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Background: Short-term forecasts of infectious disease contribute to situational awareness and capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise forecasts’ predictive performance by combining independent models into an ensemble. Here we report the performance of ensemble predictions of COVID-19 cases and deaths across Europe from March 2021 to March 2022. Methods: We created the European COVID-19 Forecast Hub, an online open-access platform where modellers upload weekly forecasts for 32 countries with results publicly visualised and evaluated. We created a weekly ensemble forecast from the equally-weighted average across individual models’ predictive quantiles. We measured forecast accuracy using a baseline and relative Weighted Interval Score (rWIS). We retrospectively explored ensemble methods, including weighting by past performance. Results: We collected weekly forecasts from 48 models, of which we evaluated 29 models alongside the ensemble model. The ensemble had a consistently strong performance across countries over time, performing better on rWIS than 91% of forecasts for deaths (N=763 predictions from 20 models), and 83% forecasts for cases (N=886 predictions from 23 models). Performance remained stable over a 4-week horizon for death forecasts but declined with longer horizons for cases. Among ensemble methods, the most influential choice came from using a median average instead of the mean, regardless of weighting component models. Conclusions: Our results support combining independent models into an ensemble forecast to improve epidemiological predictions, and suggest that median averages yield better performance than methods based on means. We highlight that forecast consumers should place more weight on incident death forecasts than case forecasts at horizons greater than two weeks. Funding: European Commission, Ministerio de Ciencia, Innovación y Universidades, FEDER; Ag

Phosphate is regulated by the kidneys and the osseus system, mainly due to the action of parathyroid hormone (PTH) and a recently described molecule, fibroblast growth factor 23 (FGF-23). We present the cases of two patients, mother and son with X-chromosome linked hypophosphatemic rickets. The genetic study was performed, and a mutation in the PHEX gene was identified, a splicing type pathogenic variant in hemizygosis. This mutation was previously described as HGMD CS126536. Hypophosphatemic rickets belongs to a group of tubulopathies characterized by hyperphosphaturia. PHEX gene mutation with function loss leads to increased FGF-23 levels. PHEX degrades FGF-23 into inactive fragments, preventing excessive phosphate excretion and the development of hypophosphatemia. In patients with PTH or vitamin D non-dependent hypophosphatemia, a diagnosis of X-chromosome linked hypophosphatemic rickets should be considered., El Fósforo es regulado por el riñón y el sistema óseo orquestado principalmente por la acción de la parathormona (PTH) y una molécula recientemente descrita como el factor de crecimiento fibroblástico 23 (FGF-23). Presentamos los casos de dos pacientes madre-hijo con Raquitismo hipofosfatémico ligado al cromosoma X. Se realizó el estudio genético identificándose una mutación en el Gen PHEX: variante patogénica tipo splicing en hemicigosis: mutación previamente descrita como HGMD CS126536.El Raquitismo Hipofosfatémico forma parte de un grupo de tubulopatías caracterizadas hiperfosfaturia. La mutación del gen PHEX con pérdida de función conduce al aumento de FGF-23.PHEX degrada el FGF-23 en fragmentos inactivos, evitando la excreción excesiva de fosfatos y el desarrollo de hipofosfatemia. En un paciente con hipofosfatemia no dependiente de la hormona PTH o de la vitamina D y de presentación familiar debe considerarse el diagnóstico de Raquitismo hipofosfatémico ligado al cromosoma X

Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast mod

Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast mod

Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast mod

L'aterosclerosi és una malaltia inflamatòria que afecta artèries grans i mitjanes. Això es produeix a causa de l'acumulació de placa a les parets. Aquest procés d'acumulació és lent i es produeix al llarg de dècades, podent arribar, en casos extrems, al trencament de la placa (la qual cosa pot produir trombes que obstrueixin el reg sanguini). S'està duent a terme una investigació per poder realitzar l'estudi tensional d'artèries afectades a partir de seccions transversals per tal de poder predir amb més precisió si aquestes tenen perill de trencament o no. En el marc de la investigació esmentada, en aquest estudi es pretén determinar quins són els paràmetres mínims necessaris per poder caracteritzar la configuració de cada secció i estudiar l'estat tensional de les artèries amb la mínima quantitat d'informació possible. Per això, en primer lloc, s'han homogeneïtzat les dades geomètriques de les seccions transversals a partir de diferents mètodes, com el mètode del conjunt de nivells (Level Set method). Un cop fet això, s'han utilitzat diferents algorismes, tant lineals (ACP) com no lineals (kACP), per a la reducció dimensional de les variables que diferenciïn les seccions d'artèries estables de les inestables i així poder representar les dades amb la menor quantitat de paràmetres possible. S'ha arribat a la conclusió que aquells paràmetres que tenen un paper més important a l'hora de poder diferenciar entre les seccions d'un grup i d'un altre són l'àrea de la secció arterial, el seu índex de remodelització, la càrrega de la placa i l'angle de les calcificacions. Tot això tenint en compte que només s'han utilitzat les dades geomètriques de seccions transversals d'artèries., La aterosclerosis es una enfermedad inflamatoria que afecta a arterias grandes y medianas. Esto se produce debido a la acumulación de placa en las paredes. Este proceso de acumulación es lento y se produce a lo largo de décadas, pudiendo llegar, en casos extremos, a la rotura de la placa (lo que puede producir trombos que obstruyan el riego sanguíneo). Se está llevando a cabo una investigación para poder realizar el estudio tensional de arterias afectadas a partir de secciones transversales para poder predecir con mayor precisión si éstas tienen peligro de rotura o no. En el marco de dicha investigación, en el presente estudio se pretende determinar cuáles son los parámetros mínimos necesarios para poder caracterizar la configuración de cada sección y estudiar el estado tensional de las arterias con la mínima cantidad de información posible. Por eso, en primer lugar, se han homogeneizado los datos geométricos de las secciones transversales a partir de diferentes métodos, como el método del conjunto de niveles (Level Set method). Una vez hecho esto, se han utilizado diferentes algoritmos, tanto lineales (ACP) como no lineales (kACP), para la reducción dimensional de las variables que diferencien las secciones de arterias estables de las inestables y así poder representar los datos con la menor cantidad de parámetros posible. Se ha llegado a la conclusión de que aquellos parámetros que tienen un papel más importante a la hora de poder diferenciar entre las secciones de un grupo y otro son el área de la sección arterial, su índice de remodelización, la carga de la placa y el ángulo de las calcificaciones. Todo esto teniendo en cuenta que sólo se han utilizado los datos geométricos de secciones transversales de arterias., Atherosclerosis is an inflammatory disease that affects large and medium arteries. This occurs due to the accumulation of plaque on its walls. This accumulation process is slow and occurs over decades, and can lead, in extreme cases, to rupture of the plaque (which can produce thrombi that obstruct the blood supply). An investigation is being carried out in order to carry out the tension study of affected arteries from their cross sections to predict with greater precision if they are in danger of rupture or not. Within the framework of this research, the present study intends to determine the minimum parameters necessary to be able to characterize the configuration of each section and study the tension state of the arteries with the minimum amount of information possible. To do this, first, the geometric data of the cross-sections have been homogenized using different methods, such as the Level Set method. Once this is done, different algorithms have been used, both linear (PCA) and non-linear (kPCA), for the dimensional reduction of the variables that differentiate the sections of stable arteries from unstable ones and thus be able to represent the data with the least amount of parameters possible. It has been concluded that those parameters that play a more important role when it comes to being able to differentiate between the sections of one group and another are the area of the arterial section, its remodeling index, the plaque load and the angle of calcifications. All this taking into account that only the geometric data of cross-sections of arteries have been taken into account.

