PK3) reduced this difference in Ctau, and AUC24 to 18% lower and 8% higher, respectively. Comparable exposures were maintained with double doses of rifampicin. Lowest Ctau during PK1, PK3, and PK4 were 12.7-, 4.8-, and 8.6-fold higher than PA-IC90, respectively, whereas 65% of PK2 Ctau were below the limit of quantification (0.03 mg/L), hence likely below PA-IC90. No participant developed significant elevation of liver enzymes, reported a serious adverse event (SAE) or experienced rebound viraemia.

CONCLUSIONS

Twice daily atazanavir/ritonavir during rifampicin co-administration was well tolerated and achieved plasma concentrations above the target.

CLINICAL TRIALS REGISTRATION

NCT04121195. Registered on 09 October 2019, https://clinicaltrials.gov/ct2/show/NCT04121195.

Biomarker signatures associated with ageing free of major chronic diseases: results from a population-based sample of the EPIC-Potsdam cohort

BACKGROUND

A number of biomarkers denoting various pathophysiological pathways have been implicated in the aetiology and risk of age-related diseases. Hence, the combined impact of multiple biomarkers in relation to ageing free of major chronic diseases, such as cancer, cardiovascular disease and type 2 diabetes, has not been sufficiently explored.

METHODS

We measured concentrations of 13 biomarkers in a random subcohort of 2,500 participants in the European Prospective Investigation into Cancer and Nutrition Potsdam study. Chronic disease-free ageing was defined as reaching the age of 70 years within study follow-up without major chronic diseases, including cardiovascular disease, type 2 diabetes or cancer. Using a novel machine-learning technique, we aimed to identify biomarker clusters and explore their association with chronic disease-free ageing in multivariable-adjusted logistic regression analysis taking socio-demographic, lifestyle and anthropometric factors into account.

RESULTS

Of the participants who reached the age of 70 years, 321 met our criteria for chronic-disease free ageing. Machine learning analysis identified three distinct biomarker clusters, among which a signature characterised by high concentrations of high-density lipoprotein cholesterol, adiponectin and insulin-like growth factor-binding protein 2 and low concentrations of triglycerides was associated with highest odds for ageing free of major chronic diseases. After multivariable adjustment, the association was attenuated by socio-demographic, lifestyle and adiposity indicators, pointing to the relative importance of these factors as determinants of healthy ageing.

CONCLUSION

These data underline the importance of exploring combinations of biomarkers rather than single molecules in understanding complex biological pathways underpinning healthy ageing.

Ruthenium complexes bearing nile red chromophore and one of its derivative: Theoretical evaluation of PDT-related properties

The outcomes of DFT-based calculations are here reported to assess the applicability of two synthesized polypyridyl Ru(II) complexes, bearing ethynyl nile red (NR) on a bpy ligand, and two analogues, bearing modified-NR, in photodynamic therapy. The absorption spectra, together with the non-radiative rate constants for the S1 - Tn intersystem crossing transitions, have been computed for this purpose. Calculations evidence that the structural modification on the chromophore destabilizes the HOMO of the complexes thus reducing the H-L gap and, consequently, red shifting the maximum absorption wavelength within the therapeutic window, up to 620 nm. Moreover, the favored ISC process from the bright state involves the triplet state closest in energy, which is also characterized by the highest SOC value and by the involvement of the whole bpy ligand bearing the chromophore in delocalising the unpaired electrons. These outcomes show that the photophysical behavior of the complexes is dominated by the chromophore.

Impact of the motivational interviewing for childhood obesity treatment: The Obemat2.0 randomized clinical trial

BACKGROUND AND OBJECTIVE

The aim was assessing a short training for healthcare providers on patient-focused counselling to treat childhood obesity in primary care, along with dietitian-led workshops and educational materials.

METHODS

Randomized clustered trial conducted with paediatrician-nurse pairs (Basic Care Units [BCU]) in primary care centres from Tarragona (Spain). BCUs were randomized to intervention (MI) (motivational interview, dietitian-led education, and educational materials) or control group (SC, standard care). Participants were 8-14-year-old children with obesity, undergoing 1-11 monthly treatment visits during 1 year at primary care centres. The primary outcome was BMI z-score reduction.

RESULTS

The study included 44 clusters (23 MI). Out of 303 allocated children, 201 (n = 106 MI) completed baseline, final visits, and at least one treatment visit and were included in the analysis. BMI z-score reduction was -0.27 (±0.31) in SC, versus -0.36 (±0.35) in MI (p = 0.036). Mixed models with centres as random effects showed greater reductions in BMI in MI than SC; differences were B = -0.11 (95% CI: -0.20, -0.01, p = 0.025) for BMI z-score, and B = -2.06 (95% CI: -3.89, -0.23, p = 0.028) for BMI %. No severe adverse events related to the study were notified.

CONCLUSION

Training primary care professionals on motivational interviewing supported by dietitians and educational materials, enhanced the efficacy of childhood obesity therapy.

Ultrafast creation of a light-induced semimetallic state in strongly excited 1T-TiSe2

Screening, a ubiquitous phenomenon associated with the shielding of electric fields by surrounding charges, has been widely adopted as a means to modify a material's properties. While most studies have relied on static changes of screening through doping or gating thus far, here we demonstrate that screening can also drive the onset of distinct quantum states on the ultrafast timescale. By using time- and angle-resolved photoemission spectroscopy, we show that intense optical excitation can drive 1T-TiSe2, a prototypical charge density wave material, almost instantly from a gapped into a semimetallic state. By systematically comparing changes in band structure over time and excitation strength with theoretical calculations, we find that the appearance of this state is likely caused by a dramatic reduction of the screening length. In summary, this work showcases how optical excitation enables the screening-driven design of a nonequilibrium semimetallic phase in TiSe2, possibly providing a general pathway into highly screened phases in other strongly correlated materials.

Implementing no-signaling correlations as a service

We deal with no-signaling correlations that include Bell-type quantum nonlocality. We consider a logical implementation using a trusted central server with encrypted connections to clients. We show that in this way it is possible to implement two-party no-signaling correlations in an asynchronous manner. While from the point of view of physics our approach can be considered as the computer emulation of the results of measurements on entangled particles, from the software engineering point of view it introduces a primitive in communication protocols that can be capable of coordinating agents without revealing the details of their actions. We present an actual implementation in the form of a Web-based application programming interface (RESTful Web API). We demonstrate the use of the API via the simple implementation of the Clauser-Horne-Shimony-Holt game.

Hypothalamic Inflammation Improves Through Bariatric Surgery, and Hypothalamic Volume Predicts Short-Term Weight Loss Response in Adults With or Without Type 2 Diabetes

OBJECTIVE

Preclinical research implicates hypothalamic inflammation (HI) in obesity and type 2 diabetes pathophysiology. However, their pathophysiological relevance and potential reversibility need to be better defined. We sought to evaluate the effect of bariatric surgery (BS) on radiological biomarkers of HI and the association between the severity of such radiological alterations and post-BS weight loss (WL) trajectories. The utility of cerebrospinal fluid large extracellular vesicles (CSF-lEVs) enriched for microglial and astrocyte markers in studying HI was also explored.

RESEARCH DESIGN AND METHODS

We included 72 individuals with obesity (20 with and 52 without type 2 diabetes) and 24 control individuals. Participants underwent lumbar puncture and 3-T MRI at baseline and 1-year post-BS. We assessed hypothalamic mean diffusivity (MD) (higher values indicate lesser microstructural integrity) and the volume of the whole and main hypothalamic subregions. CSF-lEVs enriched for glial and astrocyte markers were determined by flow cytometry.

