Development of methods for combinational approaches to cis-regulatory module interactions

The complexity and size of the higher animal genome and relative scarcity of DNA-binding factors with which to regulate it imply a complex and pleiotropic regulatory system. Cisregulatory modules (CRMs) are vitally important regulators of gene expression in higher animal cells, integrating external and internal information to determine an appropriate response in terms of gene expression by means of direct and indirect interactions with the transcriptional machinery. The interaction space available within systems of multiple CRMs, each containing several sites where one or more factors could be bound is huge. Current methods of investigation involve the removal of individual sites or factors and measuring the resulting effect on gene expression. The effects of investigations of this type may be masked by the functional redundancy present in some of these regulatory systems as a result of their evolutionary development. The investigation of CRM function is limited by a lack of technology to generate and analyse combinatorial mutation libraries of CRMs, where putative transcription factor binding sites are mutated in various combinations to achieve a holistic view of how the factors binding to those sites cooperate to bring about CRM function. The principle work of this thesis is the generation of such a library. This thesis presents the development of microstereolithography as a method for making microfluidic devices, both directly and indirectly. A microfluidic device was fabricated that was used to generate oligonucleotide mixtures necessary to synthesise combinatorial mutants of a CRM sequence from the muscle regulatory factor MyoD. In addition, this thesis presents the development of the optimisation algorithms and assembly processes necessary for successful sequence assembly. Furthermore, it was found that the CRM, in combination with other CRMs, is able to synergistically regulate gene expression in a position and orientation independent manner in three separate contexts. Finally, by testing a small portion of the available combinatorial mutant library it was shown that mutation of individual binding sites within of the CRM is not sufficient to show a significant change in the level of reporter gene expression

Assessment of thermally stabilized electrospun poly(vinyl alcohol) materials as cell permeable membranes for a novel blood salvage device

The use of Intraoperative Cell Salvage (ICS) is currently limited in oncological surgeries, due to safety concerns associated with the ability of existing devices to successfully remove circulating tumour cells. In this work, we present the first stages towards the creation of an alternative platform to current cell savers, based on the extremely selective immunoaffinity membrane chromatography principle. Non-woven membranes were produced via electrospinning using poly(vinyl alcohol) (PVA), and further heat treated at 180 °C to prevent their dissolution in aqueous environments and preserve their fibrous morphology. The effects of the PVA degree of hydrolysis (DH) (98 % vs 99 %), method of electrospinning (needleless DC vs AC), and heat treatment duration (1-8 h) were investigated. All heat treated supports maintained their cytocompatibility, whilst tensile tests indicated that the 99 % hydrolysed DC electrospun mats were stronger compared to their 98 % DH counterparts. Although, and at the described conditions, AC electrospinning produced fibres with more than double the diameter compared to those from DC electrospinning, it was not chosen for subsequent experiments because it is still under development. Evidence of unimpeded passage of SY5Y neuroblastoma cells and undiluted defibrinated sheep's blood in flow-through filtration experiments confirmed the successful creation of 3D networks with minimum resistance to mass transfer and lack of non-specific cell binding to the base material, paving the way for the development of novel, highly selective ICS devices for tumour surgeries

National Institutes of Health Stroke Scale: An Alternative Primary Outcome Measure for Trials of Acute Treatment for Ischemic Stroke

Background and Purpose- The modified Rankin Scale (mRS) at 3 months is the most commonly used primary outcome measure in stroke treatment trials, but it lacks specificity and requires long-term follow-up interviews, which consume time and resources. An alternative may be the National Institutes of Health Stroke Scale (NIHSS), early after stroke. Our aim was to evaluate whether the NIHSS assessed within 1 week after treatment could serve as a primary outcome measure for trials of acute treatment for ischemic stroke. Methods- We used data from 2 randomized controlled trials of endovascular treatment for ischemic stroke: the positive MR CLEAN (Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands; N=500) and the neutral IMS (Interventional Management of Stroke) III trial (N=656). We used a causal mediation model, with linear and ordinal logistic regression adjusted for confounders, to evaluate the NIHSS 24 hours and 5 to 7 days after endovascular treatment as primary outcome measures (instead of the mRS at 3 months) in both trials. Patients who had died before the NIHSS was assessed received the maximum score of 42. NIHSS+1 was then log10-transformed. Results- In both trials, there was a significant correlation between the NIHSS at 24 hours and 5 to 7 days and the mRS. In MR CLEAN, we found a significant effect of endovascular treatment on the mRS and on the NIHSS at 24 hours and 5 to 7 days. After adjustment for NIHSS at 24 hours and 5 to 7 days, the effect of endovascular treatment on the mRS decreased from common odds ratio 1.68 (95% CI, 1.22-2.32) to respectively 1.36 (95% CI, 0.97-1.91) and 1.24 (95% CI, 0.87-1.79), indicating that treatment effect on the mRS is in large part mediated by the NIHSS. In the IMS III trial there was no treatment effect on the NIHSS at 24 hours and 5 to 7 days, corresponding with the absence of a treatment effect on the mRS. Conclusions- The NIHSS within 1 week satisfies the requirements for a surrogate end point and may be used as a primary outcome measure in trials of acute treatment for ischemic stroke, particularly in phase II(b) trials. This could reduce stroke-outcome assessment to its essentials (ie, neurological deficit), and reduce trial duration and costs. Whether and under which conditions it could be used in phase III trials requires a debate in the field with all parties. Clinical Trial Registration- URL: http://www.isrctn.com. Unique identifier: ISRCTN10888758; https://www.clinicaltrials.gov. Unique identifier: NCT00359424

