Virtual brain twins: from basic neuroscience to clinical use.

Virtual brain twins are personalized, generative and adaptive brain models based on data from an individual's brain for scientific and clinical use. After a description of the key elements of virtual brain twins, we present the standard model for personalized whole-brain network models. The personalization is accomplished using a subject's brain imaging data by three means: (1) assemble cortical and subcortical areas in the subject-specific brain space; (2) directly map connectivity into the brain models, which can be generalized to other parameters; and (3) estimate relevant parameters through model inversion, typically using probabilistic machine learning. We present the use of personalized whole-brain network models in healthy ageing and five clinical diseases: epilepsy, Alzheimer's disease, multiple sclerosis, Parkinson's disease and psychiatric disorders. Specifically, we introduce spatial masks for relevant parameters and demonstrate their use based on the physiological and pathophysiological hypotheses. Finally, we pinpoint the key challenges and future directions.

Rationalization of a Streptavidin Based Enantioselective Artificial Suzukiase: An Integrative Computational Approach.

An Artificial Metalloenzyme (ArM) built employing the streptavidin-biotin technology has been used for the enantioselective synthesis of binaphthyls by means of asymmetric Suzuki-Miyaura cross-coupling reactions. Despite its success, it remains a challenge to understand how the length of the biotin cofactors or the introduction of mutations to streptavidin leads the preferential synthesis of one atropisomer over the other. In this study, we apply an integrated computational modeling approach, including DFT calculations, protein-ligand dockings and molecular dynamics to rationalize the impact of mutations and length of the biotion cofactor on the enantioselectivities of the biaryl product. The results unravel that the enantiomeric differences found experimentally can be rationalized by the disposition of the first intermediate, coming from the oxidative addition step, and the entrance of the second substrate. The work also showcases the difficulties facing to control the enantioselection when engineering ArM to catalyze enantioselective Suzuki-Miyaura couplings and how the combination of DFT calculations, molecular dockings and MD simulations can be used to rationalize artificial metalloenzymes.

Stringent criteria needed for germline genome editing of human IVF embryos.

Germline genome editing of IVF embryos is controversial because it is not directly health or lifesaving but is intended to prevent genetic diseases in yet-unborn future offspring. The following criteria are thus proposed for future clinical trials: (i) Due to medical risks, there should be cautious and judicious application while avoiding any non-essential usage, with rigorous patient counseling. (ii) Genome editing should only be performed on the entire batch of IVF embryos without initial PGT screening if all of them are expected to be affected by genetic disease. (iii) When there is a fair chance that some IVF embryos will not be affected by genetic diseases, initial PGT screening must be performed to identify unaffected embryos for transfer. (iv) IVF embryos with carrier status should not undergo germline genome editing. (v) If patients fail to conceive after the transfer of unaffected embryos, they should undergo another fresh IVF cycle rather than opt for genome editing of their remaining affected embryos. (vi) Only if the patient is unable to produce any more unaffected embryos in a fresh IVF cycle due to advanced maternal age or diminished ovarian reserves, can the genome editing of remaining affected embryos be permitted as a last resort.

Counseling Elective Egg Freezing Patients considering Donation of Unused Surplus Frozen Eggs for Fertility Treatment.

The majority of women who freeze their eggs for non-medical or social reasons, commonly referred to as elective egg freezing (EEF), do not eventually utilize their frozen eggs. This would result in an accumulated surplus of unused frozen eggs in fertility clinics worldwide, which represents a promising source of donation to infertile women undergoing IVF treatment. Rigorous and comprehensive counseling is needed, because the process of donating one's unused surplus frozen eggs involves complex decision-making. Prospective EEF donors can be broadly categorized into those who have achieved motherhood and those who remained childless and have given up on motherhood aspirations. A two-step systematic counseling protocol is proposed. Firstly, it is imperative to verify and ensure that these women do not want to conceive any children with their surplus frozen eggs before proceeding with further counseling and signing of consent forms. Secondly, various motivating and dissuading factors in the donation of unused surplus frozen eggs should then be comprehensively discussed with egg freezers to facilitate informed decision-making. Key motivating factors for donation include reciprocity in wanting to share the joys of motherhood among egg freezers who already have children, goodwill to help others in need, and avoiding the wastage of surplus frozen eggs after expending so much money, time, and effort. Key dissuading factors include fear of accidental incest between natural and unknown donor-conceived offspring, as well as apprehension of unexpected future contact with unknown donor-conceived offspring due to either donor anonymity being abolished in their jurisdiction or widespread consumer DNA testing.