Temporal analysis of deformations Time Series (TS) provides detailed information of various natural and humanmade displacements. Interferometric Synthetic Aperture Radar (InSAR) generates millimetre-scale products, indicating the chronicle behaviour of detected targets via TS products. Deep Learning (DL) can handle a massive load of InSAR TS to categorize significant movements from non-moving targets. To this end, we employed a supervised Convolutional Neural Network (CNN) model to distinguish five deformations trends, including Stable, Linear, Quadratic, Bilinear, and Phase Unwrapping Error (PUE). Considering several arguments in a CNN model, we trained numerous combinations to explore the most accurate combination from 5000 samples extracted from a Persistent Scatterer Interferometry (PSI) technique and Sentinel-1 images over the Granada region, Spain. The model overall accuracy exceeds 92%. Deformations of three cases of landslides were also detected over the same area, including the Cortijo de Lorenzo, El Arrecife, and Rules Viaduct areas., Peer Reviewed, Postprint (published version)

Highlights • Photogrammetry is used to construct a 3D-model of the collapsed ‘Azure Window’ coastal arch. • The 3D-model enables reconstruction and understanding of the dynamics of the collapse event. • The collapse entailed erosion at the base of the pillar, collapsing in the southwest direction. • The bridge collapsed vertically upon loss of support from the pillar. • Breakup occurred along the lithological boundary and existing joints. Abstract The Azure Window was a natural arch situated in the west coast of Gozo (Maltese Archipelago) that collapsed in March 2017. We employ a Diver Propulsion Vehicle-mounted camera system to capture data for the 3D-modeling of this collapsed arch via photogrammetry. We demonstrate use of this method to document complex underwater geomorphology spread across a large area, and draw up a geomorphic assessment of the site and collapse event on the basis of this 3D-model. The methodology enables a reconstruction and understanding of the collapse event. On account of the high-resolution attained, we are able to cross-match the principal submerged components with their pre-collapse location; this enables an understanding of the dynamics of the collapse, confirmation of rock break-up along existing joints, and mapping the distribution of the rock and debris from the collapse event. We conclude that the key stages in the collapse of the Azure Window entailed erosion at the base of the pillar, leading to the latter's collapse in the southwest direction, breaking into two main sections that separated along the lithological boundary. We also find clear evidence that separation of some sections of the pillar followed pre-existing joints. The bridge collapsed vertically upon loss of support from the pillar, breaking into two main components and many other fragments. We also document further changes at the site post-collapse. We show that this approach can be utilised to understand and characterise such events even when significant time has el

The increasing availability of Synthetic Aperture Radar (SAR) images facilitates the genera- tion of rich Differential Interferometric SAR (DInSAR) data. Temporal analysis of DInSAR products, and in particular deformation Time Series (TS), enables advanced investigations for ground deforma- tion identification. Machine Learning algorithms offer efficient tools for classifying large volumes of data. In this study, we train supervised Machine Learning models using 5000 reference samples of three datasets to classify DInSAR TS in five deformation trends: Stable, Linear, Quadratic, Bilinear, and Phase Unwrapping Error. General statistics and advanced features are also computed from TS to assess the classification performance. The proposed methods reported accuracy values greater than 0.90, whereas the customized features significantly increased the performance. Besides, the importance of customized features was analysed in order to identify the most effective features in TS classification. The proposed models were also tested on 15000 unlabelled data and compared to a model-based method to validate their reliability. Random Forest and Extreme Gradient Boosting could accurately classify reference samples and positively assign correct labels to random samples. This study indicates the efficiency of Machine Learning models in the classification and management of DInSAR TSs, along with shortcomings of the proposed models in classification of nonmoving targets (i.e., false alarm rate) and a decreasing accuracy for shorter TS., This work is part of the Spanish Grant SARAI, PID2020-116540RB-C21, funded by MCIN/ AEI/10.13039/501100011033. Additionally, it has been supported by the European Regional Devel- opment Fund (ERDF) through the project “RISKCOAST” (SOE3/P4/E0868) of the Interreg SUDOE Programme. Additionally, this work has been co-funded by the European Union Civil Protection through the H2020 project RASTOOL (UCPM-2021-PP-101048474)., Peer Reviewed, Postprint (published version)

In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement's breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.

