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Abstract Schizophrenia is thought to reflect aberrant connectivity within cortico-cortical and reentrant thalamo-cortical loops, which physiologically integrate and coordinate the function of multiple cortical and subcortical structures. Despite extensive research, reliable biomarkers of such "dys-connectivity" remain to be identified at the onset of psychosis, and before exposure to antipsychotic drugs. Because slow waves travel across the brain during sleep, they represent an ideal paradigm to study pathological conditions affecting brain connectivity. Here, we provide proof–of–concept evidence for a novel approach to investigate slow wave traveling properties in First-Episode Psychosis (FEP) with high-density electroencephalography (EEG). Whole–night sleep recordings of 5 drug-naïve FEP and 5 age- and gender-matched healthy control subjects were obtained with a 256-channel EEG system. One patient was re-recorded after 6 months and 3 years of continuous clozapine treatment. Slow wave detection and traveling properties were obtained with an open-source toolbox. Slow wave density and slow wave traveled distance (measured as the line of longest displacement) were significantly lower in patients (p

Abstract A newborn Thoroughbred filly presented with a large mass located on the ventro‐rostral aspect of the mandible. The mass was surgically removed under general anaesthesia. Upon gross examination, the mass was well circumscribed with a heterogeneous lobulated appearance. The results of histopathology and immunohistochemistry were consistent with a diagnosis of congenital fetal rhabdomyoma. On follow‐up at six months post‐surgical excision, no abnormalities were noted on clinical examination.

Abstract Background Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produced several large-scale protein-protein interaction data sets for various organisms. It is important to develop tools for dissecting their content and analyse the information they embed by data-integration and computational methods. Results Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains. The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins in common biological processes. We present here a publicly available server that allows the user to investigate protein interaction data in light of other biological information, such as their sequences, presence of specific domains, process and component ontologies. The server can be effectively used to construct a high-confidence set of mutually exclusive interactions by identifying similar features in groups of proteins sharing a common interaction partner. As an example, we describe here the identification of common motifs, function, cellular localization and domains in different datasets of yeast interactions. Conclusions The server can be used to analyse user-supplied datasets, it contains pre-processed data for four yeast Protein Protein interaction datasets and the results of their statistical analysis. These show that the presence of common motifs in proteins interacting with the same partner is a valuable source of information, it can be used to investigate the properties of the interacting proteins and provides information that can be effectively integrated with other sources. As more experimental interaction data become available, this tool will become more and more useful to gain a more detailed picture of the interactome.

Abstract Background Peritoneal fluid lactate concentration is an important diagnostic tool in horses with abdominal pain. Information on peritoneal lactate concentrations is lacking following parturition in the mare. Objectives To compare blood and peritoneal lactate concentrations in a population of mares within 36 h post‐partum, report a normal reference range and identify any impact of retained foetal membranes (RFMs). Methods This is a retrospective study evaluating healthy mares from which blood and peritoneal samples had been obtained within 36 h of parturition. Exclusion criteria included signs of abdominal pain within this period. Data was interrogated for normality using a Shapiro–Wilk test. Wilcoxon signed‐rank test and Bland–Altman analysis were used to compare blood and peritoneal lactate concentrations. Linear regression was used to compare age and breed data with peritoneal lactate concentrations. Significance was defined as p

Accurate computational identification of B-cell epitopes is crucial for the development of vaccines, therapies, and diagnostic tools. However, current structure-based prediction methods face limitations due to the dependency on experimentally solved structures. Here, we introduce DiscoTope-3.0, a markedly improved B-cell epitope prediction tool that innovatively employs inverse folding structure representations and a positive-unlabelled learning strategy, and is adapted for both solved and predicted structures. Our tool demonstrates a considerable improvement in performance over existing methods, accurately predicting linear and conformational epitopes across multiple independent datasets. Most notably, DiscoTope-3.0 maintains high predictive performance across solved, relaxed and predicted structures, alleviating the need for experimental structures and extending the general applicability of accurate B-cell epitope prediction by 3 orders of magnitude. DiscoTope-3.0 is made widely accessible on two web servers, processing over 100 structures per submission, and as a downloadable package. In addition, the servers interface with RCSB and AlphaFoldDB, facilitating large-scale prediction across over 200 million cataloged proteins. DiscoTope-3.0 is available at: https://services.healthtech.dtu.dk/service.php?DiscoTope-3.0.

