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Samantha J Thulborn,1,2 Alessandro Ceroni,3 Koirobi Haldar,4 Vijay Mistry,4 Jennifer L Cane,1,2 Christopher E Brightling,4,5 Michael R Barer,4 Mona Bafadhel1 1Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK; 2Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK; 3Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; 4Department of Immunity, Infection and Inflammation, University of Leicester, Leicester, UK; 5Institute for Lung Health, University of Leicester, Leicester, UKCorrespondence: Mona BafadhelRespiratory Medicine Unit, NDM Research Building, Old Campus Road, University of Oxford, Oxford OX3 7FZ, UKTel +44 1865 612898Email mona.bafadhel@ndm.ox.ac.ukBackground: Non-typeable Haemophilus influenzae (NTHi) is the most commonly found pathogen in the lower respiratory airways of patients with COPD. NTHi is predominantly regarded as an intracellular pathogen; however, like most pathogens, it can exist and co-exist in two broad forms: cell-associated (intracellularly or adhered to cells) or cell-dissociated (biofilm dispersed or planktonic). We sought to investigate if cell-dissociated NTHi can be detected from the sputum of COPD patients and assess this relationship to disease severity and airway inflammation.Methods: DNA was extracted from the sputum plug and cell-free supernatant to quantify absolute (cell-associated and cell-dissociated NTHi) and cell-dissociated NTHi, respectively, from 87 COPD subjects attending an observational longitudinal COPD exacerbation study. NTHi was quantified using TaqMan hydrolysis probes, targeting the OMP P6 gene using qPCR.Results: At stable state cell-dissociated NTHi was detected 56% of subjects with a median (IQR) of 9.95x102 gene copies (1.26x102 to 1.90x104). Cell-dissociated NTHi correlated with absolute NTHi levels (r=0.34, p< 0.01) but not airway inflammation or spirometry at stable state. At exacerbation, cell-dissociated NTHi correlated with lung function (FEV1 r=0.629, p=0.005; FEV1%predicted r=0.564, p=0.015; FVC r=0.476 p=0.046) and sputum neutrophilic inflammation (% neutrophils r=0.688, p=0.002; total neutrophils r=0.518, p=0.028).Conclusion: In patients with COPD, NTHi can exist in both cell-associated and cell-dissociated forms. Cell-dissociated NTHi is associated with neutrophilic airway inflammation during exacerbations of COPD and may be a driving factor in worsening lung function during these episodes.Keywords: NTHi, infection, neutrophils, COPD

Leena George,1 Adam Wright,1 Vijay Mistry,1 Amanda Sutcliffe,1 Latifa Chachi,1 Koirobi Haldar,1 Mohammadali Yavari Ramsheh,1 Matthew Richardson,1 René van der Merwe,2 Ubaldo Martin,3 Paul Newbold,3 Christopher E Brightling11Department of Respiratory Sciences, Institute for Lung Health, National Institute for Health Research Biomedical Research Centre, University of Leicester, Leicester, UK; 2Clinical Respiratory Management, MedImmune Ltd., Cambridge, UK; 3Global Medical Affairs, AstraZeneca, Gaithersburg, MD, USAAbstract: We hypothesized whether the reduction in eosinophilic airway inflammation in patients with chronic obstructive pulmonary disease (COPD) following treatment with benralizumab, a humanized, afucosylated, monoclonal antibody that binds to interleukin-5 receptor α, increases the airway bacterial load. Analysis of sputum samples of COPD patients participating in a Phase II trial of benralizumab indicated that sputum 16S rDNA load and Streptococcus pneumoniae were reduced following treatment with benralizumab. However, in vitro, eosinophils did not affect the killing of the common airway pathogens S. pneumoniae or Haemophilus influenzae. Thus, benralizumab may have an indirect effect upon airway bacterial load.Keywords: COPD, benralizumab, IL-5, bacterial load, S. pneumoniae, H. influenzae

