bluuebunny/crossref_metadata_2025 huggingface dataset:
Venous Access Problems in Sickle Cell Disease Patients: Results of Upper Extremity Thrombolysis in the setting of Catheter Related Thrombosis
Authors: Martin Jonathan G.
Published: June 2020

Purpose

Sickle cell disease is the most common monogenic disorder. All the elements of Virchow’s triad – hypercoagulability, endothelial dysfunction and impaired blood flow – are present in sickle cell disease patients, and can lead to thrombosis and vaso-occlusive crises. Central venous catheters are commonly used in sickle cell disease patients for rapid transfusion to avoid a vaso-occlusive crisis or for treatment after crises onset. However, central venous catheters themselves are an additional source for thrombus formation. We investigate a single day thrombolysis protocol for the treatment of catheter related thrombosis.

Materials and Methods

We present an Institutional Review Board approved retrospective analysis spanning from June 2016 to April 2018 evaluating upper extremity thrombolysis in the setting of catheter related thrombosis. All patients underwent a similar protocol involving peripheral upper extremity access, pharmomechanical thrombolysis, and angioplasty, which is described in detail. In 33% of the procedures, a recalcitrant stenosis was then stented. Maximal balloon size and stent sizes are included for reference.

Results

In follow up, one patient had a severe complication possibly related to the large thrombus burden, and expired. One patient who did not initially have recalcitrant stenosis and therefor did not have a stent placed during the initial procedure, had recurrent stenosis and thrombosis 6 months after the initial procedure, and had repeat pharmomechanical thrombolysis performed, with stent placement at that time. The other procedures were without complication, and the upper extremity and central venous systems remained patent at most recent follow-up, up to 30 months post procedure.

Conclusions

In the circumstance of severe catheter related thrombosis, we present a protocol which can be considered for therapeutic use without further intervention required in 78% of cases at 2 years.
How Efficient Can Non-Professional Masks Suppress COVID-19 Pandemic?
Authors: Chen Yejian , Dong Meng
Published: June 2020

The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can be transmitted via respiratory secretions. Since there are currently no specific therapeutics or vaccines available against the SARS-CoV-2, the commen non-pharmaceutical interventions (NPIs) are still the main measures to curb the COVID-19 epidemic. Face mask wearing is one important measure to suppress the pandemic. In order to know how efficient is face mask wearing in reducing the pandemic even with low efficiency non-professional face masks, we exploit physical abstraction to model the non-professional face masks made from cotton woven fabrics and characterize them by a parameter virus penetration rate (VPR) γ. Monte Carlo simulations exhibit that the effective reproduction number R of COVID-19 or similar pandemics can be approximately reduced by factor γ4 with respect to the basic reproduction number R0, if the face masks with 70% < γ < 90% are universally applied for the entire network. Furthermore, thought experiments and practical exploitation examples in country-level and city-level are enumerated and discussed to support our discovery in this study and indicate that the outbreak of a COVID-19 like pandemic can be even suppressed by the low efficiency non-professional face masks.
Impact of social media on knowledge dissemination between physicians during COVID-19 virus outbreak: A cross sectional survey
Authors: Mohamed-Hussein Aliae AR , Makhlouf Nahed A , Yassa Heba A , Makhlouf Hoda A
Published: June 2020

Background

Social media became an alternative platform for communicating during medical crisis as COVID-19 pandemic.

Aim of the study

1- to describe the use of social media by Physicians during Covid-19 outbreak 2- to determine how physicians obtain their medical information about the emerging disease 3- to determine physicians practice and how do they use the information received.

Methods

This is a cross-sectional web-based anonymous survey. Data were collected from Health Care Professional (HCPs) via fulfilling online designed questionnaire. Descriptive statistics with frequencies and percentages are presented. Results: The response rate was 66.2% (232/350). Smart phones was the most commonly used (94.8%) followed by laptops (13.4%). Facebook was used by 65.8% and WhatsApp by 52.8%. The data shared were medical newsletters (68%) and educational movies (52.2%). Source of information were mainly professional local pages (60.8%) then WHO pages (53.7%). Physicians shared trusted information (66.7%) and they confirmed the data were correct before publishing in 55.5%. They shared mainly WHO announcements and alerts (44%), professional lectures (32.1%) and 13.3% shared comics. Overall, 71% perceived lots of data about the cause of disease, clinical picture, daily spread, fatality rate and alert of the countries.

Conclusion

Physicians are active users of social media. Facebook and WhatsApp are useful platforms to spread right data about diseases during pandemics. Most physicians are positive towards data published; they watch, read and disseminate trusted informations.
Cortical re-organization after traumatic brain injury elicited using functional electrical stimulation therapy: A case report
Authors: Milosevic Matija , Nakanishi Tomoya , Sasaki Atsushi , Yamaguchi Akiko , Nomura Taishin , Popovic Milos R. , Nakazawa Kimitaka
Published: June 2020

