bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of Appropriate Use Criteria for Echocardiography in Pediatric Patients with Palpitations and Arrhythmias
Authors: Dasgupta Soham , Kelleman Michael , Sachdeva Ritu
Published: October 2020

Background:

Before the integration of the pediatric appropriate use criteria (AUC) for initial transthoracic echocardiography (TTE) in the outpatient setting with our electronic medical record (EMR), there was a high proportion of “rarely appropriate” TTEs (17.2%) ordered for palpitations/arrhythmias. We studied appropriateness ratings and applicability of pediatric AUC on the initial outpatient evaluation of children with palpitations/arrhythmias after EMR integration and the yield of abnormal TTEs for these indications.

Methods:

We obtained data after the EMR integration of the AUC at our institution. The TTE ordering physician assigned the AUC indication and the corresponding appropriateness ratings autopopulated as: appropriate (A), may be appropriate (M), and rarely appropriate (R). We recorded the abnormal TTE findings.

Results:

A total of 463 TTEs were ordered for palpitations/arrhythmias. Overall, 142 (30.7%) were for A, 263 (56.8%) for M, 41 (8.8%) for R, and 17 (3.7%) for “unclassifiable” indications. Only 14 (3.0%) had abnormal TTE findings, of which none were for indications rated R. A TTE ordered for premature ventricular contractions in a 17-year-old revealed a significant abnormality (moderate atrial septal defect).

Conclusions:

The integration of AUC with the EMR significantly improved the appropriate utilization of TTE for palpitations and arrhythmias with a decrease in the proportion of TTEs for R indications (17.2%–8.8%). Although the yield of abnormal findings on TTE performed for palpitations/arrhythmias is quite low, the AUC ratings successfully stratified the indication with no abnormalities for indications rated R. These findings can guide future revisions of AUC indications and ratings to optimize resource utilization.
Peri-Intubation Cardiac Arrest in the Pediatric Emergency Department: A Novel System of Care
Authors: Hoehn Erin F. , Dean Preston , Lautz Andrew J. , Frey Mary , Cabrera-Thurman Mary K. , Geis Gary L. , Stalets Erika , Zackoff Matthew , Pham Tena , Maxwell Andrea , Vukovic Adam , Kerrey Benjamin T.
Published: October 2020

Introduction:

Patients with physiologic disorders, such as hypoxemia or hypotension, are at high risk of peri-intubation cardiac arrest. Standardization improves emergency tracheal intubation safety, but no published reports describe initiatives to reduce the risk of cardiac arrest. This initiative aims to improve the care of children at risk of peri-intubation cardiac arrest in a pediatric emergency department (PED). We specifically aimed to increase the number of patients between those with peri-intubation cardiac arrest by 50%, from a baseline of 11–16, over 12-months.

Methods:

Our multidisciplinary team outlined a theory of improvement and designed interventions aimed at key drivers. The primary intervention was creating a PICU-ED Team (PET) and a checklist to guide the assessment and mitigation of risk for peri-intubation arrest and rapid consultation of the pediatric intensivists. The PET was iteratively refined, and we collected data by a video review of tracheal intubations.

Results:

Fifty-one patients with risk factors for peri-intubation arrest underwent tracheal -intubation in the PED from January 2016 to March 2020: 14 with PET activation since PET go-live in April 2019. None of the 14 PET patients had a peri-intubation cardiac arrest. Ninety-three percent (13/14) of PET patients were intubated in the PED, and 78% (10/13) of these patients had the first intubation attempt completed by PED physicians (balancing measures).

Conclusion:

We successfully developed the PET to mitigate the risk of peri-intubation cardiac arrest without significantly reducing key procedural opportunities for the PED. Initial data are promising, but further refinement is needed.
Profiles of HIV Care Disruptions Among Adult Patients Lost to Follow-up in Zambia: A Latent Class Analysis
Authors: Mody Aaloke , Sikombe Kombatende , Beres Laura K. , Simbeza Sandra , Mukamba Njekwa , Eshun-Wilson Ingrid , Schwartz Sheree , Pry Jake , Padian Nancy , Holmes Charles B. , Bolton-Moore Carolyn , Sikazwe Izukanji , Geng Elvin H.
Published: October 2020

Background:

Patients report varied barriers to HIV care across multiple domains, but specific barrier patterns may be driven by underlying, but unobserved, behavioral profiles.

Methods:

We traced a probability sample of patients lost to follow-up (>90 days late) as of July 31, 2015 from 64 clinics in Zambia. Among those found alive, we ascertained patient-reported reasons for care disruptions. We performed latent class analysis to identify patient subgroups with similar patterns of reasons reported and assessed the association between class membership and care status (ie, disengaged versus silently transferred to a new site).

Results:

Among 547 patients, we identified 5 profiles of care disruptions: (1) “Livelihood and Mobility” (30.6% of the population) reported work/school obligations and mobility/travel as reasons for care disruptions; (2) “Clinic Accessibility” (28.9%) reported challenges with attending clinic; (3) “Mobility and Family” (21.9%) reported family obligations, mobility/travel, and transport-related reasons; (4) “Doubting Need for HIV care” (10.2%) reported uncertainty around HIV status or need for clinical care, and (5) “Multidimensional Barriers to Care” (8.3%) reported numerous (mean 5.6) reasons across multiple domains. Patient profiles were significantly associated with care status. The “Doubting Need for HIV Care” class were mostly disengaged (97.9%), followed by the “Multidimensional Barriers to Care” (62.8%), “Clinic Accessibility” (62.4%), “Livelihood and Mobility” (43.6%), and “Mobility and Family” (23.5%) classes.

