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Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis ( Mtb ), infects approximately one-fourth of the world's population. While most infected individuals are asymptomatic, latent TB infection (LTBI) can progress to cause pulmonary TB (PTB). We recently reported an increased accumulation of mast cells (MCs) in lungs of macaques with PTB, compared with LTBI in macaques. MCs respond in vitro to Mtb exposure via degranulation and by inducing proinflammatory cytokines. In the current study, we show the dominant production of chymase by MCs in granulomas of humans and macaques with PTB. Using scRNA seq analysis, we show that MCs found in LTBI and healthy lungs in macaques are enriched in genes involved in tumor necrosis factor alpha, cholesterol and transforming growth factor beta signaling. In contrast, MCs clusters found in PTB express transcriptional signatures associated with interferon gamma, oxidative phosphorylation, and MYC signaling. Additionally, MC deficiency in the mouse model showed improved control of Mtb infection that coincided with reduced accumulation of lung myeloid cells and diminished inflammation at chronic stages. Thus, these collective results provide novel evidence for the pathological contribution of MCs during Mtb infection and may represent a novel target for host directive therapy for TB., Competing Interests: Competing interests. The authors declare no competing interests.

Early innate immune responses play an important role in determining the protective outcome of Mycobacterium tuberculosis (Mtb) infection. Nuclear factor κB (NF-κB) signaling in immune cells regulates the expression of key downstream effector molecules that mount early antimycobacterial responses. Using conditional knockout mice, we studied the effect of abrogation of NF-κB signaling in different myeloid cell types and its impact on Mtb infection. Our results show that the absence of IKK2-mediated signaling in all myeloid cells resulted in increased susceptibility to Mtb infection. In contrast, the absence of IKK2-mediated signaling in CD11c+ myeloid cells induced early proinflammatory cytokine responses, enhanced the recruitment of myeloid cells, and mediated early resistance to Mtb. Abrogation of IKK2 in MRP8-expressing neutrophils did not affect disease pathology or Mtb control. Thus, we describe an early immunoregulatory role for NF-κB signaling in CD11c-expressing phagocytes and a later protective role for NF-κB in LysM-expressing cells during Mtb infection., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: The increasing prevalence of diet-related non-communicable diseases (NCDs) in South Asia is concerning, with type 2 diabetes projected to rise to 68%, compared to the global increase of 44%. Encouraging healthy diets requires stronger policies for healthier food environments., Methods: This study reviewed and assessed food environment policies in Bangladesh, India, Pakistan, and Sri Lanka from 2020 to 2022 using the Healthy Food Environment Policy Index (Food-EPI) and compared them with global best practices. Seven policy domains and six infrastructure support domains were considered, employing 47 good practice indicators to prevent NCDs. Stakeholders from government and non-governmental sectors in South Asia (n = 148) were invited to assess policy and infrastructure support implementation using the Delphi method., Findings: Implementation of food environment policies and infrastructure support in these countries was predominantly weak. Labelling, monitoring, and leadership policies received a moderate rating, with a focus on food safety, hygiene, and quality rather than obesity prevention. Key policy gaps prioritized for attention included front-of-pack labelling, healthy food subsidies, unhealthy food taxation, restrictions on unhealthy food promotion, and improvements in school nutrition standards to combat NCDs., Interpretation: Urgent action is required to expand food policies beyond hygiene and food security measures. Comprehensive strategies targeting NCD prevention are crucial to combat the escalating burden of NCDs in the region., Funding: This research was funded by the NIHR (16/136/68 and 132960) with aid from the UK Government for global health research. Petya Atanasova also acknowledges funding from the Economic and Social Research Council (ESRC) (ES/P000703/1). The views expressed are those of the authors and not necessarily of the NIHR, the UK government or the ESRC., Competing Interests: We declare that we have no conflicts of interest., (© 2024 The Author(s).)

Osteoarthritis (OA) and diabetes mellitus (DM) have long-term deleterious chronic effects and are among the most prevalent chronic disorders. DM and its associated factors, such as hyperglycemia, have a significant contribution to the pathophysiology of OA, particularly in post-menopausal women. Women who have uncontrolled diabetes (DM) are more prone to develop osteoarthritis (OA), which may be exacerbated by poor glycemic control. Furthermore, this category of female patients with DM has an increased risk of developing fractures, even in those with initially normal bone density scores, further illustrating the correlation between DM and bone health. Additionally, multiple risk factors, including obesity, metabolic syndrome, hypertension, estrogen-based hormone therapy, and hyperuricemia, in menopausal women can lead to the development and exacerbation of OA. It is discovered that these variables have a direct or indirect impact, frequently causing inflammation and hormonal changes, which contribute to the intricate interaction between DM and OA. The management of OA and DM in women thus calls for a multi-faceted management plan including glycemic control, weight control, exercise, and specialized pain management methods catering to the specific requirements of the patients. Regularly screening for OA should be implemented for menopausal women with DM and utmost care should be provided by healthcare professionals. Regular monitoring of joint health and early management, encouraging interdisciplinary cooperation, putting preventative measures into place, and creating individualized treatment programs are essential. A thorough understanding of the link between DM and OA will ultimately lead to improved health outcomes and a better future for these individuals., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2024, Shukla et al.)

Background: Cancer treatments have many adverse effects on patient's health leading to poor cardiorespiratory capacity, muscular- degeneration, fatigue, loss of strength and physical function, altered body-composition, compromised immune-function, peripheral neuropathy, and reduced quality of life (QOL). Exercise programs can significantly increase functional capacity when tailored to individual needs, thus improving health. Exercise interventions in cancer rehabilitation, when supported by appropriate nutrition can be effective in attaining a healthy weight and body-composition. The successful rehabilitation program should also include psycho-social education aimed to reduce anxiety and improve motivation., Methods: The current study aimed to collect information on the post-treatment needs of cancer patients including barriers and expectations facing them, their caregivers and their families through consultation in focus group interviews. Cancer survivors living in the Republic of Ireland were recruited from the University Hospital Galway, community-based cancer centres, cancer support groups and social media platforms to participate in the study and attend a focus group interview. The focus group discussions were designed to obtain information on the collective views of cancer survivors on relevant topics selected. The topics were developed in consultation with a patient and public involvement (PPI) group supporting the study. The topics list was circulated to all participants prior to the focus group. The interviews were audio recorded and transcribed verbatim. Focus group transcripts were analysed subjected to a thematic framework analysis using NVivo., Results: Thirty-six participants took part in 9 focus groups. Our analysis uncovered two main themes. The first theme 'cast adrift with no direction' was grouped into three sub-themes: everything revolves around treatment; panic and fear; and what exercise should I be doing? The second theme 'everybody is different' was clustered into two sub-themes: side effects get in the way; and personalised exercise program., Conclusion: The study highlighted the lack of information and support needed by patients living with and beyond cancer. The study also highlighted the need for a personalised exercise programme designed to target the individual patient symptoms that would be ideal for the mitigation of long term symptoms and in improving QOL., (© 2024. The Author(s).)