Functional electrical stimulation therapy (FEST) can improve motor function after neurological injuries. However, little is known about cortical changes after FEST and weather it can improve motor function after traumatic brain injury (TBI). Our study examined cortical changes and motor improvements in one male participant with chronic TBI suffering from mild motor impairment affecting the right upper-limb during 3-months of FEST and during 3-months follow-up. In total, 36 sessions of FEST were applied to enable upper-limb grasping and reaching movements. Short-term assessments carried out using transcranial magnetic stimulation (TMS) showed reduced cortical silent period (CSP), indicating cortical and/or subcortical inhibition after each intervention. At the same time, no changes in motor evoked potentials (MEPs) were observed. Long-term assessments showed increased MEP corticospinal excitability after 12-weeks of FEST, which seemed to remain during both follow-ups, while no changes in CSP were observed. Similarly, long-term assessments using TMS mapping showed larger hand MEP area in the primary motor cortex (M1) after 12-weeks of FEST as well as during both follow-ups. Corroborating TMS results, functional magnetic resonance imaging (fMRI) data showed M1 activations increased during hand grip and finger pinch tasks after 12-weeks of FEST, while gradual reduction of activity compared to after the intervention was seen during follow-ups. Widespread changes were seen not only in the M1, but also sensory, parietal rostroventral, supplementary motor, and premotor areas in both contralateral and ipsilateral hemispheres, especially during the finger pinch task. Drawing test performance showed improvements after the intervention and during follow-ups. Our findings suggest that task-specific and repetitive FEST can effectively increase cortical activations by integrating voluntary motor commands and sensorimotor network through FES. Overall, our results demonstrated cortical re-organization and improved fine motor function in an individual with chronic TBI after FEST.
Modelling Singapore COVID-19 pandemic with a SEIR multiplex network model
Authors: Chung N. N. , Chew L. Y.
Published: June 2020

In this paper, we have implemented a large-scale agent-based model to study the outbreak of coronavirus infectious diseases (COVID-19) in Singapore, taking into account complex human interaction pattern. In particular, the concept of multiplex network is utilized to differentiate between social interactions that happen in households and workplaces. In addition, weak interactions among crowds, transient interactions within social gatherings, and dense human contact between foreign workers in dormitories are also taken into consideration. Such a categorization in terms of a multiplex of social network connections together with the Susceptible-Exposed-Infectious-Removed (SEIR) epidemic model have enabled a more precise study of the feasibility and efficacy of control measures such as social distancing, work from home, and lockdown, at different moments and stages of the pandemics.
HumanSYNGAP1Regulates the Development of Neuronal Activity by Controlling Dendritic and Synaptic Maturation
Authors: Llamosas Nerea , Arora Vineet , Vij Ridhima , Kilinc Murat , Bijoch Lukasz , Rojas Camilo , Reich Adrian , Sridharan BanuPriya , Willems Erik , Piper David R. , Scampavia Louis , Spicer Timothy P. , Miller Courtney A. , Holder J. Lloyd , Rumbaugh Gavin
Published: June 2020

SYNGAP1is a major genetic risk factor for global developmental delay, autism spectrum disorder, and epileptic encephalopathy.De novoloss-of-function variants in this gene cause a neurodevelopmental disorder defined by cognitive impairment, social-communication disorder, and early-onset seizures. Cell biological studies in mouse and rat neurons have shown thatSyngap1regulates developing excitatory synapse structure and function, with loss-of-function variants driving formation of larger dendritic spines and stronger glutamatergic transmission. However, studies to date have been limited to mouse and rat neurons. Therefore, it remains unknown howSYNGAP1loss-of-function impacts the development and function of human neurons. To address this, we employed CRISPR/Cas9 technology to ablateSYNGAP1protein expression in neurons derived from a human induced pluripotent stem cell line (hiPSC). Reducing SynGAP protein expression in developing hiPSC-derived neurons enhanced dendritic morphogenesis, leading to larger neurons compared to those derived from isogenic controls. Consistent with larger dendritic fields, we also observed a greater number of morphologically defined excitatory synapses in cultures containing these neurons. Moreover, neurons with reduced SynGAP protein had stronger excitatory synapses and expressed synaptic activity earlier in development. Finally, distributed network spiking activity appeared earlier, was substantially elevated, and exhibited greater bursting behavior inSYNGAP1null neurons. We conclude thatSYNGAP1regulates the postmitotic maturation of human neurons made from hiPSCs, which influences how activity develops within nascent neural networks. Alterations to this fundamental neurodevelopmental process may contribute to the etiology ofSYNGAP1-related disorders.
Multifactorial and closed head impact traumatic brain injuries cause distinct tactile hypersensitivity profiles
Authors: Wattiez A-S. , Castonguay W.C. , Gaul O.J. , Waite J.S. , Schmidt C.M. , Reis A. , Rea B.J. , Sowers L.P. , Cintrón-Pérez C.J. , Vázquez-Rosa E. , Pieper A.A. , Russo A.F.
Published: June 2020