Leena M George,1,* Richard D Haigh,1,* Vijay Mistry,1 Koirobi Haldar,1 Michael R Barer,1 Marco R Oggioni,2 Christopher E Brightling1 1Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK; 2Department of Genetics, University of Leicester, Leicester, UK *These authors contributed equally to this work Purpose: Moraxella catarrhalis is implicated in the pathogenesis of some COPD exacerbations. We sought to investigate whether the M. catarrhalis strain is variable between COPD subjects; that an exacerbation is associated with acquisition of a new strain and that certain strains are more commonly associated with exacerbations. Patients and methods: Sputum samples were collected at stable and exacerbation visits from COPD subjects from a single center as part of the COPDMAP consortium. Samples identified as M. catarrhalis positive by qPCR were recultured in liquid cultures grown to extract genomic DNA; underwent Illumina MiSeq and bacterial genome sequences were de novo assembled and Multi Locus Sequence Type (MLST) was determined. Results: Thirty-five samples were obtained from 18 subjects. These included 13 stable and 22 exacerbation samples. The diversity between samples was very large with 25 different M. catarrhalis MLSTs being identified out of the 35 samples of which 12 MSLTs have not been described previously. Change and persistence of M. catarrhalis strain were observed between stable visits, from stable to exacerbation and vice-a-versa, and between exacerbation visits. Conclusion: Sputum M. catarrhalis strains exhibit marked diversity within and between COPD subjects. Acquisition of a new strain is common between stable and exacerbation events such that no strain is specifically associated with an exacerbation. Keywords: COPD, Moraxella catarrhalis, strain change, exacerbation

Samantha J Thulborn,1 Madiha Dilpazir,2 Koirobi Haldar,3 Vijay Mistry,3 Christopher E Brightling,3 Michael R Barer,3 Mona Bafadhel1 1Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, 2Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, 3Department of Immunity, Infection & Inflammation, University of Leicester, Leicester, UK Background: Pentraxin 3 (PTX3) is an acute phase protein, involved in antibacterial resistance. Recent studies have shown PTX3 levels to be elevated in the presence of a bacterial infection and in a murine sepsis model.Objective: We aim to investigate if sputum PTX3 can be used as a biomarker for bacterial infection in subjects with COPD.Materials and methods: Sputum samples from 142 COPD patients (102 men) with a mean (range) age of 69 years (45–85) and mean (SD) post-bronchodilator percentage predicted forced expiratory volume in 1 second (FEV1) of 50% (19) were analyzed for PTX3, using a commercial assay at stable state and during an exacerbation. Association with bacteria, from culture, quantitative real-time polymerase chain reaction (qPCR) and colony-forming units (CFU) was investigated.Results: The geometric mean (95% CI) PTX3 level at stable state was 50.5 ng/mL (41.4–61.7). PTX3 levels correlated with absolute neutrophil count in sputum (r=0.37; P105 CFU/mL at stable state) with a receiver-operating characteristic (ROC) area under the curve (AUC) of 0.59 and 95% confidence interval (CI) 0.43–0.76 (P=0.21). During an exacerbation, there was a modest increase in PTX3 (fold difference 0.15, 95% of difference 0.02–0.29; P=0.02), and PTX3 fared better at identifying a bacteria-associated exacerbation (ROC AUC 0.65, 95% CI 0.52–0.78, P=0.03).Conclusion: PTX3 is associated with bacterial infection in patients with COPD, but its utility as a biomarker for identifying a bacteria-associated exacerbation warrants further studies. Keywords: TNF-inducible gene 14 protein, infection, sputum

Mona Bafadhel,1 Koirobi Haldar,2 Bethan Barker,2,3 Hemu Patel,4 Vijay Mistry,2,3 Michael R Barer,2–4 Ian D Pavord,1 Christopher E Brightling2,3 1Respiratory Medicine Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; 2Department of Infection, Immunity and Inflammation, University of Leicester, 3Institute for Lung Health, National Institute for Health Research Respiratory Biomedical Research Unit, Glenfield Hospital, University of Leicester, 4Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK Background: Potentially pathogenic microorganisms can be detected by quantitative real-time polymerase chain reaction (qPCR) in sputum from patients with COPD, although how this technique relates to culture and clinical measures of disease is unclear. We used cross-sectional and longitudinal data to test the hypotheses that qPCR is a more sensitive measure of bacterial presence and is associated with neutrophilic airway inflammation and adverse clinical outcomes.Methods: Sputum was collected from 174 stable COPD subjects longitudinally over 12 months. Microbial sampling using culture and qPCR was performed. Spirometry and sputum measures of airway inflammation were assessed.Findings: Sputum was qPCR-positive (>106 copies/mL) in 77/152 samples (Haemophilus influenzae [n=52], Moraxella catarrhalis [n=24], Streptococcus pneumoniae [n=19], and Staphylococcus aureus [n=7]). Sputum was culture-positive in 50/174 samples, with 49 out of 50 culture-positive samples having pathogen-specific qPCR bacterial loads >106 copies/mL. Samples that had qPCR copy numbers >106/mL, whether culture-positive or not, had increased sputum neutrophil counts. H. influenzae qPCR copy numbers correlated with sputum neutrophil counts (r=0.37, P106/mL three or more times in 19 patients, eight of whom were repeatedly sputum culture-positive. Persistence, whether defined by culture, qPCR, or both, was associated with a higher sputum neutrophil count, lower forced expiratory volume in 1 second (FEV1), and worsened quality of life.Interpretation: qPCR identifies a significant number of patients with potentially bacteria-associated neutrophilic airway inflammation and disease that are not identified by traditional culture-based methods. Keywords: H. influenzae, qPCR, sputum