Tuberculosis (TB) caused by Mycobacterium tuberculosis ( Mtb ) infects up to a quarter of the world's population. Although immune responses can control Mtb infection, 5%-10% of infected individuals can progress to active TB disease (progressors). A myriad of host factors regulate disease progression in TB and a better understanding of immune correlates of protection and disease is pivotal for the development of new therapeutics. Comparison of human whole blood transcriptomic metadata with that of macaque TB progressors and Mtb -infected diversity outbred mice (DO) led to the identification of differentially regulated gene (DEG) signatures, associated with TB progression or control. The current study assessed the function of Phospholipase C epsilon ( PLCƐ1 ), the top downregulated gene across species in TB progressors, using a gene-specific knockout mouse model of Mtb infection and in vitro Mtb -infected bone marrow-derived macrophages. PLCƐ1 gene expression was downregulated in TB progressors across species. PLCε1 deficiency in the mouse model resulted in increased susceptibility to Mtb infection , coincident accumulation of lung myeloid cells, and reduced ability to mount antibacterial responses. However, PLCε1 was not required for the activation and accumulation of T cells in mice. Our results suggest an important early role for PLCƐ1 in shaping innate immune response to TB and may represent a putative target for host-directed therapy., Competing Interests: The authors declare no conflict of interest.

Exercise has been repeatedly shown to be safe and beneficial for cancer survivors. However, there is no normative guideline for exercise prescription, and it is still under exploration. Therefore, this literature review aims to provide some advice for the formulation of exercise prescriptions for patients with breast cancer-related lymphedema (BCRL) from the perspective of reducing lymphedema severity. A review of relevant studies published before November 2023 was conducted using three scientific databases: PubMed, Embase, and Scopus. A total of 2696 articles were found. Eventually, 13 studies fulfilled the inclusion criteria and were included in this literature review. We concluded that daily, or nearly daily, exercise at home can be recommended. Moreover, reduced lymphedema severity may not be maintained after ceasing the exercise program, so exercise should be a lifelong practice.

Cell patterning for 3D culture has increased our understanding of how cells interact among themselves and with their environment during tissue morphogenesis. Building cell communities from the bottom up with size and compositional control is invaluable for studies of morphological transitions. Here, we detail Photolithographic DNA-programmed Assembly of Cells (pDPAC). pDPAC uses a photoactive polyacrylamide gel substrate to capture single-stranded DNA on a 2D surface in large-scale, highly resolved patterns using the photomask technology. Cells are then functionalized with a complementary DNA strand, enabling cells to be temporarily adhered to distinct locations only where their complementary strand is patterned. These temporary 2D patterns can be transferred to extracellular matrix hydrogels for 3D culture of cells in biomimetic microenvironments. Use of a polyacrylamide substrate has advantages, including a simpler photolithography workflow, lower non-specific cell adhesion, and lower stiction to ECM hydrogels during release of patterned hydrogels. The protocol is equally applicable to large (cm)-scale patterns and repetitive arrays of smaller-scale cell interaction or migration experiments., (© 2024. The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

X-box binding protein 1 (XBP1) is a transcription factor that plays a crucial role in the unfolded protein response (UPR), a cellular stress response pathway involved in maintaining protein homeostasis in the endoplasmic reticulum (EnR). While the role of XBP1 in UPR is well-characterised, emerging evidence suggests its involvement in endocrine resistance in breast cancer. The transcriptional activity of spliced XBP1 (XBP1s) is a major component of its biological effects, but the targets of XBP1s in estrogen receptor (ER)-positive breast cancer are not well understood. Here, we show that the expression of miR-378 and PPARGC1B (host gene of miR-378) is downregulated during UPR. Using chemical and genetic methods, we show that XBP1s is necessary and sufficient for the downregulation of miR-378 and PPARGC1B. Our results show that overexpression of miR-378 significantly suppressed cell growth, colony formation, and migration of ER-positive breast cancer cells. Further, we found that expression of miR-378 sensitised the cells to UPR-induced cell death and anti-estrogens. The expression of miR-378 and PPARGC1B was downregulated in breast cancer, and higher expression of miR-378 is associated with better outcomes in ER-positive breast cancer. We found that miR-378 upregulates the expression of several genes that regulate type I interferon signalling. Analysis of separate cohorts of breast cancer patients showed that a gene signature derived from miR-378 upregulated genes showed a strong association with improved overall and recurrence-free survival in breast cancer. Our results suggest a growth-suppressive role for miR-378 in ER-positive breast cancer where downregulation of miR-378 by XBP1 contributes to endocrine resistance in ER-positive breast cancer.

C/EBP homologous protein (CHOP), also known as growth arrest and DNA damage-inducible protein 153 (GADD153), belongs to the CCAAT/enhancer-binding protein (C/EBP) family. CHOP expression is induced by unfolded protein response (UPR), and sustained CHOP activation acts as a pivotal trigger for ER stress-induced apoptosis. MicroRNA-616 is located within an intron of the CHOP gene. However, the regulation of miR-616 expression during UPR and its function in breast cancer is not clearly understood. Here we show that the expression of miR-616 and CHOP (host gene of miR-616) is downregulated in human breast cancer. Both miR-5p/-3p arms of miR-616 are expressed with levels of the 5p arm higher than the 3p arm. During conditions of ER stress, the expression of miR-616-5p and miR-616-3p arms was concordantly increased primarily through the PERK pathway. Our results show that ectopic expression of miR-616 significantly suppressed cell proliferation and colony formation, whereas knockout of miR-616 increased it. We found that miR-616 represses c-MYC expression via binding sites located in its protein coding region. Furthermore, we show that miR-616 exerted growth inhibitory effects on cells by suppressing c-MYC expression. Our results establish a new role for the CHOP locus by providing evidence that miR-616 can inhibit cell proliferation by targeting c-MYC. In summary, our results suggest a dual function for the CHOP locus, where CHOP protein and miR-616 can cooperate to inhibit cancer progression.

The ADP ribosyltransferases (PARPs 1-17) regulate diverse cellular processes, including DNA damage repair. PARPs are classified on the basis of their ability to catalyze poly-ADP-ribosylation (PARylation) or mono-ADP-ribosylation (MARylation). Although PARP9 mRNA expression is significantly increased in progressive tuberculosis (TB) in humans, its participation in host immunity to TB is unknown. Here, we show that PARP9 mRNA encoding the MARylating PARP9 enzyme was upregulated during TB in humans and mice and provide evidence of a critical modulatory role for PARP9 in DNA damage, cyclic GMP-AMP synthase (cGAS) expression, and type I IFN production during TB. Thus, Parp9-deficient mice were susceptible to Mycobacterium tuberculosis infection and exhibited increased TB disease, cGAS and 2'3'-cyclic GMP-AMP (cGAMP) expression, and type I IFN production, along with upregulation of complement and coagulation pathways. Enhanced M. tuberculosis susceptibility is type I IFN dependent, as blockade of IFN α receptor (IFNAR) signaling reversed the enhanced susceptibility of Parp9-/- mice. Thus, in sharp contrast to PARP9 enhancement of type I IFN production in viral infections, this member of the MAR family plays a protective role by limiting type I IFN responses during TB.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a global cause of death. Granuloma-associated lymphoid tissue (GrALT) correlates with protection during TB, but the mechanisms of protection are not understood. During TB, the transcription factor IRF4 in T cells but not B cells is required for the generation of the T H 1 and T H 17 subsets of helper T cells and follicular helper T (T FH )-like cellular responses. A population of IRF4 + T cells coexpress the transcription factor BCL6 during Mtb infection, and deletion of Bcl6 (Bcl6 fl/fl ) in CD4 + T cells (CD4 cre ) resulted in reduction of T FH -like cells, impaired localization within GrALT and increased Mtb burden. In contrast, the absence of germinal center B cells, MHC class II expression on B cells, antibody-producing plasma cells or interleukin-10-expressing B cells, did not increase Mtb susceptibility. Indeed, antigen-specific B cells enhance cytokine production and strategically localize T FH -like cells within GrALT via interactions between programmed cell death 1 (PD-1) and its ligand PD-L1 and mediate Mtb control in both mice and macaques., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Background: Endocrine-resistant breast cancers have elevated expression of XBP1, where it drives endocrine resistance by controlling the expression of its target genes. Despite the in-depth understanding of the biological functions of XBP1 in ER-positive breast cancer, effectors of endocrine resistance downstream of XBP1 are poorly understood. The aim of this study was to identify the XBP1-regulated genes contributing to endocrine resistance in breast cancer., Methods: XBP1 deficient sub-clones in MCF7 cells were generated using the CRISPR-Cas9 gene knockout strategy and were validated using western blot and RT-PCR. Cell viability and cell proliferation were evaluated using the MTS assay and colony formation assay, respectively. Cell death and cell cycle analysis were determined using flow cytometry. Transcriptomic data was analysed to identify XBP1-regulated targets and differential expression of target genes was evaluated using western blot and qRT-PCR. Lentivirus and retrovirus transfection were used to generate RRM2 and CDC6 overexpressing clones, respectively. The prognostic value of the XBP1-gene signature was analysed using Kaplan-Meier survival analysis., Results: Deletion of XBP1 compromised the upregulation of UPR-target genes during conditions of endoplasmic reticulum (EnR) stress and sensitized cells to EnR stress-induced cell death. Loss of XBP1 in MCF7 cells decreased cell growth, attenuated the induction of estrogen-responsive genes and sensitized them to anti-estrogen agents. The expression of cell cycle associated genes RRM2, CDC6, and TOP2A was significantly reduced upon XBP1 deletion/inhibition in several ER-positive breast cancer cells. Expression of RRM2, CDC6, and TOP2A was increased upon estrogen stimulation and in cells harbouring point-mutants (Y537S, D538G) of ESR1 in steroid free conditions. Ectopic expression of RRM2 and CDC6 increased cell growth and reversed the hypersensitivity of XBP1 KO cells towards tamoxifen conferring endocrine resistance. Importantly, increased expression of XBP1-gene signature was associated with poor outcome and reduced efficacy of tamoxifen treatment in ER-positive breast cancer., Conclusions: Our results suggest that RRM2 and CDC6 downstream of XBP1 contribute to endocrine resistance in ER-positive breast cancer. XBP1-gene signature is associated with poor outcome and response to tamoxifen in ER-positive breast cancer., (© 2023. The Author(s).)