Chronic complications of traumatic brain injury (TBI) represent one of the greatest financial burdens and sources of suffering in society today. A substantial number of these patients suffer from post-traumatic headache (PTH), which is typically associated with tactile allodynia. Unfortunately, this phenomenon has been under-studied, in large part due to the lack of well-characterized laboratory animal models. We have addressed this gap in the field by characterizing the tactile sensory profile of two non-penetrating models of PTH. We show that multifactorial TBI, consisting of aspects of impact, acceleration/deceleration, and blast wave exposure, produces long term tactile hypersensitivity and central sensitization, phenotypes reminiscent of PTH in patients, in both cephalic and extracephalic regions. By contrast, closed head injury induces only transient cephalic tactile hypersensitivity, with no extracephalic consequences. Both models show more severe phenotype with repetitive daily injury for three days, compared to either one or three successive injuries in a single day, providing new insight into patterns of injury that may place patients at greater risk of developing PTH. Importantly, even after recovery from transient cephalic tactile hypersensitivity, mice subjected to closed head injury had persistent hypersensitivity to established migraine triggers, including calcitonin gene-related peptide (CGRP) and sodium nitroprusside, a nitric oxide donor. Our results offer new tools for studying PTH, as well as preclinical support for a pathophysiologic role of CGRP in this condition.

Two models of post-traumatic headache after traumatic brain injury provide novel laboratory tools and insights in relative risks of injury and therapeutic opportunities.
Neuronal Population Models Reveal Specific Linear Conductance Controllers Sufficient to Rescue Preclinical Disease Phenotypes
Authors: Allam Sushmita L. , Rumbell Timothy H. , Trong Tuan Hoang , Parikh Jaimit , Kozloski James R.
Published: June 2020

Objective

During the preclinical phase of drug development, potential drug candidates are often screened for their ability to alleviate certainin vitroelectrophysiological features among neurons. This ability is assessed by measuring treatment outcomes using the population mean, both across different cells and different animals. The go/no-go decision for progressing a drug to a clinical trial is then based on ‘average effects’, yet these measures may not be sufficient to mitigate clinical end point risk. Population-based modeling is widely used to represent the intrinsic variability of electrophysiological features among healthy, disease and drug treated neuronal phenotypes. We pursued a method for optimizing therapeutic target design by identifying a single coherent set of ion channel targets for recovery of the healthy (Wild type) cellular phenotype simultaneously across multiple measures. Specifically, we aimed to determine the set of target modulations that best recover a heterogeneous Huntington’s disease (HD) population of model neurons into a multivariate region of phenotypic measurements corresponding to the healthy excitability profile of a heterogenous Wild type (WT) population of model neurons.

Methods

Our approach combines mechanistic simulations with populations modeling of striatal neurons using evolutionary algorithms for population optimization to design ‘virtual drugs’. We introduce efficacy metrics to score population of model outcomes and use these to rank our virtual candidates.

Results

We found that virtual drugs identified using heuristic approaches performed better than single target modulators and those derived from standard classification methods. We compare a real drug to the virtual candidates and demonstrate a novelin silicotriaging method.
FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells
Authors: Warren Iyan , Moeller Michael M. , Guiggey Daniel , Chiang Alexander , Maloy Mitchell , Ogoke Ogechi , Groth Theodore , Mon Tala , Meamardoost Saber , Liu Xiaojun , Thompson Sarah , Szeglowski Antoni , Thompson Ryan , Chen Peter , Paulmurugan Ramasamy , Yarmush Martin L. , Kidambi Srivatsan , Parashurama Natesh
Published: June 2020

FOXA factors are critical members of the developmental gene regulatory network (GRN) composed of master transcription factors (TF) which regulate murine cell fate and metabolism in the gut and liver. How FOXA dictates human liver cell fate, differentiation, and simultaneously regulate metabolic pathways is poorly understood. Here, we aimed to determine the role of FOXA2 (and FOXA1 which is believed to compensate for FOXA2) in hepatic differentiation and cell metabolism in a human hepatic cell line (HepG2). siRNA targeting of FOXA1 and FOXA2 in human hepatic (HepG2) cells and during hepatic differentiation significantly downregulated albumin (p < 0.05) and GRN TF gene expression (HNF4A, HEX, HNF1B, TBX3) (p < 0.05) and significantly upregulated endoderm/gut/hepatic endoderm markers (goosecoid (GSC), FOXA3, and GATA4), gut TF (CDX2), pluripotent TF (NANOG), and neuroectodermal TF (PAX6) (p < 0.05), all consistent with a partial/transient cell reprogramming. shFOXA1/2 targeting resulted in similar findings and demonstrated evidence of reversibility. RNA-seq followed by bioinformatic analysis of shFOXA1/2 knockdown HepG2 cells demonstrated 235 significant downregulated genes and 448 upregulated genes, including upregulation of markers for alternate germ layers lineages (cardiac, endothelial, muscle) and neurectoderm (eye, neural). We found widespread downregulation of glycolysis, citric acid cycle, mitochondrial genes, and alterations in lipid metabolism, pentose phosphate pathway, and ketogenesis. Functional metabolic analysis agreed with these findings, demonstrating significantly diminished glycolysis and mitochondrial respiration, and accumulation of lipid droplets. We hypothesized that FOXA1/2 inhibit the initiation of human liver differentiationin vitro. During hPSC-hepatic differentiation, siRNA knockdown demonstrated de-differentiation and unexpectedly, activation of pluripotency factors and neuroectoderm. shRNA knockdown demonstrated similar results and activation of SOX9 (hepatobiliary). These results demonstrate complex effects of FOXA1/2 on hepatic GRN effecting de-differentiation and metabolism with applications in studies of cancer, differentiation, and organogenesis.
The role of elevated branched chain amino acids in the potent effects of vertical sleeve gastrectomy to reduce weight and improve glucose regulation in mice
Authors: Kramer Nadejda Bozadjieva , Evers Simon S. , Shin Jae Hoon , Silverwood Sierra , Wang Yibin , Burant Charles F. , Sandoval Darleen A. , Seeley Randy J.
Published: June 2020