RESULTS

Compared with control group, the obesity and type 2 diabetes groups showed a larger volume and higher MD in the hypothalamic tubular inferior region, the area encompassing the arcuate nucleus. These radiological alterations were positively associated with baseline anthropometric and metabolic measures and improved post-BS. A larger baseline tubular inferior hypothalamic volume was independently related to lesser WL 1 and 2 years after BS. CSF-lEVs did not differ among groups and were unrelated to WL trajectories.

CONCLUSIONS

These findings suggest HI improvement after BS and may support a role for HI in modulating the WL response to these interventions.

Current spectrum and outcomes of infarct-related cardiogenic shock: insights from the CULPRIT-SHOCK registry and randomized controlled trial

AIMS

We analysed consecutive patients with acute myocardial infarction complicated by cardiogenic shock (CS) who were enrolled into the CULPRIT-SHOCK randomized controlled trial (RCT) and those with exclusion criteria who were included into the accompanying registry.

METHODS AND RESULTS

In total, 1075 patients with infarct-related CS were screened for CULPRIT-SHOCK in 83 specialized centres in Europe; 369 of them had exclusion criteria for the RCT and were enrolled into the registry. Patients were followed over 1 year. The mean age was 68 years and 260 (25%) were women. 13.5%, 30.9%, and 55.6% had one-vessel, two-vessel, and three-vessel coronary artery disease (CAD), respectively. Significant left main (LM) coronary artery stenosis was present in 8.0%. 54.2% of the patients had cardiac arrest before admission. Thrombolysis in myocardial infarction (TIMI) 3 patency of the infarct vessel after percutaneous coronary intervention was achieved in 83.6% of all patients. Mechanical circulatory support was applied in one-third of patients. Total mortality after 30 days and 1 year was 47.6% and 52.9%. Mortality after 1 year was highest in patients with LM coronary artery stenosis (63.5%), followed by three-vessel (56.6%), two-vessel (49.8%), and one-vessel CAD (38.6%), respectively. Mechanical complications were rare (21/1008; 2.1%) but associated with a high mortality of 66.7% after 1 year.

CONCLUSION

In specialized centres in Europe, short- and long-term mortality of patients with infarct-related CS treated with an invasive strategy is still high and mainly depends on the extent of CAD. Therefore, there is still a need for improvement of care to improve the prognosis of infarct-related CS.

Helping Blind People Grasp: Evaluating a Tactile Bracelet for Remotely Guiding Grasping Movements

The problem of supporting visually impaired and blind people in meaningful interactions with objects is often neglected. To address this issue, we adapted a tactile belt for enhanced spatial navigation into a bracelet worn on the wrist that allows visually impaired people to grasp target objects. Participants' performance in locating and grasping target items when guided using the bracelet, which provides direction commands via vibrotactile signals, was compared to their performance when receiving auditory instructions. While participants were faster with the auditory commands, they also performed well with the bracelet, encouraging future development of this system and similar systems.

The role of animal hosts in shaping gut microbiome variation

Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Antigen-independent, autonomous B cell receptor signaling drives activated B cell DLBCL

Diffuse large B cell lymphoma of activated B cell type (ABC-DLBCL), a major cell-of-origin DLBCL subtype, is characterized by chronic active B cell receptor (BCR) signaling and NF-κB activation, which can be explained by activating mutations of the BCR signaling cascade in a minority of cases. We demonstrate that autonomous BCR signaling, akin to its essential pathogenetic role in chronic lymphocytic leukemia (CLL), can explain chronic active BCR signaling in ABC-DLBCL. 13 of 18 tested DLBCL-derived BCR, including 12 cases selected for expression of IgM, induced spontaneous calcium flux and increased phosphorylation of the BCR signaling cascade in murine triple knockout pre-B cells without antigenic stimulation or external BCR crosslinking. Autonomous BCR signaling was associated with IgM isotype, dependent on somatic BCR mutations and individual HCDR3 sequences, and largely restricted to non-GCB DLBCL. Autonomous BCR signaling represents a novel immunological oncogenic driver mechanism in DLBCL originating from individual BCR sequences and adds a new dimension to currently proposed genetics- and transcriptomics-based DLBCL classifications.

Excitation signal optimization for minimizing fluctuations in knock out slow extraction

The synchrotron is a circular particle accelerator used for high energy physics experiments, material and life science, as well as hadron cancer therapy. After acceleration to the desired energies, particle beams are commonly extracted from the synchrotron using the method of resonant slow extraction. The goal is to deliver a steady particle flux-referred to as spill-to experiments and treatment facilities over the course of seconds while slowly emptying the storage ring. Any uncontrolled intensity fluctuations in the spill are detrimental to the efficiency of beam usage, as they lead to detector pileups or detector interlocks, hindering experiments and cancer treatment. Among the most widely used extraction scheme in medical facilities is the Radio Frequency Knock Out (RF-KO) driven resonant slow extraction, where the stored beam is transversely excited with a radio frequency (RF) field and the spill intensity is controlled by the excitation signal strength. This article presents particle dynamics simulations of the RF-KO system with the focus on finding effective mechanism for minimizing the intensity fluctuations while maintaining a good extraction efficiency and other advantages of KO extraction. An improved beam excitation signal which optimizes these main objectives is found, and is rigorously compared experimentally with other commonly applied techniques.

Cellulose-Based Hydrogels for Wastewater Treatment: A Focus on Metal Ions Removal

The rapid worldwide industrial growth in recent years has made water contamination by heavy metals a problem that requires an immediate solution. Several strategies have been proposed for the decontamination of wastewater in terms of heavy metal ions. Among these, methods utilizing adsorbent materials are preferred due to their cost-effectiveness, simplicity, effectiveness, and scalability for treating large volumes of contaminated water. In this context, heavy metal removal by hydrogels based on naturally occurring polymers is an attractive approach for industrial wastewater remediation as they offer significant advantages, such as an optimal safety profile, good biodegradability, and simple and low-cost procedures for their preparation. Hydrogels have the ability to absorb significant volumes of water, allowing for the effective removal of the dissolved pollutants. Furthermore, they can undergo surface chemical modifications which can further improve their ability to retain different environmental pollutants. This review aims to summarize recent advances in the application of hydrogels in the treatment of heavy metal-contaminated wastewater, particularly focusing on hydrogels based on cellulose and cellulose derivatives. The reported studies highlight how the adsorption properties of these materials can be widely modified, with a wide range of adsorption capacity for different heavy metal ions varying between 2.3 and 2240 mg/g. The possibility of developing new hydrogels with improved sorption performances is also discussed in the review, with the aim of improving their effective application in real scenarios, indicating future directions in the field.

ESKEMAP: exact sketch-based read mapping

BACKGROUND

Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a "similar sequence". Traditionally, "similar sequence" was defined as having a high alignment score and read mappers were viewed as heuristic solutions to this well-defined problem. For sketch-based mappers, however, there has not been a problem formulation to capture what problem an exact sketch-based mapping algorithm should solve. Moreover, there is no sketch-based method that can find all possible mapping positions for a read above a certain score threshold.

RESULTS

In this paper, we formulate the problem of read mapping at the level of sequence sketches. We give an exact dynamic programming algorithm that finds all hits above a given similarity threshold. It runs in O ( | t | + | p | + ℓ 2 ) time and O ( ℓ log ℓ ) space, where |t| is the number of k -mers inside the sketch of the reference, |p| is the number of k -mers inside the read's sketch and ℓ is the number of times that k -mers from the pattern sketch occur in the sketch of the text. We evaluate our algorithm's performance in mapping long reads to the T2T assembly of human chromosome Y, where ampliconic regions make it desirable to find all good mapping positions. For an equivalent level of precision as minimap2, the recall of our algorithm is 0.88, compared to only 0.76 of minimap2.