Highlights • Photogrammetry is used to construct a 3D-model of the collapsed ‘Azure Window’ coastal arch. • The 3D-model enables reconstruction and understanding of the dynamics of the collapse event. • The collapse entailed erosion at the base of the pillar, collapsing in the southwest direction. • The bridge collapsed vertically upon loss of support from the pillar. • Breakup occurred along the lithological boundary and existing joints. Abstract The Azure Window was a natural arch situated in the west coast of Gozo (Maltese Archipelago) that collapsed in March 2017. We employ a Diver Propulsion Vehicle-mounted camera system to capture data for the 3D-modeling of this collapsed arch via photogrammetry. We demonstrate use of this method to document complex underwater geomorphology spread across a large area, and draw up a geomorphic assessment of the site and collapse event on the basis of this 3D-model. The methodology enables a reconstruction and understanding of the collapse event. On account of the high-resolution attained, we are able to cross-match the principal submerged components with their pre-collapse location; this enables an understanding of the dynamics of the collapse, confirmation of rock break-up along existing joints, and mapping the distribution of the rock and debris from the collapse event. We conclude that the key stages in the collapse of the Azure Window entailed erosion at the base of the pillar, leading to the latter's collapse in the southwest direction, breaking into two main sections that separated along the lithological boundary. We also find clear evidence that separation of some sections of the pillar followed pre-existing joints. The bridge collapsed vertically upon loss of support from the pillar, breaking into two main components and many other fragments. We also document further changes at the site post-collapse. We show that this approach can be utilised to understand and characterise such events even when significant time has el

Many countries hit by the COVID-19 epidemic consider the introduction of vaccination passes. So far, no thorough impact assessment of vaccination passes and of lower restrictions for their holders has been conducted. Here, we propose the VAP-SIRS model that accounts for susceptible, infected, and recovered subpopulations, also within the group of vaccinated pass holders. The model accounts for imperfect vaccination effectiveness, revaccinations and waning immunity. Different restrictions for pass holders and the rest of the population result in different scenarios of the epidemic evolution, some of which yield unfavourable COVID-19 dynamics and new waves. We identify critical variables that should be considered by policymakers and show how unfavourable outcomes can be avoided using adaptive policies. In particular, while pass holders could initially be allowed large freedoms, the gradual loss of immunity will require either increased restrictions for pass holders, or accelerated revaccination. In the long-term, common restrictions for both the pass holders and the rest of the population will have to be kept to avoid epidemic resurgence. Such minimum required restrictions depend on vaccination effectiveness, revaccination rate, waning rate and fraction of never-vaccinated population, and, for realistic combinations of these parameters, range between 29% and 69% reduction of contacts.

Many countries hit by the COVID-19 epidemic consider the introduction of vaccination passes. So far, no thorough impact assessment of vaccination passes and of lower restrictions for their holders has been conducted. Here, we propose the VAP-SIRS model that accounts for susceptible, infected, and recovered subpopulations, also within the group of vaccinated pass holders. The model accounts for imperfect vaccination effectiveness, revaccinations and waning immunity. Different restrictions for pass holders and the rest of the population result in different scenarios of the epidemic evolution, some of which yield unfavourable COVID-19 dynamics and new waves. We identify critical variables that should be considered by policymakers and show how unfavourable outcomes can be avoided using adaptive policies. In particular, while pass holders could initially be allowed large freedoms, the gradual loss of immunity will require either increased restrictions for pass holders, or accelerated revaccination. In the long-term, common restrictions for both the pass holders and the rest of the population will have to be kept to avoid epidemic resurgence. Such minimum required restrictions depend on vaccination effectiveness, revaccination rate, waning rate and fraction of never-vaccinated population, and, for realistic combinations of these parameters, range between 29% and 69% reduction of contacts.

Many countries hit by the COVID-19 epidemic consider the introduction of vaccination passes. So far, no thorough impact assessment of vaccination passes and of lower restrictions for their holders has been conducted. Here, we propose the VAP-SIRS model that accounts for susceptible, infected, and recovered subpopulations, also within the group of vaccinated pass holders. The model accounts for imperfect vaccination effectiveness, revaccinations and waning immunity. Different restrictions for pass holders and the rest of the population result in different scenarios of the epidemic evolution, some of which yield unfavourable COVID-19 dynamics and new waves. We identify critical variables that should be considered by policymakers and show how unfavourable outcomes can be avoided using adaptive policies. In particular, while pass holders could initially be allowed large freedoms, the gradual loss of immunity will require either increased restrictions for pass holders, or accelerated revaccination. In the long-term, common restrictions for both the pass holders and the rest of the population will have to be kept to avoid epidemic resurgence. Such minimum required restrictions depend on vaccination effectiveness, revaccination rate, waning rate and fraction of never-vaccinated population, and, for realistic combinations of these parameters, range between 29% and 69% reduction of contacts.

Many countries hit by the COVID-19 epidemic consider the introduction of vaccination passes. So far, no thorough impact assessment of vaccination passes and of lower restrictions for their holders has been conducted. Here, we propose the VAP-SIRS model that accounts for susceptible, infected, and recovered subpopulations, also within the group of vaccinated pass holders. The model accounts for imperfect vaccination effectiveness, revaccinations and waning immunity. Different restrictions for pass holders and the rest of the population result in different scenarios of the epidemic evolution, some of which yield unfavourable COVID-19 dynamics and new waves. We identify critical variables that should be considered by policymakers and show how unfavourable outcomes can be avoided using adaptive policies. In particular, while pass holders could initially be allowed large freedoms, the gradual loss of immunity will require either increased restrictions for pass holders, or accelerated revaccination. In the long-term, common restrictions for both the pass holders and the rest of the population will have to be kept to avoid epidemic resurgence. Such minimum required restrictions depend on vaccination effectiveness, revaccination rate, waning rate and fraction of never-vaccinated population, and, for realistic combinations of these parameters, range between 29% and 69% reduction of contacts.