Bethan L Barker,1 Susan McKenna,1 Vijay Mistry,1 Mitesh Pancholi,1 Hemu Patel,2 Koirobi Haldar,3 Michael R Barer,3 Ian D Pavord,4 Michael C Steiner,1 Christopher E Brightling,1 Mona Bafadhel4 1Institute for Lung Health, NIHR Respiratory Biomedical Research Unit, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom; 2Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom; 3Department of Infection, Immunity, and Inflammation, University of Leicester, Leicester, United Kingdom; 4Respiratory Medicine Unit, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom Background: Nutritional depletion is an important manifestation of chronic obstructive pulmonary disease (COPD), which has been related to systemic inflammation. It remains unclear to what degree airway inflammation contributes to the presence or progression of nutritional depletion. Objectives: To determine whether airway inflammation and lung bacterial colonization are related to nutritional status or predict progressive weight loss and muscle atrophy in patients with COPD. Methods: Body composition using dual energy X-ray absorptiometry, indices of airway inflammation, and bacterial colonization were measured in 234 COPD patients. Systemic inflammation was assessed from serum C reactive protein (CRP) and circulating total and differential leukocyte counts. Nutritional depletion was defined as a body mass index (BMI) less than 21 kg/m2 and/or fat-free mass index (FFMI) less than 15 or 17 kg/m2 in women and men, respectively. FFMI was calculated as the fat-free mass (FFM) corrected for body surface area. Measurements were repeated in 94 patients after a median 16-month follow-up. Regression analysis was used to assess the relationships of weight change and FFM change with indices of bacterial colonization and airway and systemic inflammation. Results: Nutritional depletion occurred in 37% of patients. Lung function was worsened in patients with nutritional depletion compared to those without (forced expiratory volume in 1 second 1.17 L versus 1.41 L, mean difference 0.24, 95% confidence interval 0.10 to 0.38, P

Mullite (3Al2O3·2SiO2) samples doped with 0.4 M, 0.6 M, 0.8 M, 1.0 M and 1.2 M of iron, nickel and Copper, were prepared by a sol-gel process. Prepared gels were then dried, grinded, pressed into pellets and sintered at temperatures 1100°C and 1400°C for 4 h. Phase formation, densification behavior has been investigated as a function of the metal content and sintering temperature. The density of the sintered ceramics was measured using Archimedes method. The main intention is to study the role of metal ions in influencing mullitization behavior in the case of the sol-gel reaction process, in order to provide useful information of mullite. This paper deals with the effect of metal ions on mullite formation, microstructure and densification behavior in single-phase sol-gel derived mullite. The results showed with increase in concentration of metals (Fe2+, Ni2+, Cu2+), crystallization of mullite was enhanced which is evident from X-ray diffraction upto G3 and FESEM of the composites. The density of the doped samples increases with the increase of metal ion concentration as well as with the sintering temperature. Copper-doped mullite exhibits the highest density 2.46 g cm-3 at 1400°C.