Carnosic Acid Inhibits Herpes Simplex Virus Replication by Suppressing Cellular ATP Synthesis

Acquiring resistance against antiviral drugs is a significant problem in antimicrobial therapy. In order to identify novel antiviral compounds, the antiviral activity of eight plants indigenous to the southern region of Hungary against herpes simplex virus-2 (HSV-2) was investigated. The plant extracts and the plant compound carnosic acid were tested for their effectiveness on both the extracellular and intracellular forms of HSV-2 on Vero and HeLa cells. HSV-2 replication was measured by a direct quantitative PCR (qPCR). Among the tested plant extracts, Salvia rosmarinus (S. rosmarinus) exhibited a 90.46% reduction in HSV-2 replication at the 0.47 μg/mL concentration. Carnosic acid, a major antimicrobial compound found in rosemary, also demonstrated a significant dose-dependent inhibition of both extracellular and intracellular forms of HSV-2. The 90% inhibitory concentration (IC90) of carnosic acid was between 25 and 6.25 μg/mL. Proteomics and high-resolution respirometry showed that carnosic acid suppressed key ATP synthesis pathways such as glycolysis, citrate cycle, and oxidative phosphorylation. Inhibition of oxidative phosphorylation also suppressed HSV-2 replication up to 39.94-fold. These results indicate that the antiviral action of carnosic acid includes the inhibition of ATP generation by suppressing key energy production pathways. Carnosic acid holds promise as a potential novel antiviral agent against HSV-2.

Engineering Cell Instructive Microenvironments for In Vitro Replication of Functional Barrier Organs

Multicellular organisms exhibit synergistic effects among their components, giving rise to emergent properties crucial for their genesis and overall functionality and survival. Morphogenesis involves and relies upon intricate and biunivocal interactions among cells and their environment, that is, the extracellular matrix (ECM). Cells secrete their own ECM, which in turn, regulates their morphogenetic program by controlling time and space presentation of matricellular signals. The ECM, once considered passive, is now recognized as an informative space where both biochemical and biophysical signals are tightly orchestrated. Replicating this sophisticated and highly interconnected informative media in a synthetic scaffold for tissue engineering is unattainable with current technology and this limits the capability to engineer functional human organs in vitro and in vivo. This review explores current limitations to in vitro organ morphogenesis, emphasizing the interplay of gene regulatory networks, mechanical factors, and tissue microenvironment cues. In vitro efforts to replicate biological processes for barrier organs such as the lung and intestine, are examined. The importance of maintaining cells within their native microenvironmental context is highlighted to accurately replicate organ-specific properties. The review underscores the necessity for microphysiological systems that faithfully reproduce cell-native interactions, for advancing the understanding of developmental disorders and disease progression.

GradHC: highly reliable gradual hash-based clustering for DNA storage systems

MOTIVATION

As data storage challenges grow and existing technologies approach their limits, synthetic DNA emerges as a promising storage solution due to its remarkable density and durability advantages. While cost remains a concern, emerging sequencing and synthetic technologies aim to mitigate it, yet introduce challenges such as errors in the storage and retrieval process. One crucial task in a DNA storage system is clustering numerous DNA reads into groups that represent the original input strands.

RESULTS

In this paper, we review different methods for evaluating clustering algorithms and introduce a novel clustering algorithm for DNA storage systems, named Gradual Hash-based clustering (GradHC). The primary strength of GradHC lies in its capability to cluster with excellent accuracy various types of designs, including varying strand lengths, cluster sizes (including extremely small clusters), and different error ranges. Benchmark analysis demonstrates that GradHC is significantly more stable and robust than other clustering algorithms previously proposed for DNA storage, while also producing highly reliable clustering results.

AVAILABILITY AND IMPLEMENTATION

https://github.com/bensdvir/GradHC.

Deciphering the role of PGRMC2 in the human endometrium during the menstrual cycle and in vitro decidualization using an in vitro approach

STUDY QUESTION

What is the human endometrial non-classical progesterone receptor (PGR) membrane component 2 (PGRMC2) expression pattern throughout the menstrual cycle and what role does it play during decidualization?

SUMMARY ANSWER

Endometrial PGRMC2 expression fluctuates during the human menstrual cycle and is abundantly expressed in human endometrial stromal cells (hEnSCs) during in vitro decidualization, process where PGRMC2 is involved in embryo implantation-related pathways.

WHAT IS KNOWN ALREADY

The endometrial response to progesterone is mediated by the classical and non-classical PGRs. We previously demonstrated that PGR membrane component 1 (PGRMC1) is critical for endometrial function, embryo implantation, and future placentation, however, the role(s) of PGRMC2, which is structurally similar to PGRMC1, have not been studied in the human endometrium.

STUDY DESIGN, SIZE, DURATION

This prospective study comprehensively evaluated the endometrial expression of PGRMC2 throughout the human menstrual cycle and during in vitro decidualization of hEnSCs (isolated from 77 endometrial biopsies that were collected from 66 oocyte donors), using immunohistochemistry, RT-qPCR, western blot, transcriptomic, and proteomic analyses. In addition, functional analysis was carried out to validate the implication of PGRMC2 in hEnSCs during embryo invasion using an in vitro outgrowth model.

PARTICIPANTS/MATERIALS, SETTING, METHODS

In vitro decidualization of hEnSCs was induced using co-treatment with cAMP and medroxyprogesterone 17-acetate progestin, and evaluated by measuring prolactin by ELISA and F-actin immunostaining. RT-qPCR was employed to compare expression with other PGRs. To reveal the function of PGRMC2 during the decidualization process, we specifically knocked down PGRMC2 with siRNAs and performed RNA-seq and quantitative proteomics techniques (SWATH-MS). The common differentially expressed genes (DEGs) and proteins (DEPs) were considered for downstream functional enrichment analysis. Finally, to verify its implication in the trophoblast invasion, an outgrowth model was carried out where hEnSCs with silenced PGRMC2 were co-cultured with human trophoblastic spheroids (JEG-3) following in vitro decidualization.

MAIN RESULTS AND THE ROLE OF CHANCE

In contrast to PGRMC1 and classical PGRs, endometrial PGRMC2 gene expression was significantly lower during the late- versus mid-secretory phase (P < 0.05). Accordingly, the elevated PGRMC2 protein abundance observed in the endometrial epithelial glands throughout the menstrual cycle dropped in the late secretory phase, when abundance decreased in all endometrial compartments. Nevertheless, PGRMC2 protein increased during the mid-secretory phase in stromal and glandular cells, and PGRMC2 mRNA (P < 0.0001) and protein (P < 0.001) levels were significantly enhanced in the membranes/organelles of decidualized hEnSCs, compared to non-decidualized hEnSCs. Notably, PGRMC1 and PGRMC2 mRNA were significantly more abundant than classical PGRs throughout menstrual cycle phases and in decidualized and non-decidualized hEnSCs (P < 0.05). RNA-seq and proteomics data revealed 4687 DEGs and 28 DEPs, respectively, in decidualized hEnSCs after PGRMC2 silencing. While functional enrichment analysis showed that the 2420 upregulated genes were mainly associated with endoplasmic reticulum function, vesicular transport, morphogenesis, angiogenesis, cell migration, and cell adhesion, the 2267 downregulated genes were associated with aerobic respiration and protein biosynthesis. The protein enrichment analysis showed that 4 upregulated and 24 downregulated proteins were related to aerobic respiration, cellular response, metabolism, localization of endoplasmic reticulum proteins, and ribonucleoside biosynthesis routes. Finally, PGRMC2 knockdown significantly compromised the ability of the decidualized hEnSCs to support trophoblast expansion in an outgrowth model (P < 0.05).