Many countries hit by the COVID-19 epidemic consider the introduction of vaccination passes. So far, no thorough impact assessment of vaccination passes and of lower restrictions for their holders has been conducted. Here, we propose the VAP-SIRS model that accounts for susceptible, infected, and recovered subpopulations, also within the group of vaccinated pass holders. The model accounts for imperfect vaccination effectiveness, revaccinations and waning immunity. Different restrictions for pass holders and the rest of the population result in different scenarios of the epidemic evolution, some of which yield unfavourable COVID-19 dynamics and new waves. We identify critical variables that should be considered by policymakers and show how unfavourable outcomes can be avoided using adaptive policies. In particular, while pass holders could initially be allowed large freedoms, the gradual loss of immunity will require either increased restrictions for pass holders, or accelerated revaccination. In the long-term, common restrictions for both the pass holders and the rest of the population will have to be kept to avoid epidemic resurgence. Such minimum required restrictions depend on vaccination effectiveness, revaccination rate, waning rate and fraction of never-vaccinated population, and, for realistic combinations of these parameters, range between 29% and 69% reduction of contacts.

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.

Genetic tags allow rapid localization of tagged proteins in cells and tissues. APEX, an ascorbate peroxidase, has proven to be one of the most versatile and robust genetic tags for ultrastructural localization by electron microscopy (EM). Here, we describe a simple method, APEX-Gold, which converts the diffuse oxidized diaminobenzidine reaction product of APEX into a silver/ gold particle akin to that used for immunogold labelling. The method increases the signal-to-noise ratio for EM detection, providing unambiguous detection of the tagged protein, and creates a readily quantifiable particulate signal. We demonstrate the wide applicability of this method for detection of membrane proteins, cytoplasmic proteins, and cytoskeletal proteins. The method can be combined with different EM techniques including fast freezing and freeze substitution, focussed ion beam scanning EM, and electron tomography. Quantitation of expressed APEX-fusion proteins is achievable using membrane vesicles generated by a cell-free expression system. These membrane vesicles possess a defined quantum of signal, which can act as an internal standard for determination of the absolute density of expressed APEX-fusion proteins. Detection of fusion proteins expressed at low levels in cells from CRISPR-edited mice demonstrates the high sensitivity of the APEX-Gold method.

The viral protein ICP6, encoded by herpes simplex virus 1 (HSV-1), harbours a RIP-homotypic interaction motif (RHIM), that plays a role in viral inhibition of host cell death pathways. Other members of the Herpesviridae family also encode RHIM-containing proteins that interfere with host-cell death pathways, including the M45 protein from murine cytomegalovirus, and ORF20 protein from varicella zoster virus. We have used amyloid assembly assays, electron microscopy and single molecule fluorescence spectroscopy to show that the ICP6 RHIM is amyloidogenic and can interact with host RHIM-containing proteins to form heteromeric amyloid complexes, in a manner similar to that of M45 and ORF20 RHIMs. The core tetrad sequence of the ICP6 RHIM is important for both amyloid formation and interaction with host RHIM-containing proteins. Notably, we show that the amyloid forming capacity of the ICP6 RHIM is affected by the redox environment. We propose that the formation of an intramolecular disulfide bond within ICP6 triggers the formation of amyloid assemblies that are distinct from previously characterised viral amyloids M45 and ORF20. Formation of viral-host heteromeric amyloid assemblies may underlie a general mechanism of viral adaptation against host immune machineries.

The HIV capsid is a multifunctional protein capsule that mediates the delivery of the viral genetic material into the nucleus of the target cell. Host cell proteins bind to a number of repeating binding sites on the capsid to regulate steps in the replication cycle. Here, we develop a fluorescence fluctuation spectroscopy method using self-assembled capsid particles as the bait to screen for fluorescence-labeled capsid-binding analytes (“prey” molecules) in solution. The assay capitalizes on the property of the HIV capsid as a multivalent interaction platform, facilitating high sensitivity detection of multiple prey molecules that have accumulated onto capsids as spikes in fluorescence intensity traces. By using a scanning stage, we reduced the measurement time to 10 s without compromising on sensitivity, providing a rapid binding assay for screening libraries of potential capsid interactors. The assay can also identify interfaces for host molecule binding by using capsids with defects in known interaction interfaces. Two-color coincidence detection using the fluorescent capsid as the bait further allows the quantification of binding levels and determination of binding affinities. Overall, the assay provides new tools for the discovery and characterization of molecules used by the HIV capsid to orchestrate infection. The measurement principle can be extended for the development of sensitive interaction assays, utilizing natural or synthetic multivalent scaffolds as analyte-binding platforms.

Genetic tags allow rapid localization of tagged proteins in cells and tissues. APEX, an ascorbate peroxidase, has proven to be one of the most versatile and robust genetic tags for ultrastructural localization by electron microscopy (EM). Here, we describe a simple method, APEX-Gold, which converts the diffuse oxidized diaminobenzidine reaction product of APEX into a silver/ gold particle akin to that used for immunogold labelling. The method increases the signal-to-noise ratio for EM detection, providing unambiguous detection of the tagged protein, and creates a readily quantifiable particulate signal. We demonstrate the wide applicability of this method for detection of membrane proteins, cytoplasmic proteins, and cytoskeletal proteins. The method can be combined with different EM techniques including fast freezing and freeze substitution, focussed ion beam scanning EM, and electron tomography. Quantitation of expressed APEX-fusion proteins is achievable using membrane vesicles generated by a cell-free expression system. These membrane vesicles possess a defined quantum of signal, which can act as an internal standard for determination of the absolute density of expressed APEX-fusion proteins. Detection of fusion proteins expressed at low levels in cells from CRISPR-edited mice demonstrates the high sensitivity of the APEX-Gold method.

Caveolae-associated protein 3 (cavin3) is inactivated in most cancers. We characterized how cavin3 affects the cellular proteome using genome-edited cells together with label-free quantitative proteomics. These studies revealed a prominent role for cavin3 in DNA repair, with BRCA1 and BRCA1 A-complex components being downregulated on cavin3 deletion. Cellular and cell-free expression assays revealed a direct interaction between BRCA1 and cavin3 that occurs when cavin3 is released from caveolae that are disassembled in response to UV and mechanical stress. Overexpression and RNAi-depletion revealed that cavin3 sensitized various cancer cells to UV-induced apoptosis. Supporting a role in DNA repair, cavin3-deficient cells were sensitive to PARP inhibition, where concomitant depletion of 53BP1 restored BRCA1-dependent sensitivity to PARP inhibition. We conclude that cavin3 functions together with BRCA1 in multiple cancer-related pathways. The loss of cavin3 function may provide tumor cell survival by attenuating apoptotic sensitivity and hindering DNA repair under chronic stress conditions.