P Pathiraja, S Dhar, K HaldarOxford University Hospital, Oxford, UKBackground: Minimal uterine serous cancer (MUSC) or serous endometrial intraepithelial carcinoma (EIC) has been described by many different names since 1998. There have been very few cases reported in literature since EIC/MUSC was recognized as a separate entity. The World health Organization (WHO) Classification favors the term serous EIC. Although serous EIC is confined to the uterine endometrium at initial histology diagnosis, a significant number of patients could have distal metastasis at diagnosis, without symptoms. Serous EIC is considered as being the precursor of uterine serous cancer (USC), but pure serous EIC also has an aggressive behavior similar to USC. It is therefore prudent to have an accurate diagnosis and appropriate surgical staging. There are very few published articles in literature that discuss the pure form of serous EIC. The aim of this series is to share our experience and review evidence for optimum management of serous EIC.Patients and methods: We report a series of five women treated in our institute in the last 3 years. We reviewed the relevant literature on serous EIC and various management strategies, to recommend best clinical practice.Conclusion: Pure serous EIC is a difficult histopathological diagnosis, which requires ancillary immunohistochemical staining. It can have an aggressive clinical behavior with early recurrence and poor survival. Optimum surgical staging, with appropriate adjuvant treatment, should be discussed when treating these patients.Keywords: serous EIC, minimal uterine serous cancer, papillary serous endometrial cancer

Rationale: Exacerbations of chronic obstructive pulmonary disease (COPD) are heterogeneous with respect to inflammation and etiology.Objectives: Investigate biomarker expression in COPD exacerbations to identify biologic clusters and determine biomarkers that recognize clinical COPD exacerbation phenotypes, namely those associated with bacteria, viruses, or eosinophilic airway inflammation.Methods: Patients with COPD were observed for 1 year at stable and exacerbation visits. Biomarkers were measured in sputum and serum. Viruses and selected bacteria were assessed in sputum by polymerase chain reaction and routine diagnostic bacterial culture. Biologic phenotypes were explored using unbiased cluster analysis and biomarkers that differentiated clinical exacerbation phenotypes were investigated.Measurements and Main Results: A total of 145 patients (101 men and 44 women) entered the study. A total of 182 exacerbations were captured from 86 patients. Four distinct biologic exacerbation clusters were identified. These were bacterial-, viral-, or eosinophilic-predominant, and a fourth associated with limited changes in the inflammatory profile termed “pauciinflammatory.” Of all exacerbations, 55%, 29%, and 28% were associated with bacteria, virus, or a sputum eosinophilia. The biomarkers that best identified these clinical phenotypes were sputum IL-1β, 0.89 (area under receiver operating characteristic curve) (95% confidence interval [CI], 0.83–0.95); serum CXCL10, 0.83 (95% CI, 0.70–0.96); and percentage peripheral eosinophils, 0.85 (95% CI, 0.78–0.93), respectively.Conclusions: The heterogeneity of the biologic response of COPD exacerbations can be defined. Sputum IL-1β, serum CXCL10, and peripheral eosinophils are biomarkers of bacteria-, virus-, or eosinophil-associated exacerbations of COPD. Whether phenotype-specific biomarkers can be applied to direct therapy warrants further investigation. [ABSTRACT FROM AUTHOR]

The present paper produces the subsonic solution of linearized gasdynamic equation by means of decomposition method which is divided into four parts, such as, (i) regular or ordinary decomposition, (ii) double decompoisition, (iii) modified decomposition and (iv) asymptotic decomposition. Out of these four methods, regular and modified decomposition methods have been developed for inhomogeneous partial differential equations and a few examples of inviscid gasdynamics have been considered for clear illustration of the theories. The regular decomposition method is used for linearized steady axisymmetric subsonic flow past a corrugated circular cylinder whereas the modified decomposition method is used for linearized steady plane subsonic flow past a wave shaped wall. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented which focuses on the study which investigates on the aetiological profile and antibiotic susceptibility pattern in urinary tract infection (UTI) patients in Tripura, India.