National Institutes of Health Stroke Scale An Alternative Primary Outcome Measure for Trials of Acute Treatment for Ischemic Stroke

Background and Purpose- The modified Rankin Scale (mRS) at 3 months is the most commonly used primary outcome measure in stroke treatment trials, but it lacks specificity and requires long-term follow-up interviews, which consume time and resources. An alternative may be the National Institutes of Health Stroke Scale (NIHSS), early after stroke. Our aim was to evaluate whether the NIHSS assessed within 1 week after treatment could serve as a primary outcome measure for trials of acute treatment for ischemic stroke. Methods- We used data from 2 randomized controlled trials of endovascular treatment for ischemic stroke: the positive MR CLEAN (Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands; N=500) and the neutral IMS (Interventional Management of Stroke) III trial (N=656). We used a causal mediation model, with linear and ordinal logistic regression adjusted for confounders, to evaluate the NIHSS 24 hours and 5 to 7 days after endovascular treatment as primary outcome measures (instead of the mRS at 3 months) in both trials. Patients who had died before the NIHSS was assessed received the maximum score of 42. NIHSS+1 was then log10-transformed. Results- In both trials, there was a significant correlation between the NIHSS at 24 hours and 5 to 7 days and the mRS. In MR CLEAN, we found a significant effect of endovascular treatment on the mRS and on the NIHSS at 24 hours and 5 to 7 days. After adjustment for NIHSS at 24 hours and 5 to 7 days, the effect of endovascular treatment on the mRS decreased from common odds ratio 1.68 (95% CI, 1.22-2.32) to respectively 1.36 (95% CI, 0.97-1.91) and 1.24 (95% CI, 0.87-1.79), indicating that treatment effect on the mRS is in large part mediated by the NIHSS. In the IMS III trial there was no treatment effect on the NIHSS at 24 hours and 5 to 7 days, corresponding with the absence of a treatment effect on the mRS. Conclusions- The NIHSS within 1 week satisfies the requirements for a surrogate end point and may be used as a primary outcome measure in trials of acute treatment for ischemic stroke, particularly in phase II(b) trials. This could reduce stroke-outcome assessment to its essentials (ie, neurological deficit), and reduce trial duration and costs. Whether and under which conditions it could be used in phase III trials requires a debate in the field with all parties. Clinical Trial Registration- URL: http://www.isrctn.com. Unique identifier: ISRCTN10888758; https://www.clinicaltrials.gov. Unique identifier: NCT00359424.</p

Lineage Abundance Estimation for SARS-CoV-2 in Wastewater Using Transcriptome Quantification Techniques

Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable

US Cosmic Visions: New Ideas in Dark Matter 2017: Community Report

This white paper summarizes the workshop "U.S. Cosmic Visions: New Ideas in Dark Matter" held at University of Maryland on March 23-25, 2017.Comment: 102 pages + reference

Eine Einführung in die Inverted-Classroom-Methode in der medizinischen Ausbildung

Zielgruppe: Der Workshop richtet sich an alle Personen, die sich für die Inverted Classroom Methode(ICM) interessieren und diese ggf. für eigene Lehrprojekte anwenden möchten Lernziele: Ziel des Workshops ist es, die Teilnehmer zu befähigen, die ICM auf die eigene Lehre anzuwenden. Inhalt: Der Workshop gibt eine Einführung in die ICM, skizziert ihre Vor- und Nachteile unter Einbeziehung aktueller Forschungsergebnisse und vermittelt praktische Fertigkeiten, um eigene Konzept für die Lehre entwickeln zu können. Dabei werden zusätzlich Themen wie Video-und Screencasterstellung, Open Educational Resources und Urheberrechte skizziert. Ablauf: Der Workshop selbst ist nach der ICM konzipiert. Das bedeutet, dass sich die Teilnehmer bereits im Vorfeld in einer Online-Phase das notwendige Faktenwissen aneignen, um in der Präsenzphase das erlernte Wissen in Kleingruppen anzuwenden und ICM-Konzepte für die eigene Lehre zu entwickeln. Diese Konzepte werden am Ende in der Gruppe vorgestellt und diskutier

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Fabrication of a single sub-micron pore spanning a single crystal (100) diamond membrane and impact on particle translocation

The fabrication of sub-micron pores in single crystal diamond membranes, which span the entirety of the membrane, is described for the first time, and the translocation properties of polymeric particles through the pore investigated. The pores are produced using a combination of laser micromachining to form the membrane and electron beam induced etching to form the pore. Single crystal diamond as the membrane material, has the advantages of chemical stability and durability, does not hydrate and swell, has outstanding electrical properties that facilitate fast, low noise current-time measurements and is optically transparent for combined optical-conductance sensing. The resulting pores are characterized individually using both conductance measurements, employing a microcapillary electrochemical setup, and electron microscopy. Proof-of-concept experiments to sense charged polystyrene particles as they are electrophoretically driven through a single diamond pore are performed, and the impact of this new pore material on particle translocation is explored. These findings reveal the potential of diamond as a platform for pore-based sensing technologies and pave the way for the fabrication of single nanopores which span the entirety of a diamond membrane