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.

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.

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.

Non-adherence to cardiometabolic medication as assessed by LC-MS/MS in urine and its association with kidney and cardiovascular outcomes in type 2 diabetes mellitus

AIMS/HYPOTHESIS

Non-adherence to medication is a frequent barrier in the treatment of patients with type 2 diabetes mellitus, potentially limiting the effectiveness of evidence-based treatments. Previous studies have mostly relied on indirect adherence measures to analyse outcomes based on adherence. The aim of this study was to use LC-MS/MS in urine-a non-invasive, direct and objective measure-to assess non-adherence to cardiometabolic drugs and analyse its association with kidney and cardiovascular outcomes.

METHODS

This cohort study includes 1125 participants from the PROVALID study, which follows patients with type 2 diabetes mellitus at the primary care level. Baseline urine samples were tested for 79 cardiometabolic drugs and metabolites thereof via LC-MS/MS. An individual was classified as totally adherent if markers for all drugs were detected, partially non-adherent when at least one marker for one drug was detected, and totally non-adherent if no markers for any drugs were detected. Non-adherence was then analysed in the context of cardiovascular (composite of myocardial infarction, stroke and cardiovascular death) and kidney (composite of sustained 40% decline in eGFR, sustained progression of albuminuria, kidney replacement therapy and death from kidney failure) outcomes.

RESULTS

Of the participants, 56.3% were totally adherent, 42.0% were partially non-adherent, and 1.7% were totally non-adherent to screened cardiometabolic drugs. Adherence was highest to antiplatelet and glucose-lowering agents and lowest to lipid-lowering agents. Over a median (IQR) follow-up time of 5.10 (4.12-6.12) years, worse cardiovascular outcomes were observed with non-adherence to antiplatelet drugs (HR 10.13 [95% CI 3.06, 33.56]) and worse kidney outcomes were observed with non-adherence to antihypertensive drugs (HR 1.98 [95% CI 1.37, 2.86]).

CONCLUSIONS/INTERPRETATION

This analysis shows that non-adherence to cardiometabolic drug regimens is common in type 2 diabetes mellitus and negatively affects kidney and cardiovascular outcomes.

Reaction Mechanism and Performance of Innovative 2D Germanane-Silicane Alloys: SixGe1- xH Electrodes in Lithium-Ion Batteries

The adjustable structures and remarkable physicochemical properties of 2D monoelemental materials, such as silicene and germanene, have attracted significant attention in recent years. They can be transformed into silicane (SiH) and germanane (GeH) through covalent functionalization via hydrogen atom termination. However, synthesizing these materials with a scalable and low-cost fabrication process to achieve high-quality 2D SiH and GeH poses challenges. Herein, groundbreaking 2D SiH and GeH materials with varying compositions, specifically Si0.25Ge0.75H, Si0.50Ge0.50H, and Si0.75Ge0.25H, are prepared through a simple and efficient chemical exfoliation of their Zintl phases. These 2D materials offer significant advantages, including their large surface area, high mechanical flexibility, rapid electron mobility, and defect-rich loose-layered structures. Among these compositions, the Si0.50Ge0.50H electrode demonstrates the highest discharge capacity, reaching up to 1059 mAh g-1 after 60 cycles at a current density of 75 mA g-1. A comprehensive ex-situ electrochemical analysis is conducted to investigate the reaction mechanisms of lithiation/delithiation in Si0.50Ge0.50H. Subsequently, an initial assessment of the c-Li15(SixGe1- x)4 phase after lithiation and the a-Si0.50Ge0.50 phase after delithiation is presented. Hence, this study contributes crucial insights into the (de)lithiation reaction mechanisms within germanane-silicane alloys. Such understanding is pivotal for mastering promising materials that amalgamate the finest properties of silicon and germanium.

Elucidation of the Transport Properties of Calcium-Doped High Entropy Rare Earth Aluminates for Solid Oxide Fuel Cell Applications

Solid oxide fuel cells (SOFCs) are paving the way to clean energy conversion, relying on efficient oxygen-ion conductors with high ionic conductivity coupled with a negligible electronic contribution. Doped rare earth aluminates are promising candidates for SOFC electrolytes due to their high ionic conductivity. However, they often suffer from p-type electronic conductivity at operating temperatures above 500 °C under oxidizing conditions caused by the incorporation of oxygen into the lattice. High entropy materials are a new class of materials conceptualized to be stable at higher temperatures due to their high configurational entropy. Introducing this concept to rare earth aluminates can be a promising approach to stabilize the lattice by shifting the stoichiometric point of the oxides to higher oxygen activities, and thereby, reducing the p-type electronic conductivity in the relevant oxygen partial pressure range. In this study, the high entropy oxide (Gd,La,Nd,Pr,Sm)AlO3 is synthesized and doped with Ca. The Ca-doped (Gd,La,Nd,Pr,Sm)AlO3 compounds exhibit a higher ionic conductivity than most of the corresponding Ca-doped rare earth aluminates accompanied by a reduction of the p-type electronic conductivity contribution typically observed under oxidizing conditions. In light of these findings, this study introduces high entropy aluminates as a promising candidate for SOFC electrolytes.

Assessing quality of selection procedures: Lower bound of false positive rate as a function of inter-rater reliability

Inter-rater reliability (IRR) is one of the commonly used tools for assessing the quality of ratings from multiple raters. However, applicant selection procedures based on ratings from multiple raters usually result in a binary outcome; the applicant is either selected or not. This final outcome is not considered in IRR, which instead focuses on the ratings of the individual subjects or objects. We outline the connection between the ratings' measurement model (used for IRR) and a binary classification framework. We develop a simple way of approximating the probability of correctly selecting the best applicants which allows us to compute error probabilities of the selection procedure (i.e., false positive and false negative rate) or their lower bounds. We draw connections between the IRR and the binary classification metrics, showing that binary classification metrics depend solely on the IRR coefficient and proportion of selected applicants. We assess the performance of the approximation in a simulation study and apply it in an example comparing the reliability of multiple grant peer review selection procedures. We also discuss other possible uses of the explored connections in other contexts, such as educational testing, psychological assessment, and health-related measurement, and implement the computations in the R package IRR2FPR.

Ca2+/calmodulin-dependent kinase IIδC-induced chronic heart failure does not depend on sarcoplasmic reticulum Ca2+ leak

AIMS

Hyperactivity of Ca2+/calmodulin-dependent protein kinase II (CaMKII) has emerged as a central cause of pathologic remodelling in heart failure. It has been suggested that CaMKII-induced hyperphosphorylation of the ryanodine receptor 2 (RyR2) and consequently increased diastolic Ca2+ leak from the sarcoplasmic reticulum (SR) is a crucial mechanism by which increased CaMKII activity leads to contractile dysfunction. We aim to evaluate the relevance of CaMKII-dependent RyR2 phosphorylation for CaMKII-induced heart failure development in vivo.

