Evaluation of the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in infantile epilepsy (Gene-STEPS): an international, multicentre, pilot cohort study

BACKGROUND: Most neonatal and infantile-onset epilepsies have presumed genetic aetiologies, and early genetic diagnoses have the potential to inform clinical management and improve outcomes. We therefore aimed to determine the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in this population. METHODS: We conducted an international, multicentre, cohort study (Gene-STEPS), which is a pilot study of the International Precision Child Health Partnership (IPCHiP). IPCHiP is a consortium of four paediatric centres with tertiary-level subspecialty services in Australia, Canada, the UK, and the USA. We recruited infants with new-onset epilepsy or complex febrile seizures from IPCHiP centres, who were younger than 12 months at seizure onset. We excluded infants with simple febrile seizures, acute provoked seizures, known acquired cause, or known genetic cause. Blood samples were collected from probands and available biological parents. Clinical data were collected from medical records, treating clinicians, and parents. Trio genome sequencing was done when both parents were available, and duo or singleton genome sequencing was done when one or neither parent was available. Site-specific protocols were used for DNA extraction and library preparation. Rapid genome sequencing and analysis was done at clinically accredited laboratories, and results were returned to families. We analysed summary statistics for cohort demographic and clinical characteristics and the timing, diagnostic yield, and clinical impact of rapid genome sequencing. FINDINGS: Between Sept 1, 2021, and Aug 31, 2022, we enrolled 100 infants with new-onset epilepsy, of whom 41 (41%) were girls and 59 (59%) were boys. Median age of seizure onset was 128 days (IQR 46-192). For 43 (43% [binomial distribution 95% CI 33-53]) of 100 infants, we identified genetic diagnoses, with a median time from seizure onset to rapid genome sequencing result of 37 days (IQR 25-59). Genetic diagnosis was associated with neonatal seizure onset versus infantile seizure onset (14 [74%] of 19 vs 29 [36%] of 81; p=0·0027), referral setting (12 [71%] of 17 for intensive care, 19 [44%] of 43 non-intensive care inpatient, and 12 [28%] of 40 outpatient; p=0·0178), and epilepsy syndrome (13 [87%] of 15 for self-limited epilepsies, 18 [35%] of 51 for developmental and epileptic encephalopathies, 12 [35%] of 34 for other syndromes; p=0·001). Rapid genome sequencing revealed genetic heterogeneity, with 34 unique genes or genomic regions implicated. Genetic diagnoses had immediate clinical utility, informing treatment (24 [56%] of 43), additional evaluation (28 [65%]), prognosis (37 [86%]), and recurrence risk counselling (all cases). INTERPRETATION: Our findings support the feasibility of implementation of rapid genome sequencing in the clinical care of infants with new-onset epilepsy. Longitudinal follow-up is needed to further assess the role of rapid genetic diagnosis in improving clinical, quality-of-life, and economic outcomes. FUNDING: American Academy of Pediatrics, Boston Children's Hospital Children's Rare Disease Cohorts Initiative, Canadian Institutes of Health Research, Epilepsy Canada, Feiga Bresver Academic Foundation, Great Ormond Street Hospital Charity, Medical Research Council, Murdoch Children's Research Institute, National Institute of Child Health and Human Development, National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre, One8 Foundation, Ontario Brain Institute, Robinson Family Initiative for Transformational Research, The Royal Children's Hospital Foundation, University of Toronto McLaughlin Centre

Process intensification education contributes to sustainable development goals: Part 2

Achieving the United Nations sustainable development goals requires industry and society to develop tools and processes that work at all scales, enabling goods delivery, services, and technology to large conglomerates and remote regions. Process Intensification (PI) is a technological advance that promises to deliver means to reach these goals, but higher education has yet to totally embrace the program. Here, we present practical examples on how to better teach the principles of PI in the context of the Bloom's taxonomy and summarise the current industrial use and the future demands for PI, as a continuation of the topics discussed in Part 1. In the appendices, we provide details on the existing PI courses around the world, as well as teaching activities that are showcased during these courses to aid students’ lifelong learning. The increasing number of successful commercial cases of PI highlight the importance of PI education for both students in academia and industrial staff.We acknowledge the sponsors of the Lorentz’ workshop on“Educating in PI”: The MESA+Institute of the University of Twente,Sonics and Materials (USA) and the PIN-NL Dutch Process Intensi-fication Network. DFR acknowledges support by The Netherlands Centre for Mul-tiscale Catalytic Energy Conversion (MCEC), an NWO Gravitationprogramme funded by the Ministry of Education, Culture and Sci-ence of the government of The Netherlands. NA acknowledges the Deutsche Forschungsgemeinschaft (DFG)- TRR 63¨Integrierte Chemische Prozesse in flüssigen Mehrphasen-systemen¨(Teilprojekt A10) - 56091768. The participation by Robert Weber in the workshop and thisreport was supported by Laboratory Directed Research and Devel-opment funding at Pacific Northwest National Laboratory (PNNL).PNNL is a multiprogram national laboratory operated for theUS Department of Energy by Battelle under contract DE-AC05-76RL0183

Association of Marek's Disease induced immunosuppression with activation of a novel regulatory T cells in chickens.

