Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual functions for the ssDNA-binding protein RPA in meiotic recombination

Meiotic recombination permits exchange of genetic material between homologous chromosomes. The replication protein A (RPA) complex, the predominant ssDNA-binding complex, is required for nearly all aspects of DNA metabolism, but its role in mammalian meiotic recombination remains unknown due to the embryonic lethality of RPA mutant mice. RPA is a heterotrimer of RPA1, RPA2, and RPA3. We find that loss of RPA1, the largest subunit, leads to disappearance of RPA2 and RPA3, resulting in the absence of the RPA complex. Using an inducible germline-specific inactivation strategy, we find that loss of RPA completely abrogates loading of RAD51/DMC1 recombinases to programmed meiotic DNA double strand breaks, thus blocking strand invasion required for chromosome pairing and synapsis. Surprisingly, loading of MEIOB, SPATA22, and ATR to DNA double strand breaks is RPA-independent and does not promote RAD51/DMC1 recruitment in the absence of RPA. Finally, inactivation of RPA reduces crossover formation. Our results demonstrate that RPA plays two distinct roles in meiotic recombination: an essential role in recombinase recruitment at early stages and an important role in promoting crossover formation at later stages.
Calcineurin dephosphorylates Kelch-like 3, reversing phosphorylation by angiotensin II and regulating renal electrolyte handling

Significance Calcineurin inhibitors (CNIs) are potent immunosuppressants; hypertension and hyperkalemia are common adverse effects. Activation of the renal Na-Cl cotransporter (NCC) is implicated in this toxicity; however, the mechanism is unknown. CNIs’ renal effects mimic the hypertension and hyperkalemia resulting from mutations in WNK kinases or in KLHL3-CUL3 ubiquitin ligase. WNKs activate NCC and are degraded by ubiquitylation upon their binding to KLHL3. The binding of WNKs to KLHL3 is prevented by KLHL3 mutations or by PKC-mediated KLHL3 phosphorylation at serine 433. This work shows that calcineurin dephosphorylates KLHL3S433, promoting WNK4 degradation. Conversely, CNIs inhibit KLHL3S433 dephosphorylation, preventing WNK degradation. These findings implicate calcineurin in the normal regulation of KLHL3’s binding of WNK4 and identify a direct target causing CNI-induced pathology. Calcineurin is a calcium/calmodulin-regulated phosphatase known for its role in activation of T cells following engagement of the T cell receptor. Calcineurin inhibitors (CNIs) are widely used as immunosuppressive agents; common adverse effects of CNIs are hypertension and hyperkalemia. While previous studies have implicated activation of the Na-Cl cotransporter (NCC) in the renal distal convoluted tubule (DCT) in this toxicity, the molecular mechanism of this effect is unknown. The renal effects of CNIs mimic the hypertension and hyperkalemia that result from germ-line mutations in with-no-lysine (WNK) kinases and the Kelch-like 3 (KLHL3)–CUL3 ubiquitin ligase complex. WNK4 is an activator of NCC and is degraded by binding to KLHL3 followed by WNK4’s ubiquitylation and proteasomal degradation. This binding is prevented by phosphorylation of KLHL3 at serine 433 (KLHL3S433-P) via protein kinase C, resulting in increased WNK4 levels and increased NCC activity. Mechanisms mediating KLHL3S433-P dephosphorylation have heretofore been unknown. We now demonstrate that calcineurin expressed in DCT is a potent KLHL3S433-P phosphatase. In mammalian cells, the calcium ionophore ionomycin, a calcineurin activator, reduces KLHL3S433-P levels, and this effect is reversed by the calcineurin inhibitor tacrolimus and by siRNA-mediated knockdown of calcineurin. In vivo, tacrolimus increases levels of KLHL3S433-P, resulting in increased levels of WNK4, phosphorylated SPAK, and NCC. Moreover, tacrolimus attenuates KLHL3-mediated WNK4 ubiquitylation and degradation, while this effect is absent in KLHL3 with S433A substitution. Additionally, increased extracellular K+ induced calcineurin-dependent dephosphorylation of KLHL3S433-P. These findings demonstrate that KLHL3S433-P is a calcineurin substrate and implicate increased KLHL3 phosphorylation in tacrolimus-induced pathologies.
RaCaT: An open source and easy to use radiomics calculator tool