METHODS AND RESULTS

We crossbred CaMKIIδC overexpressing [transgenic (TG)] mice with RyR2-S2814A knock-in mice that are resistant to CaMKII-dependent RyR2 phosphorylation. Ca2+-spark measurements on isolated ventricular myocytes confirmed the severe diastolic SR Ca2+ leak previously reported in CaMKIIδC TG [4.65 ± 0.73 mF/F0 vs. 1.88 ± 0.30 mF/F0 in wild type (WT)]. Crossing in the S2814A mutation completely prevented SR Ca2+-leak induction in the CaMKIIδC TG, both regarding Ca2+-spark size and frequency, demonstrating that the CaMKIIδC-induced SR Ca2+ leak entirely depends on the CaMKII-specific RyR2-S2814 phosphorylation. Yet, the RyR2-S2814A mutation did not affect the massive contractile dysfunction (ejection fraction = 12.17 ± 2.05% vs. 45.15 ± 3.46% in WT), cardiac hypertrophy (heart weight/tibia length = 24.84 ± 3.00 vs. 9.81 ± 0.50 mg/mm in WT), or severe premature mortality (median survival of 12 weeks) associated with cardiac CaMKIIδC overexpression. In the face of a prevented SR Ca2+ leak, the phosphorylation status of other critical CaMKII downstream targets that can drive heart failure, including transcriptional regulator histone deacetylase 4, as well as markers of pathological gene expression including Xirp2, Il6, and Col1a1, was equally increased in hearts from CaMKIIδC TG on a RyR WT and S2814A background.

CONCLUSIONS

S2814 phosphoresistance of RyR2 prevents the CaMKII-dependent SR Ca2+ leak induction but does not prevent the cardiomyopathic phenotype caused by enhanced CaMKIIδC activity. Our data indicate that additional mechanisms-independent of SR Ca2+ leak-are critical for the maladaptive effects of chronically increased CaMKIIδC activity with respect to heart failure.

Environmental Surveillance for Salmonella Typhi and its Association With Typhoid Fever Incidence in India and Malawi

BACKGROUND

Environmental surveillance (ES) for Salmonella Typhi potentially offers a low-cost tool to identify communities with a high burden of typhoid fever.

METHODS

We developed standardized protocols for typhoid ES, including sampling site selection, validation, characterization; grab or trap sample collection, concentration; and quantitative PCR targeting Salmonella genes (ttr, staG, and tviB) and a marker of human fecal contamination (HF183). ES was implemented over 12 months in a historically high typhoid fever incidence setting (Vellore, India) and a lower incidence setting (Blantyre, Malawi) during 2021-2022.

RESULTS

S. Typhi prevalence in ES samples was higher in Vellore compared with Blantyre; 39/520 (7.5%; 95% confidence interval [CI], 4.4%-12.4%) vs 11/533 (2.1%; 95% CI, 1.1%-4.0%) in grab and 79/517 (15.3%; 95% CI, 9.8%-23.0%) vs 23/594 (3.9%; 95% CI, 1.9%-7.9%) in trap samples. Detection was clustered by ES site and correlated with site catchment population in Vellore but not Blantyre. Incidence of culture-confirmed typhoid in local hospitals was low during the study and zero some months in Vellore despite S. Typhi detection in ES.

CONCLUSIONS

ES describes the prevalence and distribution of S. Typhi even in the absence of typhoid cases and could inform vaccine introduction. Expanded implementation and comparison with clinical and serological surveillance will further establish its public health utility.

Myoclonus and Dystonia as Recurrent Presenting Features in Patients with the SCA21-Associated TMEM240 p.Pro170Leu Variant

Background

Spinocerebellar ataxia 21 (SCA21) is a rare neurological disorder caused by heterozygous variants in TMEM240. A growing, yet still limited number of reports suggested that hyperkinetic movements should be considered a defining component of the disease.

Case Series

We describe two newly identified families harboring the recurrent pathogenic TMEM240 p.Pro170Leu variant. Both index patients and the mother of the first proband developed movement disorders, manifesting as myoclonic dystonia and action-induced dystonia without co-occurring ataxia in one case, and pancerebellar syndrome complicated by action-induced dystonia in the other. We reviewed the literature on TMEM240 variants linked to hyperkinetic disorders, comparing our cases to described phenotypes.

Discussion

Adding to prior preliminary observations, our series highlights the relevance of hyperkinetic movements as clinically meaningful features of SCA21. TMEM240 mutation should be included in the differential diagnosis of myoclonic dystonia and ataxia-dystonia syndromes.

Language outcomes of preschool children who are HIV-exposed uninfected: An analysis of a South African cohort

INTRODUCTION

There are approximately 16 million children who are HIV-exposed and uninfected (CHEU) worldwide. Studies suggest that CHEU are at risk for developmental impairment in infancy, particularly in language domains. However, there is limited research examining neurocognitive function in CHEU older than 2 years, including important pre-school years. This study aimed to investigate associations between HIV exposure without infection and neurocognitive outcomes and to determine risk factors for neurodevelopment in CHEU at age 3-4 years.

METHODS

The Drakenstein Child Health Study is a South African population-based birth cohort which enrolled women in pregnancy with ongoing follow up. Neurocognitive outcomes were assessed in children at 3.5 years by trained assessors blinded to HIV status including general cognitive function, language, and memory, measured using the Kaufmann Assessment Battery for Children, Second Edition (KABC-II). Data were compared between CHEU and children who were HIV-unexposed uninfected (CHUU) using multivariable logistic and linear regression, including testing for effect modification; sex-stratified risk factor analyses were performed.

RESULTS

A total of 497 children were included (97 [20%] CHEU; 400 [80%] CHUU; 50% male), with a mean age of 3.5 years (range 3.4-3.6). Groups had similar birth and household characteristics, although mothers of CHEU were older, on average. Overall, CHEU had lower expressive language scores compared to CHUU on unadjusted and adjusted analyses (effect size: -0.23 [95% CI -0.45, -0.01]). There were no group differences in general cognitive or memory function (p>0.05). On sex-stratified analyses, male CHEU were found to have higher odds of suboptimal cognitive development compared to male CHUU (aOR 2.28 [95% CI 1.06, 4.87], p = 0.034). Several other factors including birthweight, maternal education, maternal ART duration and HIV viral load during pregnancy were associated with cognition, memory, or expressive language outcomes in CHEU, dependent on child sex.

INTERPRETATION

The findings suggest that perinatal HIV exposure continues to be associated with impaired language development across the preschool years, highlighting the importance of targeting early interventions to optimise language outcomes. Further, the results suggest the importance of demographic, biological and HIV-related variables influencing developmental outcomes in CHEU. The greater risk of suboptimal cognitive development in male CHEU requires investigation around sex-specific mechanisms.

Grain Products: Traditional and Innovative Technologies

The current knowledge regarding various cereals, their composition, and their processing methods is extensive [...].

Human In Vitro Models of Neuroenergetics and Neurometabolic Disturbances: Current Advances and Clinical Perspectives

Neurological conditions conquer the world; they are the leading cause of disability and the second leading cause of death worldwide, and they appear all around the world in every age group, gender, nationality, and socioeconomic class. Despite the growing evidence of an immense impact of perturbations in neuroenergetics on overall brain function, only little is known about the underlying mechanisms. Especially human insights are sparse, owing to a shortage of physiologically relevant model systems. With this perspective, we aim to explore the key steps and considerations involved in developing an advanced human in vitro model for studying neuroenergetics. We discuss biological and technological strategies to meet the requirements of a predictive model, aiming at providing a guide and inspiration for future in vitro models of neuroenergetics.