The aim of this study was to investigate the potential of potato proteins and peptides as emulsifiers in the microencapsulation of fish oil by spray-drying. Microcapsules were produced using a potato protein extract, and fractions enriched in patatin and protease inhibitors. Furthermore, bioinformatically predicted emulsifier peptides from abundant potato proteins and a hydrolysate, obtained through targeted proteolysis of the extract, were investigated. During 28 days of storage at 25 °C, peptides and the hydrolysate exhibited better emulsifying properties and higher encapsulation efficiencies compared to native proteins and sodium caseinate. Significant differences (p < 0.05) were observed in the peroxide value (PV) and secondary volatile oxidation products between the microcapsules produced with peptides and native proteins. Microcapsules produced with peptides and hydrolysate showed the highest oxidative stability, not exceeding a PV of 10 meq/kg oil, and with concentrations of volatiles below the odor threshold in oil for five of the six studied compounds. These results show the emulsifying potential of potato peptides and hydrolysate for use in microencapsulation of hydrophobic bioactive ingredients such as fish oil.

The TCRDivER algorithm incorporates both clone size and sequence similarity of T cell receptors (TCR) to reveal greater complexity in TCR repertoires and novel TCR repertoire traits due to a nonlinear correlation of the two.

Abstract We recently proposed a new approach for the real-time monitoring of particle therapy treatments with the goal of achieving high sensitivities on the particle range measurement already at limited counting statistics. This method extends the Prompt Gamma (PG) timing technique to obtain the PG vertex distribution from the exclusive measurement of particle Time-Of-Flight (TOF). It was previously shown, through Monte Carlo simulation, that an original data reconstruction algorithm (Prompt Gamma Time Imaging) allows to combine the response of multiple detectors placed around the target. The sensitivity of this technique depends on both the system time resolution and the beam intensity. At reduced intensities (Single Proton Regime—SPR), a millimetric proton range sensitivity can be achieved, provided the overall PG plus proton TOF can be measured with a 235 ps (FWHM) time resolution. At nominal beam intensities, a sensitivity of a few mm can still be obtained by increasing the number of incident protons included in the monitoring procedure. In this work we focus on the experimental feasibility of PGTI in SPR through the development of a multi-channel, Cherenkov-based PG detector with a targeted time resolution of 235 ps (FWHM): the TOF Imaging ARrAy (TIARA). Since PG emission is a rare phenomenon, TIARA design is led by the concomitant optimisation of its detection efficiency and Signal to Noise Ratio (SNR). The PG module that we developed is composed of a small PbF $$_{2}$$ 2 crystal coupled to a silicon photoMultiplier to provide the time stamp of the PG. This module is currently read in time coincidence with a diamond-based beam monitor placed upstream the target/patient to measure the proton time of arrival. TIARA will be eventually composed of 30 identical modules uniformly arranged around the target. The absence of a collimation system and the use of Cherenkov radiators are both crucial to increase the detection efficiency and the SNR, respectively. A first prototype of the TIARA block detector was tested with 63 MeV protons delivered from a cyclotron: a time resolution of 276 ps (FWHM) was obtained, resulting in a proton range sensitivity of 4 mm at 2 $$\sigma$$ σ with the acquisition of only 600 PGs. A second prototype was also evaluated with 148 MeV protons delivered from a synchro-cyclotron obtaining a time resolution below 167 ps (FWHM) for the gamma detector. Moreover, using two identical PG modules, it was shown that a uniform sensitivity on the PG profiles would be achievable by combining the response of gamma detectors uniformly distributed around the target. This work provides the experimental proof-of-concept for the development of a high sensitivity detector that can be used to monitor particle therapy treatments and potentially act in real-time if the irradiation does not comply to treatment plan.