Conclusion:

There are distinct HIV care disruption profiles that are strongly associated with patients' current engagement status. Interventions targeting these unique profiles may enable more effective and tailored strategies for improving HIV treatment outcomes.
Reduction in Stigma Drivers Partially Mediates the Effect of a Stigma Reduction Intervention Among Nursing Students in India: The DriSti Cluster Randomized Controlled Trial
Authors: Srinivasan Krishnamachari , Heylen Elsa , Raj Tony , Nyblade Laura , Devadass Dhinagaran , Pereira Matilda , Ekstrand Maria L.
Published: October 2020

Background:

HIV stigma in health care settings acts as a significant barrier to health care. Stigma drivers among health professionals include transmission fears and misconceptions and pre-existing negative attitudes toward marginalized groups vulnerable to HIV. The DriSti intervention, consisted of 2 sessions with videos and interactive exercises on a computer tablet and one interactive face-to-face group session, mostly tablet administered, was designed to target key stigma drivers that included instrumental stigma, symbolic stigma, transmission misconceptions and blame to reduce HIV stigma, and discrimination among nursing students (NS) and ward staff and tested in a cluster randomized trial.

Setting:

This report focuses on second and third year NS recruited from a range of nursing schools that included private, nonprofit, and government-run nursing schools in south India.

Results:

Six hundred seventy-nine NS received intervention and 813 NS were in the wait-list control group. Twelve months outcome analyses showed significant reduction among intervention participants in endorsement of coercive policies (P < 0.001) and in the number of situations in which NS intended to discriminate against PLWH (P < 0.001). Mediation analysis revealed that the effects of intervention on endorsement of coercive policies and intent to discriminate against PLWH were partially mediated by reductions in key stigma drivers.

Conclusions:

This brief scalable stigma reduction intervention targeting key stigma drivers fills a critical gap in identifying the mechanistic pathways that aid in stigma reduction among health professionals.
Development of a Mathematical Model to Estimate the Cost-Effectiveness of HRSA's Ryan White HIV/AIDS Program
Authors: Goyal Ravi , Hu Cindy , Klein Pamela W. , Hotchkiss John , Morris Eric , Mandsager Paul , Cohen Stacy M. , Luca Dara , Gao Jessica , Jones Andrew , Addison West , O'Brien-Strain Margaret , Cheever Laura W. , Gilman Boyd
Published: October 2020

Background:

The Health Resources and Services Administration's Ryan White HIV/AIDS Program provides services to more than half of all people diagnosed with HIV in the United States. We present and validate a mathematical model that can be used to estimate the long-term public health and cost impact of the federal program.

Methods:

We developed a stochastic, agent-based model that reflects the current HIV epidemic in the United States. The model simulates everyone's progression along the HIV care continuum, using 2 network-based mechanisms for HIV transmission: injection drug use and sexual contact. To test the validity of the model, we calculated HIV incidence, mortality, life expectancy, and lifetime care costs and compared the results with external benchmarks.

Results:

The estimated HIV incidence rate for men who have sex with men (502 per 100,000 person years), mortality rate of all people diagnosed with HIV (1663 per 100,000 person years), average life expectancy for individuals with low CD4 counts not on antiretroviral therapy (1.52–3.78 years), and lifetime costs ($362,385) all met our validity criterion of within 15% of external benchmarks.

Conclusions:

The model represents a complex HIV care delivery system rather than a single intervention, which required developing solutions to several challenges, such as calculating need for and receipt of multiple services and estimating their impact on care retention and viral suppression. Our strategies to address these methodological challenges produced a valid model for assessing the cost-effectiveness of the Ryan White HIV/AIDS Program.
IgG4-Related Disease
Authors: Duggal Lalit , Singh Bhandari Gurbir , Patel Jeet , Gupta Mayank , Grover Ashok K. , Jain Neeraj
Published: October 2020

Aim

Immunoglobulin G4–related disease (IgG4-RD) is often an unrecognized, rare fibroinflammatory condition that can involve various organ systems. This study aimed to identify the different clinical patterns of this disease in a single center in North India.

Methods

Patients were diagnosed on the basis of published diagnostic criteria for IgG4-RD. Patients' presenting complaints; epidemiologic profiles; and laboratory, radiologic, and histologic findings along with the treatment and outcomes were collected and analyzed.

Results

In total, 70 patients were diagnosed with the disease. The female-to-male ratio was 0.94:1, and it increased with multiorgan involvement. The mean age of patients was 41.4 years, and the majority of the patients (65.7%) were younger than 50 years. Patients were diagnosed as possible (38.57%), probable (32.85%), and definite (28.57%) IgG4-RD. The incidence of the involvement of orbital and periorbital tissues was the highest (52.9%); however, 13% of the patients had multiple organ involvement. Patients with involvement of the retroperitoneal tissues and the lymph nodes were 8.5% and 5.7%, respectively. Increased serum IgG4 levels were found in 74.3% of the patients with single-organ involvement, whereas all patients with multiorgan involvement had increased IgG4 levels. The majority of patients (94.3%) required immunosuppressive medications along with corticosteroids. Azathioprine was the most commonly used (72.8%) immunosuppressive medication. Rituximab was used in 17.1% of the patients, of whom only one had multisystem involvement.