Thermalization of Mesh Reinforced Ultra-Thin Al-Coated Plastic Films: A Parametric Study Applied to the Athena X-IFU Instrument

The X-ray Integral Field Unit (X-IFU) is one of the two focal plane detectors of Athena, a large-class high energy astrophysics space mission approved by ESA in the Cosmic Vision 2015-2025 Science Program. The X-IFU consists of a large array of transition edge sensor micro-calorimeters that operate at ~100 mK inside a sophisticated cryostat. To prevent molecular contamination and to minimize photon shot noise on the sensitive X-IFU cryogenic detector array, a set of thermal filters (THFs) operating at different temperatures are needed. Since contamination already occurs below 300 K, the outer and more exposed THF must be kept at a higher temperature. To meet the low energy effective area requirements, the THFs are to be made of a thin polyimide film (45 nm) coated in aluminum (30 nm) and supported by a metallic mesh. Due to the small thickness and the low thermal conductance of the material, the membranes are prone to developing a radial temperature gradient due to radiative coupling with the environment. Considering the fragility of the membrane and the high reflectivity in IR energy domain, temperature measurements are difficult. In this work, a parametric numerical study is performed to retrieve the radial temperature profile of the larger and outer THF of the Athena X-IFU using a Finite Element Model approach. The effects on the radial temperature profile of different design parameters and boundary conditions are considered: (i) the mesh design and material, (ii) the plating material, (iii) the addition of a thick Y-cross applied over the mesh, (iv) an active heating heat flux injected on the center and (v) a Joule heating of the mesh. The outcomes of this study have guided the choice of the baseline strategy for the heating of the Athena X-IFU THFs, fulfilling the stringent thermal specifications of the instrument.

A Novel Methodology for Measuring Ambient Thermal Effects on Machine Tools

Large machine tools are critically affected by ambient temperature fluctuations, impacting their performance and the quality of machined products. Addressing the challenge of accurately measuring thermal effects on machine structures, this study introduces the Machine Tool Integrated Inverse Multilateration method. This method offers a precise approach for assessing geometric error parameters throughout a machine's working volume, featuring a low level of uncertainty and high speed suitable for effective temperature change monitoring. A significant innovation is found in the capability to automatically realise the volumetric error characterisation of medium- to large-sized machine tools at intervals of 40-60 min with a measurement uncertainty of 10 µm. This enables the detailed study of thermal errors which are generated due to variations in ambient temperature over extended periods. To validate the method, an extensive experimental campaign was conducted on a ZAYER Arion G™ large machine tool using a LEICA AT960™ laser tracker with four wide-angle retro-reflectors under natural workshop conditions. This research identified two key thermal scenarios, quasi-stationary and changing environments, providing valuable insights into how temperature variations influence machine behaviour. This novel method facilitates the optimization of machine tool operations and the improvement of product quality in industrial environments, marking a significant advancement in manufacturing metrology.

Ischaemic heart disease in patients with cancer

Cardiologists are encountering a growing number of cancer patients with ischaemic heart disease (IHD). Several factors account for the interrelationship between these two conditions, in addition to improving survival rates in the cancer population. Established cardiovascular (CV) risk factors, such as hypercholesterolaemia and obesity, predispose to both IHD and cancer, through specific mechanisms and via low-grade, systemic inflammation. This latter is also fuelled by clonal haematopoiesis of indeterminate potential. Furthermore, experimental work indicates that IHD and cancer can promote one another, and the CV or metabolic toxicity of anticancer therapies can lead to IHD. The connections between IHD and cancer are reinforced by social determinants of health, non-medical factors that modify health outcomes and comprise individual and societal domains, including economic stability, educational and healthcare access and quality, neighbourhood and built environment, and social and community context. Management of IHD in cancer patients is often challenging, due to atypical presentation, increased bleeding and ischaemic risk, and worse outcomes as compared to patients without cancer. The decision to proceed with coronary revascularization and the choice of antithrombotic therapy can be difficult, particularly in patients with chronic coronary syndromes, necessitating multidisciplinary discussion that considers both general guidelines and specific features on a case by case basis. Randomized controlled trial evidence in cancer patients is very limited and there is urgent need for more data to inform clinical practice. Therefore, coexistence of IHD and cancer raises important scientific and practical questions that call for collaborative efforts from the cardio-oncology, cardiology, and oncology communities.

The Discovery of New Inhibitors of Insulin-Regulated Aminopeptidase by a High-Throughput Screening of 400,000 Drug-like Compounds

With the ambition to identify novel chemical starting points that can be further optimized into small drug-like inhibitors of insulin-regulated aminopeptidase (IRAP) and serve as potential future cognitive enhancers in the clinic, we conducted an ultra-high-throughput screening campaign of a chemically diverse compound library of approximately 400,000 drug-like small molecules. Three biochemical and one biophysical assays were developed to enable large-scale screening and hit triaging. The screening funnel, designed to be compatible with high-density microplates, was established with two enzyme inhibition assays employing either fluorescent or absorbance readouts. As IRAP is a zinc-dependent enzyme, the remaining active compounds were further evaluated in the primary assay, albeit with the addition of zinc ions. Rescreening with zinc confirmed the inhibitory activity for most compounds, emphasizing a zinc-independent mechanism of action. Additionally, target engagement was confirmed using a complementary biophysical thermal shift assay where compounds causing positive/negative thermal shifts were considered genuine binders. Triaging based on biochemical activity, target engagement, and drug-likeness resulted in the selection of 50 qualified hits, of which the IC50 of 32 compounds was below 3.5 µM. Despite hydroxamic acid dominance, diverse chemotypes with biochemical activity and target engagement were discovered, including non-hydroxamic acid compounds. The most potent compound (QHL1) was resynthesized with a confirmed inhibitory IC50 of 320 nM. Amongst these compounds, 20 new compound structure classes were identified, providing many new starting points for the development of unique IRAP inhibitors. Detailed characterization and optimization of lead compounds, considering both hydroxamic acids and other diverse structures, are in progress for further exploration.

Technological and Enzymatic Characterization of Autochthonous Lactic Acid Bacteria Isolated from Viili Natural Starters

Viili, a Finnish ropy fermented milk, is traditionally manufactured through spontaneous fermentation, by mesophilic lactic acid bacteria and yeast-like fungi, or back-slopping. This study evaluated four natural viili starters as sources of lactic acid bacteria for dairy production. Back-slopping activation of the studied viili samples was monitored through pH and titratable acidity measurements and enumeration of mesophilic lactic acid bacteria. Sixty lactic acid bacteria isolates were collected, molecularly identified, and assayed for acidification performance, enzymatic activities, production of exopolysaccharides (EPSs), presence of the histidine decarboxylase (hdcA) gene of Gram-positive bacteria, and production of bacteriocins. A neat predominance of Lactococcus lactis emerged among the isolates, followed by Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Enterococcus lactis, and Lactococcus cremoris. Most isolates exhibited proteolytic activity, whereas only a few enterococci showed lipase activity. Five isolates identified as L. cremoris, L. lactis, and E. faecalis showed a good acidification performance. Most of the isolates tested positive for leucine arylamidase, whereas only one E. durans and two L. lactis isolates were positive for valine arylamidase. A few isolates also showed a positive reaction for beta-galactosidase and alpha- and beta-glucosidase. None of the isolates produced EPSs or bacteriocins. The hdcA gene was detected in five isolates identified as L. lactis and E. faecium. A few L. cremoris and L. lactis isolates for potential use as starter or adjunct cultures for dairy processing were finally identified.