Computational Study of Amyloidß42 Familial Mutations and Metal Interaction: Impact on Monomers and Aggregates Dynamical Behaviors.

One of the main hallmarks of Alzheimer's Disease is the formation of ß-amyloid plaques, whose formation may be enhanced by metal binding or the appearance of familial mutations. In the present study, the simultaneous effect of familial mutations (E22Q, E22G, E22K, and D23N) and binding to metal ions (Cu(II) or Al(III)) is studied at the Aß42 monomeric and fibrillar levels. With the application of GaMD and MD simulations, it is observed that the effects of metal binding and mutations differ in the monomeric and fibrillar forms. In the monomeric structures, without metal binding, all mutations reduce the amount of α-helix and increase, in some cases, the ß-sheet content. In the presence of Cu(II) and Al(III) metal ions, the peptide becomes less flexible, and the ß-sheet content decreases in favor of forming α-helix motifs that stabilize the system through interhelical contacts. Regarding the fibrillar structures, mutations decrease the opening of the fiber in the vertical axis, thereby stabilizing the S-shaped structure of the fiber. This effect is, in general, enhanced upon metal binding. These results may explain the different Aß42 aggregation patterns observed in familial mutations.

Insights into unique features of Drosophila CYP4G enzymes.

The cytochrome P450 enzymes of the CYP4G subfamily are some of the most intriguing insect P450s in terms of structure and function. In Drosophila, CYP4G1 is highly expressed in the oenocytes and is the last enzyme in the biosynthesis of cuticular hydrocarbons, while CYP4G15 is expressed in the brain and is of unknown function. Both proteins have a CYP4G-specific and characteristic amino acid sequence insertion corresponding to a loop between the G and H helices whose function is unclear. Here we address these enigmatic structural and functional features of Drosophila CYP4Gs. First, we used reverse genetics to generate D. melanogaster strains in which all or part of the CYP4G-specific loop was removed from CYP4G1. We showed that the full loop was not needed for proper folding of the P450, but it is essential for function, and that just a short stretch of six amino acids is required for the enzyme's ability to make hydrocarbons. Second, we confirmed by immunocytochemistry that CYP4G15 is expressed in the brain and showed that it is specifically associated with the cortex glia cell subtype. We then expressed CYP4G15 ectopically in oenocytes, revealing that it can produce of a blend of hydrocarbons, albeit to quantitatively lower levels resulting in only a partial rescue of CYP4G1 knockdown flies. The CYP4G1 structural variants studied here should facilitate the biochemical characterization of CYP4G enzymes. Our results also raise the question of the putative role of hydrocarbons and their synthesis by cortex glial cells.

[Overview of the implementation of pharmaceutical interviews in pharmacies in France: Analysis of responses to a questionnaire]. / État des lieux de la mise en place en France des entretiens pharmaceutiques en officine : analyse des réponses issues d'un questionnaire.

OBJECTIVE: To evaluate the development of pharmaceutical interviews in pharmacies in France, in order to understand the organization implemented, any limitations and the expansion of eligible pathologies. METHOD: A dematerialized questionnaire was designed and distributed between November 2022 and February 2023 to pharmacists and pharmacy students in France (mainland and overseas) via a link to a Google Form. RESULTS: Ninety-four pharmacists from 8 different regions of France responded to the survey. The 94 responses showed that 56% of pharmacists practiced pharmaceutical interviews. Among pharmacists who practiced interviews, pharmacy owners practiced significantly more interviews than other statuses within the pharmacy (67% vs. 38% P=0.014). No other factor, such as dispensary size or geographical area of practice, had a significant impact on whether or not pharmaceutical interviews were carried out. These talks are often carried out at the patient's request, and 89% of them are accompanied by documents for the patient's attention. For pharmacists who do not carry out interviews, time, staffing and remuneration are the 3 main blocking factors found in both quantitative and verbatim variables. Whether or not pharmacists carry out pharmaceutical interviews, this activity received 87% approval from the 94 respondents, and 84% of them would like to include more chronic disease themes. CONCLUSION: The survey shows that pharmacists approve of the pharmaceutical interviewing activity, but it also highlights obvious logistical obstacles linked to a lack of resources. Thus, even among pharmacists who carry out pharmaceutical interviews, this activity is still carried out relatively infrequently on a routine basis, and often by the incumbent pharmacist, who takes on the responsibility of carrying out this activity.