The potency of frontline antimalarial drug artemisinin (ART) derivatives is triggered by heme-induced cleavage of the endoperoxide bond to form reactive heme-ART alkoxy radicals and covalent heme-ART adducts, which are highly toxic to the parasite. ART-resistant (ART-R) parasites with mutations in the Plasmodium falciparum Kelch-containing protein Kelch13 (PfKekch13) exhibit impaired hemoglobin uptake, reduced yield of hemoglobin-derived heme, and thus decreased ART activation. However, any direct involvement of PfKelch13 in heme-mediated ART activation has not been reported. Here, we show that the purified recombinant PfKelch13 wild-type (WT) protein displays measurable binding affinity for iron and heme, the main effectors for ART activation. The heme-binding property is also exhibited by the native PfKelch13 protein from parasite culture. The two ART-R recombinant PfKelch13 mutants (C580Y and R539T) display weaker heme binding affinities compared to the ART-sensitive WT and A578S mutant proteins, which further translates into reduced yield of heme-ART derivatives when ART is incubated with the heme molecules bound to the mutant PfKelch13 proteins. In conclusion, this study provides the first evidence for ART activation via the heme-binding propensity of PfKelch13. This mechanism may contribute to the modulation of ART-R levels in malaria parasites through a novel function of PfKelch13., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Bangladesh reduced malaria incidence by 93% from 2008 to 2020 through the action of governmental and non-governmental organizations. The Bangladesh context is unique to South Asia because its successful public sector malaria control programs have historically not engaged corporate partners (as undertaken in Sri Lanka and proposed in India). However, ∼18 million people continue to live at risk of infection in Bangladesh and for-profit private healthcare providers, catalytic for malaria elimination in many countries, are expected to benefit the national program. We distilled (from a large and complex literature) nine distinct strategies important in other developing settings and weighed them in the context of Bangladesh's flourishing private health care sector, driven by patient demand, self-interest and aspirations for public good, as well as heterogeneity in providers and malaria-prevalence. We propose a new model dependent on five strategies and its immediate deployment considerations in high endemic areas, to empower Bangladesh's phased agenda of eliminating indigenous malaria transmission by 2030., Competing Interests: No funding was received for the formulation of this manuscript. The authors declare no competing interests., (© 2024 The Author(s).)

Vulvo-vaginal melanomas are one of the rarest gynecological oncology diseases with a poor survival compared with other malignancies. The 5-year survival varies from 13% to 32.3%. Vulvo-vaginal melanomas involving the upper 2/3rds of the vagina are usually treated with total pelvic exenteration (TPE). TPE surgery carries a 50% risk of major complications and also morbidity associated with double stomas. Central pelvic compartment resection is a novel organ-sparing surgical approach entailing radical total laparoscopic hysterectomy, bilateral salpingo-oophrectomy, laparoscopic vaginectomy and vulvectomy to reduce morbidity compared with TPE. Permanent suprapubic catheters are used if there is urethral involvement but require quality of life studies to assess their long-term outcomes., Competing Interests: Competing interests disclosure The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties., (© 2024 The Authors.)

Histone deacetylase inhibitors (HDACi) that modulate epigenetic regulation and are approved for treating rare cancers have, in disease models, also been shown to mitigate neurological conditions, including chronic pain. They are of interest as non-opioid treatments, but achieving long-term efficacy with limited dosing has remained elusive. Here we utilize a triple combination formulation (TCF) comprised of a pan-HDACi vorinostat (Vo at its FDA-approved daily dose of 50mg/Kg), the caging agent 2-hydroxypropyl-β-cyclodextrin (HPBCD) and polyethylene glycol (PEG) known to boost plasma and brain exposure and efficacy of Vo in mice and rats, of various ages, spared nerve injury (SNI) model of chronic neuropathic pain. Administration of the TCF (but not HPBCD and PEG) decreased mechanical allodynia for 4 weeks without antagonizing weight, anxiety, or mobility. This was achieved at less than 1% of the total dose of Vo approved for 4 weeks of tumor treatment and associated with decreased levels of major inflammatory markers and microglia in ipsilateral (but not contralateral) spinal cord regions. A single TCF injection was sufficient for 3-4 weeks of efficacy: this was mirrored in repeat injections, specific for the injured paw and not seen on sham treatment. Pharmacodynamics in an SNI mouse model suggested pain relief was sustained for days to weeks after Vo elimination. Doubling Vo in a single TCF injection proved effectiveness was limited to male rats, where the response amplitude tripled and remained effective for > 2 months, an efficacy that outperforms all currently available chronic pain pharmacotherapies. Together, these data suggest that through pharmacological modulation of Vo, the TCF enables single-dose effectiveness with extended action, reduces long-term HDACi dosage, and presents excellent potential to develop as a non-opioid treatment option for chronic pain., Competing Interests: Competing interests. A.V.A, K.H., M.S.A and M.V.C. are coinventors on the following patent entitled ‘Triple Combination Formulation for Treatment of Chronic Pain’ US16/209,261, published 2022-01-11.