Biosynthesis of Hesperetin, Homoeriodictyol, and Homohesperetin in a Transcriptomics-Driven Engineered Strain of Streptomyces albidoflavus

Flavonoids exhibit various bioactivities including anti-oxidant, anti-tumor, anti-inflammatory, and anti-viral properties. Methylated flavonoids are particularly significant due to their enhanced oral bioavailability, improved intestinal absorption, and greater stability. The heterologous production of plant flavonoids in bacterial factories involves the need for enough biosynthetic precursors to allow for high production levels. These biosynthetic precursors are malonyl-CoA and l-tyrosine. In this work, to enhance flavonoid biosynthesis in Streptomyces albidoflavus, we conducted a transcriptomics study for the identification of candidate genes involved in l-tyrosine catabolism. The hypothesis was that the bacterial metabolic machinery would detect an excess of this amino acid if supplemented with the conventional culture medium and would activate the genes involved in its catabolism towards energy production. Then, by inactivating those overexpressed genes (under an excess of l-tyrosine), it would be possible to increase the intracellular pools of this precursor amino acid and eventually the final flavonoid titers in this bacterial factory. The RNAseq data analysis in the S. albidoflavus wild-type strain highlighted the hppD gene encoding 4-hydroxyphenylpyruvate dioxygenase as a promising target for knock-out, exhibiting a 23.2-fold change (FC) in expression upon l-tyrosine supplementation in comparison to control cultivation conditions. The subsequent knock-out of the hppD gene in S. albidoflavus resulted in a 1.66-fold increase in the naringenin titer, indicating enhanced flavonoid biosynthesis. Leveraging the improved strain of S. albidoflavus, we successfully synthesized the methylated flavanones hesperetin, homoeriodictyol, and homohesperetin, achieving titers of 2.52 mg/L, 1.34 mg/L, and 0.43 mg/L, respectively. In addition, the dimethoxy flavanone homohesperetin was produced as a byproduct of the endogenous metabolism of S. albidoflavus. To our knowledge, this is the first time that hppD deletion was utilized as a strategy to augment the biosynthesis of flavonoids. Furthermore, this is the first report where hesperetin and homoeriodictyol have been synthesized from l-tyrosine as a precursor. Therefore, transcriptomics is, in this case, a successful approach for the identification of catabolism reactions affecting key precursors during flavonoid biosynthesis, allowing the generation of enhanced production strains.

Visual Impairment, Inclusion and Citizenship in South Africa

People with visual impairment face significant material challenges to access and inclusion in South Africa. These are in large part rooted in and supported by prejudiced assumptions about the needs, nature and capabilities of this group. The cultural and psychological face of oppression needs to be attended to. To this end, this viewpoint brings together the work of three visually impaired scholars in three key areas pertaining to the promotion of the inclusion and citizenship of visually impaired persons in South Africa. These areas are education; rehabilitation; and social inclusion and visibility. This work argues that undoing lifelong exclusion requires examining how disablism is embedded in the very fabric of our societies and operational at various levels: material, administrative, cultural and relational.

Exploring long-term breast cancer survivors' care trajectories using dynamic time warping-based unsupervised clustering

OBJECTIVES

Long-term breast cancer survivors (BCS) constitute a complex group of patients, whose number is estimated to continue rising, such that, a dedicated long-term clinical follow-up is necessary.

MATERIALS AND METHODS

A dynamic time warping-based unsupervised clustering methodology is presented in this article for the identification of temporal patterns in the care trajectories of 6214 female BCS of a large longitudinal retrospective cohort of Spain. The extracted care-transition patterns are graphically represented using directed network diagrams with aggregated patient and time information. A control group consisting of 12 412 females without breast cancer is also used for comparison.

RESULTS

The use of radiology and hospital admission are explored as patterns of special interest. In the generated networks, a more intense and complex use of certain healthcare services (eg, radiology, outpatient care, hospital admission) is shown and quantified for the BCS. Higher mortality rates and numbers of comorbidities are observed in various transitions and compared with non-breast cancer. It is also demonstrated how a wealth of patient and time information can be revealed from individual service transitions.

DISCUSSION

The presented methodology permits the identification and descriptive visualization of temporal patterns of the usage of healthcare services by the BCS, that otherwise would remain hidden in the trajectories.

CONCLUSION

The results could provide the basis for better understanding the BCS' circulation through the health system, with a view to more efficiently predicting their forthcoming needs and thus designing more effective personalized survivorship care plans.

Discovery of a Novel Pseudo-Natural Product Aurora Kinase Inhibitor Chemotype through Morphological Profiling

The pseudo-natural product (pseudo-NP) concept aims to combine NP fragments in arrangements that are not accessible through known biosynthetic pathways. The resulting compounds retain the biological relevance of NPs but are not yet linked to bioactivities and may therefore be best evaluated by unbiased screening methods resulting in the identification of unexpected or unprecedented bioactivities. Herein, various NP fragments are combined with a tricyclic core connectivity via interrupted Fischer indole and indole dearomatization reactions to provide a collection of highly three-dimensional pseudo-NPs. Target hypothesis generation by morphological profiling via the cell painting assay guides the identification of an unprecedented chemotype for Aurora kinase inhibition with both its relatively highly 3D structure and its physicochemical properties being very different from known inhibitors. Biochemical and cell biological characterization indicate that the phenotype identified by the cell painting assay corresponds to the inhibition of Aurora kinase B.

Direct mailing of HPV self-sampling kits to women aged 50-65 non-participating in cervical screening in the Czech Republic

BACKGROUND

A population-based cervical cancer screening programme is implemented in the Czech Republic. However, participation is insufficient among women over 50 years. This study aimed to estimate the potential improvement in participation through directly mailed HPV self-sampling kits (HPVssk) compared with standard invitation letters in women aged 50-65 non-participating in screening.

METHODS

The study recruited 1564 eligible women (no cervical cancer screening in the last 3 years or more, no previous treatment associated with cervical lesions or cervical cancer). Eight hundred women were mailed with an HPVssk (HPVssk group), and 764 women were sent a standard invitation letter (control group) inviting them to a routine screening (Pap test). The primary outcome was a comparison of the overall participation rate between study groups using a binominal regression model.

RESULTS

The participation rate in the HPVssk group was 13.4% [95% confidence interval (CI) 11.2-15.9%; 7.4% of women returned the HPVssk and 6.0% attended gynaecological examination] and 5.0% (95% CI 3.6-6.8%) in the control group. Using the binominal regression model, the difference between the groups was estimated as 7.6% (95% CI 5.0-10.2%; P < 0.001). In the HPVssk group, 22% of women who returned HPVssk had a positive result and 70% of them underwent a follow-up examination.

CONCLUSIONS

Compared with traditional invitation letters, the direct mailing of the HPVssk achieved a significantly higher participation rate, along with a notable HPV positivity rate among HPVssk responders. This approach offers a potentially viable method for engaging women who have not yet attended a cervical screening programme.

Association between breast feeding and food consumption according to the degree of processing in Brazil: a cohort study

BACKGROUND

The benefits of breast feeding may be associated with better formation of eating habits beyond childhood. This study was designed to verify the association between breast feeding and food consumption according to the degree of processing in four Brazilian birth cohorts.

METHODS

The duration of exclusive, predominant and total breast feeding was evaluated. The analysis of the energy contribution of fresh or minimally processed foods (FMPF) and ultra-processed foods (UPF) in the diet was evaluated during childhood (13-36 months), adolescence (11-18 years) and adulthood (22, 23 and 30 years).

RESULTS

Those who were predominantly breastfed for less than 4 months had a higher UPF consumption (β 3.14, 95% CI 0.82 to 5.47) and a lower FMPF consumption (β -3.47, 95% CI -5.91 to -1.02) at age 22 years in the 1993 cohort. Exclusive breast feeding (EBF) for less than 6 months was associated with increased UPF consumption (β 1.75, 95% CI 0.25 to 3.24) and reduced FMPF consumption (β -1.49, 95% CI -2.93 to -0.04) at age 11 years in the 2004 cohort. In this same cohort, total breast feeding for less than 12 months was associated with increased UPF consumption (β 1.12, 95% CI 0.24 to 2.19) and decreased FMPF consumption (β -1.13, 95% CI -2 .07 to -0.19). Children who did not receive EBF for 6 months showed an increase in the energy contribution of UPF (β 2.36, 95% CI 0.53 to 4.18) and a decrease in FMPF (β -2.33, 95% CI -4 .19 to -0.48) in the diet at 13-36 months in the 2010 cohort. In this cohort, children who were breastfed for less than 12 months in total had higher UPF consumption (β 2.16, 95% CI 0.81 to 3.51) and lower FMPF consumption (β -1.79, 95% CI -3.09 to -0.48).