Soft electronic skin (soft-e-skin) capable of sensing touch and pressure similar to human skin is essential in many applications, including robotics, healthcare, and augmented reality. However, most of the research effort on soft-e-skin was confined to the lab-scale demonstration. Several hurdles remain challenging, such as highly complex and expensive fabrication processes, instability in long-term use, and difficulty producing large areas and mass production. Here, we present a robust 3D printable large-area electronic skin made of a soft and resilient polymer capable of detecting touch and load, and bending with extreme sensitivity (up to 150 kPa -1 ) to touch and load, 750 times higher than earlier work. The soft-e-skin shows excellent long-term stability and consistent performance up to almost a year. In addition, we describe a fabrication process capable of producing large areas and in large numbers, yet is cost-effective. The soft-e-skin consists of a uniquely designed optical waveguide and a layer of a soft membrane with an array of soft structures which work as passive sensing nodes. The use of a soft structure gives the liberty of stretching to the soft-e-skin without considering the disjoints among the sensing nodes. We have shown the functioning of the soft-e-skin under various conditions.

Background: There are few data to support accurate interpretation of spirometry data in South Asia, a major global region with a high reported burden of chronic respiratory disease., Method: We measured lung function in 7453 healthy men and women aged ≥18 years, from Bangladesh, North India, South India, Pakistan and Sri Lanka, as part of the South Asia Biobank study. First, we assessed the accuracy of existing equations for predicting normal forced vital capacity (FVC), forced expiratory volume in 1 s (FEV 1 ) and FEV 1 /FVC ratio. Then, we used our data to derive (n=5589) and internally validate (n=1864) new prediction equations among South Asians, with further external validation among 339 healthy South Asians living in Singapore., Results: The Global Lung Initiative (GLI) and National Health and Nutrition Examination Survey consistently overestimated expiratory volumes (best fit GLI-African American, mean±sd z-score: FEV 1 -0.94±1.05, FVC -0.91±1.10; n=7453). Age, height and weight were strong predictors of lung function in our participants (p<0.001), and sex-specific reference equations using these three variables were highly accurate in both internal validation (z-scores: FEV 1 0.03±0.99, FVC 0.04±0.97, FEV 1 /FVC -0.03±0.99) and external validation (z-scores: FEV 1 0.31±0.99, FVC 0.24±0.97, FEV 1 /FVC 0.16±0.91). Further adjustment for study regions improves the model fit, with highest accuracy for estimation of region-specific lung function in South Asia., Conclusion: We present improved equations for predicting lung function in South Asians. These offer the opportunity to enhance diagnosis and management of acute and chronic lung diseases in this major global population., Competing Interests: Conflict of interest: None declared., (Copyright ©The authors 2022.)

Sonar target recognition remains an active area of research due to the complex entanglement of features from various acoustic scatterers, background clutter, and distortion by waveguide propagation effects. An equally challenging issue is due to different acoustic echoes returned from the target (including different target elements) itself. This work investigates the sonar target classification problem from a statistical perspective and aims to extract salient target feature vectors. Specifically, a multivariate statistical method is employed, canonical correlation analysis (CCA), as a feature extraction technique prior to multi-class classification of active sonar field data. The intuition behind using CCA is that persistent features slowly morph over time due to the changing aspect angles and platform positions and can be represented by maximally correlated projections of consecutive pings. CCA is applied using a sliding window, and the projections are used as feature vectors to train a neural network classifier. The smallest increase in classification accuracy when comparing the projection feature vectors to unprocessed feature vectors was 10%. The largest increase was 34%. The results are further examined through the use of confusion matrices and layer-wise relevance propagation, which distributes the trained networks output score to the input layer.

There was an average of 45,753 cancer diagnoses each year in Ireland from 2018 to 2020. Estimates state that by the year 2045, this average could increase by 50-100%. There are over 170,000 cancer survivors living in Ireland. Cancer-related fatigue (CRF) is a prevalent and debilitating side effect of cancer and cancer treatment. Research has demonstrated that exercise is an effective intervention to combat CRF. This review will examine the scope of CRF and critically analyse exercise interventions to combat CRF in cancer patients undergoing treatment. Aerobic exercise interventions and multimodal exercise (aerobic exercise, resistance exercise and flexibility exercise) interventions have been shown to improve symptoms of fatigue in cancer patients undergoing treatment. The effect of resistance training on CRF in cancer patients during treatment is not well understood. Aerobic exercise and multimodal exercise appear to combat CRF by improving one or more of the following health-related fitness parameters; aerobic capacity, muscular strength and endurance, flexibility, and body composition. A standardized process of recording the intensity and volume of aerobic, resistance and flexibility exercise should be developed. Future studies should investigate in greater detail the role of resistance training in reducing CRF among cancer patients. Qualitative methods should be developed to investigate the role the group dynamic has on cancer patients during group-based interventions. These qualitative methods may be able to determine the importance the delivery of exercise plays in reducing CRF. Biomarkers of CRF should be investigated and examined in relation to the specific dose of exercise that patients perform.