Abstract Background In a range of human disorders such as multiple myeloma (MM), immunoglobulin light chains (IgLCs) can be produced at very high concentrations. This can lead to pathological aggregation and deposition of IgLCs in different tissues, which in turn leads to severe and potentially fatal organ damage. However, IgLCs can also be highly soluble and non-toxic. It is generally thought that the cause for this differential solubility behaviour is solely found within the IgLC amino acid sequences, and a variety of individual sequence-related biophysical properties (e.g. thermal stability, dimerisation) have been proposed in different studies as major determinants of the aggregation in vivo. Here, we investigate biophysical properties underlying IgLC amyloidogenicity. Results We introduce a novel and systematic workflow, Thermodynamic and Aggregation Fingerprinting (ThAgg-Fip), for detailed biophysical characterisation, and apply it to nine different MM patient-derived IgLCs. Our set of pathogenic IgLCs spans the entire range of values in those parameters previously proposed to define in vivo amyloidogenicity; however, none actually forms amyloid in patients. Even more surprisingly, we were able to show that all our IgLCs are able to form amyloid fibrils readily in vitro under the influence of proteolytic cleavage by co-purified cathepsins. Conclusions We show that (I) in vivo aggregation behaviour is unlikely to be mechanistically linked to any single biophysical or biochemical parameter and (II) amyloidogenic potential is widespread in IgLC sequences and is not confined to those sequences that form amyloid fibrils in patients. Our findings suggest that protein sequence, environmental conditions and presence and action of proteases all determine the ability of light chains to form amyloid fibrils in patients.

Lactic acid bacteria (LAB) have an extracellular proteolytic system that includes a multi-domain, cell envelope protease (CEP) with a subtilisin homologous protease domain. These CEPs have different proteolytic activities despite having similar protein sequences. Structural characterization has previously been limited to CEP homologs of dairy- and human-derived LAB strains, excluding CEPs of plant-derived LAB strains. CEP structures are a challenge to determine experimentally due to their large size and attachment to the cell envelope. This study aims to clarify the prevalence and structural diversity of CEPs by using the structure prediction software AlphaFold 2. Domain boundaries are clarified based on a comparative analysis of 21 three-dimensional structures, revealing novel domain architectures of CEP homologs that are not necessarily restricted to specific LAB species or ecological niches. The C-terminal flanking region of the protease domain is divided into fibronectin type-III-like domains with various structural traits. The analysis also emphasizes the existence of two distinct domains for cell envelope attachment that are preceded by an intrinsically disordered cell wall spanning domain. The domain variants and their combinations provide CEPs with different stability, proteolytic activity, and potentially adhesive properties, making CEPs targets for steering proteolytic activity with relevance for both food development and human health.

Abstract Background Major depressive disorder (MDD) patients not responding to two or more different antidepressant treatments are currently considered to suffer from treatment resistant depression (TRD). Recently, intranasal esketamine has been approved by both the American Food and Drug Administration and European Medicines Agency for TRD and, more recently, in moderate to severe episode of MDD, as acute short-term treatment for the rapid reduction of depressive symptoms, which, according to clinical judgement, constitute a psychiatric emergency. There is currently no indication for obsessive–compulsive disorder (OCD) although recently published studies have already shown a rapid and significant reduction of OCD-like symptoms following ketamine administration. The etiology of OCD has not yet been fully elucidated but there is a growing evidence that glutamate signaling dysfunction in the cortico-striatal–thalamo-cortical circuitry plays an essential role. This case report exemplifies possible clinical effects of esketamine on both depressive and OCD symptoms. Case presentation We present the case of a 39-year-old man suffering from TRD. During the first evaluation at our clinic, he also reported the presence of OCD spectrum symptoms, causing him to perform time-consuming mental rituals due to pathological doubts regarding the relationship with his wife as well as intrusive thoughts regarding his mental conditions. He underwent psychometric evaluations, therapeutic drug monitoring analysis, and pharmacogenomic tests. The overall results helped to explain patient’s treatment-resistance. Moreover, we observed a significant reduction in both depressive and OCD symptoms after administration of esketamine. Conclusion This case underlines the importance of pharmacogenomic tests in profiling TRD patients and confirms the possible use of esketamine in the treatment of comorbid OCD.