CONCLUSION

Exposure to breast feeding is associated with lower UPF consumption and higher FMPF consumption in childhood, adolescence and adulthood.

Exploring the Potential of Atlantic Mesopelagic Species Processed on Board Commercial Fishing Vessels as a Source of Dietary Lipids

This study investigates the use of untapped mesopelagic species as a source of long-chain polyunsaturated omega-3 fatty acids (LC n-3 PUFAs) to meet the growing demand. The challenges faced by commercial fishing vessels, such as varying catch rates and species distribution affecting lipid levels, are addressed. Marine oils were produced post-catch using thermal separation and enzymatic hydrolysis during four commercial cruises, screening approximately 20,000 kg of mixed mesopelagic species. Maurolicus muelleri and Benthosema glaciale were the dominant species in the catch, while krill was the primary bycatch. The lipid composition varied, with B. glaciale having a higher prevalence of wax esters, while triacylglycerols and phospholipids were more predominant in the other species. LC n-3 PUFAs ranged from 19% to 44% of lipids, with an average EPA + DHA content of 202 mg/g of oil. Both processing methods achieved oil recoveries of over 90%. Estimates indicate that the mesopelagic biomass in the Northeast Atlantic could supply annual recommended levels of EPA + DHA to 1.5 million people, promoting healthy heart and brain functions. These findings offer valuable insights for considering mesopelagic species as a potential source of dietary marine lipids, laying the groundwork for further research and innovation in processing and obtaining valuable compounds from such species.

CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature

The CoMentG resource contains millions of relationships between terms of biomedical interest obtained from the scientific literature. At the core of the system is a methodology for detecting significant co-mentions of concepts in the entire PubMed corpus. That method was applied to nine sets of terms covering the most important classes of biomedical concepts: diseases, symptoms/clinical signs, molecular functions, biological processes, cellular compartments, anatomic parts, cell types, bacteria and chemical compounds. We obtained more than 7 million relationships between more than 74 000 terms, and many types of relationships were not available in any other resource. As the terms were obtained from widely used resources and ontologies, the relationships are given using the standard identifiers provided by them and hence can be linked to other data. A web interface allows users to browse these associations, searching for relationships for a set of terms of interests provided as input, such as between a disease and their associated symptoms, underlying molecular processes or affected tissues. The results are presented in an interactive interface where the user can explore the reported relationships in different ways and follow links to other resources. Database URL: https://csbg.cnb.csic.es/CoMentG/.

Flexibility of brain dynamics is increased and predicts clinical impairment in relapsing-remitting but not in secondary progressive multiple sclerosis

Large-scale brain activity has long been investigated under the erroneous assumption of stationarity. Nowadays, we know that resting-state functional connectivity is characterized by aperiodic, scale-free bursts of activity (i.e. neuronal avalanches) that intermittently recruit different brain regions. These different patterns of activity represent a measure of brain flexibility, whose reduction has been found to predict clinical impairment in multiple neurodegenerative diseases such as Parkinson's disease, amyotrophic lateral sclerosis and Alzheimer's disease. Brain flexibility has been recently found increased in multiple sclerosis, but its relationship with clinical disability remains elusive. Also, potential differences in brain dynamics according to the multiple sclerosis clinical phenotypes remain unexplored so far. We performed a brain dynamics study quantifying brain flexibility utilizing the 'functional repertoire' (i.e. the number of configurations of active brain areas) through source reconstruction of magnetoencephalography signals in a cohort of 25 multiple sclerosis patients (10 relapsing-remitting multiple sclerosis and 15 secondary progressive multiple sclerosis) and 25 healthy controls. Multiple sclerosis patients showed a greater number of unique reconfigurations at fast time scales as compared with healthy controls. This difference was mainly driven by the relapsing-remitting multiple sclerosis phenotype, whereas no significant differences in brain dynamics were found between secondary progressive multiple sclerosis and healthy controls. Brain flexibility also showed a different predictive power on clinical disability according to the multiple sclerosis type. For the first time, we investigated brain dynamics in multiple sclerosis patients through high temporal resolution techniques, unveiling differences in brain flexibility according to the multiple sclerosis phenotype and its relationship with clinical disability.

Cinchona-Based Hydrogen-Bond Donor Organocatalyst Metal Complexes: Asymmetric Catalysis and Structure Determination

In this study, we describe the synthesis of cinchona (thio)squaramide and a novel cinchona thiourea organocatalyst. These catalysts were employed in pharmaceutically relevant catalytic asymmetric reactions, such as Michael, Friedel-Crafts, and A3 coupling reactions, in combination with Ag(I), Cu(II), and Ni(II) salts. We identified several organocatalyst-metal salt combinations that led to a significant increase in both yield and enantioselectivity. To gain insight into the active catalyst species, we prepared organocatalyst-metal complexes and characterized them using HRMS, NMR spectroscopy, and quantum chemical calculations (B3LYP-D4/def2-TZVP), which allowed us to establish a structure-activity relationship.

Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness

Epigenetic clocks can measure aging and predict the incidence of diseases and mortality. Higher levels of physical fitness are associated with a slower aging process and a healthier lifespan. Microbiome alterations occur in various diseases and during the aging process, yet their relation to epigenetic clocks is not explored. To fill this gap, we collected metagenomic (from stool), epigenetic (from blood), and exercise-related data from physically active individuals and, by applying epigenetic clocks, we examined the relationship between gut flora, blood-based epigenetic age acceleration, and physical fitness. We revealed that an increased entropy in the gut microbiome of physically active middle-aged/old individuals is associated with accelerated epigenetic aging, decreased fitness, or impaired health status. We also observed that a slower epigenetic aging and higher fitness level can be linked to altered abundance of some bacterial species often linked to anti-inflammatory effects. Overall our data suggest that alterations in the microbiome can be associated with epigenetic age acceleration and physical fitness.

Narrative influence on support of a public policy: The case of nuclear power in The Netherlands

We propose a new methodology to systematically transform presurveyed argument preferences into fictional narratives, that can help people to imagine the consequences of future events, and measure how they impact willingness to pay for a public policy. We apply narrative theory to construct two short narratives that depict an imaginary future, bleak due to climate change or energy dependence, and show experimentally that exposure to these narratives increases contributions in a Public Goods game, framed as payments toward the construction of new nuclear plant in The Netherlands. Our results suggest that fictional narratives can be used (and misused) as a tool of economic policy that allows conveying relevant information to people about complex issues. We discuss the ethical use of narratives and the value of their transparent construction for democratic will-formation and policy implementation when abstract factual information can be difficult to process or comprehend.

Incidence of Diabetes Mellitus and Associated Factors in the Era of Antiretroviral Drugs With a Low Metabolic Toxicity Profile

Objective

The incidence of type 2 diabetes mellitus (T2DM) has risen dramatically. Among people living with HIV (PLHIV), chronic disease (now >15 cases/1000 in the general population worldwide) and long-term exposure to antiretroviral therapy (ART) can alter metabolic processes early, favoring insulin resistance and T2DM. We retrospectively studied the incidence of T2DM and associated factors in the Cohort of the Spanish AIDS Research Network, a prospective cohort of PLHIV enrolled at diagnosis and before initiation of ART.