Obesity and type 2 diabetes mellitus (T2D) are growing epidemics resulting in increased morbidity and mortality. An emerging body of evidence has shown that elevated levels of branched-chain amino acids (BCAA) and their metabolites are strongly positively associated with obesity, insulin-resistance and T2D. Bariatric surgery is among the best treatments for weight loss and the alleviation of T2D. Additionally, clinical studies have reported that bariatric surgery decreases the circulating levels of BCAA. The objective of these studies was to test the hypothesis that reduced BCAA levels contribute to the metabolic improvements after VSG. We find that, as in humans, circulating BCAA levels are significantly lower in VSG rats and mice compared to Sham controls. In order to increase circulating BCAA levels, we tested mice with either increased dietary intake of BCAA or impaired BCAA catabolism by total body deletion of mitochondrial phosphatase 2C, Pp2cm, a key enzyme in the rate-limiting step in BCAA catabolism. Our results show that a decrease in circulating BCAA levels is not necessary for sustained body weight loss and improved glucose tolerance after VSG. While it is clear that circulating levels of BCAAs are excellent biomarkers for metabolic status, the current data do not support a causal role in determining metabolic regulation and the response to VSG.
Robotic Assay for Drought (RoAD): An Automated Phenotyping System for Brassinosteroid and Drought Response
Authors: Xiang Lirong , Nolan Trevor M. , Bao Yin , Elmore Mitch , Tuel Taylor , Gai Jingyao , Shah Dylan , Huser Nicole M. , Hurd Ashley M. , McLaughlin Sean A. , Howell Stephen H. , Walley Justin W. , Yin Yanhai , Tang Lie
Published: June 2020

Brassinosteroids (BRs) are a group of plant steroid hormones involved in regulating growth, development, and stress responses. Many components of the BR pathway have previously been identified and characterized. However, BR phenotyping experiments are typically performed on petri plates and/or in a low-throughput manner. Additionally, the BR pathway has extensive crosstalk with drought responses, but drought experiments are time-consuming and difficult to control. Thus, we developed Robotic Assay for Drought (RoAD) to perform BR and drought response experiments in soil-grown Arabidopsis plants. RoAD is equipped with a bench scale, a precisely controlled watering system, an RGB camera, and a laser profilometer. It performs daily weighing, watering, and imaging tasks and is capable of administering BR response assays by watering plants with Propiconazole (PCZ), a BR biosynthesis inhibitor. We developed image processing algorithms for both plant segmentation and phenotypic trait extraction in order to accurately measure traits in 2-dimensional (2D) and 3-dimensional (3D) spaces including plant surface area, leaf length, and leaf width. We then applied machine learning algorithms that utilized the extracted phenotypic parameters to identify image-derived traits that can distinguish control, drought, and PCZ-treated plants. We carried out PCZ and drought experiments on a set of BR mutants and Arabidopsis accessions with altered BR responses. Finally, we extended the RoAD assays to perform BR response assays using PCZ inZea mays(maize) plants. This study establishes an automated and non-invasive robotic imaging system as a tool to accurately measure morphological and growth-related traits of Arabidopsis and maize plants, providing insights into the BR-mediated control of plant growth and stress responses.
Characterization of small molecule induced changes in Parkinson’s-related trafficking via the Nedd4 ubiquitin signaling cascade
Authors: Hatstat A. Katherine , Ahrendt Hannah D. , Foster Matthew W. , Mayne Leland , Moseley M. Arthur , Englander S. Walter , McCafferty Dewey G.
Published: June 2020

The benzdiimidazole NAB2 rescues α-synuclein-associated trafficking defects associated with early onset Parkinson’s disease in a Nedd4-dependent manner. Despite identification of E3 ubiquitin ligase Nedd4 as a putative target of NAB2, its molecular mechanism of action has not been elucidated. As such, the effect of NAB2 on Nedd4 activity and specificity was interrogated through biochemical, biophysical, and proteomic analyses. NAB2 was found to bind Nedd4 (KDapp= 42 nM), but this binding is side chain mediated and does not alter its conformation or ubiquitination kineticsin vitro. Nedd4 co-localizes with trafficking organelles, and NAB2 exposure did not alter its colocalization. Ubiquitin-enrichment coupled proteomics revealed that NAB2 stimulates ubiquitination of trafficking and transport associated proteins, most likely through modulating the substrate specificity of Nedd4, providing a putative protein network involved in the NAB2 mechanism.
Diversity analysis of amp gene sequences in the ‘CandidatusPhytoplasma meliae’
Authors: Fernández Franco D. , Conci Luis R.
Published: June 2020

