PsiNorm: a scalable normalization for single-cell RNA-seq data.

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) enables transcriptome-wide gene expression measurements at single-cell resolution providing a comprehensive view of the compositions and dynamics of tissue and organism development. The evolution of scRNA-seq protocols has led to a dramatic increase of cells throughput, exacerbating many of the computational and statistical issues that previously arose for bulk sequencing. In particular, with scRNA-seq data all the analyses steps, including normalization, have become computationally intensive, both in terms of memory usage and computational time. In this perspective, new accurate methods able to scale efficiently are desirable. RESULTS: Here, we propose PsiNorm, a between-sample normalization method based on the power-law Pareto distribution parameter estimate. Here, we show that the Pareto distribution well resembles scRNA-seq data, especially those coming from platforms that use unique molecular identifiers. Motivated by this result, we implement PsiNorm, a simple and highly scalable normalization method. We benchmark PsiNorm against seven other methods in terms of cluster identification, concordance and computational resources required. We demonstrate that PsiNorm is among the top performing methods showing a good trade-off between accuracy and scalability. Moreover, PsiNorm does not need a reference, a characteristic that makes it useful in supervised classification settings, in which new out-of-sample data need to be normalized. AVAILABILITY AND IMPLEMENTATION: PsiNorm is implemented in the scone Bioconductor package and available at https://bioconductor.org/packages/scone/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Clinical outcome and failure analysis of medial meniscus bucket-handle tear repair: a series of 96 patients with a minimum 2 year follow-up.

INTRODUCTION: The failure rate of meniscal repair remains significant, especially for bucket-handle tears. This study aimed to evaluate the clinical outcomes, failure rate and risk factors for failure of bucket-handle medial meniscal tear repairs performed during ACL reconstruction. MATERIALS AND METHODS: A retrospective analysis of prospectively collected data was performed on a consecutive series of 96 ACL reconstructions with meniscal arthroscopic suture of a bucket-handle tear of the medial meniscus with a minimum 2 year follow-up. Preoperative and postoperative evaluation at last follow-up included objective IKDC rating, instrumented differential laxity and Tegner activity level. Functional outcome was evaluated with Lysholm score at last follow-up. Failure rate, survival curves and risk factor analysis using Cox proportional hazard ratio models were performed to analyze suture repair failure. RESULTS: At IKDC rating, all patients were C or D preoperatively, whereas they where all A or B at last follow-up. Instrumented differential laxity improved from 6.77 mm (1.57) to 1.02 mm (1.15) mm at last follow-up (p = 1.9 E-18). The mean Tegner score before injury was 6.79 (± 1.47) and 6.11 (± 1.75) at last follow-up (p = 0.0011). Mean Lyholm score at last follow-up was 91.53 (± 11.6). The average entire cohort failure rate was 19% at final follow-up of 35.2 ± 9.8 months. Kaplan-Meier survival analysis demonstrated that the probability of the absence of failure decreased constantly over time. No significant difference in the objective IKDC, Lysholm or Tegner scores was observed between the failure group and the success group. Multivariate analysis revealed that younger patients and a procedure of ACL revision are more at risk for suture repair failure. In the majority of cases, the meniscal lesion observed at revision was equivalent or less extensive than the initial lesion. CONCLUSION: Despite the fact that failure rate remains high for medial meniscus bucket-handle tears, suture repair of bucket-handle tears should be encouraged taking into account the long-term consequences of menisectomy.

The challenging surgical treatment of closed distal humerus fractures in elderly and octogenarian patients: radiographic and functional outcomes with a minimum follow-up of 24 months.

