Pragmatic Trial of Hospitalization Rate in Chronic Kidney Disease.

BACKGROUND: Despite the availability of effective therapies for patients with chronic kidney disease, type 2 diabetes, and hypertension (the kidney-dysfunction triad), the results of large-scale trials examining the implementation of guideline-directed therapy to reduce the risk of death and complications in this population are lacking. METHODS: In this open-label, cluster-randomized trial, we assigned 11,182 patients with the kidney-dysfunction triad who were being treated at 141 primary care clinics either to receive an intervention that used a personalized algorithm (based on the patient's electronic health record [EHR]) to identify patients and practice facilitators to assist providers in delivering guideline-based interventions or to receive usual care. The primary outcome was hospitalization for any cause at 1 year. Secondary outcomes included emergency department visits, readmissions, cardiovascular events, dialysis, and death. RESULTS: We assigned 71 practices (enrolling 5690 patients) to the intervention group and 70 practices (enrolling 5492 patients) to the usual-care group. The hospitalization rate at 1 year was 20.7% (95% confidence interval [CI], 19.7 to 21.8) in the intervention group and 21.1% (95% CI, 20.1 to 22.2) in the usual-care group (between-group difference, 0.4 percentage points; P = 0.58). The risks of emergency department visits, readmissions, cardiovascular events, dialysis, or death from any cause were similar in the two groups. The risk of adverse events was also similar in the trial groups, except for acute kidney injury, which was observed in more patients in the intervention group (12.7% vs. 11.3%). CONCLUSIONS: In this pragmatic trial involving patients with the triad of chronic kidney disease, type 2 diabetes, and hypertension, the use of an EHR-based algorithm and practice facilitators embedded in primary care clinics did not translate into reduced hospitalization at 1 year. (Funded by the National Institutes of Health and others; ICD-Pieces ClinicalTrials.gov number, NCT02587936.).

TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat.

Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. This is reflected by the many publications and database resources describing knowledge about TFs. We previously launched the TFCheckpoint database, an integrated resource focused on human, mouse and rat dbTFs, providing users access to a comprehensive overview of these proteins. Here, we describe TFCheckpoint 2.0 (https://www.tfcheckpoint.org/index.php), comprising 13 collections of dbTFs, coTFs and GTFs. TFCheckpoint 2.0 provides an easy and versatile cross-referencing system for users to view and download collections that may otherwise be cumbersome to find, compare and retrieve.

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.

Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, and their target genes, the so called TF regulons, can be coupled with computational algorithms to estimate the activity of TFs. However, to interpret these findings accurately, regulons of high reliability and coverage are needed. In this study, we present and evaluate a collection of regulons created using the CollecTRI meta-resource containing signed TF-gene interactions for 1186 TFs. In this context, we introduce a workflow to integrate information from multiple resources and assign the sign of regulation to TF-gene interactions that could be applied to other comprehensive knowledge bases. We find that the signed CollecTRI-derived regulons outperform other public collections of regulatory interactions in accurately inferring changes in TF activities in perturbation experiments. Furthermore, we showcase the value of the regulons by examining TF activity profiles in three different cancer types and exploring TF activities at the level of single-cells. Overall, the CollecTRI-derived TF regulons enable the accurate and comprehensive estimation of TF activities and thereby help to interpret transcriptomics data.

Protein N-glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease.