Phytoplasmas are plant pathogenic bacteria transmitted by insects. As endosymbiotic bacteria that lack a cell wall, their membrane proteins are in direct contact with host cytoplasm. In phytoplasmas the immunodominant membrane proteins (IDPs), are the most abundant proteins of the cell membrane. The antigenic membrane protein (Amp), one of the three types of IDPs, is characterized by a positive selection pressure acting in their extracellular domain. In South America, the ‘CandidatusPhytoplasma meliae’ has been associated to chinaberry yellows disease. In the present work, we describe for the first time the structure, phylogeny and selection pressure of amp gene in sixteen ‘CandidatusPhytoplasma meliae’ isolates. Our results indicate that amp gene sequences preserve the structure, large extracellular domain flanked by to hydrophobic domains in the N- (signal peptide) and C-termini (transmembrane), previously described in its orthologues and high divergence in the amino acids residues from extracellular domain. Moreover, a positive selection pressure was detected predominantly in this region confirming previous reports.
ICOS signaling limits regulatory T cell accumulation and function in visceral adipose tissue
Authors: Mittelsteadt Kristen L. , Hayes Erika T. , Campbell Daniel J.
Published: June 2020

A unique population of Foxp3+regulatory T cells (TR) resides in visceral adipose tissue (VAT) that regulates adipose inflammation and helps preserve insulin sensitivity. The costimulatory molecule ICOS is highly expressed on effector (e)TRthat migrate to nonlymphoid tissues, and contributes to their maintenance and function in models of autoimmunity. In this study, we report an unexpected cell-intrinsic role for ICOS expression and downstream PI3K signaling in limiting the abundance, VAT-associated phenotype, and function of TRspecifically in VAT.Icos−/−mice and mice expressing a knock-in form of ICOS that cannot activate PI3K had increased VAT-TRabundance and elevated expression of canonical VAT-TRmarkers. Loss of ICOS signaling facilitated enhanced accumulation of TRto VAT associated with elevated CCR3 expression, and resulted in reduced adipose inflammation and heightened insulin sensitivity in the context of high-fat diet. Thus, we have uncovered a new and surprising molecular pathway that regulates VAT-TRaccumulation and function.

The authors demonstrate that loss of ICOS-dependent PI3-kinase signaling supports visceral adipose tissue (VAT) TRabundance and function, and this correlates with reduced adipose inflammation and improved insulin sensitivity after high-fat diet. This work highlights a new molecular pathway that regulates VAT-TRaccumulation and activity.
Binding of DNA origami to lipids: maximising yield and switching via strand-displacement
Authors: Daljit Singh Jasleen Kaur , Darley Es , Ridone Pietro , Gaston James P , Abbas Ali , Wickham Shelley FJ , Baker Matthew AB
Published: June 2020

Liposomes are widely used as synthetic analogues of cell membranes and for drug delivery. Lipid-binding DNA nanostructures can modify the shape, porosity and reactivity of liposomes, mediated by cholesterol-modifications. DNA nanostructures can also be designed to switch conformations by DNA strand displacement. However, the optimal conditions to facilitate stable, high-yield DNA-lipid binding while allowing controlled switching by strand-displacement are not known. Here we characterised the effect of cholesterol arrangement, DNA structure, buffer and lipid composition on DNA-lipid binding and strand displacement. We observed that binding was inhibited below pH 4, and above 200 mM NaCl or 40 mM MgCl2, was independent of lipid type, and increased with membrane cholesterol content. For simple motifs, binding yield was slightly higher for double-stranded DNA than single-stranded. For larger DNA origami tiles, 4 – 8 cholesterol modifications were optimal, while edge positions and longer spacers increased yield of lipid-binding. Strand displacement achieved controlled removal of DNA tiles from membranes, but was inhibited by overhang domains, which are used to prevent cholesterol aggregation. These findings provide design guidelines for integrating strand-displacement switching with lipid-binding DNA nanostructures. This paves the way for achieving dynamic control of membrane morphology, enabling broader applications in nanomedicine and biophysics.
Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM
Authors: Takaba Kiyofumi , Maki-Yonekura Saori , Yonekura Koji
Published: June 2020

A semi-automated protocol has been developed for rotational data collection of electron diffraction patterns by combined use of SerialEM and ParallEM, where SerialEM is used for positioning of sample crystals and ParallEM for rotational data collection. ParallEM calls standard camera control software through an AutoIt script, which adapts to software operational changes and to new GUI programs guiding other cameras. Development included periodic flashing and pausing of data collection during overnight or day-long recording with a cold field-emission beam. The protocol proved to be efficient and accurate in data collection of large-scale rotational series from two JEOL electron microscopes, a general-purpose JEM-2100 and a high-end CRYO ARM 300. Efficiency resulted from simpler steps and task specialization. It is possible to collect 12–20 rotational series from ∼ −68º to ∼ 68º at a rotation speed of 1º /s in one hour without human supervision.
Characterizing and Forecasting Emergency Department Visits Related to COVID-19 Using Chief Complaints and Discharge Diagnoses
Authors: Koshute Phillip , Holtry Rekha , Wojcik Richard , Loschen Wayne , Lewis Sheri
Published: June 2020