Effective treatments for genetic disorders that coevolved with pathogens require simultaneous betterment of both conditions. Hydroxyurea (HU) offers safe and efficacious treatment for sickle cell anemia (SCA) by reducing clinical complications, transfusions, and death rates. Despite concerns that the HU treatment for SCA would increase infection risk by the human malaria Plasmodium falciparum, (the genetic driver of the sickle mutation), HU instead reduced clinical malaria. We used physiologically relevant drug exposures that mimic in vivo pharmacokinetics in humans. Under these conditions, we showed that HU and other ribonucleotide reductase (RNR) inhibitors have significant, intrinsic killing activity in vitro against schizont stages of P falciparum in both normal and sickle red blood cells. Long-term in vitro selection with HU increased the expression of Pfrnr genes but showed a low risk of eliciting stably resistant parasites or compromising the potency of current antimalarial drugs. Additive activity devoid of antagonism by HU was observed with a wide spectrum of commonly used antimalarial treatments. These data endorse broad, safe, and long-term use of HU for SCA in malaria-endemic countries and provide a novel biological model for the treatment of a genetic disorder with simultaneous, adjunct therapy of a life-threatening infection needed in a global health setting., (© 2023 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)

Endometrial stromal sarcomas (ESSs) are a rare form of uterine malignancy representing <10% of all uterine sarcomas and <1% of all primary malignant tumours of the uterus. Invasion of the vascular system by low-grade ESS has been reported in the literature. Here we report the first case of a high-grade ESS invading the pelvic and gonadal vein and extending through the inferior vena cava to the right atrium, the diagnostic challenges and multidisciplinary management of the case., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Limited 2023. No commercial re-use. See rights and permissions. Published by BMJ.)

Maintaining protein lipoylation is vital for cell metabolism. The H-protein encoded by GCSH has a dual role in protein lipoylation required for bioenergetic enzymes including pyruvate dehydrogenase and 2-ketoglutarate dehydrogenase, and in the one-carbon metabolism through its involvement in glycine cleavage enzyme system, intersecting two vital roles for cell survival. Here, we report six patients with biallelic pathogenic variants in GCSH and a broad clinical spectrum ranging from neonatal fatal glycine encephalopathy to an attenuated phenotype of developmental delay, behavioral problems, limited epilepsy and variable movement problems. The mutational spectrum includes one insertion c.293-2&#95;293-1insT, one deletion c.122&#95;(228 + 1&#95;229-1) del, one duplication of exons 4 and 5, one nonsense variant p.Gln76*and four missense p.His57Arg, p.Pro115Leu and p.Thr148Pro and the previously described p.Met1?. Via functional studies in patient's fibroblasts, molecular modeling, expression analysis in GCSH knockdown COS7 cells and yeast, and in vitro protein studies, we demonstrate for the first time that most variants identified in our cohort produced a hypomorphic effect on both mitochondrial activities, protein lipoylation and glycine metabolism, causing combined deficiency, whereas some missense variants affect primarily one function only. The clinical features of the patients reflect the impact of the GCSH changes on any of the two functions analyzed. Our analysis illustrates the complex interplay of functional and clinical impact when pathogenic variants affect a multifunctional protein involved in two metabolic pathways and emphasizes the value of the functional assays to select the treatment and investigate new personalized options., (© The Author(s) 2022. Published by Oxford University Press.)

Hybrid rice requires adequate nitrogen (N) management in order to achieve good yields from its vegetative and reproductive development. With this backdrop, a field experiment was conducted at Regional Research Station (Coastal Saline Zone), Bidhan Chandra Krishi Viswavidyalaya, Kakdwip, West Bengal (India) to record growth and yield performance of hybrid rice (cv. PAN 2423) under varied N-fertilizer doses. A modelling approach was adopted for the first time in hybrid rice production system under coastal ecosystem of West Bengal (India). In the present study, the Agricultural Production Systems Simulator (APSIM) model was calibrated and validated for simulating a hybrid rice production system with different N rates. The APSIM based crop simulation model was found to capture the physiological changes of hybrid rice under varied N rates effectively. While studying the relationship between simulated and observed yield data, we observed that the equations developed by APSIM were significant with higher R 2 values (≥0.812). However, APSIM caused an over-estimation for calibrate data but it was rectified for validated data. The RMSE of models for all the cases was less than respective SD values and the normalized RMSE values were ≤20%. Hence, it was proved to be a good rationalized modelling and the performance of APSIM was robust. On the contrary, APSIM underestimated the calibrated amount of N (kg ha -1 ) in storage organ of hybrid rice, which was later rectified in case of validated data. A strong correlation existed between the observed and APSIM-simulated amounts of N in storage organ of hybrid rice (R 2 = 0.94** and 0.96** for the calibration and validation data sets, respectively), which indicates the robustness of the APSIM simulation study. Scenario analysis also suggests that the optimal N rate will increase from 160 to 200 kg N ha -1 for the greatest hybrid rice production in coming years under elevated CO 2 levels in the atmosphere. The APSIM-Oryza crop model had successfully predicted the variation in aboveground biomass and grain yield of hybrid rice under different climatic conditions., Competing Interests: Sukamal Sarkar is an Academic Editor for PeerJ., (© 2023 Sarkar et al.)