Conclusions

This study depicts the most common patterns of organ involvement, along with the epidemiologic, laboratory, histologic, and radiologic data and response to treatment, in IgG4-RD, with a definite ophthalmology referral bias.
Novel approaches to prediction in severe brain injury
Authors: Fidali Brian C. , Stevens Robert D. , Claassen Jan
Published: October 2020

Purpose of review

Recovery after severe brain injury is variable and challenging to accurately predict at the individual patient level. This review highlights new developments in clinical prognostication with a special focus on the prediction of consciousness and increasing reliance on methods from data science.

Recent findings

Recent research has leveraged serum biomarkers, quantitative electroencephalography, MRI, and physiological time-series to build models for recovery prediction. The analysis of high-resolution data and the integration of features from different modalities can be approached with efficient computational techniques.

Advances in neurophysiology and neuroimaging, in combination with computational methods, represent a novel paradigm for prediction of consciousness and functional recovery after severe brain injury. Research is needed to produce reliable, patient-level predictions that could meaningfully impact clinical decision making.
Magnetic Resonance Angiogram Findings of Internal Carotid Artery Narrowing and Anterior Cerebral Artery Hypoplasia Associated With Optic Atrophy After Neonatal Extracorporeal Membrane Oxygenation
Authors: Pogrebniak Alexander E. , Marcus Matthew A.
Published: October 2020

We use MRA to elucidate a potential association of unilateral optic atrophy in infancy, ipsilateral internal carotid artery narrowing after extracorporeal membrane oxygenation, and ipsilateral hypoplasia of the A1 segment of the anterior cerebral artery.
Eye Movements in Fragile X-Associated Tremor/Ataxia Syndrome
Authors: Hall Deborah A. , Leehey Maureen A. , Hagerman Randi J. , Pelak Victoria S.
Published: October 2020

Background:

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder characterized by ataxia, tremor, and parkinsonism. Eye motility abnormalities on the clinical examination of FXTAS patients have not been formally studied.

Methods:

A case–control study with fragile X gene mutation carriers with and without FXTAS and normal controls was conducted and included a videotaping of ocular items of the International Cooperative Ataxia Rating Scale (ICARS). A neuro-ophthalmologist blinded to gene status rated nystagmus, ocular pursuit, and saccades.

Results:

Forty-four cases and controls were recruited, with an average age of 55.2 years (±7.4) and 57% women. Gaze-evoked nystagmus was increased in fragile X gene carriers (odds ratio 1.44, 95% confidence interval: 0.33–7.36) but was not statistically significant. There was no difference in ocular pursuit nor saccade dysmetria between cases and controls.

Conclusion:

The results show that clinical examination findings of ocular abnormalities, using the ICARS oculomotor disorders movement subscale, are not more common in FXTAS or FMR1 premutation carriers than normal controls on examination in the clinic. Examining a larger cohort of patients with FXTAS would be an ideal next step.
Optic Disc Edema and Posterior Globe Flattening Secondary to Ocular Hypotony: Case Report and Discussion Regarding Pathophysiology and Clinical Findings
Authors: Albano de Guimarães Juliana , Teixeira Gabriela Carneiro , Silva Taiane Kelly Lima da , Moura Frederico Castelo
Published: October 2020

We describe a case of a young female patient presenting with ocular hypotension (4 mm Hg) secondary to cyclodialysis, and optic disc edema (ODE) after a blunt trauma in the right eye (right eye). MRI showed posterior globe flattening of the right eye, drawing our attention to the pathophysiology behind these findings. The combination of ODE and posterior globe flattening, as observed in the present case of ocular hypotony, is known from other conditions such as intracranial hypertension and space-flight neuro-ocular syndrome, pointing to a common pathophysiological mechanism, possibly resulting from axoplasmic stasis at the level of the lamina cribrosa due to a high translaminar pressure difference.
Structure prediction of crystals, surfaces and nanoparticles
Authors: Woodley Scott M. , Day Graeme M. , Catlow R.
Published: October 2020

We review the current techniques used in the prediction of crystal structures and their surfaces and of the structures of nanoparticles. The main classes of search algorithm and energy function are summarized, and we discuss the growing role of methods based on machine learning. We illustrate the current status of the field with examples taken from metallic, inorganic and organic systems.

This article is part of a discussion meeting issue ‘Dynamicin situmicroscopy relating structure and function’.
The influence of training load on hematological Athlete Biological Passport variables in elite cyclists
Authors: Tiffany Astolfi , von Roten Fabienne Crettaz , Bengt Kayser , Martial Saugy , Raphael Faiss
Published: October 2020

The hematological module of the Athlete Biological Passport (ABP) is used in elite sport for antidoping purposes. Its aim is to better target athletes for testing and to indirectly detect blood doping. The ABP allows to monitor hematological variations in athletes using selected primary blood biomarkers (hemoglobin concentration ([Hb] and reticulocyte percentage (Ret%)) with an adaptive Bayesian model to set individual upper and lower limits. If values fall without the individual limits, an athlete may be further targeted and ultimately sanctioned.

Since [Hb] and Ret% vary with plasma volume (PV) fluctuations, possibly caused by training load changes, we investigated the putative influence of acute and chronic training load changes on the ABP variables.

