Abstract Abstract Trypanothione is the primary thiol redox carrier in Trypanosomatids whose biosynthesis and utilization pathways contain unique enzymes that include suitable drug targets against the human parasites in this family. Overexpression of the rate-limiting enzyme, γ-glutamylcysteine synthetase (GSH1), can increase the intracellular concentration of trypanothione. Melarsoprol directly inhibits trypanothione and has predicted the effects on downstream redox biology, including ROS management and dNTP synthesis that require further investigation. Thus, we hypothesized that melarsoprol treatment would inhibit DNA synthesis, which was tested using BrdU incorporation assays and cell cycle analyses. In addition, we analysed the effects of eflornithine, which interfaces with the trypanothione pathway, fexinidazole, because of the predicted effects on DNA synthesis, and pentamidine as an experimental control. We found that melarsoprol treatment resulted in a cell cycle stall and a complete inhibition of DNA synthesis within 24 h, which were alleviated by GSH1 overexpression. In contrast, the other drugs analysed had more subtle effects on DNA synthesis that were not significantly altered by GSH1 expression. Together these findings implicate DNA synthesis as a therapeutic target that warrants further investigation in the development of antitrypanosomal drugs.

Objective: Airway foreign bodies are the leading cause of infantile deaths and fourth among preschool children. Airway foreign bodies in extremely premature neonates represent a rare but potentially lethal entity. There are very few reports in the literature describing the treatment of such a condition in premature neonates. The objectives of this report are to describe the safe removal of an airway foreign body in an extremely premature infant using urologic instruments in a trans-endotracheal tube fashion and to review the literature for other techniques that have proven safe and effective, thereby adding technical options for future cases. Methods: We reviewed the case reported and reviewed pertinent literature. Results: A 2-week old, ex-24 3/7-week, 820-g pre-mature infant was intubated with a 2.5 endotracheal tube. After intubation, a 2-cm foreign body was discovered in the distal trachea by chest x-ray. The child's respiratory status continuously deteriorated with increasing oxygen and positive pressure requirements. While remaining intubated, the child underwent direct suspension laryngoscopy, the ventilator circuitry was disconnected, and the object was successfully removed using a 1.2 mm rigid ureteroscope and 1.1 mm grasping forceps through the 2.5 endotracheal tube. Conclusion: This case report demonstrates the effectiveness of using a 1.2 mm ureteroscope and 1.2 mm urologic graspers to extract an airway foreign body from an extremely premature neonate through an endotracheal tube without paralyzing the patient. This method provides a safe and effective means of visualizing and, if necessary, manipulating the airway in a population prone to respiratory complications.

Cellular processes, including differentiation, proliferation, and migration, have been linked to the alignment (anisotropy) and orientation (directionality) of collagen fibers in the native extracellular matrix (ECM). Given the critical role that biophysical cell-matrix interactions play in regulating biological functions, several microfluidic-based methods have been used to establish 3D collagen gels with defined fiber properties; these gels have helped to establish quantitative relationships between structural ECM cues and observed cell responses. Although existing microfluidic fabrication methods provide excellent definition over collagen fiber anisotropy, they have not demonstrated the independent control over fiber anisotropy and directionality necessary to replicate in vivo collagen architecture. Therefore, to advance collagen microengineering capabilities, we present a user-friendly technology platform that uses controlled fluid flows within a non-uniform microfluidic channel network to create collagen landscapes that can be tuned as a function of extensional strain rate. Herein, we demonstrate capabilities to i) control the degree of fiber anisotropy, ii) create spatial gradients in fiber anisotropy, iii) independently define fiber directionality, and iv) generate multi-material interfaces within a 3D environment. We then address the practical issue of integrating cells into microfluidic systems by using a peel-off template technique to provide direct access to microengineered collagen gels, and demonstrate that cells respond to the defined properties of the landscape. Finally, the platform's modular capability is highlighted by integrating a sub-micrometer thick porous parylene membrane onto the microengineered collagen as a method to define cell-substrate interactions.