INTRODUCTION: The main purpose of this retrospective, non-randomized, case series study was to evaluate the clinical and radiographic outcomes of distal humerus fractures (DHFs) in a consecutive series of elderly patients operatively treated by two surgeons, and second, to identify proper indications for two elderly age ranges and two fracture pattern groups. MATERIALS AND METHODS: From January 2009 to June 2014, 51 patients (pts) underwent open reduction and internal fixation (ORIF) using the locking compression plate (LCP) distal humerus plate (DHP) system at our institution. Medical records and radiographs were retrospectively assessed. Patients were divided into 3 groups according to gender, age (pts <85 years, pts ≥85 years) and AO classification (13-B1-B2-C1-C2 or 13-C3). All subjects completed MEPS, Quick-DASH and SF-36 PCS/MCS scores at final follow-up, and statistical analysis was performed. RESULTS: 36 patients (20 women, 16 men), mean age 80.3 years, with AO type 13-B and 13-C DHFs were included with a mean follow-up of 56 months (range 24-92). The most common mechanism of trauma was a fall from ground level (55.6%). The mean MEPS was 78.9 points, Quick-DASH 28.4, SF-36 PCS 48.3 and MCS 48.9. There was statistically significant evidence that having a 13-C3 fracture leads to worse results in MEPS, Quick-DASH and SF-36. The female gender correlates with worse results in SF-36. The patients ≥85 years had a worse prognosis according to Quick-DASH and SF-36, while the AO 13-C3 pattern obtained the worst ROM outcomes versus AO 13 B1-B2-C1-C2 (normal ROM 0°-140°): mean ROM 24°-114° vs 10°-130°, mean flexion deficit 26° vs 10°, mean extension deficit 24° vs 10°, respectively). Complications were presents in 36.1% of patients, overall belonging to the AO type 13-C fracture pattern and to the group ≥85 years. CONCLUSION: These study data seem to confirm our hypothesis that plate fixation for DHFs guarantees adequate fracture osteosynthesis and satisfactory functional outcomes at medium to long-term follow-up, not only in elderly patients, but also in octogenarian osteoporotic patients (≥85 years) with 13-C1 and 13-C2 fracture patterns, while an alternative solution should be considered for type C3 fractures, even in a primary trauma setting.

Phosphorus Acquisition Efficiency and Transcriptomic Changes in Maize Plants Treated with Two Lignohumates.

Lignohumates are increasing in popularity in agriculture, but their chemistry and effects on plants vary based on the source and processing. The present study evaluated the ability of two humates (H1 and H2) to boost maize plant performance under different phosphorus (P) availability (25 and 250 µM) conditions in hydroponics, while understanding the underlying mechanisms. Humates differed in chemical composition, as revealed via elemental analysis, phenol and phytohormone content, and thermal and spectroscopic analyses. H1 outperformed H2 in triggering plant responses to low phosphorus by enhancing phosphatase and phytase enzymes, P acquisition efficiency, and biomass production. It contained higher levels of endogenous auxins, cytokinins, and abscisic acid, likely acting together to stimulate plant growth. H1 also improved the plant antioxidant capacity, thus potentially increasing plant resilience to external stresses. Both humates increased the nitrogen (N) content and acted as biostimulants for P and N acquisition. Consistent with the physiological and biochemical data, H1 upregulated genes involved in growth, hormone signaling and defense in all plants, and in P recycling particularly under low-P conditions. In conclusion, H1 showed promising potential for effective plant growth and nutrient utilization, especially in low-P plants, involving hormonal modulation, antioxidant enhancement, the stimulation of P uptake and P-recycling mechanisms.

Brown Seaweed Extract (BSE) Application Influences Auxin- and ABA-Related Gene Expression, Root Development, and Sugar Yield in Beta vulgaris L.

The molecular and phenotypic effects of a brown seaweed extract (BSE) were assessed in sugar beet (Beta vulgaris L.). Transcript levels of BSE-treated and untreated plants were studied by RNA-seq and validated by quantitative real-time PCR analysis (RT-qPCR). Root morphology, sugar yield, and processing quality traits were also analyzed to better elucidate the treatment effects. RNA-seq revealed 1019 differentially expressed genes (DEGs) between the BSE-treated and untreated plants. An adjusted p-value < 0.1 and an absolute value of log2 (fold change) greater than one was used as criteria to select the DEGs. Gene ontology (GO) identified hormone pathways as an enriched biological process. Six DEGs involved in auxin and ABA pathways were validated using RT-qPCR. The phenotypic characterization indicated that BSE treatment led to a significant increase (p < 0.05) in total root length and the length of fine roots of plants grown under hydroponics conditions. The sugar yield of plants grown under field conditions was higher (p < 0.05) in the treated field plots compared with the control treatment, without impacting the processing quality. Our study unveiled the relevant effects of BSE application in regulating auxin- and ABA-related gene expression and critical traits related to sugar beet development and yield.

Transcriptomic and physiological approaches to decipher cold stress mitigation exerted by brown-seaweed extract application in tomato.

Chilling temperatures represent a challenge for crop species originating from warm geographical areas. In this situation, biostimulants serve as an eco-friendly resource to mitigate cold stress in crops. Tomato (Solanum lycopersicum L.) is an economically important vegetable crop, but quite sensitive to cold stress, which it encounters in both open field and greenhouse settings. In this study, the biostimulant effect of a brown-seaweed extract (BSE) has been evaluated in tomato exposed to low temperature. To assess the product effects, physiological and molecular characterizations were conducted. Under cold stress conditions, stomatal conductance, net photosynthesis, and yield were significantly (p ≤ 0.05) higher in BSE-treated plants compared to the untreated ones. A global transcriptomic survey after BSE application revealed the impact of the BSE treatment on genes leading to key responses to cold stress. This was highlighted by the significantly enriched GO categories relative to proline (GO:0006560), flavonoids (GO:0009812, GO:0009813), and chlorophyll (GO:0015994). Molecular data were integrated by biochemical analysis showing that the BSE treatment causes greater proline, polyphenols, flavonoids, tannins, and carotenoids contents.The study highlighted the role of antioxidant molecules to enhance tomato tolerance to low temperature mediated by BSE-based biostimulant.