Monthly blood samples were collected over one year in 10 elite cyclists (25.6 ± 3.4 yrs, 181 ± 4 cm, 71.3 ± 4.9 kg, 6.7 ± 0.8 W.kg-1 5-min maximal power output) to calculate individual ABP profiles and monitor hematological variables. Total hemoglobin mass (Hbmass) and PV were additionally measured by carbon monoxide rebreathing. Acute and chronic training loads – respectively 5 and 42 days before sampling – were calculated considering duration and intensity (training stress score, TSS™).

[Hb] averaged 14.2 ± 0.0 (mean ± SD) g.dL-1 (range: 13.3 to 15.5 g·dl-1) over the study with significant changes over time (P = 0.004). Hbmass was 1’030 ± 87 g (range: 842 to 1116 g) with no significant variations over time (P = 0.118), whereas PV was 4309 ± 350 mL (range: 3688 to 4751 mL) with a time-effect observed over the study time (P = 0.014). Higher acute – but not chronic – training loads were associated with significantly decreased [Hb] (P <0.001). Although individual hematological variations were observed, all ABP variables remained within the individually calculated limits.

Our results support that acute training load variations significantly affect [Hb], likely due to short-term PV fluctuations, underlining the importance of considering training load when interpreting individual ABP variations for anti-doping purposes.
An ultra-sensitive, ultra-fast whole blood monocyte CD169 assay for COVID-19 screening
Authors: Michel Moïse , Malergue Fabrice , Belkacem Inès Ait , Bourgoin Pénélope , Morange Pierre-Emmanuel , Arnoux Isabelle , Miloud Tewfik , Million Matthieu , Tissot-Dupont Hervé , Mege Jean-Louis , Busnel Jean-Marc , Vitte Joana
Published: October 2020

CoVID-19 is an unprecedented epidemic, globally challenging health systems, societies, and economy. Its diagnosis relies on molecular methods, with drawbacks revealed by current use as mass screening. Monocyte CD169 upregulation has been reported as a marker of viral infections, we evaluated a flow cytometry three-color rapid assay of whole blood monocyte CD169 for CoVID-19 screening.

Outpatients (n=177) with confirmed CoVID-19 infection, comprising 80 early-stage (≤14 days after symptom onset), 71 late-stage (≥15 days), and 26 asymptomatic patients received whole blood CD169 testing in parallel with SARS-CoV-2 RT-PCR. Upregulation of monocyte CD169 without polymorphonuclear neutrophil CD64 changes was the primary endpoint. Sensitivity was 98% and 100% in early-stage and asymptomatic patients respectively, specificity was 50% and 84%. Rapid whole blood monocyte CD169 evaluation was highly sensitive when compared with RT-PCR, especially in early-stage, asymptomatic patients whose RT-PCR tests were not yet positive.

Diagnostic accuracy, easy finger prick sampling and minimal time-to-result (15-30 minutes) rank whole blood monocyte CD169 upregulation as a potential screening and diagnostic support for CoVID-19. Secondary endpoints were neutrophil CD64 upregulation as a marker of bacterial infections and monocyte HLA-DR downregulation as a surrogate of immune fitness, both assisting with adequate and rapid management of non-CoVID cases.
Application of Full Genome Analysis to Diagnose Rare Monogenic Disorders
Authors: Shieh Joseph T. , Penon-Portmann Monica , Wong Karen H.Y. , Levy-Sakin Michal , Verghese Michelle , Slavotinek Anne , Gallagher Renata C. , Mendelsohn Bryce A. , Tenney Jessica , Beleford Daniah , Perry Hazel , Chow Stephen K. , Sharo Andrew G. , Brenner Steven E. , Qi Zhongxia , Yu Jingwei , Klein Ophir D. , Martin David , Kwok Pui-Yan , Boffelli Dario
Published: October 2020

Current genetic tests for rare diseases provide a diagnosis in only a modest proportion of cases. The Full Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA’s utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application.
COVID-19 and Socioeconomic Factors: Cross-country Evidence
Authors: Jani Vishalkumar , Mavalankar Dileep
Published: October 2020

Background

COVID-19 pandemic has affected all countries across the globe in varying intensity resulting in varied numbers for total cases and deaths.

Objectives

The paper aims to understand if different socioeconomic factors have a role to play in determining the intensity of COVID-19 impact.

Methods

The study uses a country-wise number of corona cases and deaths and analyse them in a cross-country multivariate regression framework. It uses gross domestic product per capita, average temperature, population density, and median age as independent variables. The study uses testing data as a control variable.

Results

In absence of the testing variable, higher-income countries have experienced a higher number of COVID cases. The population density, median age, climate do not have significant impact. The countries with higher population density have lower deaths. Each region shows different patterns of correlation between socioeconomic factors and COVID intensity.