Methods

PLHIV were aged >18 years and ART naive at inclusion. The incidence of new diagnoses of T2DM after initiation of ART (per 1000 person-years) was calculated. Predictors of a diagnosis of T2DM were identified by a Cox proportional hazards model adjusted for statistically significant and clinically relevant variables.

Results

Cumulative incidence was 5.9 (95% CI, 5.1-6.7) per 1000 person-years, increasing significantly in persons aged >50 years to 14.4 (95% CI, 10.4-19.3). Median time to diagnosis of T2DM was 27 months. Only age and higher education were significant. Interestingly, higher education was associated with a 33% reduction in the incidence of T2DM. Having received tenofovir disoproxil fumarate + (lamivudine or emtricitabine) + rilpivirine was almost significant as a protective factor (hazard ratio, 0.49; 95% CI, .24-1.01; P = .05).

Conclusions

The incidence of T2DM in PLHIV in Spain was high, especially in persons aged >50 years. Age was the factor most closely associated with onset, and educational level was the factor most associated with reduced risk. We highlight the lack of association between HIV-related factors and T2DM and show that, within nonnucleoside reverse transcriptase inhibitors, rilpivirine could prove more benign for metabolic comorbidities.

Prognostic value of preoperative inflammatory ratios in early glottic cancer treated with transoral laser surgery

BACKGROUND

There is growing evidence regarding the prognostic utility of ratios such as neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and systemic immune-inflammatory index (SIII) in head and neck squamous cell carcinoma (HNSCC). However, most studies to date include heterogeneous series with different treatments or tumor subsites.

METHODS

We collected data from 201 patients with stage I-II glottic squamous cell carcinoma treated with transoral laser surgery. NLR, PLR, and SIII were calculated from preoperative cell blood count, cut-off points were obtained by ROC curve analysis, and survival rates were calculated.

RESULTS

High NLR (p = 0.012) and SIII (p = 0.037), but not PLR (p = 0.48), were associated with worse disease-specific survival (DSS). A similar trend was observed with overall survival (OS), although it did not reach statistical significance. On multivariable analyses, both high NLR (HR = 3.8, 95% CI = 1.5-9.9, p = 0.006) and high SIII (HR = 2.77, 95% CI = 1.1-6.9, p = 0.03) were significantly associated with shortened DSS.

CONCLUSIONS

Preoperative NLR and SIII emerge as independent prognostic biomarkers for early-stage surgically treated glottic tumors and could guide individualized follow-up.

No ageing-related increase in fibre type grouping in sprint-trained masters runners: A 10-year follow-up study

BACKGROUND

Previous research suggests that an ageing-associated remodelling and loss of motor units due to motor neuron death contributes significantly to muscle weakness in old age. In histological sections, motor unit remodelling is reflected by increased fibre type grouping. While regular exercise may not attenuate the loss of motor units during ageing, it has been suggested to facilitate reinnervation resulting in larger motor units, and a higher number and larger fibre type groups in histological sections of muscles from aged individuals.

METHODS

In a 10-year follow-up study, we assessed changes in the prevalence and size of fibre type groups in the vastus lateralis muscle from 34 male masters sprinters (40-85 years at start).

RESULTS

Over the 10 years, there was an ageing-related reduction in performance in the 60-m sprint (P < 0.001) without significant changes in fibre type composition and fibre cross-sectional area. Neither the number of fibre type groups, defined as a fibre surrounded exclusively by fibres of the same type, nor the group size changed significantly in the 10-year period.

CONCLUSIONS

These histological data show that there is limited to no significant fibre type grouping over a 10-year period in masters athletes who continued sprint run training. This observation challenges the paradigm that ageing, at least in systematically trained sprinters, is associated with motor unit remodelling.

A Photolithographable Electrolyte for Deeply Rechargeable Zn Microbatteries in On-Chip Devices

Zn batteries show promise for microscale applications due to their compatibility with air fabrication but face challenges like dendrite growth and chemical corrosion, especially at the microscale. Despite previous attempts in electrolyte engineering, achieving successful patterning of electrolyte microscale devices has remained challenging. Here, successful patterning using photolithography is enabled by incorporating caffeine into a UV-crosslinked polyacrylamide hydrogel electrolyte. Caffeine passivates the Zn anode, preventing chemical corrosion, while its coordination with Zn2+ ions forms a Zn2+-conducting complex that transforms into ZnCO3 and 2ZnCO3·3Zn(OH)2 over cycling. The resulting Zn-rich interphase product significantly enhances Zn reversibility. In on-chip microbatteries, the resulting solid-electrolyte interphase allows the Zn||MnO2 full cell to cycle for over 700 cycles with an 80% depth of discharge. Integrating the photolithographable electrolyte into multilayer microfabrication creates a microbattery with a 3D Swiss-roll structure that occupies a footprint of 0.136 mm2. This tiny microbattery retains 75% of its capacity (350 µAh cm-2) for 200 cycles at a remarkable 90% depth of discharge. The findings offer a promising solution for enhancing the performance of Zn microbatteries, particularly for on-chip microscale devices, and have significant implications for the advancement of autonomous microscale devices.

Fine-tuning tumor- and allo-immunity: advances in the use of immune checkpoint inhibitors in kidney transplant recipients

Cancer is a common complication after kidney transplantation. Kidney transplant recipients (KTR) have a 2- to 4-fold higher risk of developing cancer compared to the general population and post-transplant malignancy is the third most common cause of death in KTR. Moreover, it is well known that certain cancer types are overrepresented after transplantation, especially non-melanoma skin cancer. Immune checkpoint inhibitors (ICI) have revolutionized the treatment of cancer, with remarkable survival benefit in a subgroup of patients. ICI are monoclonal antibodies that block the binding of specific co-inhibitory signaling molecules. Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), programmed cell death protein 1 (PD-1), and its ligand programmed cell death ligand 1 (PD-L1) are the main targets of ICI. Solid organ transplant recipients (SOTR) have been excluded from clinical trials owing to concerns about tumor response, allo-immunity, and risk of transplant rejection. Indeed, graft rejection has been estimated as high as 48% and represents an emerging problem. The underlying mechanisms of organ rejection in the context of treatment with ICI are poorly understood. The search for restricted antitumoral responses without graft rejection is of paramount importance. This review summarizes the current knowledge of the use of ICI in KTR, the potential mechanisms involved in kidney graft rejection during ICI treatment, potential biomarkers of rejection, and how to deal with rejection in clinical practice.

Integration of Urinary Peptidome and Fecal Microbiome to Explore Patient Clustering in Chronic Kidney Disease

Millions of people worldwide currently suffer from chronic kidney disease (CKD), requiring kidney replacement therapy at the end stage. Endeavors to better understand CKD pathophysiology from an omics perspective have revealed major molecular players in several sample sources. Focusing on non-invasive sources, gut microbial communities appear to be disturbed in CKD, while numerous human urinary peptides are also dysregulated. Nevertheless, studies often focus on isolated omics techniques, thus potentially missing the complementary pathophysiological information that multidisciplinary approaches could provide. To this end, human urinary peptidome was analyzed and integrated with clinical and fecal microbiome (16S sequencing) data collected from 110 Non-CKD or CKD individuals (Early, Moderate, or Advanced CKD stage) that were not undergoing dialysis. Participants were visualized in a three-dimensional space using different combinations of clinical and molecular data. The most impactful clinical variables to discriminate patient groups in the reduced dataspace were, among others, serum urea, haemoglobin, total blood protein, urinary albumin, urinary erythrocytes, blood pressure, cholesterol measures, body mass index, Bristol stool score, and smoking; relevant variables were also microbial taxa, including Roseburia, Butyricicoccus, Flavonifractor, Burkholderiales, Holdemania, Synergistaceae, Enterorhabdus, and Senegalimassilia; urinary peptidome fragments were predominantly derived from proteins of collagen origin; among the non-collagen parental proteins were FXYD2, MGP, FGA, APOA1, and CD99. The urinary peptidome appeared to capture substantial variation in the CKD context. Integrating clinical and molecular data contributed to an improved cohort separation compared to clinical data alone, indicating, once again, the added value of this combined information in clinical practice.

