Miracle-dz/UniFAR-FTUs huggingface dataset:
Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA–minus RNA sequencing data

Abstract Background Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non–poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. Results We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA–minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG–positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. Conclusion By using the full potential of non–poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects.
The strategic role of manufacturing

Through empirical research a model is provided that represents strategic manufacturing effectiveness. It shows what are the important factors that directly affect strategic manufacturing effectiveness, how they relate to each other, and how they can be measured. Research is done to identify and define the stages of strategic manufacturing effectiveness. It links the four-stage framework to the concept of strategic groups and identifies two strategic groups whose effectiveness has been shown to relate positively to manufacturing competence. Details are presented on the positive effects that strategic manufacturing effectiveness has on manufacturing performance, the effects on types of industry, the sizes of firms and the types of production process used.
Splicing efficiency of minor introns in a mouse model of SMA predominantly depends on their branchpoint sequence and can involve the contribution of major spliceosome components

Spinal muscular atrophy (SMA) is a devastating neurodegenerative disease caused by reduced amounts of the ubiquitously expressed Survival of Motor Neuron (SMN) protein. In agreement with its crucial role in the biogenesis of spliceosomal snRNPs, SMN-deficiency is correlated to numerous splicing alterations in patient cells and various tissues of SMA mouse models. Among the snRNPs whose assembly is impacted by SMN-deficiency, those involved in the minor spliceosome are particularly affected. Importantly, splicing of several, but not all U12-dependent introns has been shown to be affected in different SMA models. Here, we have investigated the molecular determinants of this differential splicing in spinal cords from SMA mice. We show that the branchpoint sequence (BPS) is a key element controlling splicing efficiency of minor introns. Unexpectedly, splicing of several minor introns with suboptimal BPS is not affected in SMA mice. Using in vitro splicing experiments and oligonucleotides targeting minor or major snRNAs, we show for the first time that splicing of these introns involves both the minor and major machineries. Our results strongly suggest that splicing of a subset of minor introns is not affected in SMA mice because components of the major spliceosome compensate for the loss of minor splicing activity.
A standardized approach for case selection and genomic data analysis of maternal exomes for the diagnosis of oocyte maturation and early embryonic developmental arrest in IVF

OBJECTIVE: To develop a methodology for case selection and whole-exome sequencing (WES) analysis in infertile women due to recurrent oocyte maturation defects(OOMD) and/or preimplantation embryo lethality (PREMBL). DESIGN: Cross-sectional study. SETTING: IVF patients attending the Istanbul Memorial Hospital (2015-2021). WES and bioinformatics were performed at Igenomix and National Research Council,Italy. PATIENTS: A statistical methodology for identification of infertile endophenotypes (recurrent low oocyte maturation rate, LMR, low fertilization rate, LFR, and preimplantation developmental arrest, PDA, was developed using a large IVF dataset (11,221 couples). 28 OOMD/PREMBL infertile women were subsequently enrolled for WES. INTERVENTION: 30X-WES was performed on women's gDNA. Pathogenic variants were prioritized using a custom-made bioinformatic pipeline set to minimize false positive discoveries through resampling in control cohorts (i.e., HGDP and 1,343 WES from oocyte donors). Individual scRNAseq data from 18 human MII oocytes and antral granulosa cells(AGC) was used for genome-wide validation. MAIN OUTCOME MEASURE: Identification of High-impact variants and pathways causative of OOMD/PREMBL endophenotypes. RESULTS: Variant prioritization analysis identified 265 unique variants in 248 genes (average per sample 22.4). 87.8% of genes harbouring high-impact variants are expressed by MII oocytes and/or AGC, significantly higher compared to a random sample of 28 WES from the egg donors. Seven of the 28 women (25%) are homozygous carriers of missense pathogenic variants in known candidate genes for OOMD/PREMBL, including PATL2, NLRP5 (N=2), TLE6,PADI6, TUBB8 and TRIP13. CONCLUSIONS: This analytical framework revealed known and new genes/pathways associated with isolated recurrent OOMD/PREMBL, providing essential indications for scaling this strategy to larger studies.
Increased risk of cognitive impairment and hyperglycemia-related mortality in late middle-aged African Americans with low serum adropin levels

