bluuebunny/crossref_metadata_2025 huggingface dataset:
Semi-quantitative F-18-FDG PET/computed tomography parameters for prediction of grade in patients with renal cell carcinoma and the incremental value of diuretics
Authors: Singh Harpreet , Arora Geetanjali , Nayak Brusabhanu , Sharma Akshima , Singh Geetika , Kumari Kalpana , Jana Suman , Patel Chetan , Pandey Anil Kumar , Seth Amlesh , Kumar Rakesh
Published: March 2020

Objective

The primary objective of the study was to evaluate the correlation between semi-quantitative F-18 FDG PET parameters and renal cell carcinoma (RCC) grade and its role in predicting the histopathological grade in RCC. The secondary objective was to evaluate the role of forced diuresis in improving the diagnostic accuracy of F-18 FDG for RCC.

Methods

Thirty-three patients with radiologically proven RCC were included in the study. All patients underwent PET/CT on a dedicated PET/CT scanner (Biograph mCT; Siemens Medical Solutions, Erlangen, Germany) 45–60 min post-injection F-18-FDG. Patients were then injected 1 mg/kg body weight furosemide (upto 40 mg) and regional PET/CT images of abdomen were acquired after 2 h. For both baseline and post-diuretic F-18-FDG PET/CT scans, maximum standardized uptake value for tumor (SUVmax), mean SUV for tumor, metabolic tumor volume (MTV), tumor-to-liver (T/L) and tumor-to-kidney ratio (T/K) were calculated. Histopathology findings were considered as the reference standard. To assess the incremental value of diuresis in scan interpretation, visual analysis of scans was done.

Results

Of 33 patients, histopathology grading was available for comparison with metabolic tumor markers in all except four. Of 29 patients (mean age = 51.89 ± 13.54 years), 20 patients had clear cell (cc) type while rest had non-cc RCC. Difference between the mean values among the categories was insignificant for all parameters except T/K. Fuhrman grading was obtained in 25 patients (17 low and eight high). SUVmax, MTV and T/L were found to be significantly different between low and high grade patients. Significantly strong positive correlation was observed between Furhman grades and tumor metabolism (r ≥ 0.5). No significant difference was observed between baseline and post-diuretic scan in any of the patients.

Conclusion

Semi-quantitative F-18 FDG PET parameters (SUVmax, MTV and T/L) were found to be significantly correlated with Fuhrman grade in patients with RCC and are important markers for differentiation between low- and high-grade tumors. Furthermore, forced diuresis had no incremental value in characterization of primary RCC lesions.
Do BRAFV600E mutation and sodium-iodide symporter expression affect the response to radioactive iodine therapy in patients with papillary thyroid carcinoma?
Authors: Makboul Rania , Mostafa Nadia M. , El-Deek Heba E.M. , Aboulhagag Noha A. , Shehata Mahmoud R. , Abdelhafez Yasser G.
Published: March 2020

Objective

To report on the associations between BRAFV600E and sodium iodide symporter expressions and treatment outcomes in patients with papillary thyroid carcinoma.

Methods

Inclusion criteria included a pathologic diagnosis of papillary thyroid carcinoma of any stage, thyroidectomy followed by radioactive iodine therapy, and follow-up for at least 12 months after initial therapy. Events were classified as persistent or recurrent disease based on a clinical or investigational evidence of disease within or after, respectively, 1 year from initial therapy. Disease-free survival was calculated between the dates of surgery and confirmed event. Patients with no evidence of disease were censored at their last follow-up (censored group). BRAFV600E mutation and sodium-iodide symporter expressions were evaluated using immunohistochemistry.

Results

The study included 78 patients (60 females, 18 males) with median age 36 years (range: 20–70 years). BRAFV600E was positive in 78%, equivocal in 13%, and negative in 9%. Sodium-iodide symporter was positive in 88%. BRAFV600E mutation was significantly associated with increasing tumor size, presence of lymphovascular invasion, classic subtype of papillary thyroid carcinoma, thyroid capsular infiltration, and lymph node metastasis. Sodium-iodide symporter expression was not associated with any clinical or pathologic characteristics. Patients with negative or equivocal BRAFV600E had significantly better disease-free survival (82%, 3 events) compared to the positive group (41%, 33 events; P=0.02).