Conclusion

The majority of the cross-country variation can be attributed to the number of tests done by a country. The countries with high population density would have applied strict lockdowns and proactive testing to curb the deaths. The study essentially refutes claims around corona being a high-income group disease, cold-climate disease, or a disease impacting old-age patients more.
THE IMPACT OF LOCKDOWN ON PUBLIC HEALTH DURING THE FIRST WAVE OF COVID-19 PANDEMIC: LESSONS LEARNED FOR DESIGNING EFFECTIVE CONTAINMENT MEASURES TO COPE WITH SECOND WAVE
Authors: Coccia Mario
Published: October 2020

What is hardly known in the studies of the COVID-19 global pandemic crisis is the impact of general lockdown during the first wave of COVID-19 pandemic both public health and economic system. The main goal of this study is a comparative analysis of some European countries with a longer and shorter period of national lockdown during the first wave of COVID-19 from March to August 2020. Findings suggests that: a) countries with shorter period of lockdown have a variation of confirmed cases/population (%) higher than countries with longer period of lockdown; b) countries with shorter period of lockdown have average fatality rate (5.45%) lower than countries with longer period of lockdown (12.70%), whereas variation of fatality rate from August to March 2020 suggests a higher reduction in countries with longer period of lockdown (−1.9% vs 0.72%). However, Independent Samples Test and the Mann-Whitney test reveal that the effectiveness of longer period of lockdown versus shorter one on public health is not significant. In addition, the COVID-19 pandemic associated with longer period of lockdown has a higher negative impact on economic growth with consequential social issues in countries. Results of the impact of COVID-19 lockdowns on public health and economies of some leading countries in Europe, during the first wave of the COVID-19 pandemic, can provide vital information to design effective containment strategies in future waves of this pandemic to minimize the negative effects in society.
Longitudinal caries prevalence in a comprehensive, multi-component, school-based prevention program
Authors: Starr Jacqueline R. , Ruff Ryan R. , Palmisano Joseph , Goodson J. Max , Bukhari Omair M. , Niederman Richard
Published: October 2020

Background

Globally, children’s caries prevalence exceeds 30% and has not markedly changed in 30 years. School-based caries prevention programs may be an effective method to reduce caries prevalence, obviate traditional barriers to care, and use aerosol-free interventions. The objective of this study was to explore the clinical effectiveness of a comprehensive school-based, aerosol-free, caries prevention program.

Methods

We conducted a 6-year prospective open cohort study in 33 U.S. public elementary schools, providing care to 6,927 children in communities with and without water fluoridation. Following a dental examination, dental hygienists provided twice-yearly prophylaxis, glass ionomer sealants, glass ionomer interim therapeutic restorations, fluoride varnish, toothbrushes, fluoride toothpaste, oral hygiene instruction, and referral to community dentists as needed. We used generalized estimating equations to estimate the change in the prevalence of untreated caries over time.

Results

The prevalence of untreated caries decreased by greater than 50%: from 39% to 18% in phase 1, and from 28% to 10% in phase 2. The per-visit adjusted odds ratio of untreated decay was 0.79 (95% CI: 0.73, 0.85).

Conclusions and Practical Implications

We show that a school-based comprehensive caries prevention program was associated with substantial reductions in children’s caries, supporting the concept of expanding traditional practices to include office- and community-based aerosol-free care.
Multimodal profiling of lung granulomas reveals cellular correlates of tuberculosis control
Authors: Gideon Hannah P. , Hughes Travis K. , Tzouanas Constantine N. , Wadsworth Marc H. , Tu Ang Andy , Gierahn Todd M. , Peters Joshua M. , Hopkins Forrest F. , Wei Jun-Rong , Kummerlowe Conner , Grant Nicole L. , Nargan Kievershen , Phuah Jia Yao , Borish H. Jacob , Maiello Pauline , White Alexander G. , Winchell Caylin G. , Nyquist Sarah K. , Ganchua Sharie Keanne C. , Myers Amy , Patel Kush V , Ameel Cassaundra L. , Cochran Catherine T. , Ibrahim Samira , Tomko Jaime A , Frye Lonnie James , Rosenberg Jacob M. , Shih Angela , Chao Michael , Scanga Charles A. , Ordovas-Montanes Jose , Berger Bonnie , Mattila Joshua T. , Madansein Rajhmun , Love J. Christopher , Lin Philana Ling , Leslie Alasdair , Behar Samuel M. , Bryson Bryan , Flynn JoAnne L , Fortune Sarah M. , Shalek Alex K.
Published: October 2020

Mycobacterium tuberculosislung infection results in a complex multicellular structure, the granuloma. In some granulomas, immune activity promotes bacterial clearance; in others, bacteria persist and grow. We identified correlates of bacterial control in cynomolgus macaque lung granulomas by co-registering longitudinal PET-CT imaging, single-cell RNA-sequencing, and measures of bacterial clearance. We find that bacterial persistence occurs in granulomas enriched for mast, endothelial, fibroblast and plasma cells, signaling amongst themselves via Type II immunity and wound healing pathways. In contrast, these interactions are largely absent in granulomas that drive bacterial control, which are often those that form later in the course of infection; these restrictive lesions are characterized by cellular ecosystems enriched for Type1-Type17, stem-like, and cytotoxic T cells engaged in pro-inflammatory signaling networks that involve diverse myeloid and non-immune cell populations. There is also a temporal aspect to bacterial control, in that granulomas that arise later in infection (in the context of an established immune response) share the functional characteristics of restrictive granulomas and are more capable of killing Mtb. Taken together, our results define the complex multicellular ecosystems underlying (lack of) granuloma resolution and highlight host immune targets that can be leveraged to develop new vaccine and therapeutic strategies for TB.