Purpose The widely known field ‘Radiomics’ aims to provide an extensive image based phenotyping of e.g. tumors using a wide variety of feature values extracted from medical images. Therefore, it is of utmost importance that feature values calculated by different institutes follow the same feature definitions. For this purpose, the imaging biomarker standardization initiative (IBSI) provides detailed mathematical feature descriptions, as well as (mathematical) test phantoms and corresponding reference feature values. We present here an easy to use radiomic feature calculator, RaCaT, which provides the calculation of a large number of radiomic features for all kind of medical images which are in compliance with the standard. Methods The calculator is implemented in C++ and comes as a standalone executable. Therefore, it can be easily integrated in any programming language, but can also be called from the command line. No programming skills are required to use the calculator. The software architecture is highly modularized so that it is easily extendible. The user can also download the source code, adapt it if needed and build the calculator from source. The calculated feature values are compliant with the ones provided by the IBSI standard. Source code, example files for the software configuration, and documentation can be found online on GitHub (https://github.com/ellipfaehlerUMCG/RaCat). Results The comparison with the standard values shows that all calculated features as well as image preprocessing steps, comply with the IBSI standard. The performance is also demonstrated on clinical examples. Conclusions The authors successfully implemented an easy to use Radiomics calculator that can be called from any programming language or from the command line. Image preprocessing and feature settings and calculations can be adjusted by the user.
Relationship between β-defensin-1 gene polymorphism and susceptibility and prognosis of acute respiratory distress syndrome

Objective: The 1st exon 5′ noncoding region rs1799946 (-52A/G), rs1800972 (-44C/G), rs11362 (-20A/G) 3 single-nucleotide polymorphisms (SNPs) on human &bgr;-defensin-1 (HBD-1) gene affect its transcription and posttranscriptional mRNA stability then affect the activity of HBD-1. This study was to investigate the effects of HBD-1 gene rs1799946, rs1800972, and rs11362 locus SNPs on genetic susceptibility and prognosis of acute respiratory distress syndrome (ARDS). Methods: A total of 300 patients with ARDS (ARDS group) and 240 patients who were admitted to the intensive care unit and had a high risk of ARDS but did not progress to ARDS (control group) were included in this study. The genotypes of HBD-1 gene rs1799946, rs1800972, and rs11362 locus and serum HBD-1 were detected. Patients were followed for 60 days with development of ARDS as a primary outcome, ARDS-related mortality and organ dysfunction were secondary outcomes. Results: HBD-1 gene rs1799946 and rs11362 gene mutations were not risk factors for ARDS (P > .05). Mutation allele G of rs1800972 locus in HBD-1 gene was a risk factor for ARDS. There was no significant difference in serum HBD-1 levels between patients with different genotypes of rs1799946 and rs11362 locus in the HBD-1 gene (P > .05). HBD-1 gene rs1800972 locus wild type, heterozygous, and mutant homozygous serum levels of HBD-1 gradually decreased, the difference was statistically significant (P < .001). The 60-day survival rate of subjects with wild type, heterozygous, and mutant homozygote at the rs1800972 locus of HBD-1 gene decreased sequentially (81.7%, 48.9%, and 39.7%), and the difference was statistically significant (P < .05). Conclusion: The SNP of rs1800972 (-44C/G) in HBD-1 gene is associated with the risk of ARDS. The rs1800972 locus G allele carriers are more likely to develop ARDS and have a poor prognosis.
Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis

Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. In this study, the Axiom Microbiome Array was evaluated to determine its sensitivity, specificity and utility in microbiome analysis of veterinary clinical samples. The array contains probes designed to detect more than 12,000 species of viruses, bacteria, fungi, protozoa and archaea, yielding the most comprehensive microbial detection platform built to date. The array was able to detect Shigella and Aspergillus at 100 genome copies, and vaccinia virus DNA at 1,000 genome copies. The Axiom Microbiome Array made correct species-level calls in mock microbial community samples. When tested against serum, tissue, and fecal samples from pigs experimentally co-infected with porcine reproductive and respiratory syndrome virus and porcine circovirus type 2, the microarray correctly detected these two viruses and other common viral and bacterial microbiome species. This cost-effective and high-throughput microarray is an efficient tool to rapidly analyze large numbers of clinical and environmental samples for the presence of multiple viral and bacterial pathogens.
EEG Classification of Motor Imagery Using a Novel Deep Learning Framework