Pleural mesothelioma: a snapshot of emerging drug targets and opportunities for non-surgical therapeutic advancement.

INTRODUCTION: Pleural mesothelioma is a rare and aggressive cancer originating in the pleura, with a devastating prognosis and limited treatment options. There have been significant advancements in the management of this disease in recent years. Since 2021, nivolumab and ipilimumab immune checkpoint inhibitors have become the new standard of care for first-line treatment of pleural mesothelioma. AREAS COVERED: While a combination of chemotherapy and immune checkpoint inhibitors appears to be the next step, targeted therapies are emerging thanks to our understanding of the oncogenesis of pleural mesothelioma. Moreover, several new strategies are currently being investigated, including viral therapy, antibody-drug conjugates, and even cell therapies with CAR-T cells or dendritic cells. In this review, we will explore the various future opportunities that could potentially transform patients' lives in light of the clinical trials that have been conducted. EXPERT OPINION: Future clinical studies aim to rebiopsy patients after disease progression to identify new molecular alterations and to be associated with ancillary studies, guiding subsequent therapy decisions. Predicting and investigating treatment resistance mechanisms will lead to innovative approaches and improved treatment outcomes.

Evidence-Based Pharmaceutical Care in Community Pharmacies: A Survey of 595 French Pharmacists.

We assessed the use of evidence-based practice (EBP) among pharmacists working in community pharmacies in France and the factors linked to this practice. During 3 months in 2018, an online survey was sent to over 7000 active pharmacists and posted on pharmacists' social media sites. In total, 595 pharmacists completed the questionnaire. The responders were on average younger than the general population of community pharmacists. The 40-item questionnaire described four fictional clinical cases reflecting typical situations (conventional medicine and complementary and alternative medicine) encountered daily by community pharmacists. Multiple-choice responses were proposed and scored according to whether they reflected EBP. A high total score indicated behaviour in line with EBP. We observed 344/595 participants with a positive EBP score (57.8% [53.7-61.8%]). Univariate and multivariate analyses were used to evaluate factors that might explain adherence to EPB (the pharmacy's characteristics, the pharmacist's status, the mode of continuing education and sources of information). The majority relied on pharmaceutical industry and other biased and/or non-evidence-based sources, particularly concerning information on homeopathic products. The consultation of independent reviews, health agency recommendations and peer-reviewed scientific journals was associated with evidence-based decisions. In contrast, reliance on pharmaceutical industry documents, personal experience and informal handbooks was linked to lower EBP scores. The level of EBP use by French community pharmacists needs to be improved to ensure that good-quality, science-based advice is given to customers.

The self-association equilibrium of DNAJA2 regulates its interaction with unfolded substrate proteins and with Hsc70.

J-domain proteins tune the specificity of Hsp70s, engaging them in precise functions. Despite their essential role, the structure and function of many J-domain proteins remain largely unknown. We explore human DNAJA2, finding that it reversibly forms highly-ordered, tubular structures that can be dissociated by Hsc70, the constitutively expressed Hsp70 isoform. Cryoelectron microscopy and mutational studies reveal that different domains are involved in self-association. Oligomer dissociation into dimers potentiates its interaction with unfolded client proteins. The J-domains are accessible to Hsc70 within the tubular structure. They allow binding of closely spaced Hsc70 molecules that could be transferred to the unfolded substrate for its cooperative remodelling, explaining the efficient recovery of DNAJA2-bound clients. The disordered C-terminal domain, comprising the last 52 residues, regulates its holding activity and productive interaction with Hsc70. These in vitro findings suggest that the association equilibrium of DNAJA2 could regulate its interaction with client proteins and Hsc70.

TALAIA: a 3D visual dictionary for protein structures.