Conclusion

In patients with papillary thyroid carcinoma, BRAFV600E mutation is associated with high-risk pathological characteristics and worsened disease-free survival.
The Evaluation of a Palliative Care Advanced Practice Nursing Externship
Authors: Gentry Jennifer H. , Dahlin Constance
Published: March 2020

A growing population of persons with a serious illness will place higher demands on health care professionals to provide the palliative care needed. A Palliative Care Advanced Practice Registered Nurse (APRN) Externship was developed and implemented as a novel way to increase access to palliative care with the potential to be replicated in multiple locations. Two APRN cohorts with a total of 10 APRNs participated in a 1-week educational program, including both classroom and clinical experiences, in 1 such site. The effectiveness of the program was evaluated by participants through an electronic survey and debriefings. Active learning experiences included role play, case studies, and clinical observation and were rated as highly valuable by participants. An important theme concerning the validation of current practice was identified. Future externship programs should be refined by incorporating participant feedback and continuing to use a variety of techniques to engage learners with diverse learning styles.
Characteristics and Clinical Outcomes of Prolonged Continuous Renal Replacement Therapy in Critically Ill Pediatric Patients
Authors: Pekkucuksen Naile Tufan , Akcan Arikan Ayse , Swartz Sarah J. , Srivaths Poyyapakkam , Angelo Joseph R.
Published: March 2020

Objectives:

Paralleling improved outcomes in critically ill patients, survival for pediatric acute kidney injury has improved. Continuous renal replacement therapy is the preferred modality to optimize fluid and electrolyte management as well as nutritional support for children developing acute kidney injury in the PICU. However, some patients remain too fragile for transition to intermittent renal replacement therapies and require continuous renal replacement therapy for a prolonged period. Characteristics of this cohort and factors impacting outcomes are not well known. We aimed to describe the characteristics of pediatric patients requiring prolonged continuous renal replacement therapy and evaluate the factors impacting hospital survival.

Design:

Retrospective chart review.

Setting:

Tertiary PICU.

Patients:

Children requiring prolonged continuous renal replacement therapy. Prolonged continuous renal replacement therapy was defined as continuous renal replacement therapy dependence greater than or equal to 28 days. Primary outcome was hospital mortality.

Interventions:

None.

Measurements and Main Results:

From 2013 to 2016, 344 patients received continuous renal replacement therapy, 36 (10%) received continuous renal replacement therapy for greater than or equal to 28 days. Seventeen patients (47%) were female. Overall mortality was 44% (16/36); 69% (11/16) of nonsurvivors died of sepsis. Pediatric Logistic Organ Dysfunction score was significantly higher in nonsurvivors. Mortality rate was significantly higher in patients who were neutropenic at continuous renal replacement therapy start. Neutropenia (defined as absolute neutrophil count < 1,500/mm3) at continuous renal replacement therapy start was the only independent predictor of mortality. One in four survivors did not recover renal function and remained dialysis dependent.

Conclusions:

Prolonged continuous renal replacement therapy patients are at high risk of nonrecovery of renal function and require close monitoring. The majority of nonsurvivors in the study group died from sepsis. Neutropenia at continuous renal replacement therapy initiation was associated with increased risk of mortality. Progression of underlying disease process could explain the higher death rate in patients with neutropenia; however, inadequate treatment of infectious complications could be another explanation to explore further in future studies.
Survival and Mid-Term Neurologic Outcome After Extracorporeal Cardiopulmonary Resuscitation in Children
Authors: Kramer Peter , Mommsen Annick , Miera Oliver , Photiadis Joachim , Berger Felix , Schmitt Katharina R. L.
Published: March 2020

Objectives:

Extracorporeal cardiopulmonary resuscitation in children with refractory cardiac arrest has been shown to improve survival, however, risk factors associated with mortality and neurologic impairments are not well defined. We analyzed our recent institutional experience with pediatric extracorporeal cardiopulmonary resuscitation to identify variables associated with survival and neurocognitive outcome.