Obtaining a healthy wound environment that is conductive to healing in horses can be challenging. Negative-pressure wound therapy (NPWT) has been employed in humans to enhance wound healing for decades. The existing evidence for the effectiveness of NPWT remains uncertain in equine medicine. The aim of this review is to investigate NPWT applications and benefits in horses. A scoping review was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines for scoping reviews on three databases (PubMed, Web of Science-Thompson Reuters, and Wiley Online Library). Twenty-four manuscripts were considered. After removing duplicates, 17 papers underwent abstract screening. Of these, 16 + 1 (cited by others) were evaluated for eligibility according to PICOs, including no case reports/retrospective studies, four original articles, and three reviews. Fifteen manuscripts met the inclusion criteria. The focus of the articles was wound management; they included three reports of wounds communicating with synovial structures. Traumatic wounds and surgical-site infections are indications for NPWT. NPWT presents several advantages and few complications making it an attractive alternative to conventional wound management. However, randomized controlled trials should be performed to quantify the benefits and establish precise protocols in horses.

There has been increasing interest in the role of T cells and their involvement in cancer, autoimmune and infectious diseases. However, the nature of T cell receptor (TCR) epitope recognition at a repertoire level is not yet fully understood. Due to technological advances a plethora of TCR sequences from a variety of disease and treatment settings has become readily available. Current efforts in TCR specificity analysis focus on identifying characteristics in immune repertoires which can explain or predict disease outcome or progression, or can be used to monitor the efficacy of disease therapy. In this context, clustering of TCRs by sequence to reflect biological similarity, and especially to reflect antigen specificity have become of paramount importance. We review the main TCR sequence clustering methods and the different similarity measures they use, and discuss their performance and possible improvement. We aim to provide guidance for non-specialists who wish to use TCR repertoire sequencing for disease tracking, patient stratification or therapy prediction, and to provide a starting point for those aiming to develop novel techniques for TCR annotation through clustering.

The study of nuclear fission yields has a major impact on the characterization and understanding of the fission process and is mandatory for reactor applications. In the framework of a collaboration between the CEA, the LPSC and the ILL, a program of actinide fission yield measurements has been ongoing for several years at the LOHENGRIN spectrometer. However, the measurement of very low fission yields in the symmetry region and the heavy wing of the distributions is difficult to achieve due to the strong contamination by other masses with much higher yields and requires the development of a new experimental setup. This paper will first present the results of a new absolute measurement of the 235U(nth,f) mass yields using an ionization chamber placed at the exit of the spectrometer. Although very well documented in the literature, these yields show uncertainties lying from 3% to 10% with large discrepancies between libraries and a lack of correlation matrices. New experimental data obtained at the LOHENGRIN spectrometer will be detailed, along with the measurement method and the production of the experimental covariance matrix. The second part will show the development of a Time of Flight (ToF) line in order to improve the background rejection in the mass yield measurements. In the symmetry region, the precision of the measurement is limited by the background estimation due to the charge exchanges with the residual gas of the separator. We plan to analyze the events using a triple coincidence (∆E x E) x ToF, whereas today only (∆E x E) selection is available. The new ToF line is built using Si3N4 foils and secondary electron detectors (SED) for the start and stop detectors. We will present the choices made for the SED technology along with the progress achieved on the ToF line characterization.

T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for epitope prediction, with a particular focus on tools aimed at identifying neoepitopes, i.e. cancer-specific peptides and their potential for use in immunotherapy for cancer treatment. This review will cover how these tools work, what kind of data they use, as well as pros and cons in their respective applications.