Introduction: Cancer and its treatment using various chemotherapeutic agents can have many adverse side effects. These side effects often result in significant changes in haematological and biochemical composition of blood. As a result, the regular monitoring of serum biochemical and haematological changes plays an important role in management of disease. The present study aimed to determine the relationship between haematological and biochemical changes in neutropenic cancer patients following chemotherapy. Specifically we evaluated the association between neutrophil count and serum proteins and electrolytes., Methods: For this purpose we analysed retrospectively collected laboratory results from two independent patient cohorts. Each cohort was divided into a control group consisting of patients with normal haematological parameters and a study group which included patients with reduced neutrophil counts. Neutropenic patients (study group) were cancer patients on chemotherapy., Results and Conclusion: Blood samples of cancer patients in study group showed reduction in haemoglobin, neutrophils and platelets. Neutropenic group showed a significant reduction in serum albumin, total protein, calcium, and potassium. Our results show that patients with severe neutropenia had pronounced changes in serum protein and electrolytes and increased incidence of abnormal serum protein and electrolyte level. The changes in the neutrophil counts showed a positive correlation with the changes in serum protein and electrolyte levels. A similar trend was seen in both the patient cohorts: the discovery set (176 patients) and the validation set (200 patients). Taken together our results suggest that chemotherapy-induced neutropenia is associated with dysregulation in haemoglobin, platelets, serum proteins and electrolytes., Competing Interests: The authors declare no conflict of interest., (© 2022 The Author(s).)

Introduction: MicroRNAs (miRNAs) have been shown to be altered in both CVD and T2DM and can have an application as diagnostic and prognostic biomarkers. miRNAs are released into circulation when the cardiomyocyte is subjected to injury and damage., Objectives: Measuring circulating miRNA levels in human plasma may be of great potential use for measuring the extent of damage to cardiomyocytes and response to exercise. This review is aimed to highlight the potential application of miRNAs as biomarkers of CVD progression in T2DM, and the impact of exercise on recovery., Methods: The review aims to examine whether the health improvements following exercise in T2DM patients are reflective of changes in expression of plasma miRNAs. For this purpose, studies were identified from the literature that have established a correlation between diabetes, disease progression and plasma miRNA levels. We also reviewed studies which looked at the effect of exercise on plasma miRNA levels., Results: The review identified miRNA signatures that are affected by T2DM and DHD and a subset of these miRNAs that are also affected by different types of exercise. This approach helped us to identify those miRNAs whose expression and function can be altered by regular bouts of exercise., Conclusions: miRNAs identified as part of this review can serve as tools to monitor the cardio-protective, anti-inflammatory and metabolic effects of exercise in people suffering from T2DM. Future research should focus on regulation of these miRNAs in T2DM and how they can be altered by appropriate exercise interventions., Supplementary Information: The online version contains supplementary material available at 10.1007/s40200-022-01066-4., Competing Interests: Conflict of interestThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© The Author(s) 2022.)

Antibiotic-resistant bacteria in the genus Enterococcus are a major cause of nosocomial infections and are an emergent public health concern. Similar to a number of bacterial species, resistance to the antibiotic rifampicin (Rif R ) in enterococci is associated with mutations in the gene encoding the β subunit of RNA polymerase (rpoB). In Mycobacterium tuberculosis, Rif R rpoB mutations alter mycobacterial surface lipid expression and are associated with an altered IL-1 cytokine response in macrophages upon infection. However, it is not clear if Rif R mutations modulate host cytokine responses by other bacteria. To address this question, we utilized Enterococcus faecalis (E. faecalis). Here, we treated human monocyte-derived macrophages with heat-inactivated wild type or Rif R rpoB mutants of E. faecalis and found that Rif R mutations reduced IL-1β cytokine production. However, Rif R mutations elicited other potent pro- and anti-inflammatory responses, indicating that they can impact other immune pathways beyond IL-1R1 signaling. Our findings suggest that immunomodulation by mutations in rpoB may be conserved across diverse bacterial species and that subversion of IL-1R1 pathway is shared by Rif R bacteria., (Copyright © 2021. Published by Elsevier Ltd.)

Converting a vaccine into a thermostable dry powder is advantageous as it reduces the resource burden linked with the cold chain and provides flexibility in dosage and administration through different routes. Such a dry powder presentation may be especially useful in the development of a vaccine towards the respiratory infectious disease tuberculosis (TB). This study assesses the immunogenicity and protective efficacy of spray-dried ID93+GLA-SE, a promising TB vaccine candidate, against Mycobacterium tuberculosis (Mtb) in a murine model when administered via different routes. Four administration routes for the spray-dried ID93+GLA-SE were evaluated along with relevant controls-1) reconstitution and intramuscular injection, 2) reconstitution and intranasal delivery, 3) nasal dry powder delivery via inhalation, and 4) pulmonary dry powder delivery via inhalation. Dry powder intranasal and pulmonary delivery was achieved using a custom nose-only inhalation device, and optimization using representative vaccine-free powder demonstrated that approximately 10 and 44% of the maximum possible delivered dose would be delivered for intranasal delivery and pulmonary delivery, respectively. Spray-dried powder was engineered according to the different administration routes including maintaining approximately equivalent delivered doses of ID93 and GLA. Vaccine properties of the different spray-dried lots were assessed for quality control in terms of nanoemulsion droplet diameter, polydispersity index, adjuvant content, and antigen content. Our results using the Mtb mouse challenge model show that both intranasal reconstituted vaccine delivery as well as pulmonary dry powder vaccine delivery resulted in Mtb control in infected mice comparable to traditional intramuscular delivery. Improved protection in these two vaccinated groups over their respective control groups coincided with the presence of cytokine-producing T cell responses. In summary, our results provide novel vaccine formulations and delivery routes that can be harnessed to provide protection against Mtb infection., Competing Interests: MG, NC, MCA, RK, RV, and CF are inventors on a patent application involving spray-dried vaccine adjuvant compositions and methods, and CF is an inventor on a patent involving oil-in-water emulsions with low oil content including GLA-SE. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Gomez, Ahmed, Das, McCollum, Mellett, Swanson, Gupta, Carrigy, Wang, Barona, Bachchhav, Gerhardt, Press, Archer, Liang, Seydoux, Kramer, Kuehl, Vehring, Khader and Fox.)

MicroRNAs (miRNAs) are non-coding RNAs which modulate gene expression via multiple post-transcriptional mechanisms. They are involved in a variety of biological processes, including cell proliferation, metastasis, metabolism, tumorigenesis, and apoptosis. Dysregulation of miRNA expression has been implicated in human cancers, and they may also serve as biomarkers of disease progression and prognosis. The miR-17-92 cluster is one of the most widely studied miRNA clusters, which was initially reported as an oncogene, but was later reported to exhibit tumour suppressive effects in some human cancers. This review summarizes the recent progress and context-dependant role of this cluster in various cancers. We summarize the known mechanisms which regulate miR-17-92 expression and molecular pathways that are in turn controlled by it. We discuss examples where it acts as an oncogene or a tumour suppressor along with key targets affecting hallmarks of cancer. We discuss how cellular contexts regulate the biological effects of miR-17-92. The plausible mechanisms of its paradoxical roles are explained, and mechanisms are described that may contribute to cell fate regulation by miR-17-92. Further, we discuss recently developed strategies to target miR-17-92 cluster in human cancers. MiR-17-92 may serve as a potential biomarker for prognosis and response to therapy as well as a target for cancer prevention and therapeutics., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier Ltd.)