LARGE-SCALE DATA

Transcriptomic data are available via NCBI's Gene Expression Omnibus (GEO) under GEO Series accession number GSE251843 and proteomic data via ProteomeXchange with identifier PXD048494.

LIMITATIONS, REASONS FOR CAUTION

The functional analyses were limited by the discrete number of human endometrial biopsies. A larger sample size is required to further investigate the potential role(s) of PGRMC2 during embryo implantation and maintenance of pregnancy. Further, the results obtained in the present work should be taken with caution, as the use of a pure primary endometrial stromal population differentiated in vitro does not fully represent the heterogeneity of the endometrium in vivo, nor the paracrine communications occurring between the distinct endometrial cell types.

WIDER IMPLICATIONS OF THE FINDINGS

The repression of endometrial PGRMC2 during the late- versus mid-secretory phase, together with its overexpression during decidualization and multiple implications with embryo implantation not only highlighted the unknown roles of PGRMC2 in female reproduction but also the potential to exploit PGRMC2 signaling pathways to improve assisted reproduction treatments in the future.

STUDY FUNDING/COMPETING INTEREST(S)

This research was funded by Instituto de Salud Carlos III (ISCIII) granted to F.D. (PI20/00405 and PI23/00860), co-funded by the European Union. Y.M.-L. was supported by a predoctoral research grant from Generalitat Valenciana (ACIF/2019/262). R.G.-M. was supported by Generalitat Valenciana (CIAPOT/2022/15). P.d.C. was supported by a predoctoral grant for training in research into health (PFIS FI20/00086) from the Instituto de Salud Carlos III. I.D.-H. was supported by the Spanish Ministry of Science, Innovation and Universities (FPU18/01550). A.P. was supported by the Instituto de Salud Carlos III (PFIS FI18/00009). This research was also supported by IVI Foundation-RMA Global (1911-FIVI-103-FD). The authors declare no conflict of interest.

Epilepsy in Duchenne and Becker muscular dystrophies

OBJECTIVE

Duchenne and Becker muscular dystrophies (DMD and BMD) are dystrophinopathies caused by variants in DMD gene, resulting in reduced or absent dystrophin. These conditions, characterized by muscle weakness, also manifest central nervous system (CNS) comorbidities due to dystrophin expression in the CNS. Prior studies have indicated a higher prevalence of epilepsy in individuals with dystrophinopathy compared to the general population. Our research aimed to investigate epilepsy prevalence in dystrophinopathies and characterize associated electroencephalograms (EEGs) and seizures.

METHODS

We reviewed 416 individuals with dystrophinopathy, followed up at three centers between 2010 and 2023, to investigate the lifetime epilepsy prevalence and characterize EEGs and seizures in those individuals diagnosed with epilepsy. Associations between epilepsy and type of dystrophinopathy, genotype, and cognitive involvement were studied.

RESULTS

Our study revealed a higher epilepsy prevalence than the general population (1.4%; 95% confidence interval: 0.7-3.2%), but notably lower than previously reported in smaller dystrophinopathy cohorts. No significant differences were found in epilepsy prevalence between DMD and BMD or based on underlying genotypes. Cognitive impairment was not found to be linked to higher epilepsy rates. The most prevalent epilepsy types in dystrophinopathies resembled those observed in the broader pediatric population, with most individuals effectively controlled through monotherapy.

INTERPRETATION

The actual epilepsy prevalence in dystrophinopathies may be markedly lower than previously estimated, possibly half or even less. Our study provides valuable insights into the epilepsy landscape in individuals with dystrophinopathy, impacting medical care, especially for those with concurrent epilepsy.

Longitudinal cerebral perfusion in presymptomatic genetic frontotemporal dementia: GENFI results

INTRODUCTION

Effective longitudinal biomarkers that track disease progression are needed to characterize the presymptomatic phase of genetic frontotemporal dementia (FTD). We investigate the utility of cerebral perfusion as one such biomarker in presymptomatic FTD mutation carriers.

METHODS

We investigated longitudinal profiles of cerebral perfusion using arterial spin labeling magnetic resonance imaging in 42 C9orf72, 70 GRN, and 31 MAPT presymptomatic carriers and 158 non-carrier controls. Linear mixed effects models assessed perfusion up to 5 years after baseline assessment.

RESULTS

Perfusion decline was evident in all three presymptomatic groups in global gray matter. Each group also featured its own regional pattern of hypoperfusion over time, with the left thalamus common to all groups. Frontal lobe regions featured lower perfusion in those who symptomatically converted versus asymptomatic carriers past their expected age of disease onset.

DISCUSSION

Cerebral perfusion is a potential biomarker for assessing genetic FTD and its genetic subgroups prior to symptom onset.

HIGHLIGHTS

Gray matter perfusion declines in at-risk genetic frontotemporal dementia (FTD). Regional perfusion decline differs between at-risk genetic FTD subgroups . Hypoperfusion in the left thalamus is common across all presymptomatic groups. Converters exhibit greater right frontal hypoperfusion than non-converters past their expected conversion date. Cerebral hypoperfusion is a potential early biomarker of genetic FTD.

Fibrosis and expression of extracellular matrix proteins in human interventricular septum in aortic valve stenosis and regurgitation

Valvular heart disease leads to ventricular pressure and/or volume overload. Pressure overload leads to fibrosis, which might regress with its resolution, but the limits and details of this reverse remodeling are not known. To gain more insight into the extent and nature of cardiac fibrosis in valve disease, we analyzed needle biopsies taken from the interventricular septum of patients undergoing surgery for valve replacement focusing on the expression and distribution of major extracellular matrix protein involved in this process. Proteomic analysis performed using mass spectrometry revealed an excellent correlation between the expression of collagen type I and III, but there was little correlation with the immunohistochemical staining performed on sister sections, which included antibodies against collagen I, III, fibronectin, sarcomeric actin, and histochemistry for wheat germ agglutinin. Surprisingly, the immunofluorescence intensity did not correlate significantly with the gold standard for fibrosis quantification, which was performed using Picrosirius Red (PSR) staining, unless multiplexed on the same tissue section. There was also little correlation between the immunohistochemical markers and pressure gradient severity. It appears that at least in humans, the immunohistochemical pattern of fibrosis is not clearly correlated with standard Picrosirius Red staining on sister sections or quantitative proteomic data, possibly due to tissue heterogeneity at microscale, comorbidities, or other patient-specific factors. For precise correlation of different types of staining, multiplexing on the same section is the best approach.

Liquid Crystalline Network Microstructures for Stimuli Responsive Labels with Multi-Level Encryption

Two-photon direct laser writing enables the fabrication of shape-changing microstructures that can be exploited in stimuli responsive micro-robotics and photonics. The use of Liquid Crystalline Networks (LCN) allows to realize 3D micrometric objects that can contract along a specific direction in response to stimuli, such as temperature or light. In this paper, the fabrication of free-standing LCN microstructures is demonstrated as graphical units of a smart tag for simple physical and optical encryption. Using an array of identical pixels, information can be hidden to the observer and revealed only upon application of a specific stimulus. The reading mechanism is based on the shape-change of each pixel under stimuli and their color that combine together in a two-level encryption label. Once the stimulus is removed, the pixels recover their original shape and the message remains completely hidden. Therefore, an opto-mechanical equivalent of an "invisible ink" is realized. This new concept paves the way for introducing enhanced functionalities in smart micro-systems within a single lithography step, spanning from storage devices with physical encryption to complex motion actuators.