Recent data implicate the secreted peptide adropin in the physiology of aging. In mice, adropin improves glucose homeostasis. In humans, adropin is highly expressed in brain tissues, and correlates positively with transcriptomic signatures of mitochondrial and synaptic functions. Adropin improves performance of old mice in cognitive tests requiring learning and memory. While detected in the human circulation, no studies have investigated relationships between adropin, cognitive decline and aging. We compared serum adropin concentrations with Mini-Mental State Exam (MMSE) and animal naming test results from a cohort study of African Americans in late-middle age (baseline ages 49-65y, n=357). Using the lowest quintile of the MMSE to identify participants at risk for mild cognitive impairment (MCI) indicated lower serum concentrations (2.95{+/-}1.32 ng/ml vs. 3.31{+/-}1.56, P<0.05). Grouping into bins using 1-ng/ml increments in serum adropin concentrations further indicated an association between very low serum adropin concentrations and MCI. Using fructosamine as an indicator of moderate-term glucose levels suggested low serum adropin concentration correlate with increased risk of 10-year all-cause mortality in situations of poor glucose control. In summary, these data suggest low circulating adropin concentrations identify late-middle aged people at risk for cognitive impairment, and for all-cause mortality in situations of poor glucose control.
Genetic testing for the epilepsies: A systematic review

Numerous genetic testing options for individuals with epilepsy have emerged over the past decade without clear guidelines regarding optimal testing strategies. We performed a systematic evidence review (SER) and conducted meta‐analyses of the diagnostic yield of genetic tests commonly utilized for patients with epilepsy. We also assessed nonyield outcomes (NYOs) such as changes in treatment and/or management, prognostic information, recurrence risk determination, and genetic counseling.
Effect of a 3-Year Lifestyle Intervention in Patients with Chronic Kidney Disease: A Randomized Clinical Trial

Significance Statement Modifiable risk factors, such as low physical activity, contribute to cardiovascular mortality in patients with CKD. In a randomized trial of 160 patients with CKD, a nurse-led, multidisciplinary lifestyle intervention that included exercise training significantly increased cardiorespiratory fitness (peak O2 uptake) in patients with CKD at 12 months compared with usual care; peak O2 uptake declined to near baseline levels thereafter but remained elevated compared with usual care after 3 years of follow-up. The intervention also markedly increased exercise capacity and physical function, and prevented adverse anthropometric changes that were observed in the usual care group. Importantly, benefits of the intervention were sustained over 3 years. This study provides evidence of the effectiveness of a multidisciplinary team–supported lifestyle intervention in enhancing the health of patients with CKD. Visual Abstract Background Supervised lifestyle interventions have the potential to significantly improve physical activity and fitness in patients with CKD. Methods To assess the efficacy of a lifestyle intervention in patients with CKD to improve cardiorespiratory fitness and exercise capacity over 36 months, we conducted a randomized clinical trial, enrolling 160 patients with stage 3–4 CKD, with 81 randomized to usual care and 79 to a 3-year lifestyle intervention. The lifestyle intervention comprised care from a multidisciplinary team, including a nephrologist, nurse practitioner, exercise physiologist, dietitian, diabetes educator, psychologist, and social worker. The exercise training component consisted of an 8-week individualized and supervised gym-based exercise intervention followed by 34 months of a predominantly home-based program. Self-reported physical activity (metabolic equivalent of tasks [METs] minutes per week), cardiorespiratory fitness (peak O2 consumption [VO2peak]), exercise capacity (maximum METs and 6-minute walk distance) and neuromuscular fitness (grip strength and get-up-and-go test time) were evaluated at 12, 24, and 36 months. Results The intervention increased the percentage of patients meeting physical activity guideline targets of 500 MET min/wk from 29% at baseline to 63% at 3 years. At 12 months, both VO2peak and METs increased significantly in the lifestyle intervention group by 9.7% and 30%, respectively, without change in the usual care group. Thereafter, VO2peak declined to near baseline levels, whereas METs remained elevated in the lifestyle intervention group at 24 and 36 months. After 3 years, the intervention had increased the 6-minute walk distance and blunted declines in the get-up-and-go test time. Conclusions A 3-year lifestyle intervention doubled the percentage of CKD patients meeting physical activity guidelines, improved exercise capacity, and ameliorated losses in neuromuscular and cardiorespiratory fitness.
Progesterone-dependent and -independent modulation of luminal epithelial transcription to support pregnancy in cattle.