Expression and functions of microRNAs (miRNAs) have been widely investigated in cancer treatment-induced complications and as a response to physical activity, respectively, but few studies focus on the application of miRNAs as biomarkers in exercise-based cancer rehabilitation. Research has shown that certain miRNA expression is altered substantially due to tissue damage caused by cancer treatment and chronic inflammation. MiRNAs are released from the damaged tissue and can be easily detected in blood plasma. Levels of the miRNA present in peripheral circulation can therefore be used to measure the extent of tissue damage. Moreover, damage to tissues such as cardiac and skeletal muscle significantly affects the individual's health-related fitness, which can be determined using physiologic functional assessments. These physiologic parameters are a measure of tissue health and function and can therefore be correlated with the levels of circulating miRNAs. In this paper, we reviewed miRNAs whose expression is altered during cancer treatment and may correlate to physiological, physical, and psychological changes that significantly impact the quality of life of cancer survivors and their role in response to physical activity. We aim to identify potential miRNAs that can not only be used for monitoring changes that occur in health-related fitness during cancer treatment but can also be used to evaluate response to exercise-based rehabilitation and monitor individual progress through the rehabilitation programme.

In this work, we explore machine learning through a model-agnostic feature representation known as braiding, that employs braid manifolds to interpret multipath ray bundles. We generate training and testing data using the well-known BELLHOP model to simulate shallow water acoustic channels across a wide range of multipath scattering activity. We examine three different machine learning techniques-k-nearest neighbors, random forest tree ensemble, and a fully connected neural network-as well as two machine learning applications. The first application applies known physical parameters and braid information to determine the number of reflections the acoustic signal may undergo through the environment. The second application applies braid path information to determine if a braid is an important representation of the channel (i.e., evolving across bands of higher amplitude activity in the channel). Testing accuracy of the best trained machine learning algorithm in the first application was 86.70% and the testing accuracy of the second application was 99.94%. This work can be potentially beneficial in examining how the reflectors in the environment changeover time while also determining relevant braids for faster channel estimation.

Stem cell-based in vitro models of embryonic development have been established over the last decade. Such model systems recapitulate aspects of gametogenesis, early embryonic development, or organogenesis. They enable experimental approaches that have not been possible previously and have the potential to greatly reduce the number of animals required for research. However, each model system has its own limitations, with certain aspects, such as morphogenesis and spatiotemporal control of cell fate decisions, diverging from the in vivo counterpart. Targeted bioengineering approaches to provide defined instructive external signals or to modulate internal cellular signals could overcome some of these limitations. Here, we present the latest technical developments and discuss how bioengineering can further advance the optimization and external control of stem cell-based embryo-like structures (ELSs). In vitro models combined with sophisticated bioengineering tools will enable an even more in-depth analysis of embryonic development in the future., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

The Reflections series takes a look back on historical articles from The Journal of the Acoustical Society of America that have had a significant impact on the science and practice of acoustics.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) latently infects approximately one-fourth of the world's population. The immune mechanisms that govern progression from latent (LTBI) to active pulmonary TB (PTB) remain poorly defined. Experimentally Mtb-infected non-human primates (NHP) mirror the disease observed in humans and recapitulate both PTB and LTBI. We characterized the lung immune landscape in NHPs with LTBI and PTB using high-throughput technologies. Three defining features of PTB in macaque lungs include the influx of plasmacytoid dendritic cells (pDCs), an Interferon (IFN)-responsive macrophage population, and activated T cell responses. In contrast, a CD27 + Natural killer (NK) cell subset accumulated in the lungs of LTBI macaques. This NK cell population was also detected in the circulation of LTBI individuals. This comprehensive analysis of the lung immune landscape will improve the understanding of TB immunopathogenesis, providing potential targets for therapies and vaccines for TB control., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

An important event in the unfolded protein response (UPR) is activation of the endoplasmic reticulum (ER) kinase PERK. The PERK signalling branch initially mediates a prosurvival response, which progresses to a proapoptotic response upon prolonged ER stress. However, the molecular mechanisms of PERK-mediated cell death are not well understood. Here we show that expression of the primary miR-17-92 transcript and mature miRNAs belonging to the miR-17-92 cluster are decreased during UPR. We found that miR-17-92 promoter reporter activity was reduced during UPR in a PERK-dependent manner. Furthermore, we show that activity of the miR-17-92 promoter is repressed by ectopic expression of ATF4 and NRF2. Promoter deletion analysis mapped the region responding to UPR-mediated repression to a site in the proximal region of the miR-17-92 promoter. Hypericin-mediated photo-oxidative ER damage reduced the expression of miRNAs belonging to the miR-17-92 cluster in wild-type but not in PERK-deficient cells. Importantly, ER stress-induced apoptosis was inhibited upon miR-17-92 overexpression in SH-SY5Y and H9c2 cells. Our results reveal a novel function for ATF4 and NRF2, where repression of the miR-17-92 cluster plays an important role in ER stress-mediated apoptosis. Mechanistic details are provided for the potentiation of cell death via sustained PERK signalling mediated repression of the miR-17-92 cluster.

The aim of this interdisciplinary work is a robust signal processing and autonomous machine learning framework to associate well-known (target) as well as any potentially unknown (non-target) peaks present within gas chromatography-mass spectrometry (GC/MS/MS) raw instrument signal. Particularly, this work evaluates three machine learning algorithms abilities to autonomously associate raw signal peaks based on accuracy in training and testing. A target is a known congener that is expected to be present within the raw instrument signal and a non-target is an unknown or unexpected compound. Autonomously identifying target peaks within the GC/MS/MS and associating them with non-target peaks can help improve the analysis of collected samples. Association of peaks refers to classifying peaks as known congeners regardless if the peak is a target or non-target. Uncertainty of peaks fitted and discovered through raw instrument signals from GC/MS/MS data is assessed to create topographical illustrations of target annotated peaks among sample raw instrument signals collected across diverse locations in the Chicago area. The term "annotated peak" is used to assign peaks found at specific retention times as a known congener. Adaptive signal processing techniques are utilized to smooth data and correct baseline drifts as well as detect and separate coeluted (overlapped) peaks in the raw instrument signal to provide key feature extraction. 150 air samples are analyzed for individual polychlorinated biphenyls (PCB) with GC/MS/MS across Chicago, IL. 80% of the data is used for training classification of target PCBs and 20% of the data is evaluated to identify and associate consistently occurring non-target peaks with target PCBs. A random forest classifier is used to associate identified peaks to target PCB peaks. Geographical topographical representations of target PCBs in the raw instrument signal demonstrates how PCBs accumulate and degrade in certain locations.

Somatic mutations of the estrogen receptor 1 gene (ESR1) is an emerging mechanism of acquired resistance to endocrine therapy in hormonal breast cancers. Hotspot point mutations in the ligand- binding domain of estrogen receptor α (ER) and genomic rearrangements producing ESR1 fusion genes are the two major types of mutations that are associated with endocrine resistance. The crosstalk between X-box binding protein 1 (XBP1), a key transcription factor of the unfolded protein response (UPR) and ER signalling creates a positive feedback loop that results in increased expression of XBP1 in ER-positive breast cancer. Here we report that XBP1 co-operated with point mutants (Y537S, D538G) and fusion mutants (ESR1-YAP1, ESR1-DAB2) of ESR1 to increase their transcriptional activity. XBP1 was required for optimal expression of estrogen-regulated genes, and up to 40% of XBP1-dependent genes were estrogen-responsive genes. Knockdown of XBP1 in genome-edited MCF7 cells expressing Y537S mutant reduced their growth, re-sensitized them to anti-estrogens and attenuated the constitutive and estrogen-stimulated expression of estrogen-regulated genes. Our study provides a rationale for overcoming endocrine resistance in breast cancers expressing ESR1 mutation by combining the XBP1 targeting agents with anti-estrogen agents., (© 2020 The Authors. Published by Elsevier Ltd.)