Increased density of conspecifics caused niche contraction in a multispecific passerine assemblage

Competition is a prominent mechanism driving population dynamics and structuring community assemblage, which can be investigated by linking shifts in species' ecological niche and the densities of sympatric species because the ecological release from competitive constraints is a density-dependent process. In this work we determine how a steppe passerine community segregates their ecological niches and evaluate the role of competition in inducing changes in the ecological niche of species. We built multidimensional ecological niches (with Gaussian kernel density estimators) using data on the habitat features used by 10 bird species collected from seven sites in the natural steppes of Central Spain over 2 consecutive years. We computed distance and niche similarity metrics to explore the ecological niche partitioning of the bird community. Next, we ran multivariate linear regression models to evaluate the effects of conspecific and heterospecific density (as proxies of intraspecific and interspecific competition, respectively) on niche breadth and/or position of the three most abundant species. We found low niche overlap in the community assemblage but varying levels of niche similarity among pairs of species, which could increase the likelihood of current competition operating in the community. However, we found no effect of heterospecific density on niche breadth or position, although conspecific density was negatively related to niche breadth. Contrary to predictions of competition theory, increased density of conspecifics caused niche contraction. Our results from a multispecies system contribute to advanced knowledge of the biotic mechanisms structuring wildlife communities within the framework of ecological niche theory.

Cannabis profiling of seized samples: An intra-location variability study using gas chromatography-mass spectrometry profiles and multivariate data analysis

Yearly, cannabis belongs to the most seized drugs worldwide. During judicial investigations, illicit cannabis profiling can be performed to compare seized herbal material. However, comparison is challenging because of the natural heterogeneity of the psychoactive crop. Gas chromatography-mass spectrometry (GC-MS) profiles, consisting of eight cannabinoids, were used to study the intra-location (within) and inter-location (between) variabilities. Decision thresholds were derived from the 95% and 99% confidence limits, applying Pearson correlation coefficients for the intra-location samples. The false negatives and false positives (FPs) determined the discriminative power of different pretreatments applied to obtain the lowest FP error rate possible. Initially, a 97 samples data set was used and with log transformation as pretreatment, a decrease in FPs from 38% and 45% FPs to 17% and 22%, for both confidence limits, respectively, was seen relative to internal standard normalization that was used as reference. An additional intra-plantation variability study with 130 samples verified whether the initial model contained sufficient within-location information, but this was not the case. Hence, a combined data matrix was constructed with all seized samples. Log transformation provided the best FP results for both limits, that is, an improvement from 58% and 64% to 21% and 26%, respectively, was seen. The representativeness of these 'linked' thresholds was demonstrated using both cross-validation and an external set, for which similar FP results as for the calibration set were obtained. By applying data pretreatment, a significant improvement was observed to distinguish seized samples. However, the FP rate is still not at an acceptable level to defend in court.

Artificial intelligence in endocrinology: a comprehensive review

BACKGROUND AND AIM

Artificial intelligence (AI) has emerged as a promising technology in the field of endocrinology, offering significant potential to revolutionize the diagnosis, treatment, and management of endocrine disorders. This comprehensive review aims to provide a concise overview of the current landscape of AI applications in endocrinology and metabolism, focusing on the fundamental concepts of AI, including machine learning algorithms and deep learning models.

METHODS

The review explores various areas of endocrinology where AI has demonstrated its value, encompassing screening and diagnosis, risk prediction, translational research, and "pre-emptive medicine". Within each domain, relevant studies are discussed, offering insights into the methodology and main findings of AI in the treatment of different pathologies, such as diabetes mellitus and related disorders, thyroid disorders, adrenal tumors, and bone and mineral disorders.

RESULTS

Collectively, these studies show the valuable contributions of AI in optimizing healthcare outcomes and unveiling new understandings of the intricate mechanisms underlying endocrine disorders. Furthermore, AI-driven approaches facilitate the development of precision medicine strategies, enabling tailored interventions for patients based on their individual characteristics and needs.

CONCLUSIONS

By embracing AI in endocrinology, a future can be envisioned where medical professionals and AI systems synergistically collaborate, ultimately enhancing the lives of individuals affected by endocrine disorders.

Diet Quality and Multimorbidity in Older Adults: A Prospective Cohort Study

BACKGROUND

The role of diet quality in the accumulation of multiple chronic conditions is mostly unknown. This study examined diet quality in association with the number of chronic conditions and the rate of multimorbidity development among community-dwelling older adults.

METHODS

We used data from 2 784 adults aged ≥65 years from the Seniors-ENRICA 2 cohort. Diet quality was assessed at baseline (2015-17) with the Alternate Healthy Eating Index-2010 (AHEI-2010) and the Mediterranean Diet Adherence Screener (MEDAS). Information on medical diagnoses was obtained from electronic clinical records up to 2021.

RESULTS

Higher adherence to the AHEI-2010 was associated with a lower number of total chronic conditions (β [95% CI] quartile 4 vs 1: -0.57 [-0.86 to 0.27], p trend < .001] and cardiometabolic conditions (-0.30 [-0.44 to -0.17], p trend < .001) at baseline, while higher adherence to the MEDAS was associated with a lower number of total chronic conditions (-0.30 [-0.58 to -0.02], p trend = .01) and neuropsychiatric and neurodegenerative conditions (-0.09 [-0.17 to -0.01], p trend = .01). After a median follow-up of 5.2 years (range: 0.1-6.1 years) higher adherence to the AHEI-2010 was associated with a lower increase in chronic conditions (β [95% confidence interval] quartile 4 vs 1: -0.16 [-0.30 to -0.01], p trend = .04) and with lower rate of chronic disease accumulation.

CONCLUSIONS

Higher diet quality, as measured by the AHEI-2010, was associated with a lower number of chronic health conditions and a lower rate of multimorbidity development over time.

Small RNA-seq and clinical evaluation of tRNA-derived fragments in multiple myeloma: Loss of mitochondrial i-tRFHisGTG results in patients' poor treatment outcome

Despite the substantial progress in multiple myeloma (MM) therapy nowadays, treatment resistance and disease relapse remain major clinical hindrances. Herein, we have investigated tRNA-derived fragment (tRF) profiles in MM and precursor stages (smoldering MM/sMM; monoclonal gammopathy of undetermined significance/MGUS), aiming to unveil potential MM-related tRFs in ameliorating MM prognosis and risk stratification. Small RNA-seq was performed to profile tRFs in bone marrow CD138+ plasma cells, revealing the significant deregulation of the mitochondrial internal tRFHisGTG (mt-i-tRFHisGTG) in MM versus sMM/MGUS. The screening cohort of the study consisted of 147 MM patients, and mt-i-tRFHisGTG levels were quantified by RT-qPCR. Disease progression was assessed as clinical end-point for survival analysis, while internal validation was performed by bootstrap and decision curve analyses. Screening cohort analysis highlighted the potent association of reduced mt-i-tRFHisGTG levels with patients' bone disease (p = 0.010), osteolysis (p = 0.023) and with significantly higher risk for short-term disease progression following first-line chemotherapy, independently of patients' clinical data (HR = 1.954; p = 0.036). Additionally, mt-i-tRFHisGTG-fitted multivariate models led to superior risk stratification of MM patients' treatment outcome and prognosis compared to disease-established markers. Notably, our study highlighted mt-i-tRFHisGTG loss as a powerful independent indicator of post-treatment progression of MM patients, leading to superior risk stratification of patients' treatment outcome.