Background: High-Grade Serous Ovarian Carcinoma (HGSOC) is the most prevalent and lethal subtype of ovarian cancer, but has a paucity of clinically-actionable biomarkers due to high degrees of multi-level heterogeneity. Radiogenomics markers have the potential to improve prediction of patient outcome and treatment response, but require accurate multimodal spatial registration between radiological imaging and histopathological tissue samples. Previously published co-registration work has not taken into account the anatomical, biological and clinical diversity of ovarian tumours., Methods: In this work, we developed a research pathway and an automated computational pipeline to produce lesion-specific three-dimensional (3D) printed moulds based on preoperative cross-sectional CT or MRI of pelvic lesions. Moulds were designed to allow tumour slicing in the anatomical axial plane to facilitate detailed spatial correlation of imaging and tissue-derived data. Code and design adaptations were made following each pilot case through an iterative refinement process., Results: Five patients with confirmed or suspected HGSOC who underwent debulking surgery between April and December 2021 were included in this prospective study. Tumour moulds were designed and 3D-printed for seven pelvic lesions, covering a range of tumour volumes (7 to 133 cm 3 ) and compositions (cystic and solid proportions). The pilot cases informed innovations to improve specimen and subsequent slice orientation, through the use of 3D-printed tumour replicas and incorporation of a slice orientation slit in the mould design, respectively. The overall research pathway was compatible with implementation within the clinically determined timeframe and treatment pathway for each case, involving multidisciplinary clinical professionals from Radiology, Surgery, Oncology and Histopathology Departments., Conclusions: We developed and refined a computational pipeline that can model lesion-specific 3D-printed moulds from preoperative imaging for a variety of pelvic tumours. This framework can be used to guide comprehensive multi-sampling of tumour resection specimens., Competing Interests: MC-O: 52 North Health Ltd. employee and shareholder, GE HealthCare research support, GSK speakers’ bureau. JB: Tailor Bio co-founder, stock options, AstraZeneca consulting and advisory roles, honoraria, Clovis Oncology consulting and advisory roles, GSK honoraria, holder of patents TAm-Seq v2 method for ctDNA estimation; enhanced detection of target DNA by fragment size analysis; methods for predicting treatment response in cancers. ES: Lucida Medical co-founder and shareholder, GE HealthCare research support, speakers’ bureau, Canon research support, speakers’ bureau. 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 © 2023 Delgado-Ortet, Reinius, McCague, Bura, Woitek, Rundo, Gill, Gehrung, Ursprung, Bolton, Haldar, Pathiraja, Brenton, Crispin-Ortuzar, Jimenez-Linan, Escudero Sanchez and Sala.)

Chromosomal instability is a major challenge to patient stratification and targeted drug development for high-grade serous ovarian carcinoma (HGSOC). Here we show that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and methylation status. We identify five prevalent clonal driver SCNAs (chromosomal amplifications encompassing MYC, PIK3CA, CCNE1, KRAS and TERT) from multi-regional HGSOC data and reason that their strong selection should prioritise them as key biomarkers for targeted therapies. We use primary HGSOC spheroid models to test interactions between in vitro targeted therapy and SCNAs. MYC chromosomal copy number is associated with in-vitro and clinical response to paclitaxel and in-vitro response to mTORC1/2 inhibition. Activation of the mTOR survival pathway in the context of MYC-amplified HGSOC is statistically associated with increased prevalence of SCNAs in genes from the PI3K pathway. Co-occurrence of amplifications in MYC and genes from the PI3K pathway is independently observed in squamous lung cancer and triple negative breast cancer. In this work, we show that identifying co-occurrence of clonal driver SCNA genes could be used to tailor therapeutics for precision medicine., (© 2022. The Author(s).)

