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The mRNA-seq data analysis is a powerful technology for inferring information from biological systems of interest. Specifically, the sequenced RNA fragments are aligned with genomic reference sequences, and we count the number of sequence fragments corresponding to each gene for each condition. A gene is identified as differentially expressed (DE) if the difference in its count numbers between conditions is statistically significant. Several statistical analysis methods have been developed to detect DE genes based on RNA-seq data. However, the existing methods could suffer decreasing power to identify DE genes arising from overdispersion and limited sample size, where overdispersion refers to the empirical phenomenon that the variance of read counts is larger than the mean of read counts. We propose a new differential expression analysis procedure: heterogeneous overdispersion genes testing (DEHOGT) based on heterogeneous overdispersion modeling and a post-hoc inference procedure. DEHOGT integrates sample information from all conditions and provides a more flexible and adaptive overdispersion modeling for the RNA-seq read count. DEHOGT adopts a gene-wise estimation scheme to enhance the detection power of differentially expressed genes when the number of replicates is limited as long as the number of conditions is large. DEHOGT is tested on the synthetic RNA-seq read count data and outperforms two popular existing methods, DESeq2 and EdgeR, in detecting DE genes. We apply the proposed method to a test dataset using RNAseq data from microglial cells. DEHOGT tends to detect more differently expressed genes potentially related to microglial cells under different stress hormones treatments., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Yuan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Aim: This randomized controlled trial evaluated the impact of a partially exposed non-absorbable membrane (dPTFE) in Alveolar Ridge Preservation (ARP) procedures on clinical, tomographic, immunoenzymatic, implant-related, and patient-centered outcomes., Materials and Methods: Patients with a hopeless maxillary single-rooted tooth demanding rehabilitation with implants were included. Patients were randomized into two groups: dPTFE (n = 22)-tooth extraction followed by ARP using a partially exposed dPTFE membrane; USH (n = 22)-unassisted socket healing. Clinical and tomographic analyses were performed at baseline and after 3 months. After 3 months, patients received one dental implant. Implant stability quotient was obtained following implant placement. Bone-related markers were analyzed in bone biopsies using an immunoenzymatic assay., Results: Greater gain in Keratinized Mucosa Width (KMW) was observed in the dPTFE (1.33 ± 0.98 mm) compared to USH (0.59 ± 0.98 mm) (Mann-Whitney test, Z = 2,28, p < 0.05). USH showed a reduction of pain/discomfort, edema, and interference with daily life from the seventh day (Friedman/Wilcoxon test, maxT = 7.48, 8.00, and 5.92, respectively, p < 0.05). dPTFE presents a reduction of edema and interference with daily life from the 7th day and pain/discomfort from the 14th day (Friedman/Wilcoxon test, maxT = 5.40, 5.26, and 4.78, respectively, p < 0.05). The dPTFE group presented higher pain/discomfort in the 35 and 42 days and higher edema from 7 to 42 days postoperatively than USH group (Mann-Whitney test, p < 0.05). No differences between groups were observed in the tomographic measures, immunoenzymatic analysis, and implant stability (p > 0.05)., Conclusion: dPTFE was superior to USH by increasing KMW gain. However, dPTFE without bone graft presented similar bone loss compared to USH. This clinical trial was not registered prior to participant recruitment and randomization (NCT04329351)., (© 2023 Wiley Periodicals LLC.)

Background: The role of Numb, a protein that is important for cell fate and development and that, in human muscle, is expressed at reduced levels with advanced age, was investigated; adult mice skeletal muscle and its localization and function within myofibres were determined., Methods: Numb expression was evaluated by western blot. Numb localization was determined by confocal microscopy. The effects of conditional knock out (cKO) of Numb and the closely related gene Numb-like in skeletal muscle fibres were evaluated by in situ physiology, transmission and focused ion beam scanning electron microscopy, three-dimensional reconstruction of mitochondria, lipidomics, and bulk RNA sequencing. Additional studies using primary mouse myotubes investigated the effects of Numb knockdown on cell fusion, mitochondrial function, and calcium transients., Results: Numb protein expression was reduced by ~70% (P < 0.01) at 24 as compared with 3 months of age in gastrocnemius and tibialis anterior muscle. Numb was localized within muscle fibres as bands traversing fibres at regularly spaced intervals in close proximity to dihydropyridine receptors. The cKO of Numb and Numb-like reduced specific tetanic force by 36% (P < 0.01), altered mitochondrial spatial relationships to sarcomeric structures, increased Z-line spacing by 30% (P < 0.0001), perturbed sarcoplasmic reticulum organization and reduced mitochondrial volume by over 80% (P < 0.01). Only six genes were differentially expressed in cKO mice: Itga4, Sema7a, Irgm2, Vezf1, Mib1, and Tmem132a. Several lipid mediators derived from polyunsaturated fatty acids through lipoxygenases were up-regulated in Numb cKO skeletal muscle: 12-HEPE was increased by ~250% (P < 0.05) and 17,18-EpETE by ~240% (P < 0.05). In mouse primary myotubes, Numb knockdown reduced cell fusion (~20%, P < 0.01) and delayed the caffeine-induced rise in cytosolic calcium concentrations by more than 100% (P < 0.01)., Conclusions: These findings implicate Numb as a critical factor in skeletal muscle structure and function and suggest that Numb is critical for calcium release. We therefore speculate that Numb plays critical roles in excitation-contraction coupling, one of the putative targets of aged skeletal muscles. These findings provide new insights into the molecular underpinnings of the loss of muscle function observed with sarcopenia., (© 2022 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of Society on Sarcopenia, Cachexia and Wasting Disorders. This article has been contributed to by US Government employees and their work is in the public domain in the USA.)