Modelling lipid rafts formation through chemo-mechanical interplay triggered by receptor-ligand binding

Cell membranes, mediator of many biological mechanisms from adhesion and metabolism up to mutation and infection, are highly dynamic and heterogeneous environments exhibiting a strong coupling between biochemical events and structural re-organisation. This involves conformational changes induced, at lower scales, by lipid order transitions and by the micro-mechanical interplay of lipids with transmembrane proteins and molecular diffusion. Particular attention is focused on lipid rafts, ordered lipid microdomains rich of signalling proteins, that co-localise to enhance substance trafficking and activate different intracellular biochemical pathways. In this framework, the theoretical modelling of the dynamic clustering of lipid rafts implies a full multiphysics coupling between the kinetics of phase changes and the mechanical work performed by transmembrane proteins on lipids, involving the bilayer elasticity. This mechanism produces complex interspecific dynamics in which membrane stresses and chemical potentials do compete by determining different morphological arrangements, alteration in diffusive walkways and coalescence phenomena, with a consequent influence on both signalling potential and intracellular processes. Therefore, after identifying the leading chemo-mechanical interactions, the present work investigates from a modelling perspective the spatio-temporal evolution of raft domains to theoretically explain co-localisation and synergy between proteins' activation and raft formation, by coupling diffusive and mechanical phenomena to observe different morphological patterns and clustering of ordered lipids. This could help to gain new insights into the remodelling of cell membranes and could potentially suggest mechanically based strategies to control their selectivity, by orienting intracellular functions and mechanotransduction.

Less Favorable Nutri-Score Consumption Ratings Are Prospectively Associated with Abdominal Obesity in Older Adults

Nutri-Score is a front-of-package (FOP) labeling designed to assist consumers in selecting healthier options at the point of purchase and ultimately enhance their health. This study aims to evaluate the association between the Nutri-Score system and incident abdominal obesity (AO) in community-dwelling older adults. A prospective cohort of 628 individuals aged ≥ 60 were recruited in Spain between 2008-2010 and were reexamined between 2015-2017. Dietary intake was evaluated utilizing a validated computerized dietary history. Food was categorized based on the Nutri-Score system into five levels from A (green, representing the best quality) to E (red, representing the poorest quality). A five-color Nutri-Score dietary index (5-CNS DI) in g/day/kg was calculated for each participant. AO was determined by a waist circumference (WC) of ≥102 cm for men and ≥88 cm for women. Logistic regression models were adjusted for the main potential confounders. During a mean six-year follow-up, 184 incident cases of AO occurred. The odds ratio (OR) and 95% confidence interval (CI) for AO, when comparing the highest and lowest quartiles of the 5-CNS DI, were 2.45 (1.17-5.14), with a p-value for trend of 0.035. In sensitivity analyses, the OR was 2.59 (1.22-5.52, p-trend: 0.032) after adjustment for WC at baseline, and 1.75 (0.74-4.18, p-trend: 0.316) after adjustment for ultra-processed food consumption. In conclusion, less favorable food-consumption ratings in the Nutri-Score are associated with incident AO in the elderly. These findings support the use of this FOP system to potentially improve metabolic health.

Metabolic Profiling as an Approach to Differentiate T-Cell Acute Lymphoblastic Leukemia Cell Lines Belonging to the Same Genetic Subgroup

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive tumor mainly affecting children and adolescents. It is driven by multiple genetic mutations that together define the leukemic phenotype. Interestingly, based on genetic alterations and/or deregulated expression, at least six genetic subgroups have been recognized. The TAL/LMO subgroup is one of the most represented genetic subgroups, characterizing 30-45% of pediatric T-ALL cases. The study of lipid and metabolic profiles is increasingly recognized as a valuable tool for comprehending the development and progression of tumors. In this study, metabolic and lipidomic analysis via LC/MS have been carried out on four T-ALL cell lines belonging to the TAL/LMO subgroup (Jurkat, Molt-4, Molt-16, and CCRF-CEM) to identify new potential metabolic biomarkers and to provide a subclassification of T-ALL cell lines belonging to the same subgroup. A total of 343 metabolites were annotated, including 126 polar metabolites and 217 lipid molecules. The statistical analysis, for both metabolic and lipid profiles, shows significant differences and similarities among the four cell lines. The Molt-4 cell line is the most distant cell line and CCRF-CEM shows a high activity in specific pathways when compared to the other cell lines, while Molt-16 and Jurkat show a similar metabolic profile. Additionally, this study highlighted the pathways that differ in each cell line and the possible enzymes involved using bioinformatic tools, capable of predicting the pathways involved by studying the differences in the metabolic profiles. This experiment offers an approach to differentiate T-ALL cell lines and could open the way to verify and confirm the obtained results directly in patients.

Networks of gut bacteria relate to cardiovascular disease in a multi-ethnic population: the HELIUS study

AIMS

Gut microbiota have been linked to blood lipid levels and cardiovascular diseases (CVDs). The composition and abundance of gut microbiota trophic networks differ between ethnicities. We aim to evaluate the relationship between gut microbiotal trophic networks and CVD phenotypes.

METHODS AND RESULTS

We included cross-sectional data from 3860 individuals without CVD history from 6 ethnicities living in the Amsterdam region participating in the prospective Healthy Life in Urban Setting (HELIUS) study. Genetic variants were genotyped, faecal gut microbiota were profiled, and blood and anthropometric parameters were measured. A machine learning approach was used to assess the relationship between CVD risk (Framingham score) and gut microbiota stratified by ethnicity. Potential causal relationships between gut microbiota composition and CVD were inferred by performing two-sample Mendelian randomization with hard CVD events from the Pan-UK Biobank and microbiome genome-wide association studies summary data from a subset of the HELIUS cohort (n = 4117). Microbial taxa identified to be associated with CVD by machine learning and Mendelian randomization were often ethnic-specific, but some concordance across ethnicities was found. The microbes Akkermansia muciniphila and Ruminococcaceae UCG-002 were protective against ischaemic heart disease in African-Surinamese and Moroccans, respectively. We identified a strong inverse association between blood lipids, CVD risk, and the combined abundance of the correlated microbes Christensenellaceae-Methanobrevibacter-Ruminococcaceae (CMR). The CMR cluster was also identified in two independent cohorts and the association with triglycerides was replicated.

CONCLUSION

Certain gut microbes can have a potentially causal relationship with CVD events, with possible ethnic-specific effects. We identified a trophic network centred around Christensenellaceae, Methanobrevibacter, and various Ruminococcaceae, frequently lacking in South-Asian Surinamese, to be protective against CVD risk and associated with low triglyceride levels.