This paper introduces a feature extraction technique that identifies highly informative features from sonar magnitude spectra for automated target classification. The approach involves creating feature representations through convolution of a two-dimensional Gabor wavelet and acoustic color magnitudes to capture elastic waves. This feature representation contains extracted localized features in the form of Gabor stripes, which are representative of unique targets and are invariant of target aspect angle. Further processing removes non-informative features through a threshold-based culling. This paper presents an approach that begins connecting model-based domain knowledge with machine learning techniques to allow interpretation of the extracted features while simultaneously enabling robust target classification. The relative performance of three supervised machine learning classifiers, specifically a support vector machine, random forest, and feed-forward neural network are used to quantitatively demonstrate the representations' informationally rich extracted features. Classifiers are trained and tested with acoustic color spectrograms and features extracted using the algorithm, interpreted as stripes, from two public domain field datasets. An increase in classification performance is generally seen, with the largest being a 47% increase from the random forest tree trained on the 1-31 kHz PondEx10 data, suggesting relatively small datasets can achieve high classification accuracy if model-cognizant feature extraction is utilized.

Estrogen receptor 1 (ESR1, which encodes estrogen receptor-alpha) is a key driver gene for the initiation and progression of hormone receptor-positive breast cancer. Estrogen receptor-alpha (ER) is expressed in up to 70% of cases, and patients are routinely treated with endocrine therapies. However, the development of resistance over time is common and occurs in one-third of ER-positive breast tumors, leading to disease progression and death. X-box binding protein 1 (XBP1), a key component of the unfolded protein response (UPR) and ER signaling pathway, generates a positive feedback regulatory loop that leads to increased expression of XBP1 and ER in luminal breast cancer. In this review, we highlight new insights into the mechanisms of crosstalk between XBP1 and ER signaling and its clinical implications. Next, we describe the key signaling nodes that play an important role in XBP1-mediated endocrine resistance in breast cancer. Further, we discuss XBP1 gene mutations in breast cancer and the role of these mutations in the emergence of endocrine resistance and response to treatment. Finally, we discuss the current state and future directions for targeting XBP1 in combination with standard endocrine therapy to improve clinical outcomes in endocrine-resistant breast cancer patients., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Forces and relative movement between cells and extracellular matrix (ECM) are crucial to the self-organization of tissues during development. However, the spatial range over which these dynamics can be controlled in engineering approaches is limited, impeding progress toward the construction of large, structurally mature tissues. Herein, shape-morphing materials called "kinomorphs" that rationally control the shape and size of multicellular networks are described. Kinomorphs are sheets of ECM that change their shape, size, and density depending on patterns of cell contractility within them. It is shown that these changes can manipulate structure-forming behaviors of epithelial cells in many spatial locations at once. Kinomorphs are built using a new photolithographic technology to pattern single cells into ECM sheets that are >10× larger than previously described. These patterns are designed to partially mimic the branch geometry of the embryonic kidney epithelial network. Origami-inspired simulations are then used to predict changes in kinomorph shapes. Last, kinomorph dynamics are shown to provide a centimeter-scale program that sets specific spatial locations in which ≈50 µm-diameter epithelial tubules form by cell coalescence and structural maturation. The kinomorphs may significantly advance organ-scale tissue construction by extending the spatial range of cell self-organization in emerging model systems such as organoids., (© 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome . This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration., (Copyright © 2020 Cullen, Aneja, Beyhan, Cho, Woloszynek, Convertino, McCoy, Zhang, Anderson, Alvarez-Ponce, Smirnova, Karstens, Dorrestein, Li, Sen Gupta, Cheung, Powers, Zhao and Rosen.)

The main contribution of this interdisciplinary work is a robust computational framework to autonomously discover and quantify previously unknown associations between well-known (target) and potentially unknown (non-target) toxic industrial air pollutants. In this work, the variability of polychlorinated biphenyl (PCB) data is evaluated using a combination of statistical, signal processing, and graph-based informatics techniques to interpret the raw instrument signal from gas chromatography-mass spectrometry (GC/MS/MS) data sets. Specifically, minimum mean-squared techniques from the adaptive signal processing literature are extended to detect and separate coeluted (overlapped) peaks in the raw instrument signal. A graph-based visualization is provided which bridges two complementary approaches to quantitative pollution studies: (i) peak-cognizant target analysis (limits data analysis to few well-known compounds) and (ii) chemometric analysis (statistical large-scale data analysis) that is agnostic of specific compounds. Further, peak fitting techniques based on L2 error minimization are employed to autonomously calculate the amount of each PCB present with a normalized mean square error of -18.4851 dB. Graph-based visualization of associations between known and unknown compounds are developed through principal component analysis and both fuzzy c-means (FCM) and k-means clustering techniques are implemented and compared. The efficiency of these methods are compared using 150 air samples analyzed for individual PCBs with GC/MS/MS against traditional target-only techniques that perform analysis across only the known (target) PCBs. Parameter optimization techniques are employed to evaluate the relative contribution of PCB signals against ten potential source signals representing legacy signatures from historical manufacture of Aroclors and modern sources of PCBs produced as by products of pigment and polymer manufacturing. Aroclors 1232, 1254, 1016, and 1221 as well as non-Aroclor 3, 3', dichlorobiphenyl (PCB 11) were found in many of the samples as unique source signals that describe PCB mixtures in air samples collected from Chicago, IL.

Recent evidence has shown that the miR-17-92 cluster can function either as oncogene or tumor suppressor in human cancers. The function of miR-17-92 in subtypes of breast cancer remains largely unknown. The expression of miR-17-92 is elevated in triple negative breast cancer (TNBC) but reduced in estrogen receptor (ER)-positive breast cancer (ERPBC). We show that increased expression of miRNAs belonging to the miR-17-92 cluster is associated with poor outcome in TNBC, whereas the expression of miR-17-92 miRNAs is with good outcome in ERPBC. We show that ectopic expression of miR-17-92 inhibited cell growth and invasion of ER-positive and HER2-enriched cells. On the contrary, miR-17-92 expression enhanced cell growth and invasion of TNBC cells. Further, we found that miR-17-92 expression sensitized MCF7 cells to chemotherapeutic compounds, whereas it rendered SKBR3 cells resistant to them. We found that expression of ADORA1 was reduced by miR-17-92-expressing breast cancer cells, specifically in ERPBC. We observed an inverse correlation between the expression of ADORA1 and miR-17-92 in human breast cancer. Treatment with DPCPX, a selective ADORA1 antagonist, abolished the difference in the growth of control and miR-17-92 overexpressing MCF7 cells and identified ADORA1 as a key functional target of miR-17-92 in ERPBC. Furthermore, increased expression of ADORA1 in ERPBC is associated with a poor outcome. Our observations underscore the context-dependent role of miR-17-92 in breast cancer subtypes and suggest that miR-17-92 could serve as novel prognostic markers in breast cancer., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The lungs are the most vulnerable site for air-borne infections. Immunologic compartmentalization of the lungs into airway lumen and interstitium has paved the way to determine the immune status of the site of pathogen entry, which is crucial for the outcome of any air-borne infections. Vaccination via the nasal route with Mycobacterium indicus pranii (MIP), a prospective candidate vaccine against tuberculosis (TB), has been reported to confer superior protection as compared to the subcutaneous (s.c.) route in small-animal models of TB. However, the immune mechanism remains only partly understood. Here, we showed that intranasal (i.n.) immunization of mice with MIP resulted in a significant recruitment of CD4 + and CD8 + T-cells expressing activation markers in the lung airway lumen. A strong memory T-cell response was observed in the lung airway lumen after i.n. MIP vaccination, compared with s.c. vaccination. The recruitment of these T-cells was regulated primarily by CXCR3-CXCL11 axis in "MIP i.n." group. MIP-primed T-cells in the lung airway lumen effectively transferred protective immunity into naïve mice against Mycobacterium tuberculosis (M.tb) infection and helped reducing the pulmonary bacterial burden. These signatures of protective immune response were virtually absent or very low in unimmunized and subcutaneously immunized mice, respectively, before and after M.tb challenge. Our study provides mechanistic insights for MIP-elicited protective response against M.tb infection., (Copyright © 2019 Gupta, Saqib, Singh, Pal, Nishikanta and Bhaskar.)

