Flatfoot Reconstruction for Painful Pediatric Idiopathic Flexible Flatfoot: Prospective Study Demonstrates Improved Alignment, Function, and Patient-reported Outcomes.

BACKGROUND: This prospective study was undertaken to report outcomes following reconstructive surgery for patients with painful pediatric idiopathic flexible flatfoot. METHODS: Twenty-five patients with pediatric idiopathic flexible flatfoot were evaluated pre- and post flatfoot reconstruction with lateral column lengthening (LCL). All patients had lengthening of the Achilles or gastrocnemius, while 13 patients had medial side soft tissue (MSST) procedures, 7 underwent medial cuneiform plantarflexion osteotomy (MCPO), and 5 had medializing calcaneal osteotomy. Measures of static foot alignment-both radiographic parameters and clinical arch height indices-were compared, as were measures of dynamic foot alignment and loading, including arch height flexibility and pedobarography. Preoperative and postoperative patient-reported outcome (PRO) scores were compared between those treated with or without MSST procedures. RESULTS: The median subject age was 13.8 years (range: 10.3 to 16.5) at the time of surgery. All radiographic parameters improved with surgery ( P <0.001). The mean sitting arch height index showed a modest increase after surgery ( P =0.023). Arch height flexibility was similar after surgery. The mean center-of-pressure excursion index increased from 14.1% to 24.0% ( P <0.001), and the mean first metatarsal head (MH) peak pressure dropped ( P <0.001), while the mean fifth MH peak pressure increased ( P =0.018). The ratio of peak pressure in the fifth MH to peak pressure in the second MH increased ( P =0.010). The ratio of peak pressure in the first MH to peak pressure in the second MH decreased when an MCPO was not used ( P <0.002), but it remained stable when an MCPO was included. Mean scores in all PRO domains improved ( P <0.001). Patients treated without MSST procedures showed no difference in PROMIS Pain Interference scores compared to those without MSST procedures. CONCLUSIONS: Flatfoot reconstruction surgery using an LCL with plantarflexor lengthening results in improved PROs. LCL changes but does not normalize the distribution of MH pressure loading. The addition of an MCPO can prevent a significant reduction in load-sharing by the first MH.

Comparative Analysis of Transcriptome and sRNAs Expression Patterns in the Brachypodium distachyon- Magnaporthe oryzae Pathosystems.

The hemibiotrophic fungus Magnaporthe oryzae (Mo) is the causative agent of rice blast and can infect aerial and root tissues of a variety of Poaceae, including the model Brachypodium distachyon (Bd). To gain insight in gene regulation processes occurring at early disease stages, we comparatively analyzed fungal and plant mRNA and sRNA expression in leaves and roots. A total of 310 Mo genes were detected consistently and differentially expressed in both leaves and roots. Contrary to Mo, only minor overlaps were observed in plant differentially expressed genes (DEGs), with 233 Bd-DEGs in infected leaves at 2 days post inoculation (DPI), compared to 4978 at 4 DPI, and 138 in infected roots. sRNA sequencing revealed a broad spectrum of Mo-sRNAs that accumulated in infected tissues, including candidates predicted to target Bd mRNAs. Conversely, we identified a subset of potential Bd-sRNAs directed against fungal cell wall components, virulence genes and transcription factors. We also show a requirement of operable RNAi genes from the DICER-like (DCL) and ARGONAUTE (AGO) families for fungal virulence. Overall, our work elucidates the extensive reprogramming of transcriptomes and sRNAs in both plant host (Bd) and fungal pathogen (Mo), further corroborating the critical role played by sRNA species in the establishment of the interaction and its outcome.

Combined inhibition of IL1, CXCR1/2, and TGFß signaling pathways modulates in-vivo resistance to anti-VEGF treatment.

Resistance of tumors to antiangiogenic therapies is becoming increasingly relevant. We recently identified interleukin-1 (IL1), CXC receptors (CXCR)1/2 ligands, and transforming growth factor ß (TGFß) among the proinflammatory factors that were expressed at higher levels in murine models resistant to the antivascular endothelial growth factor (anti-VEGF) antibody bevacizumab. Here, we hypothesized that the combined inhibition of these proinflammatory signaling pathways might reverse this anti-VEGF resistance. Bevacizumab-resistant FGBR pancreatic cancer cells were treated in vitro with bevacizumab, the recombinant human IL1 receptor antagonist anakinra, the monoclonal antibody against TGFß receptor type II TR1, and a novel recombinant antibody binding CXCR1/2 ligands. The FGBR cells treated with these agents in combination had significantly higher levels of E-cadherin and lower levels of vimentin, IL6, phosphorylated p65, and SMAD2, and showed significantly lower migration rates than did their controls treated with the same agents without bevacizumab or with a single agent bevacizumab as a control. Consistently, the combination of these agents with bevacizumab reduced the FGBR tumor burden and significantly prolonged mice survival compared with bevacizumab in monotherapy. Tumors from mice receiving the combination treatment showed significantly lower expression of IL6 and phosphorylated SMAD2, higher expression of E-cadherin and lower levels of vimentin, and a significantly lower infiltration by CD11b cells compared with bevacizumab-treated controls. This study suggests that inhibition of IL1, CXCR1/2, and TGFß signaling pathways is a potential therapeutic approach to modulate the acquired resistance to anti-VEGF treatment by reversing epithelial-mesenchymal transition and inhibiting CD11b proangiogenic myeloid cells' tumor infiltration.