Design:

Retrospective observational study.

Setting:

Pediatric cardiology and congenital heart surgery departments of a tertiary referral heart center.

Patients:

Seventy-two consecutive children (median age, 0.3 yr [0.0–1.9 yr]) who underwent extracorporeal cardiopulmonary resuscitation at our institution during the study period from 2005 to 2016.

Interventions:

Not applicable.

Measurements and Main Results:

Median duration of resuscitation was 60 minutes (42–80 min) and median extracorporeal support duration was 5.4 days (2.2–7.9 d). Forty-three (59.7%) extracorporeal cardiopulmonary resuscitation events occurred during off-hours, however, neither duration of resuscitation (65 min [49–89 min] vs 51 min [35–80 min]; p = 0.16) nor survival (34.9% vs 37.9%; p = 0.81) differed significantly compared to working hours. Congenital heart disease was present in 84.7% of the patients. Survival to hospital discharge was 36.1%; younger age, higher lactate levels after resuscitation, acute kidney injury, renal replacement therapy, hepatic injury, and complexity of prior cardiothoracic surgical procedures were significantly associated with mortality. At mid-term follow-up (median, 4.1 yr [3.7–6.1 yr]), 22 patients (84.6% of discharge survivors) were still alive with 77.3% having a favorable neurologic outcome. High lactate levels, arrest location other than ICU, and requirement for renal replacement therapy were associated with unfavorable neurologic outcome. Interestingly, longer duration of resuscitation did not negatively impact survival or neurologic outcome.

Conclusions:

Extracorporeal cardiopulmonary resuscitation is a valuable tool for the treatment of children with refractory cardiac arrest and a favorable neurologic outcome can be achieved in the majority of survivors even after prolonged resuscitation. Mortality after extracorporeal cardiopulmonary resuscitation in postcardiac surgery children is associated with procedural complexity.
Using Quality Improvement to Reduce IV Acetaminophen Use in a PICU
Authors: Howell Katelyn A. , Ruggles Cassandra A. , Thompson Marlene , Metzger Kelly Z. , Christopher Jean A. , Bigham Michael T.
Published: March 2020

Objectives:

Improve medication-related variable ICU costs by increasing value related to a locally identified high-frequency/high-cost medication, IV acetaminophen.

Design:

Structured quality improvement initiative using the Institute for Healthcare Improvement’s Model for Improvement.

Setting:

Twenty-three–bed tertiary PICU.

Patients:

All patients admitted to the PICU receiving IV acetaminophen during the study period of 2015–2018.

Interventions:

PICU staff survey, education to close nurse/provider knowledge gap, optimization of order sets and electronic health record order entry, improving oral/enteral medication transition, and optimization of pharmacy dispensing.

Measurements and Main Results:

The primary outcome of interest was IV acetaminophen doses per patient day reported as a 12-month rolling average. Baseline IV acetaminophen prescribing prior to the study period was initially 0.55 doses per patient day, and in 2014, there were 3,042 doses administered. IV acetaminophen is $43 per dose. The rolling 12-month average post intervention was 0.33 doses per patient day. Enteral and rectal doses increased from 0.42 to 0.58 doses per patient day. Opioid utilization varied throughout the study. A 40% reduction in IV acetaminophen equated to a $35,507 cost savings in a single year.

Conclusions:

IV acetaminophen is prescribed with high frequency and impacts variable PICU costs. Value can be improved by optimizing IV acetaminophen prescribing.
Testing for Common Respiratory Viruses in Children Admitted to Pediatric Intensive Care: Epidemiology and Outcomes
Authors: Moynihan Katie M. , McGarvey Tambra , Barlow Andrew , Heney Claire , Gibbons Kristen , Clark Julia E. , Schlebusch Sanmarié , Schlapbach Luregn J.
Published: March 2020

Objectives:

Viral infections are common in children, but there is a lack of data on severe viral infections in critically ill children. We investigated testing for viral infections in children requiring PICU admission and describe the epidemiology and outcomes.