BACKGROUND: Diabetes is expected to directly impact renal glycosylation, yet to date, there has not been a comprehensive evaluation of alterations in N-glycan composition in the glomeruli of patients with diabetic kidney disease (DKD). METHODS: We used untargeted mass spectrometry imaging to identify N-glycan structures in healthy and sclerotic glomeruli in FFPE sections from needle biopsies of five patients with DKD and three healthy kidney samples. Regional proteomics was performed on glomeruli from additional biopsies from the same patients to compare the abundances of enzymes involved in glycosylation. Secondary analysis of single nuclei transcriptomics (snRNAseq) data was used to inform on transcript levels of glycosylation machinery in different cell types and states. RESULTS: We detected 120 N-glycans, and among them identified twelve of these protein post-translated modifications that were significantly increased in glomeruli. All glomeruli-specific N-glycans contained an N-acetyllactosamine (LacNAc) epitope. Five N-glycan structures were highly discriminant between sclerotic and healthy glomeruli. Sclerotic glomeruli had an additional set of glycans lacking fucose linked to their core, and they did not show tetra-antennary structures that are common in healthy glomeruli. Orthogonal omics analyses revealed lower protein abundance and lower gene expression involved in synthesizing fucosylated and branched N-glycans in sclerotic podocytes. In snRNAseq and regional proteomics analyses, we observed that genes and/or proteins involved in sialylation and LacNAc synthesis were also downregulated in DKD glomeruli, but this alteration remained undetectable by our spatial N-glycomics assay. CONCLUSIONS: Integrative spatial glycomics, proteomics, and transcriptomics revealed protein N-glycosylation characteristic of sclerotic glomeruli in DKD.

Virus-like particle-mediated delivery of structure-selected neoantigens demonstrates immunogenicity and antitumoral activity in mice.

BACKGROUND: Neoantigens are patient- and tumor-specific peptides that arise from somatic mutations. They stand as promising targets for personalized therapeutic cancer vaccines. The identification process for neoantigens has evolved with the use of next-generation sequencing technologies and bioinformatic tools in tumor genomics. However, in-silico strategies for selecting immunogenic neoantigens still have very low accuracy rates, since they mainly focus on predicting peptide binding to Major Histocompatibility Complex (MHC) molecules, which is key but not the sole determinant for immunogenicity. Moreover, the therapeutic potential of neoantigen-based vaccines may be enhanced using an optimal delivery platform that elicits robust de novo immune responses. METHODS: We developed a novel neoantigen selection pipeline based on existing software combined with a novel prediction method, the Neoantigen Optimization Algorithm (NOAH), which takes into account structural features of the peptide/MHC-I interaction, as well as the interaction between the peptide/MHC-I complex and the TCR, in its prediction strategy. Moreover, to maximize neoantigens' therapeutic potential, neoantigen-based vaccines should be manufactured in an optimal delivery platform that elicits robust de novo immune responses and bypasses central and peripheral tolerance. RESULTS: We generated a highly immunogenic vaccine platform based on engineered HIV-1 Gag-based Virus-Like Particles (VLPs) expressing a high copy number of each in silico selected neoantigen. We tested different neoantigen-loaded VLPs (neoVLPs) in a B16-F10 melanoma mouse model to evaluate their capability to generate new immunogenic specificities. NeoVLPs were used in in vivo immunogenicity and tumor challenge experiments. CONCLUSIONS: Our results indicate the relevance of incorporating other immunogenic determinants beyond the binding of neoantigens to MHC-I. Thus, neoVLPs loaded with neoantigens enhancing the interaction with the TCR can promote the generation of de novo antitumor-specific immune responses, resulting in a delay in tumor growth. Vaccination with the neoVLP platform is a robust alternative to current therapeutic vaccine approaches and a promising candidate for future personalized immunotherapy.

Improving the coverage area and flake size of ReS2through machine learning in APCVD.

Machine learning is playing a crucial role in optimizing material synthesis, particularly in scenarios where several parameters related to growth exhibit different and significant outcomes. An example of such complexity is the growth of atomically thin semiconductors through chemical vapor deposition (CVD), where multiple parameters can influence the thermodynamics and reaction kinetics involved in the synthesis. Herein, we performed a set of orthogonal experiments, varying the key parameters such as temperature, carries gas flux and precursor position to identify the optimal conditions for maximizing covered area and the size of rhenium disulfide (ReS2) crystals. The experimental results were used to establish correlations among the three thermodynamic variables through an artificial neural network. Contour plots were then generated to visualize the impact on the coverage and flake size of the crystals. This study demonstrates the capability of machine learning to enhance the potential of CVD-growth for the integration of 2D semiconductors like ReS2at larger scales.