A dual-omics approach for profiling plant responses to biostimulant applications under controlled and field conditions.

A comprehensive approach using phenomics and global transcriptomics for dissecting plant response to biostimulants is illustrated with tomato (Solanum lycopersicum cv. Micro-Tom and Rio Grande) plants cultivated in the laboratory, greenhouse, and open field conditions. Biostimulant treatment based on an Ascophyllum nodosum extract (ANE) was applied as a foliar spray with two doses (1 or 2 l ha-1) at three different phenological stages (BBCH51, BBCH61, and BBCH65) during the flowering phase. Both ANE doses resulted in greater net photosynthesis rate, stomatal conductance, and fruit yield across all culture conditions. A global transcriptomic analysis of leaves from plants grown in the climate chamber, revealed a greater number of differentially expressed genes (DEGs) with the low ANE dose compared to the greater one. The second and third applications induced broader transcriptome changes compared to the first one, indicating a cumulative treatment effect. The functional enrichment analysis of DEGs highlighted pathways related to stimulus-response and photosynthesis, consistent with the morpho-physiological observations. This study is the first comprehensive dual-omics approach for profiling plant responses to biostimulants across three different culture conditions.

The outcomes of surgical management of failed two-stage revision knee arthroplasty.

Background Joint infection following total knee arthroplasty has significant consequences on both the patient and healthcare system. Two stage revision arthroplasties is viewed as the gold standard in management. However, recurrence of infection following this procedure is a growing clinical problem for a multitude of reasons. Despite a variety of surgical options for management of failure of two-stage revision arthroplasty, the potential for complications and functional limitation remains high, and the optimal strategy is yet to be determined. Methods We performed a systematic review of all papers reporting on the outcomes of the surgical management of failure of two-stage revision arthroplasty published up to and including January 2020. Data was extracted on patient demographics, study design, methodological quality, indication for surgery, surgical technique, clinical and functional outcomes, and complications. Results Nine papers with a total of 273 patients were found and analysed All surgical techniques had mixed results in term of clinical and functional outcomes, and the rate of complications was high in all studies. Knee arthrodesis had the lower risk of failure than repeat 2 stage revision. Poor patient immunological status and limb status were weakly associated with increased risk of failure. Conclusion Despite failure of two-stage revision arthroplasty being a growing clinical issue, we were not able to identify any consistently superior surgical technique for the management of this scenario. Knee arthrodesis appears to provide the best results for improving quality of life and reducing infection recurrence, although the complication rate is high and the functional outcomes appear to be worse. Further larger and prospective studies are needed to elucidate optimal surgical management in different patient subsets.

Transcriptional and Physiological Analyses to Assess the Effects of a Novel Biostimulant in Tomato.

This work aimed to study the effects in tomato (Solanum lycopersicum L.) of foliar applications of a novel calcium-based biostimulant (SOB01) using an omics approach involving transcriptomics and physiological profiling. A calcium-chloride fertilizer (SOB02) was used as a product reference standard. Plants were grown under well-watered (WW) and water stress (WS) conditions in a growth chamber. We firstly compared the transcriptome profile of treated and untreated tomato plants using the software RStudio. Totally, 968 and 1,657 differentially expressed genes (DEGs) (adj-p-value < 0.1 and |log2(fold change)| ≥ 1) were identified after SOB01 and SOB02 leaf treatments, respectively. Expression patterns of 9 DEGs involved in nutrient metabolism and osmotic stress tolerance were validated by real-time quantitative reverse transcription PCR (RT-qPCR) analysis. Principal component analysis (PCA) on RT-qPCR results highlighted that the gene expression profiles after SOB01 treatment in different water regimes were clustering together, suggesting that the expression pattern of the analyzed genes in well water and water stress plants was similar in the presence of SOB01 treatment. Physiological analyses demonstrated that the biostimulant application increased the photosynthetic rate and the chlorophyll content under water deficiency compared to the standard fertilizer and led to a higher yield in terms of fruit dry matter and a reduction in the number of cracked fruits. In conclusion, transcriptome and physiological profiling provided comprehensive information on the biostimulant effects highlighting that SOB01 applications improved the ability of the tomato plants to mitigate the negative effects of water stress.