Trypanothione is the primary thiol redox carrier in Trypanosomatids whose biosynthesis and utilization pathways contain unique enzymes that include suitable drug targets against the human parasites in this family. Overexpression of the rate-limiting enzyme, γ-glutamylcysteine synthetase (GSH1), can increase the intracellular concentration of trypanothione. Melarsoprol directly inhibits trypanothione and has predicted the effects on downstream redox biology, including ROS management and dNTP synthesis that require further investigation. Thus, we hypothesized that melarsoprol treatment would inhibit DNA synthesis, which was tested using BrdU incorporation assays and cell cycle analyses. In addition, we analysed the effects of eflornithine, which interfaces with the trypanothione pathway, fexinidazole, because of the predicted effects on DNA synthesis, and pentamidine as an experimental control. We found that melarsoprol treatment resulted in a cell cycle stall and a complete inhibition of DNA synthesis within 24 h, which were alleviated by GSH1 overexpression. In contrast, the other drugs analysed had more subtle effects on DNA synthesis that were not significantly altered by GSH1 expression. Together these findings implicate DNA synthesis as a therapeutic target that warrants further investigation in the development of antitrypanosomal drugs.

ABSTRACTFibrillar collagens are structural proteins in the extracellular matrix (ECM), and cellular processes, including differentiation, proliferation, and migration, have been linked to the orientation (directionality) and alignment (anisotropy) of collagen fibers. Given the importance of cell-substrate interactions in driving biological functions, several microfluidic approaches have demonstrated three-dimensional (3D) collagen gels with defined fiber properties that enable quantitative correlations between structural cues and observed cell responses. Although existing methods provide excellent definition over collagen fiber anisotropy, independent control over both anisotropy and directionality (that we collectively refer to as the collagen landscape) has not been demonstrated. Therefore, to advance collagen microengineering capabilities, we present a user-friendly approach that uses controlled fluid flows within a non-uniform microfluidic channel network to create well-defined collagen landscapes. We demonstrate capabilities including i) control over fiber anisotropy, ii) spatial gradients in fiber anisotropy, iii) defined fiber directionality, and iv) multi-material interfaces. We then show that cells respond to the microengineered topographic cues by aligning along the anisotropy domains and following fiber directionality. Finally, this platform’s modular capability is demonstrated by integrating an ultrathin porous parylene (UPP) membrane on the microengineered collagen as a mask to control cell-substrate interactions.

Objectives/HypothesisObstructive sleep apnea (OSA) and sickle cell disease (SCD) represent two complex disease processes. Current guidelines recommend that children with SCD receive polysomnography (PSG) after presenting with signs or symptoms of sleep‐disordered breathing (SDB). Recent studies suggest a disproportionately elevated prevalence of SDB in the population of children with SCD, and traditional risk factors may not be evident within these patients. Further objective testing might be needed to screen all pediatric patients with SCD, even in the absence of overt signs or symptoms of OSA to prevent complications of both conditions.Study DesignProspective cohort study.MethodsInstitutional review board approval was obtained. An eight‐question OSA risk assessment screening questionnaire was presented prospectively to 100 consecutive patients with SCD in the pediatric hematology clinic regardless of complaints of SDB.ResultsOut of 100 patients, 51 were female. The average age, body mass index (BMI), BMI percentile, and I'M SLEEPY score of the entire cohort were 3.97 years, 15.97%, 55.4%, and 1.63%, respectively. Nineteen patients had a positive sleep apnea screening score and were referred for PSG. The average age BMI, BMI percentile, and I'M SLEEPY score for those 19 patients were 3.77%, 16.67%, 65%, and 3.95%, respectively. Ten patients completed PSG, with seven diagnosed with OSA.ConclusionsThis pilot study demonstrates a higher incidence of SDB and OSA in children with SCD relative to the general pediatric population. Although more PSG reports and further testing is needed to determine whether the results hold, preliminary data indicate that children with SCD should at least undergo OSA screening in the office regardless of overt symptoms.Level of Evidence3 Laryngoscope, 131:E1022–E1028, 2021