Successful applications of brain-computer interface (BCI) approaches to motor imagery (MI) are still limited. In this paper, we propose a classification framework for MI electroencephalogram (EEG) signals that combines a convolutional neural network (CNN) architecture with a variational autoencoder (VAE) for classification. The decoder of the VAE generates a Gaussian distribution, so it can be used to fit the Gaussian distribution of EEG signals. A new representation of input was developed by combining the time, frequency, and channel information from the EEG signal, and the CNN-VAE method was designed and optimized accordingly for this form of input. In this network, the classification of the extracted CNN features is performed via the deep network VAE. Our framework, with an average kappa value of 0.564, outperforms the best classification method in the literature for BCI Competition IV dataset 2b with a 3% improvement. Furthermore, using our own dataset, the CNN-VAE framework also yields the best performance for both three-electrode and five-electrode EEGs and achieves the best average kappa values 0.568 and 0.603, respectively. Our results show that the proposed CNN-VAE method raises performance to the current state of the art.
Movement dynamics of divisome proteins and PBP2x:FtsW in cells of Streptococcus pneumoniae

Significance This study answers two long-standing questions about FtsZ dynamics and its relationship to septal peptidoglycan (PG) synthesis in Streptococcus pneumoniae. In previous models, FtsZ concertedly moves from midcell septa to MapZ rings that have reached the equators of daughter cells. Instead, the results presented here show that FtsZ, FtsA, and EzrA filaments/bundles move continuously out from early septa as part of MapZ rings. In addition, this study establishes that the movement of bPBP2x:FtsW complexes in septal PG synthesis depends on and likely mirrors new PG synthesis and is not correlated with the treadmilling of FtsZ filaments/bundles. These findings are consistent with a mechanism where septal FtsZ rings organize directional movement of bPBP2x:FtsW complexes dependent upon PG substrate availability. Bacterial cell division and peptidoglycan (PG) synthesis are orchestrated by the coordinated dynamic movement of essential protein complexes. Recent studies show that bidirectional treadmilling of FtsZ filaments/bundles is tightly coupled to and limiting for both septal PG synthesis and septum closure in some bacteria, but not in others. Here we report the dynamics of FtsZ movement leading to septal and equatorial ring formation in the ovoid-shaped pathogen, Streptococcus pneumoniae. Conventional and single-molecule total internal reflection fluorescence microscopy (TIRFm) showed that nascent rings of FtsZ and its anchoring and stabilizing proteins FtsA and EzrA move out from mature septal rings coincident with MapZ rings early in cell division. This mode of continuous nascent ring movement contrasts with a failsafe streaming mechanism of FtsZ/FtsA/EzrA observed in a ΔmapZ mutant and another Streptococcus species. This analysis also provides several parameters of FtsZ treadmilling in nascent and mature rings, including treadmilling velocity in wild-type cells and ftsZ(GTPase) mutants, lifetimes of FtsZ subunits in filaments and of entire FtsZ filaments/bundles, and the processivity length of treadmilling of FtsZ filament/bundles. In addition, we delineated the motion of the septal PBP2x transpeptidase and its FtsW glycosyl transferase-binding partner relative to FtsZ treadmilling in S. pneumoniae cells. Five lines of evidence support the conclusion that movement of the bPBP2x:FtsW complex in septa depends on PG synthesis and not on FtsZ treadmilling. Together, these results support a model in which FtsZ dynamics and associations organize and distribute septal PG synthesis, but do not control its rate in S. pneumoniae.
Knowledge-Aided Structured Covariance Matrix Estimator Applied for Radar Sensor Signal Detection