Pelvic Tilt in Adults With Cerebral Palsy and Its Relationship With Prior Hamstrings Lengthening.

BACKGROUND: Current studies assessing the change in pelvic tilt for ambulatory patients with cerebral palsy (CP) after surgical hamstring lengthening (SHL) lack a comparison cohort without prior SHL and are limited to younger patients. This study presents gait data of middle-aged adults with CP, primarily focusing on the pelvis, and compares pelvic tilt, trunk tilt, and knee flexion between those with and without prior SHL. MATERIALS AND METHODS: A consecutive series of 54 adults with CP, a mean age of 36±13 years, and Gross Motor Function Classification System (GMFCS) levels I-III were included. Thirty-two (59%) had SHL performed at a mean age of 8±5 years. Three-dimensional gait analysis data prospectively collected at a mean of 28±14 years postoperatively were retrospectively analyzed. Chi-square tests were used to compare demographic and surgical history data and statistical parameter mapping was used to compare knee flexion during stance and pelvic and trunk tilts during the gait cycle between SHL and SHL-naive groups. RESULTS: Age, GMFCS level, sex, race, topography, and ethnicity were not different between the groups (P=.217-.612). Anterior pelvic tilt throughout gait was significantly greater in the SHL group compared with the SHL-naive group (63%-87%; P=.033). This difference was augmented after accounting for other surgical history and revision SHL (0%-32%, P=.019; and 46%-93%, P=.007). CONCLUSION: Within a cohort of adults with CP, GMFCS levels I-III, and a mean age of 36 years, those with a history of SHL, performed a mean of 28 years prior to 3-dimensional gait analysis, walked with increased anterior pelvic tilt compared with those without a history of SHL. [Orthopedics. 202x;4x(x):xx-xx.].

Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes.

Structural variations (SVs) are larger polymorphisms (> 50 bp in length), which consist of insertions, deletions, inversions, duplications, and translocations. They can have a strong impact on agronomical traits and play an important role in environmental adaptation. The development of long-read sequencing technologies, including Oxford Nanopore, allows for comprehensive SV discovery and characterization even in complex polyploid crop genomes. However, many of the SV discovery pipeline benchmarks do not include complex plant genome datasets. In this study, we benchmarked insertion and deletion detection by popular long-read alignment-based SV detection tools for crop plant genomes. We used real and simulated Oxford Nanopore reads for two crops, allotetraploid Brassica napus (oilseed rape) and diploid Solanum lycopersicum (tomato), and evaluated several read aligners and SV callers across 5×, 10×, and 20× coverages typically used in re-sequencing studies. We further validated our findings using maize and soybean datasets. Our benchmarks provide a useful guide for designing Oxford Nanopore re-sequencing projects and SV discovery pipelines for crop plants.

Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs.

Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.], rice (Oryza sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.). Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic diversity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.

Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon.

RNA interference (RNAi) is a biological process in which small RNAs regulate gene silencing at the transcriptional or posttranscriptional level. The trigger for gene silencing is double-stranded RNA generated from an endogenous genomic locus or a foreign source, such as a transgene or virus. In addition to regulating endogenous gene expression, RNAi provides the mechanistic basis for small RNA-mediated communication between plant hosts and interacting pathogenic microbes, known as cross-kingdom RNAi. Two core protein components, Argonaute (AGO) and Dicer (DCL), are central to the RNAi machinery of eukaryotes. Plants encode for several copies of AGO and DCL genes; in Arabidopsis thaliana, the AGO protein family contains 10 members, and the DCL family contains four. Little is known about the conservation and specific roles of these proteins in monocotyledonous plants, which account for the most important food staples. Here, we utilized in silico tools to investigate the structure and related functions of AGO and DCL proteins from the model grass Brachypodium distachyon. Based on the presence of characteristic domains, 16 BdAGO- and 6 BdDCL-predicted proteins were identified. Phylogenetic analysis showed that both protein families were expanded in Brachypodium as compared with Arabidopsis. For BdDCL proteins, both plant species contain a single copy of DCL1 and DCL4; however, Brachypodium contains two copies each of DCL2 and DCL3. Members of the BdAGO family were placed in all three functional clades of AGO proteins previously described in Arabidopsis. The greatest expansion occurred in the AtAGO1/5/10 clade, which contains nine BdAGOs (BdAGO5/6/7/9/10/11/12/15/16). The catalytic tetrad of the AGO P-element-induced wimpy testis domain (PIWI), which is required for endonuclease activity, is conserved in most BdAGOs, with the exception of BdAGO1, which lacks the last D/H residue. Three-dimensional modeling of BdAGO proteins using tertiary structure prediction software supported the phylogenetic classification. We also predicted a provisional interactome network for BdAGOs, their localization within the cell, and organ/tissue-specific expression. Exploring the specifics of RNAi machinery proteins in a model grass species can serve as a proxy for agronomically important cereals such as barley and wheat, where the development of RNAi-based plant protection strategies is of great interest.