Experimental fission studies for reaction physics or nuclear spectroscopy can profit from fast, efficient, and radiation-resistant fission fragment (FF) detectors. When such experiments are performed in-beam in intense thermal neutron beams, additional constraints arise in terms of target-detector interface, beam-induced background, etc. Therefore, wide gap semi-conductor detectors were tested with the aim of developing innovative instrumentation for such applications. The detector characterization was performed with mass- and energy-separated fission fragment beams at the ILL (Institut Laue Langevin) LOHENGRIN spectrometer. Two single crystal diamonds, three polycrystalline and one diamond-on-iridium as well as a silicon carbide detector were characterized as solid state ionization chamber for FF detection. Timing measurements were performed with a 500-µm thick single crystal diamond detector read out by a broadband amplifier. A timing resolution of ∼10.2 ps RMS was obtained for FF with mass A = 98 at 90 MeV kinetic energy. Using a spectroscopic preamplifier developed at INFN-Milano, the energy resolution measured for the same FF was found to be slightly better for a ∼50-µm thin single crystal diamond detector (∼1.4% RMS) than for the 500-µm thick one (∼1.6% RMS), while a value of 3.4% RMS was obtained with the 400-µm silicon carbide detector. The Pulse Height Defect (PHD), which is significant in silicon detectors, was also investigated with the two single crystal diamond detectors. The comparison with results from α and triton measurements enabled us to conclude that PHD leads to ∼50% loss of the initial generated charge carriers for FF. In view of these results, a possible detector configuration and integration for in-beam experiments has been discussed.

Background Methods We evaluated the impact of a high percentage of leukemia blast contamination in patient-derived starting material (SM) on CAR T-cell drug product (DP) manufacturing. In vitro as well as in vivo models were employed to identify characteristics of the construct associated with better profile of safety in case of inadvertent B-cell leukemia transduction during CAR T-cell manufacturing.Results The presence of large amounts of CD19+ cells in SM did not affect the transduction level of DPs, as well as the CAR T-cell rate of expansion at the end of standard production of 14 days. DPs were deeply characterized by flow cytometry and molecular biology for Ig-rearrangements, showing that the level of B-cell contamination in DPs did not correlate with the percentage of CD19+ cells in SM, in the studied patient cohort. Moreover, we investigated whether CAR design may affect the control of CAR+ leukemia cells. We provided evidences that CAR.CD19 short linker (SL) prevents complete epitope masking in CD19+CAR+ leukemia cells and we demonstrated in vitro and in vivo that CD19 +CAR(SL)+leukemic cells are killed by CAR.CD19 T-cells.Conclusions Taken together, these data suggest that a VL-VH SL may result in a safe CAR-T product, even when manufacturing starts from biological materials characterized by heavy contamination of leukemia blasts.

Abstract Background The development of accurate epitope prediction tools is important in facilitating disease diagnostics, treatment and vaccine development. The advent of new approaches making use of antibody and TCR sequence information to predict receptor-specific epitopes have the potential to transform the epitope prediction field. Development and validation of these new generation of epitope prediction methods would benefit from regularly updated high-quality receptor-antigen complex datasets. Results To address the need for high-quality datasets to benchmark performance of these new generation of receptor-specific epitope prediction tools, a webserver called SCEptRe (Structural Complexes of Epitope-Receptor) was created. SCEptRe extracts weekly updated 3D complexes of antibody-antigen, TCR-pMHC and MHC-ligand from the Immune Epitope Database and clusters them based on antigen, receptor and epitope features to generate benchmark datasets. SCEptRe also provides annotated information such as CDR sequences and VDJ genes on the receptors. Users can generate custom datasets based by selecting thresholds for structural quality and clustering parameters (e.g. resolution, R-free factor, antigen or epitope sequence identity) based on their need. Conclusions SCEptRe provides weekly updated, user-customized comprehensive benchmark datasets of immune receptor-epitope structural complexes. These datasets can be used to develop and benchmark performance of receptor-specific epitope prediction tools in the future. SCEptRe is freely accessible at http://tools.iedb.org/sceptre.