Application of arbitrary and individualized load quantification strategies over the weekly microcycle in professional soccer players.

The aims of this study were to: (a) determine the differences in external load quantification between arbitrary and individual speed thresholds over the weekly microcycle in professional soccer players, and (b) analyse the association between internal load and different external load quantification strategies (ELQSs). Ten professional outfield players were monitored during training sessions and official matches using 10 Hz GPS devices over a 6-week in-season period. The absolute and relative ("R" before the distance category) distances covered were calculated for the following external load variables: medium-intensity running distance (MIR), high-intensity running (HIR), sprint distance (SD), and very high-intensity running (VHIR). Individualized thresholds were determined based on maximal sprinting speed (MSS) and the last speed achieved during the 30-15 Intermittent Fitness Test (VIFT) of each player. In terms of match-day workload, significant differences (p < 0.05) were observed between arbitrary and individualized strategies (i.e., MSS and VIFT) for the distance covered in MIR, HIR, SD, VHIR, RHIR, RSD, and RVHIR. The MSS strategy compared to arbitrary thresholds revealed significant differences (p < 0.05) for distance covered in HIR, RHIR, and VHIR during all training sessions. The present results showed that arbitrary thresholds lead to underestimation of external load absolute and relative metrics compared to the MSS strategy throughout the microcycle. The VIFT strategy mainly revealed differences in external load quantification regarding MD compared to arbitrary thresholds. Individualized speed threshold strategies did not achieve better associations with internal load measures in comparison with arbitrary thresholds in professional soccer players.

Synthesis of Fluorescent Pyrrolo[1,2-a]pyrimidines from Fischer Carbene Complexes as Building Blocks.

A novel synthetic methodology is reported for the synthesis of fluorescent pyrrolo[1,2-a]pyrimidines. Fischer carbene complexes served as the synthetic platform for (3+3) cyclization to form the heterocyclic moiety. The reaction process furnished two products, their ratio being modulated by the metal, base, and solvent. The selectivity exhibited was studied by analyzing the potential energy surface with density functional theory tools. The photophysical properties of absorption and emission were also evaluated. The dyes absorbed at wavelengths of 240-440 nm, depending on the substituents. The maximum emission wavelength was in the range of 470-513 nm, with quantum yields of 0.36-1.0 and a high Stokes shift range of 75-226 nm.

Extended BODIPYs as Red-NIR Laser Radiation Sources with Emission from 610 nm to 750 nm.

Herein, we report the synthetic access to a set of π-extended BODIPYs featuring a penta-arylated (phenyl and/or thiophene) dipyrrin framework. We take advantage of the full chemoselective control of 8-methylthio-2,3,5,6-tetrabromoBODIPY when we conduct the Liebeskind-Srogl cross-coupling (LSCC) to functionalize exclusively the meso-position, followed by the tetra-Suzuki reaction to arylate the halogenated sites. All these laser dyes display absorption and emission bands in the red edge of the visible spectrum reaching the near-infrared with thiophene functionalization. The emission efficiency, both fluorescence and laser, of the polyphenylBODIPYs can be enhanced upon decoration of the peripheral phenyls with electron donor/acceptor groups at para positions. Alternatively, the polythiopheneBODIPYs show an astonishing laser performance despite the charge transfer character of the emitting state. Therefore, these BODIPYs are suitable as a palette of stable and bright laser sources covering the spectral region from 610 nm to 750 nm.

Synthesis of Polysubstituted Symmetrical BODIPYs via Fischer Carbene Complexes: Theoretical, Photophysical and Electrochemical Evaluation.