One-Sentence Summary

Bacterial control in TB lung granulomas correlates with distinct cellular immune microenvironments and time of formation after infection.
1Cross Sectional Study of Middle East Respiratory Syndrome (Mers-Cov Infection) in Camels at Selected Sites of Amibara District, Afar Region, Ethiopia
Authors: Sibhatu Demeke , Mamo Gezahagne , Aklillu Fasil , Zewde Demeke , Walelign Elias , Muluneh Ayelech , Aliey Abdi , Mirkena Tadele , Tewolde Nega , Gari Getachew , van ‘t Klooster Gijs , Elmasry Ihab , VonDobschuetz Sophie , Peiris Malik , Chu Daniel , Perera Ranawaka APM , Jobire Yilma
Published: October 2020

Background

A Cross sectional study of Middle East Respiratory Syndrome Corona virus (MERS-CoV) in Camel was conducted between February 2018 to April 2019 in three selected sites of Amibara district of Afar region, Northeast Ethiopia. The study was aimed to observe the current sero-prevalence status of MERS-CoV, assess the presence of active cases through detection RNA Viral particle and investigate possible risk factors of MERS-CoV in camels. A total of 589 sera were collected and tested with indirect Enzyme linked ImmunoSorbent Assay (iELISA).

Result

The overall seroprevalance of MERS-CoV was 87.3% (n=514/589, 95% CI: 84.5-89.9). Association of different risk factors with seroprevalance revealed that origin (X2=13.39,P=0.001), sex (X2=4.5 P=0.034), age ((X2=185.7, P=0.001) season (X2=41.7, P=0.000) and reproduction status (X2=96.1, P=0.001) displayed a statistical significant difference among the groups (P<0.05) while herd size did not show a Significant difference among groups (p>0.05). In multivariable logistic regression analysis, age (OR=7.39, 95% CI:3.43-15.91), season (OR=4.83, 95% CI:-2.14-10.90), and in adult female camel reproduction status (OR=7.39,95% C I:3.43-15.91) showed statistically significant difference among the groups for MERS CoV antibody detection while risk factors of origin, animal sex and herd size difference were statistically insignificant. A total of 857 nasal swab samples were collected for the detection of MERS-CoV RNA particle. However, all swab samples tested by Real-time reverse transcription polymerase chain reaction (RT-PCR) technique were Negative for the virus.

Conclusion

In conclusion, the present study revealed a high seroprevalance of MERS CoV in adult camels. However, in spite of high seroprevalance the lack of any RNA viral particle in the study suggests the need for further in depth longitudinal study to detect the circulating virus focusing on juveniles and young camels whereby seroprevalance of antibody is low when compared with adult camel in order to get the active virus before the camel develop antibody. Moreover, the zoonotic significance and potential transmission routes of MERS CoV to pastoral communities should also be investigated and design strategy for the preparedness in control of the diseases in Ethiopia.
BioSamplr: An open source, low cost automated sampling system for bioreactors
Authors: Efromson John P. , Li Shuai , Lynch Michael D.
Published: October 2020

Autosampling from bioreactors reduces error, increases reproducibility and offers improved aseptic handling when compared to manual sampling. Additionally, autosampling greatly decreases the hands-on time required for a bioreactor experiment and enables sampling 24 hrs a day. We have designed, built and tested a low cost, open source, automated bioreactor sampling system, the BioSamplr. The BioSamplr can take up to ten samples from a bioreactor at a desired sample interval and cools them to a desired temperature. The device, assembled from low cost and 3D printed components, is controlled wirelessly by a Raspberry Pi, and records all sampling data to a log file. The cost and accessibility of the BioSamplr make it useful for laboratories without access to more expensive and complex autosampling systems.
Drug self-administration in head-restrained mice for simultaneous multiphoton imaging
Authors: Vollmer Kelsey M. , Doncheck Elizabeth M. , Grant Roger I. , Winston Kion T. , Romanova Elizaveta V. , Bowen Christopher W. , Siegler Preston N. , Bobadilla Ana-Clara , Trujillo-Pisanty Ivan , Kalivas Peter W. , Otis James M.
Published: October 2020

Multiphoton microscopy is one of several new technologies providing unprecedented insight into the activity dynamics and function of neural circuits. Unfortunately, many of these technologies require experimentation in head-restrained animals, greatly limiting the behavioral repertoire that can be studied with each approach. This issue is especially evident in drug addiction research, as no laboratories have coupled multiphoton microscopy with simultaneous intravenous drug self-administration, the gold standard of behavioral paradigms for investigating the neural mechanisms of drug addiction. Such experiments would be transformative for addiction research as one could measure or perturb an array of behavior and drug-related adaptations in precisely defined neural circuit elements over time, including but not limited to dendritic spine plasticity, neurotransmitter release, and neuronal activity. Here, we describe a new experimental assay wherein mice self-administer drugs of abuse while head-restrained, allowing for simultaneous multiphoton imaging. We demonstrate that this approach enables longitudinal tracking of activity in single neurons from the onset of drug use to relapse. The assay can be easily replicated by interested labs for relatively little cost with readily available materials and can provide unprecedented insight into the neural underpinnings of substance use disorder.
The RNA Structurome in the Asexual Blood Stages of Malaria PathogenPlasmodium falciparum
Authors: Alvarez Diana Renteria , Ospina Alejandra , Barwell Tiffany , Zheng Bo , Dey Abhishek , Li Chong , Basu Shrabani , Shi Xinghua , Kadri Sabah , Chakrabarti Kausik
Published: October 2020