Caveolae-associated protein 3 (cavin3) is inactivated in most cancers. We characterized how cavin3 affects the cellular proteome using genome-edited cells together with label-free quantitative proteomics. These studies revealed a prominent role for cavin3 in DNA repair, with BRCA1 and BRCA1 A-complex components being downregulated on cavin3 deletion. Cellular and cell-free expression assays revealed a direct interaction between BRCA1 and cavin3 that occurs when cavin3 is released from caveolae that are disassembled in response to UV and mechanical stress. Overexpression and RNAi-depletion revealed that cavin3 sensitized various cancer cells to UV-induced apoptosis. Supporting a role in DNA repair, cavin3-deficient cells were sensitive to PARP inhibition, where concomitant depletion of 53BP1 restored BRCA1-dependent sensitivity to PARP inhibition. We conclude that cavin3 functions together with BRCA1 in multiple cancer-related pathways. The loss of cavin3 function may provide tumor cell survival by attenuating apoptotic sensitivity and hindering DNA repair under chronic stress conditions.

Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.

Purpose: High myopia (HM) is an eye disorder with both environmental and genetic factors involved. Many genetic factors responsible for HM were recognized worldwide, but little is known about genetic variants underlying HM in Central Europe. Thus, the aim of this study was to identify rare sequence variants involved in HM in families from Central Europe to better understand the genetic basis of HM. Materials and methods: We assessed 17 individuals from 7 unrelated Central European families with hereditary HM using exome sequencing (ES). Segregation of selected variants in other available family members was performed using Sanger sequencing. Results: Detected 73 rare variants were selected for verification. We observed 2 missense variants, c.938C>T in SLC35E2B - encoding solute carrier family 35 member E2B, and c.1642G>C in FLRT3 - encoding fibronectin leucine rich transmembrane protein, segregating with HM in one family. Conclusions: FLRT3 and/or SLC35E2B could represent disease candidate genes and identified sequence variants might be responsible for HM in the studied family., Funding Agencies|National Science Centre in PolandNational Science Centre, Poland [2013/08/T/NZ5/00754]; Ministry of Science and Higher Education in PolandMinistry of Science and Higher Education, Poland [27/GM/2017, 2 P05A 095 29]; United States National Institutes of Health, National Human Genome Research Institute/National Heart Lung and Blood Institute [UM1 HG006542]

We propose a new approach for the comparison of mass spectra using a metric known in the computer science under the name of Earth Mover's Distance and in mathematics as the Wasserstein distance. We argue that this approach allows for natural and robust solutions to various problems in the analysis of mass spectra. In particular, we show an application to the problem of deconvolution, in which we infer proportions of several overlapping isotopic envelopes of similar compounds. Combined with the previously proposed generator of isotopic envelopes, IsoSpec, our approach works for a wide range of masses and charges in the presence of several types of measurement inaccuracies. To reduce the computational complexity of the solution, we derive an effective implementation of the Interior Point Method as the optimization procedure. The software for mass spectral comparison and deconvolution based on Wasserstein distance is available at https://github.com/mciach/wassersteinms.

Herpesviruses are known to encode a number of inhibitors of host cell death, including RIP Homotypic Interaction Motif (RHIM)-containing proteins. Varicella zoster virus (VZV) is a member of the alphaherpesvirus subfamily and is responsible for causing chickenpox and shingles. We have identified a novel viral RHIM in the VZV capsid triplex protein, open reading frame (ORF) 20, that acts as a host cell death inhibitor. Like the human cellular RHIMs in RIPK1 and RIPK3 that stabilise the necrosome in TNF-induced necroptosis, and the viral RHIM in M45 from murine cytomegalovirus that inhibits cell death, the ORF20 RHIM is capable of forming fibrillar functional amyloid complexes. Notably, the ORF20 RHIM forms hybrid amyloid complexes with human ZBP1, a cytoplasmic sensor of viral nucleic acid. Although VZV can inhibit TNF-induced necroptosis, the ORF20 RHIM does not appear to be responsible for this inhibition. In contrast, the ZBP1 pathway is identified as important for VZV infection. Mutation of the ORF20 RHIM renders the virus incapable of efficient spread in ZBP1- expressing HT-29 cells, an effect which can be reversed by the inhibition of caspases. Therefore we conclude that the VZV ORF20 RHIM is important for preventing ZBP1-driven apoptosis during VZV infection, and propose that it mediates this effect by sequestering ZBP1 into decoy amyloid assemblies.

CAV1 (caveolin 1) expression and secretion is associated with prostate cancer (PCa) disease progression, but the mechanisms underpinning CAV1 release remain poorly understood. Numerous studies have shown CAV1 can be secreted within exosome-like vesicles, but antibody-mediated neutralization can mitigate PCa progression; this is suggestive of an inverted (non-exosomal) CAV1 topology. Here we show that CAV1 can be secreted from specific PCa types in an inverted vesicle-associated form consistent with the features of bioactive CAV1 secretion. Characterization of the isolated vesicles by electron microscopy, single-molecule fluorescence microscopy and proteomics reveals they represent a novel class of exosomes ~40 nm in diameter containing ~50-60 copies of CAV1 and, strikingly, are released via a non-canonical secretory macroautophagy/autophagy pathway. This study provides novel insights into a mechanism whereby CAV1 translocates from a normal plasma membrane distribution to an inverted secreted form implicated in PCa disease progression. Abbreviations: 3-MA: 3-methyladenine; APEX: a modified soybean ascorbate peroxidase; ATG5: autophagy related 5; ATG9A: autophagy related 9A; ATG12: autophagy related 12; BHK: baby hamster kidney; C-exosomes: caveolin-exosomes; CAMKK2/CAMKKβ: calckum/calmodulin dependent protein kinase kinase 2; CAV1: caveolin 1; DAB: 3,3′-diaminobenzidine; DAPK: death associated protein kinase; EEA1: early endosome antigen 1; EM: electron microscopy; FCS: fluorescence correlation spectroscopy; GBP: GFP/YFP-binding peptide; GFP: green fluorescent protein; GOLGA2: golgin A2; ILVs: intralumenal vesicles; LC3: microtubule-associated protein 1 light chain 3; MBP: maltose binding protein; MTORC1: mechanistic target of rapamycin kinase complex 1; MVBs: multivesicular bodies; PBS: phosphate-buffered saline; PCa: prostate cancer; PI3K: phosphoinositide 3-kinase; PM: plasma membrane; SFM: serum-free medium; TSG101: tumor susceptibility 101; WCL: whole cell lysat