The patent literature should reflect the past 30 years of engineering efforts directed toward developing monoclonal antibody therapeutics. Such information is potentially valuable for rational antibody design. Patents, however, are designed not to convey scientific knowledge, but to provide legal protection. It is not obvious whether antibody information from patent documents, such as antibody sequences, is useful in conveying engineering know-how, rather than as a legal reference only. To assess the utility of patent data for therapeutic antibody engineering, we quantified the amount of antibody sequences in patents destined for medicinal purposes and how well they reflect the primary sequences of therapeutic antibodies in clinical use. We identified 16,526 patent families covering major jurisdictions (e.g., US Patent and Trademark Office (USPTO) and World Intellectual Property Organization) that contained antibody sequences. These families held 245,109 unique antibody chains (135,397 heavy chains and 109,712 light chains) that we compiled in our Patented Antibody Database (PAD, http://naturalantibody.com/pad). We find that antibodies make up a non-trivial proportion of all patent amino acid sequence depositions (e.g., 11% of USPTO Full Text database). Our analysis of the 16,526 families demonstrates that the volume of patent documents with antibody sequences is growing, with the majority of documents classified as containing antibodies for medicinal purposes. We further studied the 245,109 antibody chains from patent literature to reveal that they very well reflect the primary sequences of antibody therapeutics in clinical use. This suggests that the patent literature could serve as a reference for previous engineering efforts to improve rational antibody design.

The cell envelope proteinase (CEP) of Lactococcus lactis is a large extracellular protease covalently linked to the peptidoglycan of the cell wall. Strains of L. lactis are typically auxotrophic for several amino acids and in order to grow to high cell densities in milk they need an extracellular protease. The structure of the entire CEP enzyme is difficult to determine experimentally due to the large size and due to the attachment to the cell surface. We here describe the use of a combination of structure prediction tools to create a structural model for the entire CEP enzyme of Lactococcus lactis. The model has implications for how the bacterium interacts with casein micelles during growth in milk, and it has implications regarding the energetics of the proteolytic system. Our model for the CEP indicates that the catalytic triad is activated through a structural change caused by interaction with the substrate. The CEP of L. lactis might become a useful model for the mode of action for enzymes belonging to the large class of S8 proteinases with a PA (protease associated) domain and a downstream fibronectin like domain.

Approximately 30% of Major Depressive Disorder (MDD) patients develop treatment-resistant depression (TRD). Among the different causes that make TRD so challenging in both clinical and research contexts, major roles are played by the inadequate understanding of MDD pathophysiology and the limitations of current pharmacological treatments. Nevertheless, the field of psychiatry is facing exciting times. Combined with recent advances in genome editing techniques, human induced pluripotent stem cell (hiPSC) technology is offering novel and unique opportunities in both disease modelling and drug discovery. This technology has allowed innovative disease-relevant patient-specific in vitro models to be set up for many psychiatric disorders. Such models hold great potential in enhancing our understanding of MDD pathophysiology and overcoming many of the well-known practical limitations inherent to animal and post-mortem models. Moreover, the field is approaching the advent of (es)ketamine, a glutamate N-methyl- d -aspartate (NMDA) receptor antagonist, claimed as one of the first and exemplary agents with rapid (in hours) antidepressant effects, even in TRD patients. Although ketamine seems poised to transform the treatment of depression, its exact mechanisms of action are still unclear but greatly demanded, as the resulting knowledge may provide a model to understand the mechanisms behind rapid-acting antidepressants, which may lead to the discovery of novel compounds for the treatment of depression. After reviewing insights into ketamine’s mechanisms of action (derived from preclinical animal studies) and depicting the current state of the art of hiPSC technology below, we will consider the implementation of an hiPSC technology-based TRD model for the study of ketamine’s fast acting antidepressant mechanisms of action.