RNA as an effector of biological functions often adopts secondary and tertiary structural folds.Plasmodium falciparumis a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle inP. falciparumin human red blood cells. Our comprehensive analysis, combining high-throughput nuclease mapping of RNA structures by duplex RNA-seq, immunoaffinity purification and RNA analysis, collectively measured differentially base-paired RNA regions during the parasite development. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, ~71% of the genes with secondary structures are found to be protein coding mRNAs. Mapping pattern of these base-paired RNAs corresponded to all parts of protein-coding mRNAs, including 5’ UTR, CDS and 3’ UTR. In addition to histone family genes which are known to form secondary structures in their mRNAs, transcripts from genes which are important for transcriptional and post-transcriptional control, such as unique plant-like transcription factor family,ApiAP2, DNA/RNA binding protein family,Alba, ribosomal proteins and eukaryotic initiation factors involved in translational control and the ones important for RBC invasion and cytoadherence also show strong accumulation of duplex RNA reads in various asexual stages. Intriguingly, our study determined a positive relationship between mRNA structural contents and translation efficiency inP. falciparumasexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.
ALS monocyte-derived microglia reveal cytoplasmic TDP-43 accumulation, DNA damage, and cell-specific impairment of phagocytosis associated with disease progression
Authors: Quek Hazel , Cuní-López Carla , Stewart Romal , Colletti Tiziana , Notaro Antonietta , Sun Yifan , Guo Christine C. , Lupton Michelle K. , Nguyen Tam Hong , Oikari Lotta E. , Roberts Tara L. , Lim Yi Chieh , La Bella Vincenzo , White Anthony R.
Published: October 2020

Aims

Amyotrophic lateral sclerosis (ALS) is a multifactorial neurodegenerative disease characterised by the loss of upper and lower motor neurons. Neuroinflammation mediated by microglial activation is evident in post-mortem brain tissues, and in brain imaging of patients with ALS. However, the exact role of microglia in ALS remains to be elucidated partly due to the lack of an accurate microglial model system that is able to recapitulate the clinical pathology of ALS. Moreover, direct sampling of microglia from patients with ALS is not feasible, further limiting the study of microglial function in ALS. To address this shortcoming, we describe an approach that generates monocyte-derived microglia (MDMi) that are capable of expressing molecular markers, and functional characteristics similar to resident human brain microglia. Importantly, MDMi can be routinely and reproducibly generated from ALS patient blood, and reveal patient heterogeneity associated with age, sex and disease subgroup.

Methods

MDMi were successfully established from all 30 ALS patients, including 15 patients with slow disease progression, 6 with intermediate progression, and 9 with rapid progression, together with 20 non-affected heathy controls (HC).

Results

Our ALS MDMi model recapitulated canonical pathological features of ALS including non-phosphorylated and phosphorylated-TDP-43-positive pathological inclusions. We further observed significantly impaired phagocytosis, altered cytokine expression and microglial morphology, as well as elevated DNA damage in ALS compared to HC MDMi. Abnormal phagocytosis was observed in all ALS cases, and was correlated to the progression of disease. Moreover, in-depth analysis of individual microglia revealed cell-specific variation in phagocytic function that was significantly altered, and exacerbated in rapid disease progression.

Conclusions

Our approach enabled us to generate ALS patient microglia from peripheral blood samples using a rapid, robust, cost-effective, and reproducible protocol. We have shown that ALS monocyte-derived microglia have significantly altered functional behaviour compared to age-matched HCs, with a major deficit in phagocytic activity. This is also the first demonstration of abnormal TDP-43 localisation in microglia grown from ALS patients. Overall, this approach is highly applicable to monitor disease progression and can be applied as a functional readout in clinical trials for anti-neuroinflammatory agents. Additionally, this model system can be used as a basis for personalised therapeutic treatment for ALS, as well as other neurodegenerative diseases.
Ultra-fast Prediction of Somatic Structural Variations by Reduced Read Mapping via Pan-Genomek-mer Sets
Authors: Choi Min-Hak , Sohn Jang-il , Yi Dohun , Menon A Vipin , Kim Yeon Jeong , Kyung Sungkyu , Shin Seung-Ho , Na Byunggook , Joung Je-Gun , Yoon Sungro , Koh Youngil , Baek Daehyun , Kim Tae-Min , Nam Jin-Wu
Published: October 2020

Genome rearrangements often result in copy number alterations of cancer-related genes and cause the formation of cancer-related fusion genes. Current structural variation (SV) callers, however, still produce massive numbers of false positives (FPs) and require high computational costs. Here, we introduce an ultra-fast and high-performing somatic SV detector, called ETCHING, that significantly reduces the mapping cost by filtering reads matched to pan-genome and normalk-mer sets. To reduce the number of FPs, ETCHING takes advantage of a Random Forest classifier that utilizes six breakend-related features. We systematically benchmarked ETCHING with other SV callers on reference SV materials, validated SV biomarkers, tumor and matched-normal whole genomes, and tumor-only targeted sequencing datasets. For all datasets, our SV caller was much faster (≥15X) than other tools without compromising performance or memory use. Our approach would provide not only the fastest method for largescale genome projects but also an accurate clinically practical means for real-time precision medicine.
Structural basis of rotavirus RNA chaperone displacement and RNA annealing
Authors: Bravo Jack P. K. , Bartnik Kira , Venditti Luca , Gail Emma H. , Davidovich Chen , Lamb Don C , Tuma Roman , Calabrese Antonio N. , Borodavka Alexander
Published: October 2020