MOTIVATION: Graphical analysis of the molecular structure of proteins can be very complex. Full-atom representations retain most geometric information but are generally crowded, and key structural patterns can be challenging to identify. Non-full-atom representations could be more instructive on physicochemical aspects but be insufficiently detailed regarding shapes (e.g. entity beans-like models in coarse grain approaches) or simple properties of amino acids (e.g. representation of superficial electrostatic properties). In this work, we present TALAIA a visual dictionary that aims to provide another layer of structural representations.TALAIA offers a visual grammar that combines simple representations of amino acids while retaining their general geometry and physicochemical properties. It uses unique objects, with differentiated shapes and colors to represent amino acids. It makes easier to spot crucial molecular information, including patches of amino acids or key interactions between side chains. Most conventions used in TALAIA are standard in chemistry and biochemistry, so experimentalists and modelers can rapidly grasp the meaning of any TALAIA depiction. RESULTS: We propose TALAIA as a tool that renders protein structures and encodes structure and physicochemical aspects as a simple visual grammar. The approach is fast, highly informative, and intuitive, allowing the identification of possible interactions, hydrophobic patches, and other characteristic structural features at first glance. The first implementation of TALAIA can be found at https://github.com/insilichem/talaia.

Tertiary care for infertile couples: aetiological diagnoses and conventional treatment outcomes in Kisangani, Democratic Republic of the Congo.

BACKGROUND: In sub-Saharan Africa, tubal factors are described as the main aetiological factors of infertility. Under these conditions, medically assisted procreation is particularly indicated. However, Assisted Reproductive Technology centres are less available. Thus, infertile couples are quickly oriented towards available alternative conventional treatments. The present study aimed to determine the aetiological factors of infertility, the outcomes of the therapeutic options offered, and the factors associated with the success of conventional treatment among infertile couples seeking tertiary care in Kisangani. METHODS: A cross-sectional study was conducted at two tertiary health facilities in Kisangani. Infertile couples who provided consent underwent specific examinations necessary for the exploration of infertility and were treated and followed up for a minimum of 6 months. The therapeutic options that were offered were expectant attitude, medical treatment, surgical treatment or transfer to an in vitro fertilization unit. The pregnancy diagnosis was performed by ultrasound. RESULTS: A total of 272 infertile couples underwent specific examinations, were treated and were followed up for a minimum of 6 months. Many determinant causes were mostly linked to wives rather than husbands. Overall, only 34 women among 211 who were treated became pregnant during the follow-up period; 61 couples were advised to resort to IVF or adoption, but the couples for whom expectant the attitude was indicated immediately rejected it. The patients who therapeutically succeeded at the end of the treatment were those who were younger than 35 years (OR = 2.27; 95% CI = 1.06-4.87; P = 0.017), had a duration of infertility of less than five years (OR = 6.08; 95% CI = 1.79-20.69; P = 0.001) and had secondary infertility (OR = 6.08; 95% CI = 1.79-20.69; P = 0.001). CONCLUSION: Kisangani faces a major issue in the treatment of infertility. Treatment of patients using conventional methods is limited by the predominance of tubal factors as aetiological determinants of infertility. The low pregnancy rate found in this study provided additional evidence of this. This paper represents a serious plea to national policy-makers to encourage them to pay attention to issues surrounding infertility.

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that-in the case of the interdependent tumor cell morphology and adapted immune response-reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM.

The Pattern of RNA Editing Changes in Pleural Mesothelioma upon Epithelial-Mesenchymal Transition.

Pleural mesothelioma (PM) is a cancer where epithelioid, biphasic and sarcomatoid histotypes are observed. Sarcomatoid PM is characterized by mesenchymal features. Multi-omics have been used to characterize the epithelial-to-mesenchymal (EMT) phenotype at the molecular level. We contribute to this effort by including the analysis of RNA editing. We extracted samples with the highest vs. lowest Epithelial score from two PM cohorts and observed increased RNA editing in introns and decreased RNA editing in 3'UTR upon EMT. The same was observed in primary PM primary cultures stratified by transcriptomics analysis into two groups, one of them enriched with mesenchymal features. Our data demonstrate that, as has been observed in other cancer types, RNA editing associates to EMT phenotype in PM.

Computational assessment of the impact of Cu(II) and Al(III) on ß-amyloid42 fibrils: Binding sites, structural stability, and possible physiological implications.