Abstract Background Although the etiology of chronic lymphocytic leukemia (CLL), the most common type of adult leukemia, is still unclear, strong evidence implicates antigen involvement in disease ontogeny and evolution. Primary and 3D structure analysis has been utilised in order to discover indications of antigenic pressure. The latter has been mostly based on the 3D models of the clonotypic B cell receptor immunoglobulin (BcR IG) amino acid sequences. Therefore, their accuracy is directly dependent on the quality of the model construction algorithms and the specific methods used to compare the ensuing models. Thus far, reliable and robust methods that can group the IG 3D models based on their structural characteristics are missing. Results Here we propose a novel method for clustering a set of proteins based on their 3D structure focusing on 3D structures of BcR IG from a large series of patients with CLL. The method combines techniques from the areas of bioinformatics, 3D object recognition and machine learning. The clustering procedure is based on the extraction of 3D descriptors, encoding various properties of the local and global geometrical structure of the proteins. The descriptors are extracted from aligned pairs of proteins. A combination of individual 3D descriptors is also used as an additional method. The comparison of the automatically generated clusters to manual annotation by experts shows an increased accuracy when using the 3D descriptors compared to plain bioinformatics-based comparison. The accuracy is increased even more when using the combination of 3D descriptors. Conclusions The experimental results verify that the use of 3D descriptors commonly used for 3D object recognition can be effectively applied to distinguishing structural differences of proteins. The proposed approach can be applied to provide hints for the existence of structural groups in a large set of unannotated BcR IG protein files in both CLL and, by logical extension, other contexts where it is relevant to characterize BcR IG structural similarity. The method does not present any limitations in application and can be extended to other types of proteins.

Esketamine (ESK) has been approved as a rapid-acting intranasal treatment for treatment-resistant depression (TRD). Although existing studies have investigated the efficacy of ESK in the 4-week induction phase, our knowledge about long-term ESK efficacy remains poor. The aim of this systematic review was to summarize the available data on long-term ESK efficacy for TRD. A systematic search was performed including articles in English, up to 31 March 2021. The search found 7 relevant studies, involving 1024 adult TRD patients. Continuing treatment with ESK after the 4-week induction phase may be associated with stable efficacy in relapse prevention among TRD patients. Conversely, the long-term antidepressant effectiveness upon discontinuation of ESK might be limited, although data from three studies had a moderate to high risk of bias. Overall, the results on the effectiveness of this compound in the long term are mixed. According to our findings, ESK treatment should be continued following the induction phase to reach a stable efficacy in relapse prevention, while the long-term antidepressant and anti-suicidal effects of ESK after discontinuation are inconsistent. Currently, the level of proof of ESK efficacy in long-term TRD treatment remains low and more RCTs with larger sample sizes and active comparators are needed.

Antibodies are important for immunity and exist in several classes (IgM, IgD, IgA, IgG, IgE). They are composed of symmetric dimeric molecules with two antigen binding regions (Fab) and a constant part (Fc), usually depicted as Y-shaped molecules. Rheumatoid factors found in patients with rheumatoid arthritis are autoantibodies binding to IgG and paradoxically appear to circulate in blood alongside with their antigen (IgG) without reacting with it. Here, it is shown that rheumatoid factors do not react with native IgG in solution, and that their epitopes only become accessible upon certain physico-chemical treatments (e.g. heat treatment at 57 °C), by physical adsorption on a hydrophobic surface or by antigen binding. Moreover, chemical cross-linking in combination with mass spectrometry showed that the native state of IgG is a compact (closed) form and that the Fab parts of IgG shield the Fc region and thereby control access of rheumatoid factors and presumably also some effector functions. It can be inferred that antibody binding to pathogen surfaces induces a conformational change, which exposes the Fc part with its effector sites and rheumatoid factor epitopes. This has strong implications for understanding antibody structure and physiology and necessitates a conceptual reformulation of IgG models.

Epsins are part of the internalization machinery pivotal to control clathrin-mediated endocytosis. Here, we report that epsin family members are expressed in mouse embryonic stem cells (mESCs) and that epsin1/2 knockdown alters both mESC exits from pluripotency and their differentiation. Furthermore, we show that epsin1/2 knockdown compromises the correct polarization and division of mESC-derived neural progenitors and their conversion into expandable radial glia-like neural stem cells. Finally, we provide evidence that Notch signaling is impaired following epsin1/2 knockdown and that experimental restoration of Notch signaling rescues the epsin-mediated phenotypes. We conclude that epsins contribute to control mESC exit from pluripotency and allow their neural differentiation by appropriate modulation of Notch signaling.