In cattle, starting 4-5 days after estrus, pre-implantation embryonic development occurs in the confinement of the uterine lumen. Cells in the endometrial epithelial layer control the molecular traffic to and from the lumen and, thereby determine luminal composition. Starting early post-estrus, endometrial function is regulated by sex-steroids, but the effects of progesterone on luminal cells transcription have not been measured in vivo. First objective was to determine the extent to which progesterone controls transcription in luminal epithelial cells 4 d (D4) after estrus. Second objective was to discover luminal transcripts that predict pregnancy outcomes, when the effect of progesterone is controlled. Endometrial luminal epithelial cells were collected from embryo transfer recipients on D4 using a cytological brush and their transcriptome determined by RNASeq. Pregnancy by embryo transfer was measured on D30 (25 pregnant and 18 non-pregnant). Progesterone concentration on D4 was associated positively (n= 182) and negatively (n= 58) with gene expression. Progesterone-modulated transcription indicated an increase in oxidative phosphorylation, biosynthetic activity and proliferation of epithelial cells. When these effects of progesterone were controlled, different genes affected positively (n= 22) and negatively (n= 292) odds of pregnancy. These set of genes indicated that a receptive uterine environment was characterized by the inhibition of phosphoinositide signaling and innate immune system responses. A panel of 25 genes predicted the pregnancy outcome with sensitivity and specificity ranging from 64-96% and 44-83%, respectively. In conclusion, in the early diestrus, both progesterone-dependent and -independent mechanisms regulate luminal epithelial transcription associated with pregnancy outcomes in cattle.
Dynamic characteristics of shaped micro-actuators solved using the differential quadrature method

This study examined the dynamic characteristics of nonlinear electrostatic pull-in behavior for shaped actuators in micro-electro-mechanical systems (MEMS). The natural frequencies of a fixed–fixed shaped beam vibrating around its statically deflected position were calculated using the differential quadrature method (DQM). The proposed model included the nonlinear interaction between the curved electrostatic field force and the shaped micro-beam, as well as the mid-plane stretching, axial residual stress and electrical field fringing effect. Very good agreement existed between the results simulated using the proposed model and the measured data. This work also investigated the micro-beam and electrode shape effect on the natural frequencies of the actuator system. Analytical results indicate that the variation in the micro-beam and the electrode shapes might not only influence the electrostatic field distribution but also significantly alter the dynamic characteristics of the micro-actuator. Analytical results demonstrate that the shaped micro-beam with curved electrode can increase the working voltage range approximately six times compared to the rectangular micro-beam and flat electrode.
Relay vibration protection simulation experimental platform based on signal reconstruction of MATLAB software

Abstract For conceptual analysis of the principle of relay vibration protection, this article establishes the simulation system model of directional current protection in MATLAB/Simulink environment through the protection algorithm. Various outcomes have been achieved for the proposed approach during the faulty conditions. The outcomes obtained during the fault period reveals that the waveform of three-phase current changes greatly, and the amplitude of three-phase current at power supply side increases sharply. After 0.02s signal acquisition and processing, the action signal acts after 0.07s, and the fault is removed. In case of two-phase short-circuit, two-phase grounding short-circuit and other faults, the fault can be removed smoothly after signal acquisition and processing. In this paper, the directional current protection simulation system based on microcomputer protection model is built, and the changes of voltage, current and action signal are demonstrated through GUI interface, and analyzed and verified.
Whole Genome Analysis of Polyadenylation Sites in Long Non-coding RNAs in Oryza Sativa

Polyadenylation [poly(A)] has been shown to widely contribute to regulating gene expression involving complex mechanisms. Recent analysis of eukaryotic genomes has uncovered a large number of long non-coding RNAs (lncRNAs), however, the characteristic of lncRNAs is still unclear. In this study, we focus on the study of poly(A) sites of lncRNAs in Oryza sativa using genome-wide high-throughput sequencing data. Around 23% lncRNAs have at least one poly(A) site and most of them have multiple poly(A) sites. Interestingly, poly(A) sites are more likely to be located in upstream regions of lncRNAs than in downstream regions. Moreover, poly(A) sites of lncRNAs are expressed at a lower level than those of mRNAs, and lncRNAs with poly(A) sites are more conserved than those without poly(A) sites. These results will provide a new perspective for the study of the mechanism of APA of lncRNAs in plants.
Replicating a Study of Ransomware in Germany

Ransomware is a pertinent threat to businesses and end user data. While several attacks on enterprises are reported and give insights into the prevalence of such ransomware attacks, this prevalence in the general population is hard to estimate since they are not monitored by an official entity. A 2019 study by Simoiu et al. surveyed a representative sample of American consumers to estimate it for the US population. One year later, we aimed to replicate this effort for a representative German population (N=963) to study the spread of ransomware in a different context. Our findings suggest some differences between the two samples concerning payment methods and the participants’ way of dealing with ransomware. Other aspects, like the ransom amounts and behavioral changes after an attack, were largely similar. We extend prior work by examining disagreements and uncertainty in judging whether a ransomware attack occurred for participants and researchers alike.
Patching Non-Uniform Extraordinary Points with Sharp Features