The formation of biofilms is critical for the successful and stable colonization of mucosal surfaces by microbes, which often build three-dimensional environments by exuding exopolysaccharides and other macromolecules such as proteins, lipids, and even DNA. It is not just bacteria, but fungi such as yeast, that form these adherent interacting communities. Historically, biofilms have been studied in the context of pathogenesis, but only recently it has been recognized that important relationships among members of host-associated microbiomes are maintained within the context of biofilms. Host immune responses impact biofilm formation in various ways; for example, it is likely that formation of stable biofilms by non-pathogens improves barrier defenses by not just filling available niche spaces but also by helping to ward off pathogens directly. Recently, it was found that soluble immune effector molecules such as immunoglobulin A (IgA) in mammals serve essential roles in modulating complex biofilm communities in ways that benefit the host. Additional lines of evidence from other secreted immune effectors, such as the variable region-containing chitin-binding proteins (VCBPs) in protochordates, now suggest that this phenomenon is much more widespread than previously recognized. The activity of these immune molecules also likely serves roles beyond those of simple defense strategies; rather, they may be improving the outcome of symbiotic interactions benefiting the host. Thus, traditional immune assays that are aimed at studying the function of secreted immune effectors, such as agglutination assays, should take into account the possibility that the first observation may not be the last if the microbes under study are not directly killed. Here, we describe a series of simple approaches to characterize biofilm formation when bacteria (or yeast) are cultured in the presence of a secreted immune effector. To model this approach, we use microbes isolated from the gut of Ciona robusta, each grown in the presence or absence of VCBPs. The approaches defined here are amenable to diverse model systems and their microbes., (© 2022. Springer Science+Business Media, LLC, part of Springer Nature.)

The surprise question (SQ), "Would you be surprised if your patient died within a year?", has been studied in the cancer population as a prognostic prompt. Studies have almost exclusively directed the SQ to physicians, whereas perspectives of nurses remain underevaluated. We asked the SQ for patients admitted to an inpatient medical oncology service to medical oncology, palliative care, and hospital medicine teams and bedside nurses. We performed a 1-year retrospective chart review to identify how concordant various provider types were in their prognostic estimations and identified the missed opportunity rate (MOR) defined as the number of patients who died within a particular time frame but who the providers had predicted would be alive and may not have had a palliative approach. Oncologists had higher MORs for the 6-month and 1-year SQ when compared with hospital medicine providers. Bedside nurses were least concordant in their estimations of prognosis and had higher MORs for all time frames of the SQ. Missed opportunities might have significant implications for the end-of-life care for cancer patients, and continued research is needed to understand what influences provider prognostication and how this impacts palliative care utilization for patients with life-limiting disease.

Context: Various modalities have been used to pretreat skeletal muscle to attenuate inflammation., Objective: To determine the effects of short-wave diathermy (SWD) preheating treatment on inflammation and stress markers after eccentric exercise., Design: Controlled laboratory study., Setting: University laboratory setting., Patients or Other Participants: Fifteen male (age = 22 ± 4.9 years, height = 179.75 ± 9.56 cm, mass = 82.22 ± 12.67 kg) college-aged students., Intervention(s): Seven participants were selected randomly to receive 40 minutes of SWD heat treatment (HT), and 8 participants served as the control (CON) group and rested without SWD. Both groups completed 7 sets of 10 repetitions of a high-intensity eccentric exercise protocol (EEP) at 120% of the 1-repetition maximum (1-RM) leg extension., Main Outcome Measure(s): We biopsied muscles on days 1, 3 (24 hours post-EEP), and 4 (48 hours post-EEP) and collected blood samples on days 1, 2 (4 hours post-EEP), 3, and 4. We determined 1-RM on day 2 (24 hours post-SWD) and measured 1-RM on days 3 and 4. We analyzed the muscle samples for interleukin 6 (IL-6), tumor necrosis factor α, and heat shock protein 70 and the blood for serum creatine kinase., Results: We found a group × time interaction for intramuscular IL-6 levels after SWD (F2,26 = 7.13, P = .003). The IL-6 decreased in HT (F1,6 = 17.8, P = .006), whereas CON showed no change (P > .05). We found a group × time interaction for tumor necrosis factor α levels (F2,26 = 3.71, P = .04), which increased in CON (F2,14 = 7.16, P = .007), but saw no changes for HT (P > .05). No group × time interactions were noted for 1-RM, heat shock protein 70, or creatine kinase (P > .05)., Conclusions: The SWD preheating treatment provided a treatment effect for intramuscular inflammatory myokines induced through high-intensity eccentric exercise but did not affect other factors associated with intense exercise and inflammation.