Trypanosomatid parasites threaten the health of more than 1 billion people worldwide. Because their genomes are highly diverged from those of well-established eukaryotes, conservation is not always useful in assigning gene functions. However, it is precisely among the trypanosomatid-specific genes that ideal therapeutic targets might be found. Forward genetics approaches are an effective way to identify novel gene functions. We used an ORFeome approach to clone a large percentage of Trypanosoma brucei genes and generate a gain-of-function parasite library. This library was used in a genetic screen to identify genes that promote resistance to the clinically significant yet highly toxic drug melarsoprol. Hits arising from the screen demonstrated the library’s usefulness in identifying known pathways and uncovered novel aspects of resistance mediated by proteins localized to the flagellum and mitochondrion. The powerful new genetic tools generated herein are expected to promote advances in trypanosomatid biology and therapeutic development in the years to come.

Trypanosoma brucei is an early branching protozoan that causes Human and Animal African Trypanosomiasis. Forward genetics approaches are powerful tools for uncovering novel aspects of Trypanosomatid biology, pathogenesis, and therapeutic approaches against trypanosomiasis. Here we have generated a T. brucei ORFeome consisting of over 90% of the targeted genome and used it to make an inducible Gain-of-Function library for broadly applicable forward genetic screening. Using a critical drug of last resort, melarsoprol, we conducted a proof of principle genetic screen. Hits arising from this screen support the significance of trypanothione, a key player in redox metabolism, as a target of melarsoprol and implicate novel proteins of the flagellum and mitochondria in drug resistance. This study has produced two powerful new genetic tools for kinetoplastida research, which are expected to promote major advances in kinetoplastida biology and therapeutic development in the years to come.

Computational models are powerful tools for investigating brain function in health and disease. However, biologically detailed neuronal and circuit models are complex and implemented in a range of specialized languages, making them inaccessible and opaque to many neuroscientists. This has limited critical evaluation of models by the scientific community and impeded their refinement and widespread adoption. To address this, we have combined advances in standardizing models, open source software development and web technologies to develop Open Source Brain, a platform for visualizing, simulating, disseminating and collaboratively developing standardized models of neurons and circuits from a range of brain regions. Model structure and parameters can be visualized and their dynamical properties explored through browser-controlled simulations, without writing code. Open Source Brain makes neural models transparent and accessible and facilitates testing, critical evaluation and refinement, thereby helping to improve the accuracy and reproducibility of models, and their dissemination to the wider community.

Objectives: Velopharyngeal insufficiency (VPI) may be due to functional or anatomic causes, and can lead to speech deficits, communication difficulty, and emotional strain on patients and their caregivers. The VPI Effects on Life Outcomes (VELO) instrument quantifies quality of life outcomes in VPI patients both before and after VPI surgery. This study aims to identify pre-operative patient characteristics associated with better post-operative quality of life. Methods: This study is a retrospective chart review of 51 patients who underwent VPI surgery between 2009 and 2018 at a tertiary free-standing children's hospital. A 26-item parent-proxy VELO questionnaire was administered by telephone to parents to assess their child's quality of life post-VPI surgery. Results: Twenty-seven parents responded to the VELO questionnaire. Average post-operative VELO score was significantly higher in non-syndromic patients as compared with syndromic patients. Average post-operative VELO score was not significantly different between patients with and without submucous cleft (SMC) or those with mild to moderate versus severe pre-operative hypernasality. On multivariate analysis, absence of genetic syndrome, lack of submucous cleft, and presence of severe-pre-operative hypernasality were significantly and positively associated with increased post-operative VELO scores. Conclusion: Children who undergo VPI surgery are more likely to have better post-operative quality of life outcomes if their VPI was not associated with a genetic syndrome or submucous cleft. Non-syndromic and non-SMC patients with severe pre-operative hypernasality may benefit significantly from VPI surgery and have improved post-operative quality of life.

The OpenWorm project has the ambitious goal of producing a highly detailed in silico model of the nematode Caenorhabditis elegans A crucial part of this work will be a model of the nervous system encompassing all known cell types and connections. The appropriate level of biophysical detail required in the neuronal model to reproduce observed high-level behaviours in the worm has yet to be determined. For this reason, we have developed a framework, c302, that allows different instances of neuronal networks to be generated incorporating varying levels of anatomical and physiological detail, which can be investigated and refined independently or linked to other tools developed in the OpenWorm modelling toolchain.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.