This paper proposes channel estimation using energy efficient transmission of signal dictionaries for shallow water acoustic communications. Specifically, the multi-columned structure of the channel delay spread is exploited to design partially sampled dictionary in a two-dimensional (2-D) frequency representation of the channel. The key contribution of this work is to achieve considerable energy saving in the transmission of complex exponential signals, designed specifically for real-time shallow water channel estimation at the receiver. This is accomplished by harnessing 2-D frequency localization with compressive transmission and modified-compressive sensing with prior information to exploit the sparse structure of the rapidly fluctuating shallow water acoustic channel in real time. The proposed technique reduces demands on transmitted signal energy by harnessing the reconstruction ability of sparse sensing while retaining key non-sparse channel elements that represent important multipath phenomena. Numerical evidence based on experimental channel estimates demonstrates the efficacy of the proposed work.

Very few adjuvants inducing Th1 immune response have been developed and are under clinical investigation. Hence, there is the need to find an adjuvant that elicits strong Th1 immune response which should be safe when injected in the host along with vaccines. Mycobacterium indicus pranii (MIP), a non-pathogenic vaccine candidate, has shown strong immunomodulatory activity in leprosy/tuberculosis/cancer and in genital warts patients where its administration shifted the host immune response towards Th1 type. These findings prompted us to study the components of MIP in detail for their Th1 inducing property. Since mycobacterial cell wall is very rich in immunostimulatory components and is known to play important role in immune modulation, we investigated the activity of MIP cell wall using Ovalbumin antigen (OVA) as model antigen. 'Whole cell wall' (CW) and 'aqueous soluble cell wall fractions' (ACW) induced significant Th1 immune response while 'cell wall skeleton' (CWS) induced strong Th2 type of immune response. Finally, functional activity of fractions having Th1 inducing activity was evaluated in mouse model of melanoma. CW demonstrated significant anti-tumor activity similar to whole MIP. Anti-tumor activity of CW could be correlated with enhanced tumor antigen specific Th1 immune response observed in tumor draining lymph nodes., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Young children are infected by a diverse range of enteric pathogens in high disease burden settings, suggesting pathogen contamination of the environment is equally diverse. This study aimed to characterize across- and within-neighborhood diversity in enteric pathogen contamination of public domains in urban informal settlements of Kisumu, Kenya, and to assess the relationship between pathogen detection patterns and human and domestic animal sanitation conditions. Microbial contamination of soil and surface water from 166 public sites in three Kisumu neighborhoods was measured by enterococcal assays and quantitative reverse transcription polymerase chain reaction (qRT-PCR) for 19 enteric pathogens. Regression was used to assess the association between observed sanitary indicators of contamination with enterococci and pathogen presence and concentration, and pathogen diversity. Seventeen types of pathogens were detected in Kisumu public domains. Enteric pathogens were codetected in 33% of soil and 65% of surface water samples. Greater pathogen diversity was associated with the presence of domestic animal feces but not with human open defecation, deteriorating latrines, flies, or disposal of human feces. Sanitary conditions were not associated with enterococcal bacteria, specific pathogen concentrations, or "any pathogen". Young children played at 40% of observed sites. Managing domestic animal feces may be required to reduce enteric pathogen environmental contamination in high-burden settings.

BCG (Bacillus Calmette-Guérin) is the only available vaccine against TB and is also used for the treatment of superficial bladder cancer. BCG-mediated protection against TB and bladder cancer has been shown to rely on its ability to induce superior CD4 + and CD8 + T cell responses. As the magnitude of T cell responses is defined by dendritic cell (DC) lifespan, we examined the effect of BCG on DC survival and its underlying mechanisms. It was observed that BCG stimulation enhanced DC survival and prolonged DC lifespan in a dose-dependent manner. Live BCG led to a higher DC survival compared with heat-killed BCG. FITC-Annexin V staining showed that BCG promoted DC survival by inhibiting apoptosis. Consistently, higher expressions of anti-apoptotic proteins Bcl-2 and Bcl-x L were observed in BCG-stimulated DCs. Pharmacological inhibition of Bcl-2 and Bcl-x L drastically reduced the DC survival efficacy of BCG. Comparable survival of BCG-stimulated wild-type and MyD88 -/- DCs suggested that MyD88 signaling is dispensable for BCG-induced DC survival. NF-κB is one of the key regulators of innate immune responses. We observed that pharmacological inhibition of NF-κB abrogated BCG-mediated increase in DC survival and expression of anti-apoptotic proteins. These findings provide a novel insight into the effect of BCG on DC physiology., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2018. Published by The Company of Biologists Ltd.)

Nuclear receptor coactivators (NCOAs) function as coactivators for nuclear receptors as well as several other transcription factors and potentiate their transcriptional activity. NCOAs play an important role in biology of hormone-dependent and -independent cancers. MCB-613 is a recently described, small molecule stimulator of NCOAs and anti-neoplastic compound that leads to the death of tumour cells due to increased cellular stress. In the present study we investigated the molecular mechanism of MCB-613-induced cell death. We report that absence of NCOA3 leads to compromised activation of PERK signalling pathway during unfolded protein response (UPR). We found that chemical and genetic inhibition of NCOA3 attenuated the expression of PERK at mRNA and protein level. We show that loss of NCOA3 renders cells hypersensitive to UPR induced cell death. Our results show that MCB-613 induced cell death is attenuated in NCOA3 knockout HeLa cells and MCB-613 leads to enhanced PERK signalling in wild-type HeLa cells. The knockdown of PERK provides resistance to MCB-613 mediated cell death while knockdown of XBP1 and ATF6 have no such effect. Our results suggest that hyperstimulation of NCOA3 by MCB-613 induces cell death by evoking constitutive PERK signalling. Taken together our results point to NCOA3 as an important determinant in regulating cell fate during ER stress, with too little and too much NCOA3 both producing deleterious effects., Competing Interests: CONFLICTS INTEREST Authors declare no competing financial interests.

Mycobacterium indicus pranii (MIP) is a potent vaccine candidate against tuberculosis (TB) as it has demonstrated significant protection in animal models of tuberculosis as well as in clinical trials. Higher protective efficacy of MIP against TB as compared to BCG provoked the efforts to gain insight into the molecular mechanisms underlying MIP mediated protection against Mycobacterium tuberculosis (M.tb). Autophagy, initially described as a cell survival mechanism during starvation, also plays a key role in host resistance to M.tb. Virulent mycobacteria like M.tb, suppresses host autophagy response to increase its survival in macrophages. Since mycobacterial species have been shown to vary widely in their autophagy-inducing properties, in the present study, we examined the autophagy inducing efficacy of MIP and its role in MIP-mediated protection against M.tb. MIP was found to be potent inducer of autophagy in macrophages. Induced autophagy was responsible for reversal of the phagosome maturation block and phagolysosome fusion inhibition in M.tb infected macrophages, which ultimately lead to significantly enhanced clearance of M.tb from the macrophages. This is an important study which further delineated the underlying mechanisms for significant immunotherapeutic activity observed in TB patients / animal models of tuberculosis, given MIP therapy along with chemotherapy.