Noncontiguous operon atlas for the Staphylococcus aureus genome

Bacteria synchronize the expression of genes with related functions by organizing genes into operons so that they are cotranscribed together in a single polycistronic messenger RNA. However, some cellular processes may benefit if the simultaneous production of the operon proteins coincides with the inhibition of the expression of an antagonist gene. To coordinate such situations, bacteria have evolved noncontiguous operons (NcOs), a subtype of operons that contain one or more genes that are transcribed in the opposite direction to the other operon genes. This structure results in overlapping transcripts whose expression is mutually repressed. The presence of NcOs cannot be predicted computationally and their identification requires a detailed knowledge of the bacterial transcriptome. In this study, we used direct RNA sequencing methodology to determine the NcOs map in the Staphylococcus aureus genome. We detected the presence of 18 NcOs in the genome of S. aureus and four in the genome of the lysogenic prophage 80α. The identified NcOs comprise genes involved in energy metabolism, metal acquisition and transport, toxin-antitoxin systems, and control of the phage life cycle. Using the menaquinone operon as a proof of concept, we show that disarrangement of the NcO architecture results in a reduction of bacterial fitness due to an increase in menaquinone levels and a decrease in the rate of oxygen consumption. Our study demonstrates the significance of NcO structures in bacterial physiology and emphasizes the importance of combining operon maps with transcriptomic data to uncover previously unnoticed functional relationships between neighbouring genes.

The Association between the rs3747406 Polymorphism in the Glucocorticoid-Induced Leucine Zipper Gene and Sepsis Survivals Depends on the SOFA Score

The variability in mortality in sepsis could be a consequence of genetic variability. The glucocorticoid system and the intermediate TSC22D3 gene product-glucocorticoid-induced leucine zipper-are clinically relevant in sepsis, which is why this study aimed to clarify whether TSC22D3 gene polymorphisms contribute to the variance in sepsis mortality. Blood samples for DNA extraction were obtained from 455 patients with a sepsis diagnosis according to the Sepsis-III criteria and from 73 control subjects. A SNP TaqMan assay was used to detect single-nucleotide polymorphisms (SNPs) in the TSC22D3 gene. Statistical and graphical analyses were performed using the SPSS Statistics and GraphPad Prism software. C-allele carriers of rs3747406 have a 2.07-fold higher mortality rate when the sequential organ failure assessment (SOFA) score is higher than eight. In a multivariate COX regression model, the SNP rs3747406 with a SOFA score ≥ 8 was found to be an independent risk factor for 30-day survival in sepsis. The HR was calculated to be 2.12, with a p-value of 0.011. The wild-type allele was present in four out of six SNPs in our cohort. The promoter of TSC22D3 was found to be highly conserved. However, we discovered that the C-allele of rs3747406 poses a risk for sepsis mortality for SOFA Scores higher than 6.

EPOPTIS: A Monitoring-as-a-Service Platform for Internet-of-Things Applications

The technology landscape has been dynamically reshaped by the rapid growth of the Internet of Things, introducing an era where everyday objects, equipped with smart sensors and connectivity, seamlessly interact to create intelligent ecosystems. IoT devices are highly heterogeneous in terms of software and hardware, and many of them are severely constrained. This heterogeneity and potentially constrained nature creates new challenges in terms of security, privacy, and data management. This work proposes a Monitoring-as-a-Service platform for both monitoring and management purposes, offering a comprehensive solution for collecting, storing, and processing monitoring data from heterogeneous IoT networks for the support of diverse IoT-based applications. To ensure a flexible and scalable solution, we leverage the FIWARE open-source framework, also incorporating blockchain and smart contract technologies to establish a robust integrity verification mechanism for aggregated monitoring and management data. Additionally, we apply automated workflows to filter and label the collected data systematically. Moreover, we provide thorough evaluation results in terms of CPU and RAM utilization and average service latency.

Circulating Cancer-Associated Macrophage-like Cells as a Blood-Based Biomarker of Response to Immune Checkpoint Inhibitors

Evidence has been provided that circulating cancer-associated macrophage-like cell (CAM-L) numbers increase in response to chemotherapy, with an inverse trend compared to circulating tumor cells (CTCs). In the era of evolving cancer immunotherapy, whether CAM-Ls might have a potential role as predictive biomarkers of response has been unexplored. We evaluated whether a serial blood evaluation of CTC to CAM-L ratio might predict response to immune checkpoint inhibitors in a cohort of non-small-cell lung cancer patients. At baseline, CTCs, CAM-Ls, and the CTC/CAM-L ratio significantly correlate with both progression-free survival (PFS) and overall survival (OS). The baseline CTC/CAM-L ratio was significantly different in early progressors (4.28 ± 3.21) compared to long responders (0.42 ± 0.47) (p = 0.001). In patients treated with immune checkpoint inhibitors, a CTC/CAM-L ratio ≤ 0.25 at baseline is associated with better PFS and OS. A baseline CTC/CAM-L ratio ≤ 0.25 is statistically significant to discriminate early progressions from durable response. The results of the present pilot study suggest that CAM-Ls together with CTCs could play an important role in evaluating patients treated with cancer immunotherapy.

Detection and genotyping of zoonotic microsporidia in the endangered Iberian lynx (Lynx pardinus)

Microsporidia is a diverse group of obligate, intracellular, and spore-forming parasites that infect a wide range of animals. Among them, Enterocytozoon bieneusi and Encephalitozoon spp. are the most frequently reported species in humans. Limited information is available about the presence and molecular diversity of microsporidian species in the endangered Iberian lynx (Lynx pardinus). Presence of Enterocytozoon bieneusi and Encephalitozoon spp. was investigated by molecular methods in wild and captive Iberian lynxes from Spain. Overall, E. bieneusi was detected in 3.2% (8/251) of the animals examined. None of the samples tested were positive for Encephalitozoon spp. Four known (D, EbfelA, PigEBITS7, and Type IV) and a novel (named as LynxSpEb1) E. bieneusi genotypes were identified. All the genotypes found belonged to the zoonotic Group 1 of E. bieneusi. This study provides the first genotyping data of E. bieneusi in Iberian lynx in Spain. Our result indicate that the Iberian lynx does not seem to play a relevant role in the epidemiology of Encephalitozoon spp., and that this endangered felid is likely acting as spillover host rather than a true reservoir of E. bieneusi. Additional studies should be conducted to assess the impact of this parasite in the health status of the endangered Iberian lynx.

The socioeconomic impact of the COVID-19 lockdown on families affected by childhood respiratory illnesses in Cape Town, South Africa

The COVID-19 pandemic impacted families globally, directly and indirectly. Children presenting with respiratory illnesses are affected by emerging health systems and socioeconomic changes in the COVID-19 era. We explored the socioeconomic impacts of the COVID-19 lockdown on families with a respiratory illness diagnosed in their child in Cape Town, South Africa. This study was nested in a prospective observational cohort of children presenting with respiratory symptoms presumptive of COVID-19. We conducted 21 semi-structured interviews to explore the socioeconomic impact of the COVID-19 pandemic on families with a child affected by respiratory illnesses. We used case descriptive analysis and thematically organised common and divergent experiences. We found that socioeconomic challenges in low-income communities were exacerbated: 1) loss of pre-COVID sources of income (loss of income, employment and working hours), 2) shrinking employment opportunities due to business closures and strict preventative measures, 3) family network dependence to cope with financial pressures, 4) impact on education, implicating additional pressures due to lack of resources for adequate home schooling and 5) caregivers' mental health and wellbeing being impacted, causing stress and anxiety due to loss of income. This study shows that the COVID-19 lockdown impacted the socioeconomic aspects of families caring for a child with a respiratory illness. Care became more complicated and adversely impacted the family's emotional well-being and health-seeking behaviour. These impacts should be more carefully considered in order to strengthen health services and global health messaging in future pandemics.