A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant-Microbe Interactions.

Small RNA (sRNA) molecules are key factors in the communication between hosts and their interacting pathogens, where they function as effectors that can modulate both host defense and microbial virulence/pathogenicity through a mechanism termed cross-kingdom RNA interference (ck-RNAi). Consistent with this recent knowledge, sRNAs and their double-stranded RNA precursor have been adopted to control diseases in crop plants, demonstrating a straight forward application of the new findings to approach agricultural problems. Despite the great interest in natural ck-RNAi, it is astonishing to find just a few additional examples in the literature since the first report was published in 2013. One reason might be that the identification of sRNA effectors is hampered both by technical challenges and lack of routine bioinformatics application strategies. Here, we suggest a practical procedure to find, characterize, and validate sRNA effectors in plant-microbe interaction. The aim of this review is not to present and discuss all possible tools, but to give guidelines toward the best established software available for the analysis.

A circulating TH2 cytokines profile predicts survival in patients with resectable pancreatic adenocarcinoma.

Surgery is the only potentially curative option for patients with pancreatic ductal adenocarcinoma (PDAC), but metastatic relapse remains common. We hypothesized that the expression levels of inflammatory cytokines could predict recurrence of PDAC, thus allowing to select patients who most likely could benefit from surgical resection. We prospectively collected plasma at diagnosis from 287 patients with pancreatic resectable neoplasms. The expression levels of 23 cytokines were measured in 90 patients with PDAC by using a multiplex analyte profiling assay. Levels higher than cutoff identified of the TH2 cytokines interleukin (IL)4, IL5, IL6 of macrophage inflammatory protein (MIP)1α, granulocyte-macrophage colony-stimulating factor (GM-CSF), and monocyte chemoattractant protein (MCP)1, and of IL17α, IFNγ-induced protein (IP)10, and IL1b were significantly associated with a shorter median OS. In particular, levels of IL4 and IP10 higher than cutoff identified, and level of TH1 cytokines TNFα and INFγ, and of IL9 and IL1Rα lower than cutoff identified were significantly associated with a shorter DFS. In the multivariate analysis, high IP10 was confirmed as negatively associated with OS (HR = 3.097, p = 0.014) and IL4 and TNFα remain negatively (HR = 2.75, p = 0.002) and positively (HR = 0.224, p = 0.049) associated with DFS, respectively. Simultaneous expression of low IL4 and high TNFα identified patients with best prognosis (HR = 0.313, p < 0.0001). In conclusion, we demonstrated that, among a series of cytokines, IL4 is the most significant independent prognostic factor for DFS in resectable PDAC patients, and it could be useful to select patients with high risk of early recurrence who may avoid an unnecessary resection.

Targeted delivery of photosensitizers: efficacy and selectivity issues revealed by multifunctional ORMOSIL nanovectors in cellular systems.

PEGylated and non-PEGylated ORMOSIL nanoparticles prepared by microemulsion condensation of vinyltriethoxy-silane (VTES) were investigated in detail for their micro-structure and ability to deliver photoactive agents. With respect to pure silica nanoparticles, organic modification substantially changes the microstructure and the surface properties. This in turn leads to a modulation of both the photophysical properties of embedded photosensitizers and the interaction of the nanoparticles with biological entities such as serum proteins. The flexibility of the synthetic procedure allows the rapid preparation and screening of multifunctional nanosystems for photodynamic therapy (PDT). Selective targeting of model cancer cells was tested by using folate, an integrin specific RGD peptide and anti-EGFR antibodies. Data suggest the interference of the stealth-conferring layer (PEG) with small targeting agents, but not with bulky antibodies. Moreover, we showed that selective photokilling of tumour cells may be limited even in the case of efficient targeting because of intrinsic transport limitations of active cellular uptake mechanisms or suboptimum localization.