Higher risk of cerebral palsy, seizures/epilepsy, visual- and hearing impairments, cancer, injury and child abuse in children with congenital anomalies: Data from the EUROlinkCAT study

AIM

The aim is to examine the risk of cerebral palsy, seizures/epilepsy, visual- and hearing impairments, cancer, injury/poisoning and child abuse in children with and without a congenital anomaly up to age 5 and 10 years.

METHODS

This is a population-based data linkage cohort study linking information from the European Surveillance of Congenital Anomalies network (EUROCAT) and birth registries to hospital discharge databases. We included 91 504 live born children with major congenital anomalies born from 1995 to 2014 from nine EUROCAT registries in five countries and 1 960 727 live born children without congenital anomalies (reference children). Prevalence and relative risk (RR) were estimated for each of the co-morbidities using Kaplan-Meier survival estimates.

RESULTS

Children with congenital anomalies had higher risks of the co-morbidities than reference children. The prevalences in the reference children were generally very low. The RR was 13.8 (95% CI 12.5-15.1) for cerebral palsy, 2.5 (95% CI 2.4-2.6) for seizures/epilepsy, 40.8 (95% CI 33.2-50.2) for visual impairments, 10.0 (95% CI 9.2-10.9) for hearing loss, 3.6 (95% CI 3.2-4.2) for cancer, 1.5 (95% CI 1.4-1.5) for injuries/poisoning and 2.4 (95% CI 1.7-3.4) for child abuse.

CONCLUSION

Children with congenital anomalies were more likely to be diagnosed with the specified co-morbidities compared to reference children.

Role of calcium integrin-binding protein 1 in the mechanobiology of the liver endothelium

Liver sinusoidal endothelial cells (LSECs) dysfunction is a key process in the development of chronic liver disease (CLD). Progressive scarring increases liver stiffness in a winch-like loop stimulating a dysfunctional liver cell phenotype. Cellular stretching is supported by biomechanically modulated molecular factors (BMMFs) that can translocate into the cytoplasm to support mechanotransduction through cytoskeleton remodeling and gene transcription. Currently, the molecular mechanisms of stiffness-induced LSECs dysfunction remain largely unclear. Here we propose calcium- and integrin-binding protein 1 (CIB1) as BMMF with crucial role in LSECs mechanobiology in CLD. CIB1 expression and translocation was characterized in healthy and cirrhotic human livers and in LSECs cultured on polyacrylamide gels with healthy and cirrhotic-like stiffnesses. Following the modulation of CIB1 with siRNA, the transcriptome was scrutinized to understand downstream effects of CIB1 downregulation. CIB1 expression is increased in LSECs in human cirrhosis. In vitro, CIB1 emerges as an endothelial BMMF. In human umbilical vein endothelial cells and LSECs, CIB1 expression and localization are modulated by stiffness-induced trafficking across the nuclear membrane. LSECs from cirrhotic liver tissue both in animal model and human disease exhibit an increased amount of CIB1 in cytoplasm. Knockdown of CIB1 in LSECs exposed to high stiffness improves LSECs phenotype by regulating the intracellular tension as well as the inflammatory response. Our results demonstrate that CIB1 is a key factor in sustaining cellular tension and stretching in response to high stiffness. CIB1 downregulation ameliorates LSECs dysfunction, enhancing their redifferentiation, and reducing the inflammatory response.

Tuning Fluorescence and Singlet Oxygen Quantum Yields of Subporphyrazines by Axial Functionalization

The axial functionalization of Subporphyrazines (SubPzs) with unreported alkoxy groups, carboxy and carboperoxy rests, as well as sulfanyl, aryl and amino groups, forming B-O, B-S, B-C, and B-N bonds, respectively, has been investigated. The studied oxygen nucleophiles include aromatic and sterically demanding aliphatic alcohols, along with carboxylic acids and peracids. In general, direct substitution of the chloro-SubPz by oxygen nucleophiles of diverse nature proceeds smoothly, with yields of the isolated alkoxy and carboxy-substituted SubPzs ranging from 49 to 100 %. Conversely, direct substitution with sulphur, carbon and nitrogen nucleophiles do not afford the corresponding substituted SubPzs. In these cases, a stepwise procedure involving an axial triflate-SubPz intermediate was employed, affording only the phenyl-SubPz in 8 % yield. The major compound under these conditions was the unreported SubPz μ-oxo dimer, presumably arising from substitution of the triflate-SubPz by the in situ generated hydroxy-SubPz. This result indicates a quite low reactivity of the TfO-SubPz intermediate with carbon, sulphur and nitrogen nucleophiles. All SubPzs prepared in this work exhibited fluorescence at 510-515 nm with quantum yields ranging from 0.1 to 0.24. Additionally, all SubPzs generated singlet oxygen, with ΦΔ values ranging from 0.15 to 0.57, which show no apparent correlation with the axial substituents.

Overcoming constraints to measuring O2 diffusivity and consumption of intact roots

A method using O2 microsensors enables detailed quantification of respiratory O2 consumption and diffusive resistance to O2 of individual root cell layers.

Phytohormones in a universe of regulatory metabolites: lessons from jasmonate

Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells. Increasing evidence indicates that currently recognized plant hormones are part of a larger group of regulatory metabolites that have acquired signaling properties during the evolution of land plants. This rich assortment of chemical signals reflects the tremendous diversity of plant secondary metabolism, which offers evolutionary solutions to the daunting challenges of sessility and other unique aspects of plant biology. A major gap in our current understanding of plant regulatory metabolites is the lack of insight into the direct targets of these compounds. Here, we illustrate the blurred distinction between classical phytohormones and other bioactive metabolites by highlighting the major scientific advances that transformed the view of jasmonate from an interesting floral scent to a potent transcriptional regulator. Lessons from jasmonate research generally apply to other phytohormones and thus may help provide a broad understanding of regulatory metabolite-protein interactions. In providing a framework that links small-molecule diversity to transcriptional plasticity, we hope to stimulate future research to explore the evolution, functions, and mechanisms of perception of a broad range of plant regulatory metabolites.

Potential effects of a mobile stroke unit on time to treatment and outcome in patients treated with thrombectomy or thrombolysis: A Danish-German cross-border analysis

BACKGROUND AND PURPOSE

A mobile stroke unit (MSU) reduces delays in stroke treatment by allowing thrombolysis on board and avoiding secondary transports. Due to the beneficial effect in comparison to conventional emergency medical services, current guidelines recommend regional evaluation of MSU implementation.

METHODS

In a descriptive study, current pathways of patients requiring a secondary transport for mechanical thrombectomy were reconstructed from individual patient records within a Danish (n = 122) and an adjacent German region (n = 80). Relevant timestamps included arrival times (on site, primary hospital, thrombectomy centre) as well as the initiation of acute therapy. An optimal MSU location for each region was determined. The resulting time saving was translated into averted disability-adjusted life years (DALYs).

RESULTS

For each region, the optimal MSU location required a median driving time of 35 min to a stroke patient. Time savings in the German region (median [Q1; Q3]) were 7 min (-15; 31) for thrombolysis and 35 min (15; 61) for thrombectomy. In the Danish region, the corresponding time savings were 20 min (8; 30) and 43 min (25; 66). Assuming 28 thrombectomy cases and 52 thrombolysis cases this would translate to 9.4 averted DALYs per year justifying an annual net MSU budget of $0.8M purchasing power parity dollars (PPP-$) in the German region. In the Danish region, the MSU would avert 17.7 DALYs, justifying an annual net budget of PPP-$1.7M.