The common dolphinfish (Coryphaena hippurus) is an epipelagic thermophilic species with a worldwide distribution in tropical and subtropical regions that is characterized by its migratory behavior and fast growth rates. This species is targeted by artisanal small-scale and recreational fisheries in most regions where it is found. This paper updates and analyzes the global scientific knowledge on the biology and ecology of this species, which was last revised at a regional level 20 years ago. This review showed an increase in knowledge about the population structure and regional differences in biological traits, in parallel with a notable lack of mechanistic and even empirical knowledge about the ecology of this species, which hampers a good understanding of the population dynamics and the potential impacts of environmental change. This paper also updates the information about the Mediterranean dolphinfish fishery, where the main four countries that exploit this species deploy 30% of fish aggregation devices (FAD) worldwide. The results suggest, among other effects, some temporal synchronicity in landings across countries, potential interannual stock movement affecting inter-country catches, diverging trends in prices and insufficient quality in the estimates of fishing effort. The authors propose a suite of specific measures to ameliorate this lack of knowledge and to better manage this complex living resource.

The common dolphinfish (Coryphaena hippurus) is an epipelagic thermophilic species with a worldwide distribution in tropical and subtropical regions that is characterized by its migratory behavior and fast growth rates. This species is targeted by artisanal small-scale and recreational fisheries in most regions where it is found. This paper updates and analyzes the global scientific knowledge on the biology and ecology of this species, which was last revised at a regional level 20 years ago. This review showed an increase in knowledge about the population structure and regional differences in biological traits, in parallel with a notable lack of mechanistic and even empirical knowledge about the ecology of this species, which hampers a good understanding of the population dynamics and the potential impacts of environmental change. This paper also updates the information about the Mediterranean dolphinfish fishery, where the main four countries that exploit this species deploy 30% of fish aggregation devices (FAD) worldwide. The results suggest, among other effects, some temporal synchronicity in landings across countries, potential interannual stock movement affecting inter-country catches, diverging trends in prices and insufficient quality in the estimates of fishing effort. The authors propose a suite of specific measures to ameliorate this lack of knowledge and to better manage this complex living resource.

The murine cytomegalovirus protein M45 protects infected mouse cells from necroptotic death and, when heterologously expressed, can protect human cells from necroptosis induced by tumour necrosis factor receptor (TNFR) activation. Here, we show that the N-terminal 90 residues of the M45 protein, which contain a RIP homotypic interaction motif (RHIM), are sufficient to confer protection against TNFR-induced necroptosis. This N-terminal region of M45 drives rapid self-assembly into homo-oligomeric amyloid fibrils and interacts with the RHIMs of the human kinases RIPK1 and RIPK3, and the Z-DNA binding protein 1 (ZBP1), to form heteromeric amyloid fibrils in vitro. Mutation of the tetrad residues in the M45 RHIM attenuates homo- and hetero-amyloid assembly by M45, suggesting that the amyloidogenic nature of the M45 RHIM underlies its biological activity. The M45 RHIM preferentially interacts with RIPK3 and ZBP1 over RIPK1 and alters the properties of the host RHIM protein assemblies. Our results indicate that M45 mimics the interactions made by RIPK1 or ZBP1 with RIPK3, thereby forming heteromeric amyloid structures, which may explain its ability to inhibit necroptosis.

The massive use of Information and Communications Technology (ICT) is increasing the amount of energy drained by the telecommunication infrastructure and its footprint on the environment. With the advent of the smartphone, mobile traffic is massively growing driven by both the rising number of user subscriptions and an increasing average data volume per subscription. This is putting a lot of pressure on the mobile network operators side, which are enforced to boost their infrastructure capacity by densifying the network with more Base Stations (BSs) and resources, which translates to a growth in the energy consumption and related costs. Hence, any future development in the ICT sector and its infrastructure has definitely to cope with their environmental and economical sustainability, where energy management is essential. In this thesis, we discuss the role of energy in the design of eco-friendly cost-effective sustainable mobile networks and, in particular, we elaborate on the use of Energy Harvesting (EH) hardware as a means to decrease the environmental footprint of the 5G network. Specifically, we investigate energy management strategies in 5G mobile networks with the main goals of: (i) improving the energy balance across base stations and other network elements, (ii) understanding how the energy can be exchanged either among network elements and the electrical grid, and (iii) investigating how renewable energy sources can be utilized within network elements to maximize the utility for the overall network in terms of better performance for the users (e.g., throughput, coverage, etc.), and lower energy consumption (i.e., carbon footprint) for the 5G network infrastructure. Therefore, we address, formulate and solve some of the problems related to the energy management in different scenarios within the 5G mobile network. The main covered topics are: (i) Wireless Energy Transfer where we investigate the tradeoffs involved in the recharging process from base stations