This study deals with the problem of covariance matrix estimation for radar sensor signal detection applications with insufficient secondary data in non-Gaussian clutter. According to the Euclidean mean, the authors combined an available prior covariance matrix with the persymmetric structure covariance estimator, symmetric structure covariance estimator, and Toeplitz structure covariance estimator, respectively, to derive three knowledge-aided structured covariance estimators. At the analysis stage, the authors assess the performance of the proposed estimators in estimation accuracy and detection probability. The analysis is conducted both on the simulated data and real sea clutter data collected by the IPIX radar sensor system. The results show that the knowledge-aided Toeplitz structure covariance estimator (KA-T) has the best performance both in estimation and detection, and the knowledge-aided persymmetric structure covariance estimator (KA-P) has similar performance with the knowledge-aided symmetric structure covariance estimator (KA-S). Moreover, compared with existing knowledge-aided estimator, the proposed estimators can obtain better performance when secondary data are insufficient.
Health Benefits of Physical Activity Related to an Urban Riverside Regeneration

The promotion of physical activity through better urban design is one pathway by which health and well-being improvements can be achieved. This study aimed to quantify health and health-related economic impacts associated with physical activity in an urban riverside park regeneration project in Barcelona, Spain. We used data from Barcelona local authorities and meta-analysis assessing physical activity and health outcomes to develop and apply the “Blue Active Tool”. We estimated park user health impacts in terms of all-cause mortality, morbidity (ischemic heart disease; ischemic stroke; type 2 diabetes; cancers of the colon and breast; and dementia), disability-adjusted life years (DALYs) and health-related economic impacts. We estimated that 5753 adult users visited the riverside park daily and performed different types of physical activity (walking for leisure or to/from work, cycling, and running). Related to the physical activity conducted on the riverside park, we estimated an annual reduction of 7.3 deaths (95% CI: 5.4; 10.2), and 6.2 cases of diseases (95% CI: 2.0; 11.6). This corresponds to 11.9 DALYs (95% CI: 3.4; 20.5) and an annual health-economic impact of 23.4 million euros (95% CI: 17.2 million; 32.8 million). The urban regeneration intervention of this riverside park provides health and health-related economic benefits to the population using the infrastructure.
Energy-Efficient IoT Service Brokering with Quality of Service Support †

The Internet of Things (IoT) is becoming real, and recent studies highlight that the number of IoT devices will significantly grow in the next decade. Such massive IoT deployments are typically made available to applications as a service by means of IoT platforms, which are aware of the characteristics of the connected IoT devices–usually constrained in terms of computation, storage and energy capabilities–and dispatch application’s service requests to appropriate devices based on their capabilities. In this work, we develop an energy-aware allocation policy that aims at maximizing the lifetime of all the connected IoT devices, whilst guaranteeing that applications’ Quality of Service (QoS) requirements are met. To this aim, we formally define an IoT service allocation problem as a non-linear Generalized Assignment Problem (GAP). We then develop a time-efficient heuristic algorithm to solve the problem, which is shown to find near-optimal solutions by exploiting the availability of equivalent IoT services provided by multiple IoT devices, as expected especially in the case of massive IoT deployments.
Molecular identification of Wolbachia and Sodalis glossinidius in the midgut of Glossina fuscipes quanzensis from the Democratic Republic of Congo

During the last 30 years, investigations on the microbiome of different tsetse species have generated substantial data on the bacterial flora of these cyclical vectors of African trypanosomes, with the overarching goal of improving the control of trypanosomiases. It is in this context that the presence of Wolbachia and Sodalis glossinidius was studied in wild populations of Glossina fuscipes quanzensis from the Democratic Republic of Congo. Tsetse flies were captured with pyramidal traps. Of the 700 Glossina f. quanzensis captured, 360 were dissected and their midguts collected and analyzed. Sodalis glossinidius and Wolbachia were identified by PCR. The Wolbachia-positive samples were genetically characterized with five molecular markers. PCR revealed 84.78% and 15.55% midguts infected by Wolbachia and S. glossinidius, respectively. The infection rates varied according to capture sites. Of the five molecular markers used to characterize Wolbachia, only the fructose bis-phosphate aldolase gene was amplified for about 60% of midguts previously found with Wolbachia infections. The sequencing results confirmed the presence of Wolbachia and revealed the presence of S. glossinidius in the midgut of Glossina f. quanzensis. A low level of midguts were naturally co-infected by both bacteria. The data generated in this study open a framework for investigations aimed at understanding the contribution of these symbiotic microorganisms to the vectorial competence of Glossina fuscipes quanzensis.
Viable Neisseria meningitidis is commonly present in saliva in healthy young adults: Non-invasive sampling and enhanced sensitivity of detection in a follow-up carriage study in Portuguese students