Extending the non-uniform rational B-spline (NURBS) representation to arbitrary topology is one of the most important steps to define the iso-geometric analysis (IGA) suitable geometry. The approach needs to be NURBS-compatible and can handle non-uniform knot intervals. To achieve this goal, we present a novel patching solution which define one Bézier patch for each non-zero knot interval control grid face. The construction can reproduce the bi-cubic NURBS in the regular face and define bi-quintic Bézier patches for irregular faces. The method can also support non-uniform sharp features along the extraordinary points. Experimental results demonstrate that the new surfaces can improve the surface quality for non-uniform parameterization.
Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation

How the eukaryotic 43S preinitiation complex scans along the 5′ untranslated region (5′UTR) of a capped mRNA to locate the correct start codon remains elusive. Here, we directly track yeast 43S-mRNA binding, scanning, and 60S subunit joining by real-time single-molecule fluorescence spectroscopy. Once engaged with the mRNA, 43S scanning occurs at >100 nucleotides per second, independent of multiple cycles of ATP-hydrolysis by RNA helicases. The scanning ribosomes can proceed through RNA secondary structures, but 5′UTR hairpin sequences near start codons drive scanning ribosomes at start codons back in the 5′ direction, requiring rescanning to arrive once more at a start codon. Direct observation of scanning ribosomes provides a mechanistic framework for translational regulation by 5′UTR structures and upstream near-cognate start codons. One Sentence Summary Direct observation of scanning eukaryotic ribosomes establishes a quantitative framework of scanning and its regulation.
Transcriptomic modulation in response to an intoxication with deltamethrin in Triatoma infestans, vector of Chagas disease

Background Triatoma infestans is the main vector of Chagas disease in the Southern Cone. The resistance to pyrethroid insecticides developed by populations of this species impairs the effectiveness of vector control campaigns in wide regions of Argentina. The study of the global transcriptomic response to pyrethroid insecticides is important to deepen the knowledge about detoxification in triatomines. Methodology and findings We used RNA-Seq to explore the early transcriptomic response of T. infestans after intoxication with deltamethrin. We were able to assemble a complete transcriptome of this vector and found evidence of differentially expressed genes belonging to diverse families such as chemosensory and odorant-binding proteins, ABC transporters and heat-shock proteins. Moreover, genes related to transcription and translation, energetic metabolism and cuticle rearrangements were also modulated. Finally, we characterized the repertoire of previously uncharacterized detoxification-related gene families in T. infestans and Rhodnius prolixus. Conclusions and significance Our work contributes to the understanding of the detoxification response in vectors of Chagas disease. Given the absence of genomic information from T. infestans, the analysis presented here constitutes a resource for molecular and physiological studies in this species. The results increase the knowledge on detoxification processes in vectors of Chagas disease, and provide relevant information to explore new potential insecticide resistance mechanisms in these insects. Author summary Chagas disease affects millions of people worldwide. In the Southern Cone, the development of pyrethroid resistant populations from T. infestans is related to vector persistence and affects the efficiency of vector control campaigns. Several studies have explored the causes of insecticide resistance in T. infestans populations. However, the global transcriptomic response after insecticide treatment has not been analyzed in this species so far. In this study, we obtained transcriptomic information which allowed us to characterize important gene families despite the absence of genomic information. Furthermore, we performed a quantitative analysis of gene expression after deltamethrin intoxication. The results provided here increase the knowledge on detoxification processes in vectors of Chagas disease, which is essential for the design of new vector control strategies.
EFFECTS OF AIR BLOWING ON TURBULENT FLOW OVER A CIRCULAR CYLINDER

This study analyzes the flow over a two-dimensional (2D) circular cylinder at a turbulent Reynolds number of 20,000 and its control by air blowing from several slots located on the surface of the cylinder, computationally. CFD simulations are performed by using Unsteady Reynolds-Averaged Navier-Stokes (URANS) equations and Spalart-Allmaras turbulence model. Uncontrolled flow simulation results are validated using the experimental results available in literature for drag coefficient, Strouhal number, time-averaged pressure coefficient distribution on the circumference of the cylinder and mean velocity values at the downstream. Air blowing from several slots located on the cylinder is used as an actuator for forcing the flow. Blowing from four slots located on the circumference of the cylinder with a velocity magnitude of 50% of the free stream velocity yields a drag reduction of 23% compared to the uncontrolled case. Additionally, near wake region is further examined by application of Proper Orthogonal Decomposition (POD) technique. A Fast Fourier Transform (FFT) based spatial filtering procedure is employed in order to separate the effects of small-scale turbulent structures in the wake region. The FFT-filtered snapshot-based POD analysis shows that approximately 99% of the total energy of the flow can be represented by considering only the most energetic first two modes where the effects of von Karman vortex street can be seen appropriately both for uncontrolled and controlled flow cases.