Protein hydrolysates show great promise as bioactive food and feed ingredients and for valorization of side-streams from e.g., the fish processing industry. We present a novel approach for hydrolysate characterization that utilizes proteomics data for calculation of weighted mean peptide properties (length, molecular weight, and charge) and peptide-level abundance estimation. Using a novel bioinformatic approach for subsequent prediction of biofunctional properties of identified peptides, we are able to provide an unprecedented, in-depth characterization. The study further characterizes bulk emulsifying, foaming, and in vitro antioxidative properties of enzymatic hydrolysates derived from cod frame by application of Alcalase and Neutrase, individually and sequentially, as well as the influence of heat pre-treatment. All hydrolysates displayed comparable or higher emulsifying activity and stability than sodium caseinate. Heat-treatment significantly increased stability but showed a negative effect on the activity and degree of hydrolysis. Lower degrees of hydrolysis resulted in significantly higher chelating activity, while the opposite was observed for radical scavenging activity. Combining peptide abundance with bioinformatic prediction, we identified several peptides that are likely linked to the observed differences in bulk emulsifying properties. The study highlights the prospects of applying proteomics and bioinformatics for hydrolysate characterization and in food protein science.

We measured the radiation tolerance of commercially available diamonds grown by the Chemical Vapor Deposition process by measuring the charge created by a 120 GeV hadron beam in a 50 μm pitch strip detector fabricated on each diamond sample before and after irradiation. We irradiated one group of samples with 70 MeV protons, a second group of samples with fast reactor neutrons (defined as energy greater than 0.1 MeV), and a third group of samples with 200 MeV pions, in steps, to (8.8±0.9) × 1015 protons/cm2, (1.43±0.14) × 1016 neutrons/cm2, and (6.5±1.4) × 1014 pions/cm2, respectively. By observing the charge induced due to the separation of electron–hole pairs created by the passage of the hadron beam through each sample, on an event-by-event basis, as a function of irradiation fluence, we conclude all datasets can be described by a first-order damage equation and independently calculate the damage constant for 70 MeV protons, fast reactor neutrons, and 200 MeV pions. We find the damage constant for diamond irradiated with 70 MeV protons to be 1.62±0.07(stat)±0.16(syst)× 10−18 cm2/(p μm), the damage constant for diamond irradiated with fast reactor neutrons to be 2.65±0.13(stat)±0.18(syst)× 10−18 cm2/(n μm), and the damage constant for diamond irradiated with 200 MeV pions to be 2.0±0.2(stat)±0.5(syst)× 10−18 cm2/(π μm). The damage constants from this measurement were analyzed together with our previously published 24 GeV proton irradiation and 800 MeV proton irradiation damage constant data to derive the first comprehensive set of relative damage constants for Chemical Vapor Deposition diamond. We find 70 MeV protons are 2.60 ± 0.29 times more damaging than 24 GeV protons, fast reactor neutrons are 4.3 ± 0.4 times more damaging than 24 GeV protons, and 200 MeV pions are 3.2 ± 0.8 more damaging than 24 GeV protons. We also observe the measured data can be described by a universal damage curve for all proton, neutron, and pion irradiations we performed of Chemical Vapor Deposition diamond. Finally, we confirm the spatial uniformity of the collected charge increases with fluence for polycrystalline Chemical Vapor Deposition diamond, and this effect can also be described by a universal curve.

The paper aim is to describe the major findings of a PhD research having the objective of defining and developing an instrument (Green City Circle) for the design of existing urban districts, through a circular approach and with the point of view of resilience and energy efficiency. The research approach is multi-disciplinary, aiming to evaluate both risk resilience and slower processes on an eco-systemic perspective. The paper aims to reflect upon these questions by deepening the study of a set of Key Performance Indicator and of alternative scenarios composition. The instrument’s target has been selected into local public bodies as major enablers of local regeneration.