Aim: To identify glycosylation-related genes in the HT29 derivative cell line, HT29-MTX-E12, showing differential expression on infection with Helicobacter pylori ( H. pylori )., Methods: Polarised HT29-MTX-E12 cells were infected for 24 h with H. pylori strain 26695. After infection RNA was isolated from both infected and non-infected host cells. Sufficient infections were carried out to provide triplicate samples for microarray analysis and for qRT-PCR analysis. RNA was isolated and hybridised to Affymetrix arrays. Analysis of microarray data identified genes significantly differentially expressed upon infection. Genes were grouped into gene ontology functional categories. Selected genes associated with host glycan structure (glycosyltransferases, hydrolases, lectins, mucins) were validated by real-time qRT-PCR analysis., Results: Infection of host cells was confirmed by the isolation of live bacteria after 24 h incubation and by PCR amplification of bacteria-specific genes from the host cell RNA. H. pylori do not survive incubation under the adopted culture conditions unless they associate with the adherent mucus layer of the host cell. Microarray analysis identified a total of 276 genes that were significantly differentially expressed ( P < 0.05) upon H. pylori infection and where the fold change in expression was greater than 2. Six of these genes are involved in glycosylation-related processes. Real-time qRT-PCR demonstrated significant downregulation (1.8-fold, P < 0.05) of the mucin MUC20. REG4 was heavily expressed and significantly downregulated (3.1-fold, P < 0.05) upon infection. Gene ontology analysis was consistent with previous studies on H. pylori infection., Conclusion: Gene expression data suggest that infection with H. pylori causes a decrease in glycan synthesis, resulting in shorter and simpler glycan structures., Competing Interests: Conflict-of-interest statement: The authors declare no conflicts-of-interest.

BCG, the only approved vaccine protects against severe form of childhood tuberculosis but its protective efficacy wanes in adolescence. BCG has reduced the incidence of infant TB considerably in endemic areas; therefore prime-boost strategy is the most realistic measure for control of tuberculosis in near future. Mycobacterium indicus pranii (MIP) shares significant antigenic repertoire with Mtb and BCG and has been shown to impart significant protection in animal models of tuberculosis. In this study, MIP was given as a booster to BCG vaccine which enhanced the BCG mediated immune response, resulting in higher protection. MIP booster via aerosol route was found to be more effective in protection than subcutaneous route of booster immunization. Pro-inflammatory cytokines like IFN-γ, IL-12 and IL-17 were induced at higher level in infected lungs of 'BCG-MIP' group both at mRNA expression level and in secretory form when compared with 'only BCG' group. BCG-MIP groups had increased frequency of multifunctional T cells with high MFI for IFN-γ and TNF-α in Mtb infected mice. Our data demonstrate for the first time, potential application of MIP as a booster to BCG vaccine for efficient protection against tuberculosis. This could be very cost effective strategy for efficient control of tuberculosis., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Background: Comprehensive two-dimensional gas chromatography [Formula: see text] provides high-resolution separations across hundreds of compounds in a complex mixture, thus unlocking unprecedented information for intricate quantitative interpretation. We exploit this compound diversity across the [Formula: see text] topography to provide quantitative compound-cognizant interpretation beyond target compound analysis with petroleum forensics as a practical application. We focus on the [Formula: see text] topography of biomarker hydrocarbons, hopanes and steranes, as they are generally recalcitrant to weathering. We introduce peak topography maps (PTM) and topography partitioning techniques that consider a notably broader and more diverse range of target and non-target biomarker compounds compared to traditional approaches that consider approximately 20 biomarker ratios. Specifically, we consider a range of 33-154 target and non-target biomarkers with highest-to-lowest peak ratio within an injection ranging from 4.86 to 19.6 (precise numbers depend on biomarker diversity of individual injections). We also provide a robust quantitative measure for directly determining "match" between samples, without necessitating training data sets., Results: We validate our methods across 34 [Formula: see text] injections from a diverse portfolio of petroleum sources, and provide quantitative comparison of performance against established statistical methods such as principal components analysis (PCA). Our data set includes a wide range of samples collected following the 2010 Deepwater Horizon disaster that released approximately 160 million gallons of crude oil from the Macondo well (MW). Samples that were clearly collected following this disaster exhibit statistically significant match [Formula: see text] using PTM-based interpretation against other closely related sources. PTM-based interpretation also provides higher differentiation between closely correlated but distinct sources than obtained using PCA-based statistical comparisons. In addition to results based on this experimental field data, we also provide extentive perturbation analysis of the PTM method over numerical simulations that introduce random variability of peak locations over the [Formula: see text] biomarker ROI image of the MW pre-spill sample (sample [Formula: see text] in Additional file 4: Table S1). We compare the robustness of the cross-PTM score against peak location variability in both dimensions and compare the results against PCA analysis over the same set of simulated images. Detailed description of the simulation experiment and discussion of results are provided in Additional file 1: Section S8., Conclusions: We provide a peak-cognizant informational framework for quantitative interpretation of [Formula: see text] topography. Proposed topographic analysis enables [Formula: see text] forensic interpretation across target petroleum biomarkers, while including the nuances of lesser-known non-target biomarkers clustered around the target peaks. This allows potential discovery of hitherto unknown connections between target and non-target biomarkers.

Shallow water acoustic channel estimation techniques are presented at the intersection of time, frequency, and sparsity. Specifically, a mathematical framework is introduced that translates the problem of channel estimation to non-uniform sparse channel recovery in two-dimensional frequency domain. This representation facilitates disambiguation of slowly varying channel components against high-energy transients, which occupy different frequency ranges and also exhibit significantly different sparsity along their local distribution. This useful feature is exploited to perform non-uniform sampling across different frequency ranges, with compressive sampling across higher Doppler frequencies and close to full-rate sampling at lower Doppler frequencies, to recover both slowly varying and rapidly fluctuating channel components at high precision. Extensive numerical experiments are performed to measure relative performance of the proposed channel estimation technique using non-uniform compressive sampling against traditional compressive sampling techniques as well as sparsity-constrained least squares across a range of observation window lengths, ambient noise levels, and sampling ratios. Numerical experiments are based on channel estimates from the SPACE08 experiment as well as on a recently developed channel simulator tested against several field trials.

The endoplasmic reticulum (ER) responds to changes in intracellular homeostasis through activation of the unfolded protein response (UPR). UPR can facilitate the restoration of cellular homeostasis, via the concerted activation of three ER stress sensors, namely IRE1, PERK and ATF6. Global approaches in several cellular contexts have revealed that UPR regulates the expression of many miRNAs that play an important role in the regulation of life and death decisions during UPR. Here we show that expression of miR-424(322)-503 cluster is downregulated during UPR. IRE1 inhibitor (4 μ8C) and deficiency of XBP1 had no effect on downregulation of miR-424(322)-503 during UPR. Treatment of cells with CCT030312, a selective activator of EIF2AK3/PERK signalling, leads to the downregulation of miR-424(322)-503 expression. The repression of miR-424(322)-503 cluster during conditions of ER stress is compromised in PERK-deficient MEFs. miR-424 regulates the expression of ATF6 via a miR-424 binding site in its 3' UTR and attenuates the ATF6 transcriptional activity during UPR. Further miR-424 had no effect on IRE1-XBP1 axis but enhanced the regulated IRE1-dependent decay (RIDD). Our results suggest that miR-424 constitutes an obligatory fine-tuning mechanism where PERK-mediated downregulation of miR-424(322)-503 cluster regulates optimal activation of IRE1 and ATF6 during conditions of ER stress.