A series of new symmetrical highly substituted BODIPYs 6 a-l was synthesized through a prefunctionalization approach in 35 %-89 % yields from the pyrrole core. This strategy allowed modulation of the substituents at the different positions based on the choice of Fischer's alkynyl carbenes, oxazolones and aldehydes used as precursors. The substituent variation at positions 2, 6, 3 and 5 had the greatest effect on the modulation of their photophysical properties such as absorption (λabs ) and emission (λem ) wavelengths, extinction coefficient (ϵ), quantum yields (ϕ), Stokes shifts (Δν), fluorescence decay, radiative (krad ) and non-radiative (knr ) constants and the CIE 1931 coordinates. Theoretical calculations allowed to corroborate the effect of the substituents of meso-position on the modification of the dihedral angles. Cyclic voltammetry studies revealed that the BODIPY series presents similar redox potential behavior, being electrochemically active even in successive cycles, which suggests that transport by diffusion is the dominant process.

Influence of the Weekly and Match-play Load on Muscle Injury in Professional Football Players.

The aim of this investigation was to examine the impact of the weekly training load and the match running patterns prior to a muscle injury as potential risk factors of muscle injury in professional football players. Forty male professional football players participated in the investigation. Running distances at different intensities 5 min and 15 min prior to the injury were compared to the same time-points in official matches of the same player with no injury events. Furthermore, the cummulative session rating of perceived exertion (sRPE) and training load of the week prior to the injury were compared to a control week (mean value of training weeks without injury). Nineteen players suffered 31 non-contact muscle injuries during matches. The distance covered at 21-24 km/h (p<0.001; effect size (ES)=0.62) and at>24 km/h (p=0.004; ES=0.51) over the 5-min period prior to the injury was greater than in matches without injury. The cumulative sRPE (p=0.014; ES=1.33) and training volume (p=0.002; ES=2.45) in the week prior to the injury was higher than in a control week. The current data suggest that the combination of a training week with a high load and a short period of high intensity running during the match might increase the risk of muscle injury in professional footballers.

Cooperative Terrestrial-Underwater Wireless Optical Links by Using an Amplify-and-Forward Strategy.

In this paper, we analyze a combined terrestrial-underwater optical communication link for providing high-speed optical connectivity between onshore and submerge systems. For this purpose, different transmission signaling schemes were employed to obtain performance results in terms of average bit error rate (ABER). In this sense, from the starting point of a known conditional bit-error-rate (CBER) in the absence of turbulence, the behavior of the entire system is obtained by applying an amplify-and-forward (AF) based dual-hop system: The first link is a terrestrial free-space optical (FSO) system assuming a Málaga distributed turbulence and, the second one, is an underwater FSO system with a Weibull channel model. To obtain performance results, a semi-analytical simulation procedure is applied, using a hyper-exponential fitting technique previously proposed by the authors and leading to BER closed-form expressions and high-accuracy numerical results.

Performance Analysis of a Vertical FSO Link with Energy Harvesting Strategy.

In this paper we investigate the application of free space optical (FSO) communications, energy harvesting, and unmanned aerial vehicles (UAVs) as key technology enablers of a cost-efficient backhaul/fronthaul framework for 5G and beyond (5G+) networks. This novel approach is motivated by several facts. First, the UAVs, acting as relay nodes, represent an easy-to-deploy and adaptive network that can provide line-of-sight between the base stations and the gateways connected to the core network. Second, FSO communications offer high data rates between the UAVs and the network nodes, while avoiding any potential interference with the 5G radio access networks. Third, energy harvesting in the optical domain has the potential to extend the UAVs' battery life. Nevertheless, the presence of atmospheric turbulence, atmospheric attenuation, and pointing errors in the FSO links severely degrades their performance. For this reason an accurate yet tractable modelling framework is required to fully understand whether an UAV-FSO backhaul/fronthaul network with energy harvesting can be applied. To this end, we consider a composite channel attenuation model that includes the effect of turbulence fading, pointing errors, and atmospheric attenuation. Using this model, we derive analytical closed-form expressions of the average harvested energy as a function of the FSO link parameters. These expressions can be used to improve energy harvesting efficiency in FSO link design. We have applied our proposed expressions to evaluate the energy harvested in vertical FSO links for a variety of real scenarios under a modified on-off keying (OOK) scheme optimized for energy harvesting. From the simulations carried out in this paper, we demonstrate that significant values of harvested energy can be obtained. Such performance enhancement can complement the existing deployment charging stations.