CONCLUSION

The effects of an MSU can be calculated from individual patient pathways and reflect differences in the hospital infrastructure between Denmark and Germany.

Study on the Properties of PLA- and PP-Based Films for Food Applications Incorporating Orange Peel Extract from Agricultural by-Products

The aim of this work was to develop active packaging based on polypropylene (PP) and polylactic acid (PLA) matrices using a high value by-product extracted from orange peel as an active compound for food packaging applications. Different films with and without orange peel extract (OPE) based on PP and PLA were obtained via cast extrusion and characterized in terms of their mechanical, thermal, optical, and sealing properties. The films obtained were transparent, but when OPE was incorporated, the transmittance spectrum decreased, causing slight coloration. Mechanical properties were affected by the incorporation of OPE, as elongation at break and tensile strength increased in the cross-direction of the PP film, although the main differences found were related to the polymer itself. In addition, sealing strength also increased via the incorporation of OPE in the PP matrix. However, thermal properties were not affected by OPE in the PP matrix but slightly decreased stability in PLA. Regarding antimicrobial activity in in vitro studies, no inhibition of the growth of Listeria innocua, Saccharomyces cerevisiae, Aspergillus niger, or Escherichia coli was observed. Finally, antioxidant activity was observed in in vitro studies with 2,2-Diphenyl-1picrylhydrazyl (DPPH) radical. The results of this study showed that the obtention of materials with OPE incorporated into the PLA and PP matrix is feasible. The new materials obtained can be used for applications of oxidation-sensitive fresh products.

Cationic Azobenzenes as Light-Responsive Crosslinkers for Alginate-Based Supramolecular Hydrogels

Azobenzene photoswitches are fundamental components in contemporary approaches aimed at light-driven control of intelligent materials. Significant endeavors are directed towards enhancing the light-triggered reactivity of azobenzenes for such applications and obtaining water-soluble molecules able to act as crosslinkers in a hydrogel. Here, we report the rational design and the synthesis of azobenzene/alginate photoresponsive hydrogels endowed with fast reversible sol-gel transition. We started with the synthesis of three cationic azobenzenes (AZOs A, B, and C) and then incorporated them in sodium alginate (SA) to obtain photoresponsive supramolecular hydrogels (SMHGs). The photoresponsive properties of the azobenzenes were investigated by UV-Vis and 1H NMR spectroscopy. Upon irradiation with 365 nm UV light, the azobenzenes demonstrated efficient trans-to-cis isomerization, with complete isomerization occurring within seconds. The return to the trans form took several hours, with AZO C exhibiting the fastest return, possibly due to higher trans isomer stability. In the photoresponsive SMHGs, the minimum gelation concentration (MGC) of azobenzenes was determined for different compositions, indicating that small amounts of azobenzenes could induce gel formation, particularly in 5 wt% SA. Upon exposure to 365 nm UV light, the SMHGs exhibited reversible gel-sol transitions, underscoring their photoresponsive nature. This research offers valuable insights into the synthesis and photoresponsive properties of cationic, water-soluble azobenzenes, as well as their potential application in the development of photoresponsive hydrogels.

Use of Unmanned Surface Vehicles (USVs) in Water Chemistry Studies

Unmanned surface vehicles (USVs) equipped with integrated sensors are a tool valuable to several monitoring strategies, offering enhanced temporal and spatial coverage over specific timeframes, allowing for targeted examination of sites or events of interest. The elaboration of environmental monitoring programs has relied so far on periodic spot sampling at specific locations, followed by laboratory analysis, aiming at the evaluation of water quality at a catchment scale. For this purpose, automatic telemetric stations for specific parameters have been installed by the Institute of Marine Biological Resources and Inland Waters of Hellenic Centre for Marine Research (IMBRIW-HCMR) within several Greek rivers and lakes, providing continuous and temporal monitoring possibilities. In the present work, USVs were deployed by the Athens Water and Sewerage Company (EYDAP) as a cost-effective tool for the environmental monitoring of surface water bodies of interest, with emphasis on the spatial fluctuations of chlorophyll α, electrical conductivity, dissolved oxygen and pH, observed in Koumoundourou Lake and the rivers Acheloos, Asopos and Kifissos. The effectiveness of an innovative heavy metal (HM) system installed in the USV for the in situ measurements of copper and lead was also evaluated herewith. The results obtained demonstrate the advantages of USVs, setting the base for their application in real-time monitoring of chemical parameters including metals. Simultaneously, the requirements for accuracy and sensitivity improvement of HM sensors were noted, in order to permit full exploitation of USVs' capacities.

Advanced Detection of Failed LEDs in a Short Circuit for Automotive Lighting Applications

This paper addresses the issue of LED short-circuit fault detection in signaling and lighting systems in the automotive industry. The conventional diagnostic method commonly implemented in newer vehicles relies on measuring the voltage drop across different LED branches and comparing it with threshold values indicating faults caused by open circuits or LED short circuits. With this algorithm, detecting cases of a few LEDs short-circuited within a branch, particularly a single malfunctioning LED, is particularly challenging. In this work, two easily implementable algorithms are proposed to address this issue within the vehicle's control unit. One is based on a mathematical prediction model, while the other utilizes a neural network. The results obtained offer a 100% LED short-circuit fault detection rate in the majority of analyzed cases, representing a significant improvement over the conventional method, even in scenarios involving a single malfunctioning LED within a branch. Additionally, the neural network-based model can accurately predict the number of failed LEDs.

Absorption and Fluorescence Emission Investigations on Supramolecular Assemblies of Tetrakis-(4-sulfonatophenyl)porphyrin and Graphene Quantum Dots

The one-pot synthesis of N-doped graphene quantum dots (GQDs), capped with a positively charged polyamine (trien), has been realized through a microwave-assisted pyrolysis on solid L-glutamic acid and trien in equimolar amounts. The resulting positively charged nanoparticles are strongly emissive in aqueous solutions and are stable for months. The interaction with the anionic tetrakis(4-sulphonatophenyl)porphyrin (TPPS4) has been investigated at neutral and mild acidic pH using a combination of UV/vis absorption spectroscopy together with static and time-resolved fluorescence emission. At pH = 7, the experimental evidence points to the formation of a supramolecular adduct mainly stabilized by electrostatic interactions. The fluorescence emission of the porphyrin is substantially quenched while GQDs remain still emissive. On decreasing the pH, protonation of TPPS4 leads to formation of porphyrin J-aggregates through the intermediacy of the charged quantum dots.

Comprehensive Two-Dimensional Gas Chromatography with a TOF MS Detector-An Effective Tool to Trace the Signature of Grape Varieties

Varietal volatile compounds are characteristic of each variety of grapes and come from the skins of the grapes. This work focuses on the development of a methodology for the analysis of free compounds in grapes from Trincadeira, Cabernet Sauvignon, Syrah, Castelão and Tinta Barroca from the 2021 and 2022 harvests, using HS-SPME-GC × GC-TOFMS. To achieve this purpose, a previous optimization step of sample preparation was implemented, with the optimized conditions being 4 g of grapes, 2 g of NaCl, and 2 mL of H2O. The extraction conditions were also optimized, and it was observed that performing the extraction for 40 min at 60 °C was the best for identifying more varietal compounds. The fiber used was a triple fiber of carboxen/divinylbenzene/polydimethylsiloxane (CAR/DVB/PDMS). In addition to the sample preparation, the analytical conditions were also optimized, enabling the adequate separation of analytes. Using the optimized methodology, it was possible to identify fifty-two free volatile compounds, including seventeen monoterpenes, twenty-eight sesquiterpenes, and seven C13-norisoprenoids. It was observed that in 2021, more free varietal volatile compounds were identifiable compared to 2022. According to the results obtained through a linear discriminant analysis (LDA), the differences in volatile varietal signature are observed both among different grape varieties and across different years.