Marek’s Disease Virus (MDV) is an alphaherpesvirus that infects chickens, transforms CD4+ T cells and causes deadly lymphomas. In addition, MDV induces immunosuppression early during infection by inducing cell death of the infected lymphocytes, and potentially due to activation of regulatory T (Treg)-cells. Furthermore, immunosuppression also occurs during the transformation phase of the disease; however, it is still unknown how the disease can suppress immune response prior or after lymphoma formation. Here, we demonstrated that chicken TGF-beta+ Treg cells are found in different lymphoid tissues, with the highest levels found in the gut-associated lymphoid tissue (cecal tonsil: CT), fostering an immune-privileged microenvironment exerted by TGF-beta. Surprisingly, significantly higher frequencies of TGF-beta+ Treg cells are found in the spleens of MDV-susceptible chicken lines compared to the resistant line, suggesting an association between TGF-beta+ Treg cells and host susceptibility to lymphoma formation. Experimental infection with a virulent MDV elevated the levels of TGF-beta+ Treg cells in the lungs as early as 4 days post infection, and during the transformation phase of the disease in the spleens. In contrast to TGF-beta+ Treg cells, the levels of CD4+CD25+ T cells remained unchanged during the infection and transformation phase of the disease. Furthermore, our results demonstrate that the induction of TGF-beta+ Treg cells is associated with pathogenesis of the disease, as the vaccine strain of MDV did not induce TGF-beta+ Treg cells. Similar to human haematopoietic malignant cells, MDV-induced lymphoma cells expressed high levels of TGF-beta but very low levels of TGF-beta receptor I and II genes. The results confirm that COX-2/ PGE2 pathway is involved in immunosuppression induced by MDV-lymphoma cells. Taken together, our results revealed a novel TGF-beta+ Treg subset in chickens that is activated during MDV infection and tumour formation.Biotechnology and Biological Sciences Research Counci

1,25-Dihydroxyvitamin D3 modulates the phenotype and function of Monocyte derived dendritic cells in cattle

Abstract Background The active form of the vitamin D3, 1,25-Dihydroxyvitamin D3 (1,25-(OH)2D3) has been shown to have major effects not only on physiological processes but also on the regulation of the immune system of vertebrates. Dendritic cells are specialised antigen presenting cells which are in charge of the initiation of T-cell dependant immune responses and as such are key regulators of responses towards pathogens. In this study we set out to evaluate the effects of 1,25-(OH)2D3 on the phenotype of cattle monocyte-derived dendritic cells (MoDCs) and how the conditioning with this vitamin affects the function of these myeloid cells. Results MoDCs were generated from CD14+ monocytes with bovine IL-4 and GM-CSF with or without 1,25-(OH)2D3 supplementation for 10 days. Vitamin D conditioned MoDCs showed a reduced expression of co-stimulatory and antigen presenting molecules, as well as a reduced capability of endocytose ovalbumin. Furthermore, the capacity of MoDCs to induce proliferation in an allogeneic mixed leukocyte reaction was abolished when MoDCs were generated in presence of 1,25-(OH)2D3. LPS induced maturation of 1,25-(OH)2D3conditioned MoDCs resulted in lower secretion of IL-12 and higher IL-10 than that observed in MoDCs. Conclusions The typical immunotolerant phenotype observed in cattle DCs after exposure to 1,25-(OH)2D3 has a significant effect on the functionality of these immune cells, inhibiting the T-cell stimulatory capacity of MoDCs. This could have profound implications on how the bovine immune system deals with pathogens, particularly in diseases such as tuberculosis or paratuberculosis

Process intensification education contributes to sustainable development goals : part 1

In 2015 all the United Nations (UN) member states adopted 17 sustainable development goals (UN-SDG) as part of the 2030 Agenda, which is a 15-year plan to meet ambitious targets to eradicate poverty, protect the environment, and improve the quality of life around the world. Although the global community has progressed, the pace of implementation must accelerate to reach the UN-SDG time-line. For this to happen, professionals, institutions, companies, governments and the general public must become cognizant of the challenges that our world faces and the potential technological solutions at hand, including those provided by chemical engineering. Process intensification (PI) is a recent engineering approach with demonstrated potential to significantly improve process efficiency and safety while reducing cost. It offers opportunities for attaining the UN-SDG goals in a cost-effective and timely manner. However, the pedagogical tools to educate undergraduate, graduate students, and professionals active in the field of PI lack clarity and focus. This paper sets out the state-of-the-art, main discussion points and guidelines for enhanced PI teaching, deliberated by experts in PI with either an academic or industrial background, as well as representatives from government and specialists in pedagogy gathered at the Lorentz Center (Leiden, The Netherlands) in June 2019 with the aim of uniting the efforts on education in PI and produce guidelines. In this Part 1, we discuss the societal and industrial needs for an educational strategy in the framework of PI. The terminology and background information on PI, related to educational implementation in industry and academia, are provided as a preamble to Part 2, which presents practical examples that will help educating on Process Intensification

Suspended SOI waveguide with sub-wavelength grating cladding for mid-infrared

We present a new type of mid-infrared silicon-on-insulator (SOI) waveguide. The waveguide comprises a sub-wavelength lattice of holes acting as lateral cladding while at the same time allowing for the bottom oxide (BOX) removal by etching. The waveguide loss is determined at the wavelength of 3.8 µm for structures before and after being underetched using both vapor phase and liquid hydrofluoric acid (HF). A propagation loss of 3.4 dB/cm was measured for a design with a 300 nm grating period and 150 nm holes after partial removal (560 nm) of BOX by vapor phase HF etching. We also demonstrate an alternative design with 550 nm period and 450 nm holes, which allows a faster and complete removal of the BOX by liquid phase HF etching, yielding the waveguide propagation loss of 3.6 dB/cm