Rationale and design of the Kidney Precision Medicine Project.

Chronic kidney disease (CKD) and acute kidney injury (AKI) are common, heterogeneous, and morbid diseases. Mechanistic characterization of CKD and AKI in patients may facilitate a precision-medicine approach to prevention, diagnosis, and treatment. The Kidney Precision Medicine Project aims to ethically and safely obtain kidney biopsies from participants with CKD or AKI, create a reference kidney atlas, and characterize disease subgroups to stratify patients based on molecular features of disease, clinical characteristics, and associated outcomes. An additional aim is to identify critical cells, pathways, and targets for novel therapies and preventive strategies. This project is a multicenter prospective cohort study of adults with CKD or AKI who undergo a protocol kidney biopsy for research purposes. This investigation focuses on kidney diseases that are most prevalent and therefore substantially burden the public health, including CKD attributed to diabetes or hypertension and AKI attributed to ischemic and toxic injuries. Reference kidney tissues (for example, living-donor kidney biopsies) will also be evaluated. Traditional and digital pathology will be combined with transcriptomic, proteomic, and metabolomic analysis of the kidney tissue as well as deep clinical phenotyping for supervised and unsupervised subgroup analysis and systems biology analysis. Participants will be followed prospectively for 10 years to ascertain clinical outcomes. Cell types, locations, and functions will be characterized in health and disease in an open, searchable, online kidney tissue atlas. All data from the Kidney Precision Medicine Project will be made readily available for broad use by scientists, clinicians, and patients.

Fischer Carbene Complexes: A Glance at Two Decades of Research on Higher-Order Cycloaddition Reactions.

The structure of Fischer carbene complexes (FCCs) is electron deficient. If bearing an α,ß-unsaturated system, it can generate a wide variety of compounds by undergoing many different transformations, including higher-order cycloadditions. The latter are described as pericyclic reactions in which more than six electrons participate. These reactions have been employed in various areas of organic synthesis, resulting in highly selective compounds with a broad range of scaffolds. The first studies on higher-order cycloadditions involving FCCs frequently yielded competing byproducts. Many groups have attempted to increase selectivity by exploring distinct reaction conditions, reagents and co-catalysts (e. g., metal-mediated cycloadditions). The present review is the first to focus exclusively on using higher-order cycloadditions involving FCCs to synthesize carbocycles and heterocycles. Based on two decades of reports, an analysis is made of the main aspects of the mechanisms proposed for higher-order cycloadditions and the structural diversity obtained by the substituent effect.

Organocatalytic Cascade Reactions for the Diversification of Thiopyrano-Piperidone Fused Rings Utilizing Trienamine Activation.

An aminocatalytic privileged diversity-oriented synthesis (ApDOS) strategy utilizing trienamine catalysis for the construction of diverse and complex thiopyrans-piperidone fused rings through a thia-Diels-Alder/nucleophilic ring-closing sequence by using dithioamides as activated heterodienophiles is reported. Following this strategy, a super cascade reaction to assemble nine fused rings can be achieved by employing a bis-dithioamide. Additionally, by linking an indole moiety on the dithioamide, a Pictet-Spengler type reaction can be promoted once the cascade sequence has been achieved, leading to more complex penta- hexa- and heptacyclic fused ring derivatives in a one-pot process. This investigation opens new perspectives for the synthesis of a new class of complex and diverse thiopyrans that contribute to populate new relevant regions in the chemical space.