In response to the unprecedented public health challenge posed by the SARS CoV-2 virus (COVID-19) in the United States, we and our colleagues at the Johns Hopkins University Applied Physics Laboratory (JHU/APL) have developed a model of COVID-19 progression using emergency department (ED) visit data from the National Capital Region (NCR). We obtained ED visits counts through targeted queries of the NCR Electronic Surveillance System for the Early Notification of Community-Based Epidemics (ESSENCE). To focus on ED visits by COVID-19 patients, we adjusted the query results for typical ED visit volumes and for reductions in ED volumes due to COVID-19 precautions. With these ED visit data, we fitted a logistic growth model to characterize and forecast the increase in cumulative COVID-19 ED visits. Our model achieves the best fit when we assume that the first NCR visit occurred in early January. We estimate that approximately 15,000 COVID-19 ED visits occurred prior to May 2020 and that approximately 17,000 more visits will occur in subsequent months. We plan to deploy an operational pilot of this model in the NCR ESSENCE environment, assisting local public health authorities as they brace for a second wave of COVID-19. Additionally, we will iteratively assess potential model refinements, aiming to maximize our model’s relevance for local public health authorities’ situational awareness and decision-making.
Ramularia leaf spot disease of barley is highly host genotype-dependent and suppressed by continuous drought stress in the field
Authors: Hoheneder Felix , Hofer Katharina , Groth Jennifer , Herz Markus , Heß Michael , Hückelhoven Ralph
Published: June 2020

Since the 1980s, Ramularia leaf spot (RLS) is an emerging barley disease world-wide. The control of RLS is increasingly aggravated by a recent decline in fungicide efficacy and a lack of RLS-resistant cultivars. Furthermore, climate change increases drought periods in Europe, enhances variable weather conditions and thus will have an impact on severity of plant diseases. Hence, identification of RLS-resistant cultivars and understanding of disease progression under abiotic stress are important aims in integrated disease management under climate change. In the present study, we evaluated quantitative RLS resistance of 15 spring barley genotypes under drought, controlled irrigation and field conditions between 2016 and 2019 and monitored microclimatic conditions within the canopy. We identified genotypes that show robust quantitative resistance to RLS in different field environments. Our findings suggest that long-lasting drought periods create unfavourable conditions for the disease and supports that the extent and duration of leaf wetness is a key factor for RLS epidemics.
Optimizing nucleic acid extraction and transcriptome evaluation from low-input, fixed clinical samples
Authors: Campbell Katie M. , Medina Egmidio , Carretero Ignacio Baselga , Teper Yaroslav , Elumalai Rangasamy , Miller Raymond , Pal Kasturi , Pitzer Jessica , Daviso Eugenio , Carstens Carsten , Laugharn James , Hugo Willy , Chen Jia Ming , Vega-Crespo Agustin , Jilani Sameeha , Garcilazo Ivan Perez , Dong Ling , Li Xinmin , Hu-Lieskovan Siwen , Ribas Antoni
Published: June 2020

Tumor biopsies are commonly formalin-fixed and paraffin-embedded (FFPE) for long-term and efficient storage. However, FFPE preservation can greatly compromise the quality of samples, the extraction of nucleic acids, and feasibility of downstream studies, including RNA sequencing. These challenges are especially evident in the studies of clinical trial samples, where the sizes of biopsies often limit the amount of material available for study. Here, we evaluate two nucleic acid extraction kits (Covaris truXTRAC FFPE tNA Plus, QIAGEN miRNeasy FFPE) and three hybridized-capture-based RNA sequencing library preparations (Agilent SureSelect XT RNA Direct, Agilent SureSelect XT HS, and Illumina TruSeq RNA Exome) to evaluate the impact of these sample processing steps on transcriptome evaluation in a melanoma biopsy procured in a clinical setting and preserved by FFPE. While there exist many options for extraction and library preparation that are appropriate for RNA sequencing from FFPE samples, we observed that combinations of experimental approaches may have subtle impacts on downstream analysis, including gene expression quantification and fusion detection.
Pleiotropy allows recovery of phenotypic plasticity in constant environments
Authors: Kingma Enzo , Diepeveen Eveline T. , de la Cruz Leila Iñigo , Laan Liedewij
Published: June 2020

Phenotypic plasticity confers a fitness advantage to an organism by tailoring phenotype to environmental circumstances. The extent to which phenotypic plasticity emerges as an adaptive response is still unknown, however it is predicted that the emergence and maintenance of phenotypic plasticity occurs only during evolution in fluctuating environments. Interestingly, experimental studies have shown that phenotypic plasticity can be preserved for several generations during evolution in a constant environment. Here, we evolve a mutant strain ofSaccharomyces cerevisiaethat has reduced plasticity in a constant and fluctuating environment. Subsequently we compared the adaptive response of the evolved cell, both at the phenotype and genotype level. As predicted by current theory, we find that evolution in a fluctuating environment results in a recovery of phenotypic plasticity. Surprisingly, evolution in a constant environment can lead to a similar recovery of plasticity due to a pleiotropic coupling of different traits. Thus, plasticity can emerge in both fluctuating and constant environments and its prevalence may mainly be determined by network structure. In addition, pleiotropic interactions may be an important structural component of biological networks that can facilitate the recovery of phenotypic plasticity without the requirement to continuously encounter environmental fluctuations.
Adaptive evolution of phenotypic switching during environmental change
Authors: Trivedi Urvish , Rebsdorf Maria R. , Cueva Angel R. , Rumbaugh Kendra P. , Burmølle Mette , Sørensen Søren J. , Madsen Jonas S.
Published: June 2020