Rotavirus genomes are distributed between eleven distinct RNA molecules, all of which must be selectively co-packaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 auto-regulates its chaperone activity through its C-terminal region (CTR) that promotes RNA-RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, whilst accelerating RNA release from NSP2. Cryo-electron microscopy reconstructions of an NSP2-RNA complex reveal a highly conserved acidic patch poised towards RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation whilst promoting inter-molecular RNA interactions may be a widespread strategy of RNA chaperone recycling.
Implementation of a crossed-slit system for fast alignment of sealed polycapillary X-ray optics
Authors: Zymaková Anna , Khakurel Krishna , Picchiotti Alessandra , Błachucki Wojciech , Szlachetko Jakub , Rebarz Mateusz , Uhlig Jens , Andreasson Jakob
Published: October 2020

A new modification of a table-top laser-driven water-jet plasma X-ray source has been successfully implemented and commissioned at the Extreme Light Infrastructure (ELI) Beamlines user facility. In order to preserve the broadband nature of the source for spectroscopic experiments, a polycapillary lens was initially chosen as the focusing element. Generally, polycapillary X-ray optics have a narrow photon acceptance angle and small field of view, making alignment complicated and time-consuming. This contribution demonstrates a straightforward, reliable and reproducible procedure for aligning polycapillary focusing optics with broadband X-rays. The method involves a pre-alignment step where two X-ray slits are mounted orthogonally on opposite sides of a 3D-printed cylindrical polycapillary holder. This helps to precisely determine the optical axis of the X-ray beam. Subsequent mounting of the polycapillary in the pre-aligned holder with the slits removed allowed for immediate transmission of the X-ray photons through the optics and has provided a good starting point for fine alignment.
Backside-illuminated scientific CMOS detector for soft X-ray resonant scattering and ptychography
Authors: Desjardins Kewin , Medjoubi Kadda , Sacchi Maurizio , Popescu Horia , Gaudemer Roland , Belkhou Rachid , Stanescu Stefan , Swaraj Sufal , Besson Adrien , Vijayakumar Jaianth , Pautard Stéphanie , Noureddine Arafat , Mercère Pascal , Da Silva Paulo , Orsini Fabienne , Menneglier Claude , Jaouen Nicolas
Published: October 2020

The impressive progress in the performance of synchrotron radiation sources is nowadays driven by the so-called `ultimate storage ring' projects which promise an unprecedented improvement in brightness. Progress on the detector side has not always been at the same pace, especially as far as soft X-ray 2D detectors are concerned. While the most commonly used detectors are still based on microchannel plates or CCD technology, recent developments of CMOS (complementary metal oxide semiconductor)-type detectors will play an ever more important role as 2D detectors in the soft X-ray range. This paper describes the capabilities and performance of a camera equipped with a newly commercialized backside-illuminated scientific CMOS (sCMOS-BSI) sensor, integrated in a vacuum environment, for soft X-ray experiments at synchrotron sources. The 4 Mpixel sensor reaches a frame rate of up to 48 frames s−1 while matching the requirements for X-ray experiments in terms of high-intensity linearity (>98%), good spatial homogeneity (<1%), high charge capacity (up to 80 ke−), and low readout noise (down to 2 e− r.m.s.) and dark current (3 e− per second per pixel). Performance evaluations in the soft X-ray range have been carried out at the METROLOGIE beamline of the SOLEIL synchrotron. The quantum efficiency, spatial resolution (24 line-pairs mm−1), energy resolution (<100 eV) and radiation damage versus the X-ray dose (<600 Gy) have been measured in the energy range from 40 to 2000 eV. In order to illustrate the capabilities of this new sCMOS-BSI sensor, several experiments have been performed at the SEXTANTS and HERMES soft X-ray beamlines of the SOLEIL synchrotron: acquisition of a coherent diffraction pattern from a pinhole at 186 eV, a scattering experiment from a nanostructured Co/Cu multilayer at 767 eV and ptychographic imaging in transmission at 706 eV.
Fast convolution-based performance estimation method for diffraction-limited source with imperfect X-ray optics
Authors: Hu Lingfei , Sutter John P. , Wang Hongchang
Published: October 2020

Although optical element error analysis is always an important part of beamline design for highly coherent synchrotron radiation or free-electron laser sources, the usual wave optics simulation can be very time-consuming, which limits its application at the early stage of the beamline design. In this work, a new theoretical approach has been proposed for quick evaluations of the optical performance degradation due to optical element error. In this way, time-consuming detailed simulations can be applied only when truly necessary. This approach treats the imperfections as perturbations that convolve with the ideal performance. For simplicity, but not by necessity, the Gaussian Schell-model has been used to show the application of this theoretical approach. The influences of the finite aperture size and height error of a focusing mirror are analysed using the proposed theory. The physical explanation of the performance degradation acquired from the presented approach helps to give a better definition of the critical range of error spatial frequencies that most affect the performance of a mirror. An example comparing two mirror surface errors with identical power spectral density functions is given. These two types of mirror surface errors result in very different intensity profiles. The approach presented in this work could help beamline designers specify the error tolerances on general optical elements more accurately.