Supercapacitors have been achieving great interest in energy storage systems for the past couple of decades. Such devices with superior performance, mainly, depending on the material architecture of the electrodes. We report on the preparation of Tellurium nanotubes (Te-tubes diameter ∼100 nm and length ∼700 nm), with variable doping of conducting network reduced graphene oxide (rGO) to fabricate high-performance electrode characteristics of rGO @ Te. The prepared material was characterized using XRD, FTIR, FESEM, and Raman spectroscopy techniques, including Brunauer-Emmett-Teller, Barrett-Joyner-Halenda measurements. FTIR study revealed that 15% rGO @ Te has a wide C-O vibration band at ∼ 1,100-1,300 cm -1 , over other compositions. FESEM study shows the Te-tubes dispersion in rGO layers. The EDX study revealed that 15% of the composition has an optimistic concentration of C and O elements. In other compositions, either at lower/higher rGO concentration, an uneven count of C and O is observed. These support efficient charge dynamics to achieve superior ultra-capacitor characteristics, thereby achieving specific capacitance C sp 170 + F/g @ 10 mV/s in a symmetric configuration. The reported values are thirty times higher than pristine Te-tubes (∼5 F/g). This finding suggests that rGO @ Te is a promising candidate for supercapacitor., Competing Interests: The 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 Rani, Alegaonkar, Biswas, Jewariya, Kanta Haldar and Alegaonkar.)

Kabuki syndrome (KS) is a rare genetic disorder typically characterized by facial abnormalities, developmental delay, cognitive dysfunction, and organ impairment. In this report, fibroblast cells obtained from a KS patient containing a heterozygous KMT2D c.12592 C>T mutation (p.R4198X) were reprogrammed using non-integrative Sendai virus to generate three induced pluripotent stem cell (iPSC) clones. The iPSC lines retained the KS patient mutation, and displayed normal karyotypes, pluripotency marker expression, and the ability to differentiate into the three germ layers., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)

Emerging resistance to artemisinin drugs threatens the elimination of malaria. Resistance is widespread in South East Asia (SEA) and Myanmar. Neighboring Bangladesh, where 90% of infections occur in the Chittagong Hill Tracts (CHTs), lacks recent assessment. We undertook a prospective study in the sole district-level hospital in Bandarban, a CHT district with low population densities but 60% of reported malaria cases. Thirty patients presented with malaria in 2018. An increase to 68 patients in 2019 correlated with the district-level rise in malaria, rainfall, humidity, and temperature. Twenty-four patients (7 in 2018 and 17 in 2019) with uncomplicated Plasmodium falciparum monoinfection were assessed for clearing parasites after starting artemisinin combination therapy (ACT). The median (range) time to clear half of the initial parasites was 5.6 (1.5 to 9.6) h, with 20% of patients showing a median of 8 h. There was no correlation between parasite clearance and initial parasitemia, blood cell counts, or mutations of P. falciparum gene Pfkelch13 (the molecular marker of artemisinin resistance [AR]). The in vitro ring-stage survival assay (RSA) revealed one (of four) culture-adapted strains with a quantifiable resistance of 2.01% ± 0.1% (mean ± standard error of the mean [SEM]). Regression analyses of in vivo and in vitro measurements of the four CHT strains and WHO-validated K13 resistance mutations yielded good correlation ( R 2 = 0.7; ρ = 0.9, P  < 0.005), strengthening evaluation of emerging AR with small sample sizes, a challenge in many low/moderate-prevalence sites. There is an urgent need to deploy multiple, complementary approaches to understand the evolutionary dynamics of the emergence of P. falciparum resistant to artemisinin derivatives in countries where malaria is endemic. IMPORTANCE Malaria elimination is a Millennium Development Goal. Artemisinins, fast-acting antimalarial drugs, have played a key role in malaria elimination. Emergence of artemisinin resistance threatens the global elimination of malaria. Over the last decade, advanced clinical and laboratory methods have documented its spread throughout South East Asia and Myanmar. Neighboring Bangladesh lies in the historical path of dissemination of antimalarial resistance to the rest of the world, yet it has not been evaluated by combinations of leading methods, particularly in the highland Chittagong Hill Tracts adjacent to Myanmar which contain >90% of malaria in Bangladesh. We show the first establishment of capacity to assess clinical artemisinin resistance directly in patients in the hilltops and laboratory adaptation of Bangladeshi parasite strains from a remote, sparsely populated malaria frontier that is responsive to climate. Our study also provides a generalized model for comprehensive monitoring of drug resistance for countries where malaria is endemic.