Microbes are faced with environmental fluctuations and it is therefore important to understand how change affects bacterial evolution and population dynamics. Here, we evolved a model bacterium,Pseudomonas aeruginosaPA14, under both constant and changing conditions where settlement by biofilm formation or migration by swimming motility was induced. In changing environments, a heterogeneous population evolved with both specialists and generalists. Interestingly, over time, generalists were outcompeted despite being better at both phenotypes compared to the ancestor. However, generalists became dominant when faced with local competition after resettlement. Reintroduction into a burn wound model, the environment PA14 originally was isolated from, further suggested a tradeoff between niche breadth and peak fitness in agreement with the evolution experiments. Mutations in the c-di-GMP system were key for adaptation of the phenotypes. No mutants lost their ability to regulate c-di-GMP, but generalists acquired mutations that optimized their phenotypic response by efficiently adjusting c-di-GMP levels.
Comprehensive and Integrated Genomic Characterization of Human Immunome in Cancer
Authors: Li Yongsheng , Triplett Todd , Burgman Brandon , Sun Ming , McGrail Daniel J. , Qi Dan , Shukla Sachet , Wu Erxi , Wu Catherine J. , Capasso Anna , Eckhardt S. Gail , Georgiou George , Li Bo , Sahni Nidhi , Yi S. Stephen
Published: June 2020

Genetic alterations in immune-related pathways are common hallmarks of cancer. However, to realize the full potential of immunotherapy, a comprehensive understanding of immune networks and how mutations impact network structure and functional output across cancer types is instrumental. Herein we systematically interrogated somatic mutations that could express neoantigens and alter immune responses in cancer patients compared to wild-type controls. To do so, we developed a network-based immunogenomics model (NIPPER) with scoring systems to prioritize critical genes and mutations eliciting differential HLA binding affinity and alternate responses to immunotherapy. These mutations are enriched in essential protein domains and often alter tumor infiltration by immune cells, affecting T cell receptor repertoire and B cell clonal expansion. Furthermore, we devised an interactome network propagation framework integrated with drug associated gene signatures to identify potential immunomodulatory drug candidates. Together, our systems-level analysis results help interpret the heterogeneous immune responses among patients, and serve as a resource for future functional studies and targeted therapeutics.

Significance

Cancer cells induce specific immune-related pathway perturbations by mutations, transcriptional dysregulation, and integration of multi-omics data can help identify critical molecular determinants for effective targeted therapeutics.
Circadian clock neurons maintain phase control over daily behavioral activity patterns under diverse environmental conditions
Authors: Lorber Clara , Stanewsky Ralf , Lamaze Angélique
Published: June 2020

Proper timing of rhythmic locomotor behavior is the consequence of integrating environmental conditions and internal time within the circadian clock. The 150 clock neurons in theDrosophila melanogasterbrain are organized in various clusters, controlling different aspects of the daily activity rhythms. For example, during regular 12 hr light : 12 hr dark cycles at constant temperature (LD), so called Morning (M) neurons control the activity peak in the morning, while Evening (E-) neurons regulate the activity increase at the end of the day. During the remaining times of day and night, flies are inactive, giving rise to the crepuscular behavior observed in LD. Here, we investigate if the same neuronal groups also control behavioral activity under very different environmental conditions of constant light and temperature cycles (LLTC). While the morning activity is completely absent in LLTC, a single pronounced activity peak occurs at the end of the thermophase. We show that the same E-neurons operating in LD, also regulate the evening peak in LLTC. Interestingly, neuronal activity of E-neurons is inversely correlated with behavioral activity, suggesting an inhibitory action on locomotion. Surprisingly, the E-cells responsible for synchronization to temperature cycles belong to the clock neurons containing the circadian photoreceptor Cryptochrome, previously suggested to be more important for synchronization to LD. Our results therefore support a more deterministic function of the different clock neuronal subgroups, independent of specific environmental conditions.

Significance statement

Master circadian clocks in the brains of mammals and fruit fly are composed of neurons expressing varying types of neuropeptides and transmitters. This diversity along with anatomical differences indicate diverse functions of different clock neurons. InDrosophila, so-called Morning (M) and Evening (E) neurons control locomotor activity at the respective time of day during normal day/night (LD) cycles. Recent reports point to a certain degree of plasticity with regard to circadian clock neuron function, depending on specific environmental conditions. Here we show that one neuronal group, the E-neurons, instead behave as if hard-wired to their output targets. Surprisingly they direct activity to occur during the evening both under LD conditions, as well as during temperature cycles in constant light.
Promiscuous esterases counterintuitively are less flexible than specific ones
Authors: Nutschel Christina , Coscolín Cristina , Mulnaes Daniel , David Benoit , Ferrer Manuel , Jaeger Karl-Erich , Gohlke Holger
Published: June 2020

Understanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention. Here, we exploit comprehensive experimental information on the substrate promiscuity of 147 esterases tested against 96 esters together with computationally efficient rigidity analyses to understand the molecular origin of the observed promiscuity range. Unexpectedly, our data reveal that promiscuous esterases are significantly less flexible than specific ones, are significantly more thermostable, and have a significantly increased specific activity. These results may be reconciled with a model according to which structural flexibility in the case of specific esterases serves for conformational proofreading. Our results signify that esterase sequence space can be screened by rigidity analyses for promiscuous esterases as starting points for further exploration in biotechnology and synthetic chemistry.
Temperature restriction in entomopathogenic bacteria
Authors: Hapeshi Alexia , Healey Joseph R.J. , Mulley Geraldine , Waterfield Nicholas R.
Published: June 2020

Temperature plays an important role in bacteria-host interactions and can be a determining factor for host switching. In this study we sought to investigate the reasons behind growth temperature restriction in the entomopathogenic enterobacteriumPhotorhabdus. Photorhabdushas a complex dual symbiotic and pathogenic life cycle. The genus consists of 19 species but only one subgroup, previously all classed together asP. asymbiotica, have been shown to cause human disease. These clinical isolates necessarily need to be able to grow at 37 °C, whilst the remaining species are largely restricted to growth temperatures below 34 °C and are therefore unable to infect mammalian hosts. Here, we have isolated spontaneous mutant lines ofP. laumondiiDJC that were able to grow up to 36 °C-37 °C. Following whole genome sequencing of 29 of these mutants we identified a single gene, encoding a protein with a RecG-like helicase domain, that for the majority of isolates contained single nucleotide polymorphisms. Importantly, provision of the wild-type allele of this gene intransrestored the temperature restriction, confirming the mutations are recessive, and the dominant effect of the protein product of this gene. The gene appears to be part of a short three cistron operon, which we have termed the Temperature Restricting Locus (TRL). Transcription reporter strains revealed that this operon is induced upon the switch from 30 °C to 37 °C, leading to replication arrest of the bacteria. TRL is absent from all of the human pathogenic species so far examined, although its presence is not uniform in different strains of theP. luminescenssubgroup. In a wider context, the presence of this gene is not limited toPhotorhabdus, being found in phylogenetically diverse proteobacteria. We therefore suggest that this system may play a more fundamental role in temperature restriction in diverse species, relating to as yet cryptic aspects of their ecological niches and life cycle requirements.
Identifying key factors for improving ICA-based decomposition of EEG data in mobile and stationary experiments
Authors: Klug Marius , Gramann Klaus
Published: June 2020

Recent developments in EEG hardware and analyses approaches allow for recordings in both stationary and mobile settings. Irrespective of the experimental setting, EEG recordings are contaminated with noise that has to be removed before the data can be functionally interpreted. Independent component analysis (ICA) is a commonly used tool to remove artifacts such as eye movement, muscle activity, and external noise from the data and to analyze activity on the level of EEG effective brain sources. While the effectiveness of filtering the data as one key preprocessing step to improve the decomposition has been investigated previously, no study thus far compared the different requirements of mobile and stationary experiments regarding the preprocessing for ICA decomposition. We thus evaluated how movement in EEG experiments, the number of channels, and the high-pass filter cutoff during preprocessing influence the ICA decomposition. We found that for commonly used settings (stationary experiment, 64 channels, 0.5 Hz filter), the ICA results are acceptable. However, high-pass filters of up to 2 Hz cutoff frequency should be used in mobile experiments, and more channels require a higher filter to reach an optimal decomposition. Fewer brain ICs were found in mobile experiments, but cleaning the data with ICA proved to be important and functional even with 16 channels. Based on the results, we provide guidelines for different experimental settings that improve the ICA decomposition.
An untargeted metabolomics strategy to measure differences in metabolite uptake and excretion by mammalian cell lines
Authors: Muelas Marina Wright , Roberts Ivayla , Mughal Farah , O’Hagan Steve , Day Philip J. , Kell Douglas B.
Published: June 2020

Introduction

It is widely but erroneously believed that drugs get into cells by passing through the phospholipid bilayer portion of the plasma and other membranes. Much evidence shows, however, that this is not the case, and that drugs cross biomembranes by hitchhiking on transporters for other natural molecules to which these drugs are structurally similar. Untargeted metabolomics can provide a method for determining the differential uptake of such metabolites.

Objectives

Blood serum contains many thousands of molecules and provides a convenient source of biologically relevant metabolites. Our objective was to measure them.

Methods

We develop an untargeted LC-MS/MS method to detect a broad range of compounds present in human serum. We apply this to the analysis of the time course of the uptake and secretion of metabolites in serum by several human cell lines, by analysing changes in the serum that represents the extracellular phase (the ‘exometabolome’ or metabolic footprint).

Results

Our method measures some 4,000-5,000 metabolic features in both ES+and ES−modes. We show that the metabolic footprints of different cell lines differ greatly from each other.

Conclusion

Our new, 15-minute untargeted metabolome method allows for the robust and convenient measurement of differences in the uptake of serum compounds by cell lines following incubation in serum, and its relation to differences in transporter expression.