“Gröbner Bases Theory” & Ontology could be implemented as explained An Insight into Higher Order Logic (HOL) based Ontology Neuroinformatics Framework by Considering Ontology Oriented Concepts & Language/s based on HOL/Grobner Bases/Scala/Jikes RVM/JVM Technologies/IoT Computing Environments. keywords : explained in the abstract/title itself. **** Readers Please make a note : This communication is written in free style.No particular format was followed.Intended for rapid publication.

It has been 30 years since the 'mind of the worm' was published in Philosophical Transactions B (White et al 1986 Phil. Trans. R. Soc. Lond. B314, 1-340). Predicting Caenorhabditis elegans' behaviour from its wiring diagram has been an enduring challenge since then. This special theme issue of Philosophical Transactions B combines research from neuroscientists, physicists, mathematicians and engineers to discuss advances in neural activity imaging, behaviour quantification and multiscale simulations, and how they are bringing the goal of whole-animal modelling at cellular resolution within reach.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.

To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system-based simulation engine known as Sibernetic, which implements the smoothed particle-hydrodynamics algorithm. The model includes an elastic body-wall cuticle subject to hydrostatic pressure. This cuticle is then driven by body-wall muscle cells that contract and relax, whose positions and shape are mapped from C. elegans anatomy, and determined from light microscopy and electron micrograph data. We show that by using different muscle activation patterns, this model is capable of producing C. elegans-like behaviours, including crawling and swimming locomotion in environments with different viscosities, while fitting multiple additional known biomechanical properties of the animal. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.

The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization working towards an integrative simulation of the nematode Caenorhabditis elegans, with the aim of providing a powerful new tool to understand how the organism's behaviour arises from its fundamental biology. In this perspective, we give an overview of the history and philosophy of OpenWorm, descriptions of the constituent sub-projects and corresponding open-science management practices, and discuss current achievements of the project and future directions. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.

We simulate C. elegans’ forward crawling with a cell network composed of the AVB interneuron pair, 18 B-type and 19 D-type motorneurons and 95 body muscles, considering three key hypotheses; I. AVB interneurons get activated from their upstream neurons, and excite B-type motor neurons. II. Simultaneously, a central pattern generator (CPG) in the head, produces periodic stimuli for the B-type motorneuron network. Input stimuli from the CPG is injected into the first dorsal and ventral motor neurons (DB01 and VB01). These signals then propagate in a coordinated manner through the rest of the B-type motorneurons. III. At the same time, a proprioceptive feedback function is assumed amongst B-type motorneurons that establishes synchronized traveling waves in the muscles. Simulation of the cell network and the worm’s crawling is performed in the c302 and Sibernetic platforms of the OpenWorm project. See a video demonstration here https: //youtu.be/iyV7y8nFdDU.

A prerequisite for simulating the biophysics of complex biological tissues and whole organisms are computational descriptions of biological matter that are flexible and can interface with materials of different viscosities, such as liquid. The landscape of software that is easily available to do such work is limited and lacks essential features necessary for combining elastic matter with simulations of liquids. Here we present an open source software package called Sibernetic, designed for the physical simulation of biomechanical matter (membranes, elastic matter, contractile matter) and environments (liquids, solids and elastic matter with variable physical properties). At its core, Sibernetic is built as an extension to Predictive-Corrective Incompressible Smoothed Particle Hydrodynamics (PCISPH). Sibernetic is built on top of OpenCL, making it possible to run simulations on CPUs or GPUs, and has 3D visualization support built on top of OpenGL. Several test examples of the software running and reproducing physical experiments, as well as performance benchmarks, are presented and future directions are discussed. (C) 2016 Elsevier Ltd. All rights reserved.

Presentation and supplemental materials (readings, etc) from the OpenWorm Open House, held on the internet on October 25, 2016. Materials for nine 5-minute presentations and two 45-minute workshops.

The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.