Enteropathogenic Escherichia coli (EPEC) is one the most prevalent pathogens infecting children worldwide, with one of the major symptoms including watery diarrhoea. During EPEC infection, bacterial effector proteins are injected into epithelial cells by a type three secretion system (T3SS). Bacterial effectors have evolved to manipulate the host defence system and hijack crucial innate immunity signalling pathways. This thesis aims to provide a deeper insight into the most important protein interactions during EPEC infection. It studies and elaborates on different stages of the infection: colonisation, signalling and cell hijacking. Using cell-free protein expression, single molecule fluorescence techniques and a protein interaction proximity assay we studied the assembly process of the T3SS and its docking to the host plasma membrane. We also screened the main effector proteins causing disease against host proteins involved in inflammation, apoptosis and cell survival pathways. Our laboratory has observed that many innate immune proteins signal through the formation of higherorder assembly structures. We investigated the ability of EPEC bacterial effectors to affect the formation of these polymer-like assemblies. Our experiments uncovered a novel interaction between EspF and the tumour necrosis factor receptor-associated factor 2 (TRAF2). We characterized the behaviour of TRAF2 and TRAF2-EspF interaction in vitro and in cells. We discovered that bacterial proteins can not only bind to some host proteins but also alter the formation of the higher-order assemblies (oligomers or aggregates) that some immune proteins carry out to serve as scaffold or to amplify signal transduction. Finally, using proteomics and cell culture techniques, we validated the data obtained in the protein screen and obtained information about the most affected pathways during EPEC infection and the cell location of the effectors. Overall, this research contributes to understanding how EPEC ca

Epidemiological studies show increasing prevalence rates of cognitive decline and hearing loss with age, particularly after the age of 65 years. These conditions are reported to be associated, although conclusive evidence of causality and implications is lacking. Nevertheless, audiological and cognitive assessment among elderly people is a key target for comprehensive and multidisciplinary evaluation of the subject's frailty status. To evaluate the use of tools for identifying older adults at risk of hearing loss and cognitive decline and to compare skills and abilities in terms of hearing and cognitive performances between older adults and young subjects, we performed a prospective cross-sectional study using supraliminal auditory tests. The relationship between cognitive assessment results and audiometric results was investigated, and reference ranges for different ages or stages of disease were determined. Patients older than 65 years with different degrees of hearing function were enrolled. Each subject underwent an extensive audiological assessment, including tonal and speech audiometry, Italian Matrix Sentence Test, and speech audiometry with logatomes in quiet. Cognitive function was screened and then verified by experienced clinicians using the Montreal Cognitive Assessment Score, the Geriatric Depression Scale, and further investigations in some. One hundred twenty-three subjects were finally enrolled during 2016-2019: 103 were >65 years of age and 20 were younger participants (as controls). Cognitive functions showed a correlation with the audiological results in post-lingual hearing-impaired patients, in particular in those affected by slight to moderate hearing loss and aged more than 70 years. Audiological testing can thus be useful in clinical assessment and identification of patients at risk of cognitive impairment. The study was limited by its sample size (CI 95%; CL 10%), strict dependence on language, and hearing threshold. Further investigation

Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.

The automatic classification of applications and services is an invaluable feature for new generation mobile networks. Here, we propose and validate algorithms to perform this task, at runtime, from the raw physical channel of an operative mobile network, without having to decode and/or decrypt the transmitted flows. Towards this, we decode Downlink Control Information (DCI) messages carried within the LTE Physical Downlink Control CHannel (PDCCH). DCI messages are sent by the radio cell in clear text and, in this paper, are utilized to classify the applications and services executed at the connected mobile terminals. Two datasets are collected through a large measurement campaign: one labeled, used to train the classification algorithms, and one unlabeled, collected from four radio cells in the metropolitan area of Barcelona, in Spain. Among other approaches, our Convolutional Neural Network (CNN) classifier provides the highest classification accuracy of 99%. The CNN classifier is then augmented with the capability of rejecting sessions whose patterns do not conform to those learned during the training phase, and is subsequently utilized to attain a fine grained decomposition of the traffic for the four monitored radio cells, in an online and unsupervised fashion.

Supplementation with copper (Cu) improves deer antler characteristics, but it could modify meat quality and increase its Cu content to levels potentially harmful for humans. Here, we studied the effects of Cu bolus supplementation by means on quality and composition of sternocephalicus (ST) and rectus abdominis (RA) muscles (n=13 for each one) from yearling male red deer fed with a balanced diet. Each intraruminal bolus, containing 3.4 g of Cu, was administered orally in the treatment group to compare with the control group. Meat traits studied were pH at 24 h postmortem (pH24), colour, chemical composition, cholesterol content, fatty acid (FA) composition, amino acid (AA) profile and mineral content. In addition, the effect of Cu supplementation on mineral composition of liver and serum (at 0 and 90 days of treatment) was analysed. No interactions between Cu supplementation and muscle were observed for any trait. Supplementation with Cu increased the protein content of meat (P<0.01). However, Cu content of meat, liver and serum was not modified by supplementation. In fact, Cu content of meat (1.20 and 1.34 mg/kg for Cu supplemented and control deer, respectively) was much lower in both groups than 5 mg/kg of fresh weight allowed legally for food of animal origin. However, bolus of Cu tended to increase the meat content of zinc and significantly increased (P<0.05) the hepatic contents of sodium and lead. Muscles studied had different composition and characteristics. The RA muscle had significantly higher protein content (P<0.001), monounsaturated FA content (P<0.05) and essential/non-essential AA ratio (P<0.01) but lower pH24 (P<0.01) and polyunsaturated FA content (P=0.001) than the ST muscle. In addition, RA muscle had 14.4% less cholesterol (P=0.001) than ST muscle. Also, mineral profile differed between muscles with higher content of iron, significantly higher (P<0.001) content of zinc and lower content of calcium, magnesium and phosphorus (P<0.05) for ST muscle

Antler growth is a costly yearly process supplied by daily nutrition and body reserves. Conditions for antler growth are rarely optimal. Thus, certain decrease in antler quality due to depletion of resources, known as physiological exhaustion, is frequently observed along the main beam. Testosterone promotes the mineralization in the last phase of antler growth, and its concentration change in male deer according to the socio-sexual environment: it is greater in single males housed only with females than in males housed only with other males (female effect). We hypothesised that the socio-sexual environment affect antler mineralization; especially in the top of the antler which is the last part mineralising and subjected to the described physiological exhaustion, but also the one mineralising when testosterone levels are higher. We tested this in antlers of pampas deer (Ozotoceros bezoarticus) from captive animals living in the two social contexts described. All the animals had an ad libitum high nutrition plan, so results are not due to nutritional differences. The antlers from males living with females suffered a lower physiological exhaustion (i.e., lower percent decrease in the top compared to the base of the antler) in the two most important minerals: Ca and P, but also similar tendencies in other bone-biology related trace elements like Sr and Li. Our results highlight that the socio-sexual environment, particularly living continuously in close contact with females, promotes antler mineralization probably through modifications in testosterone secretion.