Psammaplin A and Its Analogs Attenuate Oxidative Stress in Neuronal Cells through Peroxisome Proliferator-Activated Receptor γ Activation

Psammaplins are sulfur containing bromotyrosine alkaloids that have shown antitumor activity through the inhibition of class I histone deacetylases (HDACs). The cytotoxic properties of psammaplin A (1), the parent compound, are related to peroxisome proliferator-activated receptor γ (PPARγ) activation, but the mechanism of action of its analogs psammaplin K (2) and bisaprasin (3) has not been elucidated. In this study, the protective effects against oxidative stress of compounds 1-3, isolated from the sponge Aplysinella rhax, were evaluated in SH-SY5Y cells. The compounds improved cell survival, recovered glutathione (GSH) content, and reduced reactive oxygen species (ROS) release at nanomolar concentrations. Psammaplins restored mitochondrial membrane potential by blocking mitochondrial permeability transition pore opening and reducing cyclophilin D expression. This effect was mediated by the capacity of 1-3 to activate PPARγ, enhancing gene expression of the antioxidant enzymes catalase, nuclear factor E2-related factor 2 (Nrf2), and glutathione peroxidase. Finally, HDAC3 activity was reduced by 1-3 under oxidative stress conditions. This work is the first description of the neuroprotective activity of 1 at low concentrations and the mechanism of action of 2 and 3. Moreover, it links for the first time the previously described effects of 1 in HDAC3 and PPARγ signaling, opening a new research field for the therapeutic potential of this compound family.

Carbonic Anhydrases: Different Active Sites, Same Metal Selectivity Rules

Carbonic anhydrases are mononuclear metalloenzymes catalyzing the reversible hydration of carbon dioxide in organisms belonging to all three domains of life. Although the mechanism of the catalytic reaction is similar, different families of carbonic anhydrases do not have a common ancestor nor do they exhibit significant resemblance in the amino acid sequence or the structure and composition of the metal-binding sites. Little is known about the physical principles determining the metal affinity and selectivity of the catalytic centers, and how well the native metal is protected from being dislodged by other metal species from the local environment. Here, we endeavor to shed light on these issues by studying (via a combination of density functional theory calculations and polarizable continuum model computations) the thermodynamic outcome of the competition between the native metal cation and its noncognate competitor in various metal-binding sites. Typical representatives of the competing cations from the cellular environments of the respective classes of carbonic anhydrases are considered. The calculations reveal how the Gibbs energy of the metal competition changes when varying the metal type, structure, composition, and solvent exposure of the active center. Physical principles governing metal competition in different carbonic anhydrase metal-binding sites are delineated.

Kinetic Assessment of Kraft and Thermally Upgraded Kraft Papers Aged in Five Alternative Dielectric Fluids

The lifespan of an electrical transformer, primarily determined by the condition of its solid insulation, is well known under various operating conditions when mineral oil is the coolant in these machines. However, there is a trend toward replacing this oil with biodegradable fluids, especially esters; therefore, an understanding of the ageing of solid insulation with these fluids is essential. Currently available data do not allow for the selection of the best ester among those available on the market, as each study applies different conditions, making it impossible to compare results. Thus, this paper analyses the degradation of Kraft and Thermally Upgraded Kraft papers with the following five most promising commercial esters: sunflower, rapeseed, soybean, palm, and synthetic. The materials underwent accelerated thermal ageing at 130, 150, and 170 °C, and the integrity of the papers was evaluated through their polymerisation degree and the obtaining of the degradation kinetic models. The wide range of materials studied in this work, which were subjected to the same treatments, allows for a comparison of the esters, revealing significant differences in the impact of the alternative fluids. Sunflower, rapeseed, and soybean esters provided the best paper protection, i.e., the degree of polymerisation of Kraft paper in the tests at 150 °C decreased by 71% with these fluids, compared to the 83% reduction with mineral oil, 79% reduction with palm ester, and 75% reduction with synthetic ester. Furthermore, different kinetic models were obtained to predict the degradation; it was concluded that the Emsley model provides the best fit. Additionally, it was found that the behaviour of a dielectric fluid with one type of paper cannot be extrapolated, which is only noticeable in broad-scope studies.

Rapid Compensation for Noisy Voluntary Movements in Adults with Primary Tic Disorders

BACKGROUND

It has been proposed that tics and premonitory urges in primary tic disorders (PTD), like Tourette syndrome, are a manifestation of sensorimotor noise. However, patients with tics show no obvious movement imprecision in everyday life. One reason could be that patients have strategies to compensate for noise that disrupts performance (ie, noise that is task-relevant).

OBJECTIVES

Our goal was to unmask effects of elevated sensorimotor noise on the variability of voluntary movements in patients with PTD.

METHODS

We tested 30 adult patients with PTD (23 male) and 30 matched controls in a reaching task designed to unmask latent noise. Subjects reached to targets whose shape allowed for variability either in movement direction or extent. This enabled us to decompose variability into task-relevant versus less task-relevant components, where the latter should be less affected by compensatory strategies than the former. In alternating blocks, the task-relevant target dimension switched, allowing us to explore the temporal dynamics with which participants adjusted movement variability to changes in task demands.

RESULTS

Both groups accurately reached to targets, and adjusted movement precision based on target shape. However, when task-relevant dimensions of the target changed, patients initially produced movements that were more variable than controls, before regaining precision after several reaches. This effect persisted across repeated changes in the task-relevant dimension across the experiment, and therefore did not reflect an effect of novelty, or differences in learning.

CONCLUSIONS

Our results suggest that patients with PTD generate noisier voluntary movements compared with controls, but rapidly compensate according to current task demands. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Effects of Environmental Enrichment on Exposure to Human-Relevant Mixtures of Endocrine Disrupting Chemicals in Zebrafish

Fish models used for chemical exposure in toxicological studies are normally kept in barren tanks without any structural environmental enrichment. Here, we tested the combined effects of environmental enrichment and exposure to two mixtures of endocrine disrupting chemicals (EDCs) in zebrafish. Firstly, we assessed whether developmental exposure to an EDC mixture (MIX G1) combined with rearing the fish in an enriched environment influenced behaviour later in life. This was evaluated using locomotion tracking one month after exposure, showing a significant interaction effect between enrichment and the MIX G1 exposure on the measured locomotion parameters. After three months, we assessed behaviour using custom-made behaviour tanks, and found that enrichment influenced swimming activity. Control fish from the enriched environment were more active than control fish from the barren environment. Secondly, we exposed adult zebrafish to a separate EDC mixture (MIX G0) after rearing them in a barren or enriched environment. Behaviour and hepatic mRNA expression for thyroid-related genes were assessed. There was a significant interaction effect between exposure and enrichment on swimming activity and an effect of environment on latency to approach the group of conspecifics, where enriched fish took more time to approach the group, possibly indicating that they were less anxious. Hepatic gene expression of a thyroid-related gene (thrb) was significantly affected by EDC exposure, while enrichment had no discernible impact on the expression of the measured genes. In conclusion, environmental enrichment is important to consider when studying the effects of EDCs in fish.