Effect of the substituents of new coumarin-imidazo[1,2-a]heterocyclic-3-acrylate derivatives on nonlinear optical properties: a combined experimental-theoretical approach.

A series of new coumarin-imidazo[1,2-a]heterocyclic-3-acrylate derivatives 7a-h were synthesized by the Heck reaction between the corresponding 3-(imidazo[1,2-a]pyrimidines)-(2-yl)-2H-chromen-2-ones 4a-e and methyl acrylate in 45-87% yields. The effect of the distinct substituents on third-order nonlinear optical properties was examined, experimentally measuring their nonlinear refractive indexes by the Z-scan technique. Density functional theory and time-dependent density functional theory were utilized with the B3LYP, CAM-B3LYP, PBE (PBEPBE), and M062X functionals on Gaussian09 software to calculate the vertical excitation, relaxation of the brightest excited states, conformation, HOMO-LUMO gaps, oscillator strength, polarizability, and hyperpolarizabilities of all derivatives. Although all acrylates showed a nonlinear response at a certain level of power, the compounds bearing a diethylamino electron-donating group exhibited higher nonlinear refractive index values (∼10-9 cm2 W-1), which is in agreement with the trend in the computational calculations of the first and second hyperpolarization. According to the structural analysis, the electron-withdrawing group (acrylate) is mainly responsible for the loss of coplanarity because of increasing the dihedral angle between the coumarin and imidazo[1,2-a]heterocyclic moieties (to 39.1°). On the other hand, the unsubstituted compound 4a presented the greatest nonlinearity due to its almost coplanar structure (n2 ∼ 10-8 cm2 W-1), highlighting the importance of this feature.

Secondary hypereosinophilic syndrome: an unusual manifestation in a patient with syringotropic mycosis fungoides and human immunodeficiency virus infection.

Syringotropic mycosis fungoides is a very rare variant of cutaneous T-cell lymphomas characterised by prominent involvement of the eccrine glands. Hypereosinophilic syndrome refers to a rare group of conditions that are associated with persistent eosinophilia with organ involvement. It is classified into idiopathic, primary and secondary (reactive). We report herein an unusual case of hypereosinophilic syndrome with great impact on morbidity, which developed in a patient with human immunodeficiency virus infection and long-time misdiagnosed syringotropic mycosis fungoides.

Patient Dossier: Healthcare queries over distributed resources.

As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain greatly hinders these developments, including ethical and legal issues, fragmentation of the relevant data in different locations, and a level of (meta)data complexity that requires great expertise across technical, clinical, and biological domains. We propose the Patient Dossier paradigm as a way to organize new innovative healthcare services that sorts the current limitations. The Patient Dossier conceptual framework identifies the different issues and suggests how they can be tackled in a safe, efficient, and responsible way while opening options for independent development for different players in the healthcare sector. An initial implementation of the Patient Dossier concepts in the Rbbt framework is available as open-source at https://github.com/mikisvaz and https://github.com/Rbbt-Workflows.

Selective synthesis of trisubstituted pyrroles through the reactions of alkynyl Fischer carbene complexes with oxazolones.

An efficient and simple synthesis of novel trisubstituted 1H-pyrroles 4a-qvia 1,3-dipolar cycloaddition of Δ3-trifluoromethyloxazolones 2a-d with both chromium and tungsten alkynyl Fischer carbene complexes (1a-h) is described. An unexpected and unreported -CF3 group elimination process was observed in the pyrrole structure. Our experimental and theoretical data suggested that the metal fragment may be responsible for this phenomenon. The dipolar cycloaddition proceeded efficiently to produce a single regioisomer, which was unambiguously established through NMR and single-crystal X-ray diffraction studies. Nevertheless, the reaction of alkynyl carbenes bearing an α,ß,γ,δ-unsaturated moiety with excess oxazolone 2a produced a polycyclic compound 6 speculatively formed through a cascade reaction involving 1,6-, 1,4- and 1,2-nucleophilic addition steps.