BACKGROUND: The identification of early biomarkers of psychotic experiences (PEs) is of interest because early diagnosis and treatment of those at risk of future disorder is associated with improved outcomes. The current study investigated early lipidomic and coagulation pathway protein signatures of later PEs in subjects from the Avon Longitudinal Study of Parents and Children cohort. METHODS: Plasma of 115 children (12 years of age) who were first identified as experiencing PEs at 18 years of age (48 cases and 67 controls) were assessed through integrated and targeted lipidomics and semitargeted proteomics approaches. We assessed the lipids, lysophosphatidylcholines (n = 11) and phosphatidylcholines (n = 61), and the protein members of the coagulation pathway (n = 22) and integrated these data with complement pathway protein data already available on these subjects. RESULTS: Twelve phosphatidylcholines, four lysophosphatidylcholines, and the coagulation protein plasminogen were altered between the control and PEs groups after correction for multiple comparisons. Lipidomic and proteomic datasets were integrated into a multivariate network displaying a strong relationship between most lipids that were significantly associated with PEs and plasminogen. Finally, an unsupervised clustering approach identified four different clusters, with one of the clusters presenting the highest case-control ratio (p < .01) and associated with a higher concentration of smaller low-density lipoprotein cholesterol particles. CONCLUSIONS: Our findings indicate that the lipidome and proteome of subjects who report PEs at 18 years of age are already altered at 12 years of age, indicating that metabolic dysregulation may contribute to an early vulnerability to PEs and suggesting crosstalk between these lysophosphatidylcholines, phosphatidylcholines, and coagulation and complement proteins., Funding Agencies:Health Research Board HRA-POR-2013-282 HRBCSA2012/8 European Research Council 647783 724809 European Union FP7 collaborative project METSY 602478 National Institute for Health Research Biomedical Research Centre at University Hospitals Bristol NHS Foundation Trust and the University of Bristol Irish Health Research Board Clinician Scientist Award UK Medical Research Council 102215/2/13/2

Multi-Access Edge Computing (MEC) is a paradigm for handling delay sensitive services that require ultra-low latency at the access network. With it, computing and communications are performed within one Base Station (BS) site, where the computation resources are in the form of Virtual Machines (VMs) (computer emulators) in the MEC server. MEC and Energy Harvesting (EH) BSs, i.e., BSs equipped with EH equipments, are foreseen as a key towards next-generation mobile networks. In fact, EH systems are expected to decrease the energy drained from the electricity grid and facilitate the deployment of BSs in remote places, extending network coverage and making energy self-sufficiency possible in remote/rural sites. In this paper, we propose an online optimization algorithm called ENergy Aware and Adaptive Management (ENAAM), for managing remote BS sites through foresighted control policies exploiting (short-term) traffic load and harvested energy forecasts. Our numerical results reveal that ENAAM achieves energy savings with respect to the case where no energy management is applied, ranging from 56% to 66% through the scaling of computing resources, and keeps the server utilization factor between 30% and 96% over time (with an average of 75%). Notable benefits are also found against heuristic energy management techniques., Comment: arXiv admin note: substantial text overlap with arXiv:1902.05358

The innate immune system uses a multitude of receptors and intracellular signalling pathways to sense pathogens and danger signals. Recent studies have discovered that an array of these intracellular signalling proteins assemble into oligomeric signalling platforms, consequently amplifying the transmission of signal from the stimulated receptor to the activation of relevant transcription machinery. Unexpectedly, it was also discovered that some of these proteins present in innate immune signalling can form fibrils. These fibrils can elongate in a prion-like manner to create super-sized signalling platforms. Through screening over 100 innate immune intracellular signalling proteins using single molecule fluorescence, we defined the oligomerisation and aggregation propensity of these proteins, tracking the specific signature of polymerisation. We identified multiple candidates forming super-sized protein aggregates; and were able to conclude that 19 of these proteins could self-propagate aggregation, just as prions do. 4 of these proteins had been previously published as being ‘prion-like’, leaving 15 novel prion-like polymers identified.Our observations suggest that prion-like polymerisation underlies the backbone of intracellular communication and drives the complex interplay that exists among the major signalling cascades of the innate immune system. Our disease-associated mutagenesis data highlights the crucial functions that these large signalling platforms have in the optimal execution of defence against pathogens and intracellular homeostasis and will contribute to the development of therapies aimed at aiding and regulating this critical first line of defence.

α-Synuclein (αS) is an intrinsically disordered protein that is associated with Parkinson’s disease (PD) through its ability to self-assemble into oligomers and fibrils. Inhibition of this oligomerization cascade is an interesting approach to developing therapeutical strategies and β-synuclein (βS) has been described as a natural negative regulator of this process. However, the biological background and molecular mechanisms by which this inhibition occurs is unclear. Herein, we focused on assessing the effect of βS on the aggregation of five αS pathological mutants linked to early-onset PD (A30P, E46K, H50Q, G51D and A53T). By coupling single molecule fluorescence spectroscopy to a cell-free protein expression system, we validated the ability of βS to act as a chaperone of αS, effectively inhibiting its aggregation. Interestingly, we found that βS does so in a selective manner, i.e., is a more effective inhibitor for certain αS pathological mutants—A30P and G51D—as compared to E46K, H50Q and A53T. Moreover, two-color coincidence experiments proved that this discrepancy is due to a preferential incorporation of βS into smaller oligomers of αS. This was validated by showing that the chaperoning effect was lost when proteins were mixed after being expressed individually. This study highlights the potential of fluorescence spectroscopy to deconstruct αS aggregation cascade and its interplay with βS.