One of Alzheimer's disease major hallmarks is the aggregation of ß-amyloid peptide, a process in which metal ions play an important role. In the present work, an integrative computational study has been performed to identify the metal-binding regions and determine the conformational impact of Cu(II) and Al(III) ion binding to the ß-amyloid (Aß42) fibrillary structure. Through classical and Gaussian accelerated molecular dynamics, it has been observed that the metal-free fiber shows a hinge fan-like motion of the S-shaped structure, maintaining the general conformation. Upon metal coordination, distinctive patterns are observed depending on the metal. Cu(II) binds to the flexible N-terminal region and induces structural changes that could ultimately disrupt the fibrillary structure. In contrast, Al(III) binding takes place with the residues Glu22 and Asp23, and its binding reinforces the core stability of the system. These results give clues on the molecular impact of the interaction of metal ions with the aggregates and sustain their non-innocent roles in the evolution of the illness.

Delineating epileptogenic networks using brain imaging data and personalized modeling in drug-resistant epilepsy.

Precise estimates of epileptogenic zone networks (EZNs) are crucial for planning intervention strategies to treat drug-resistant focal epilepsy. Here, we present the virtual epileptic patient (VEP), a workflow that uses personalized brain models and machine learning methods to estimate EZNs and to aid surgical strategies. The structural scaffold of the patient-specific whole-brain network model is constructed from anatomical T1 and diffusion-weighted magnetic resonance imaging. Each network node is equipped with a mathematical dynamical model to simulate seizure activity. Bayesian inference methods sample and optimize key parameters of the personalized model using functional stereoelectroencephalography recordings of patients' seizures. These key parameters together with their personalized model determine a given patient's EZN. Personalized models were further used to predict the outcome of surgical intervention using virtual surgeries. We evaluated the VEP workflow retrospectively using 53 patients with drug-resistant focal epilepsy. VEPs reproduced the clinically defined EZNs with a precision of 0.6, where the physical distance between epileptogenic regions identified by VEP and the clinically defined EZNs was small. Compared with the resected brain regions of 25 patients who underwent surgery, VEP showed lower false discovery rates in seizure-free patients (mean, 0.028) than in non-seizure-free patients (mean, 0.407). VEP is now being evaluated in an ongoing clinical trial (EPINOV) with an expected 356 prospective patients with epilepsy.

Viral Mimicry Response Is Associated With Clinical Outcome in Pleural Mesothelioma.

Introduction: The aim of this study was to investigate endogenous retrovirus (ERV) expression and type I interferon (IFN) activation in human pleural mesothelioma (PM) and their association with clinical outcome. Methods: The expression of ERV was determined from PM cohorts and mesothelial precursor RNA sequencing data. The expression of ERV was confirmed by quantitative polymerase chain reaction (qPCR). Methylation of genomic DNA was assessed by quantitative methylation-specific PCR. DNA demethylation was induced in cells by demethylating agent 5-Aza-2'-deoxycytidine (5-Aza-CdR) treatment. To block type I IFN signaling, the cells were treated with ruxolitinib or MAVS silencing. The expression of IFN-stimulated genes (ISGs) was determined by qPCR and Western blot. Circulating ERVs were detected by qPCR. Results: Long terminal repeats (LTRs) represent the most abundant transposable elements up-regulated in PM. Within the LTR, ERVmap_1248 and LTR7Y, which are specifically enriched in PM, were further analyzed. The 5-Aza-CdR treatment increased the levels of ERVmap_1248 expression and induced ERVmap_1248 promoter demethylation in mesothelial cells. In addition, ERVmap_1248 promoter was more demethylated in the mesothelioma tissue compared with nontumor tissue. The 5-Aza-CdR treatment of the mesothelial cells also increased the levels of ISGs. Basal ISG expression was higher in the mesothelioma cells compared with the mesothelial cells, and it was significantly decreased by ruxolitinib treatment or MAVS silencing. Furthermore, ISG expression was higher in the tumor tissue with high expression levels of ERVmap_1248. High expression of ERVmap_1248 was associated with longer overall survival and BAP1 mutations. ERVmap_1248 and LTR7Y can be detected in the PM plasma. Conclusions: We provide clues for patient stratification especially for immunotherapy where best clinical responses are associated with an activated basal immune response.