Introduction and aims Improved sensitivity and efficiency of detection and quantification of carriage of Neisseria meningitidis (Nm) in young people is important for evaluation of the impact of vaccines upon transmission and associated population-wide effects. Saliva collection is quick, non-invasive and facilitates frequent sampling, but has been reported to yield low sensitivity by culture. We re-evaluated this approach in a follow-up cross sectional study using direct and culture-amplified PCR. Material/Methods In April 2016 we collected paired oropharyngeal swabs (OPS) and saliva samples from 1005 healthy students in Portugal into STGG broth and stored them at -80°C until DNA extraction and batched qPCR analysis. Samples were also cultured on GC agar plates for 72h and PCR done on DNA extracts from overall growth. Nm isolates were also sought from a selection of 50 samples. qPCR amplification targets were superoxide dismutase sodC and capsular locus/genogroup-specific genes (B, C, W, X and Y) and, for cultured isolates only, porA. Cycle threshold values of ≤36 were considered positive. Results 556 tests (460 samples, 363 subjects, 36.1%) were positive for Nm (sodC) and 65 (45, 36, 3.6%) for MenB. More salivas were positive by direct sodC qPCR (211, 21.0%) than OPS (126, 12.5%) but fewer were positive by culture-amplified qPCR (94 vs. 125). For both sample types, many that were negative on direct qPCR came positive on culture-amplification and Nm was consistently isolated from salivas in which culture amplified the PCR signal. Using both methods on both samples yielded 36.1% Nm and 5.5% encapsulated Nm carriage rates while direct qPCR on OPS alone detected 12.5% and 2.2%. Conclusions Detectable MenB carriage rates (2.9%) were lower than 4 years earlier (6.8%) in this population (p = 0.0003). Viable meningococci were often present in saliva. Although evidence of encapsulated Nm was less frequent in saliva than OPS, collection is more acceptable to subjects allowing more frequent sampling. Use of culture-amplification increases detection sensitivity in both sample types, especially when combined with direct PCR. Combining these samples and/or methodologies could greatly enhance the power of carriage studies to detect the impact of vaccines upon carriage and transmission.
Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides

Ceramides are central intermediates of sphingolipid metabolism that also function as potent messengers in stress signaling and apoptosis. Progress in understanding how ceramides execute their biological roles is hampered by a lack of methods to manipulate their cellular levels and metabolic fate with appropriate spatiotemporal precision. Here, we report on clickable, azobenzene-containing ceramides, caCers, as photoswitchable metabolic substrates to exert optical control over sphingolipid production in cells. Combining atomic force microscopy on model bilayers with metabolic tracing studies in cells, we demonstrate that light-induced alterations in the lateral packing of caCers lead to marked differences in their metabolic conversion by sphingomyelin synthase and glucosylceramide synthase. These changes in metabolic rates are instant and reversible over several cycles of photoswitching. Our findings disclose new opportunities to probe the causal roles of ceramides and their metabolic derivatives in a wide array of sphingolipid-dependent cellular processes with the spatiotemporal precision of light.
A Spotlight on Viruses—Application of Click Chemistry to Visualize Virus-Cell Interactions

The replication of a virus within its host cell involves numerous interactions between viral and cellular factors, which have to be tightly controlled in space and time. The intricate interplay between viral exploitation of cellular pathways and the intrinsic host defense mechanisms is difficult to unravel by traditional bulk approaches. In recent years, novel fluorescence microscopy techniques and single virus tracking have transformed the investigation of dynamic virus-host interactions. A prerequisite for the application of these imaging-based methods is the attachment of a fluorescent label to the structure of interest. However, their small size, limited coding capacity and multifunctional proteins render viruses particularly challenging targets for fluorescent labeling approaches. Click chemistry in conjunction with genetic code expansion provides virologists with a novel toolbox for site-specific, minimally invasive labeling of virion components, whose potential has just recently begun to be exploited. Here, we summarize recent achievements, current developments and future challenges for the labeling of viral nucleic acids, proteins, glycoproteins or lipids using click chemistry in order to study dynamic processes in virus-cell interactions.