Design:

Multicenter retrospective study. Results of viral testing for nine respiratory viruses using polymerase chain reaction were collected.

Participants:

Children less than 16 years old nonelectively admitted to PICU over a 6-year period.

Setting:

Two tertiary PICUs in Queensland, Australia.

Interventions:

None.

Main Outcome Measures:

Primary outcome was PICU length of stay. Secondary outcomes included need for and duration of intubation and mortality in PICU. Univariate and multivariate regression analyses were performed, adjusting for age, indigenous status, comorbidities, and severity of illness.

Results:

Of 6,426 nonelective admissions, 2,956 (46%) were polymerase chain reaction tested for a virus of which 1,353 (46%) were virus positive. Respiratory syncytial virus was the most common pathogen identified (n = 518, 33%), followed by rhinovirus/enterovirus and adenovirus. Across all patients who underwent polymerase chain reaction testing, identification of a respiratory virus was not significantly associated with longer overall length of stay (multivariate odds ratio, 1.08; 95% CI, 0.99–1.17; p = 0.068) or longer intubation (p = 0.181), whereas the adjusted odds for intubation and mortality were significantly lower (p < 0.01). Subgroup analyses restricted to patients with acute respiratory infections (n = 1,241), bronchiolitis (n = 761), pneumonia (n = 311), confirmed bacterial infection (n = 345), and malignancy (n = 95) showed that patients positive for a virus on testing had significantly longer PICU length of stay (multivariate p < 0.05). In children with pneumonia, identification of a respiratory virus was associated with significantly increased duration of ventilation (p = 0.003). No association between positive test results for multiple viruses and outcomes was observed.

Conclusion:

Viral infections are common in critically ill children. Viral infections were associated with lower intubation and mortality rates compared with all children testing negative for viral infections. In several subgroups studied, identification of viral pathogens was associated with longer PICU length of stay while mortality was comparable. Prospective studies are required to determine the benefit of routine testing for respiratory viruses at the time of PICU admission.
The Effect of Patient- and Treatment-Related Factors on Circuit Lifespan During Continuous Renal Replacement Therapy in Critically Ill Children
Authors: Cortina Gerard , McRae Rosemary , Chiletti Roberto , Butt Warwick
Published: March 2020

Objectives:

To examine the effects of patient and treatment variables on circuit lifespan in critically ill children requiring continuous renal replacement therapy.

Design:

Retrospective observational study based on a prospective registry.

Setting:

Tertiary referral 30-bed PICU.

Patients:

One hundred sixty-one critically ill children undergoing continuous renal replacement therapy during an 8-year period (2007–2014) were included in the study.

Interventions:

Continuous renal replacement therapy.

Measurements and Main Results:

During the study period, 161 patients received a total of 22,190 hours of continuous renal replacement therapy, with a median duration of 74.75 hours (interquartile range, 32–169.5) per patient. Of the 572 filter circuits used, 276 (48.3%) were changed due to circuit clotting and 262 (45.8%) were electively changed. Median circuit life was 24.62 hours (interquartile range, 10.6–55.3) for all filters and significantly longer for those electively removed as compared to those prematurely removed because of clotting (35.50 hr [interquartile range, 16.9–67.6] vs 22.00 hr [interquartile range, 13.8–42.5]; p < 0.001). Multivariate regression analyses revealed that admission diagnosis (p < 0.001), anticoagulation type (p < 0.001), access type (p = 0.016), and circuit size (p = 0.027) were associated with prolonged circuit life, as well as, in patients on heparin anticoagulation, with higher doses of heparin (p < 0.001) and a prolonged activated partial thromboplastin time (p < 0.001).

Conclusions:

In this study, circuit lifespan in pediatric continuous renal replacement therapy was low and appeared to depend upon the patient’s diagnosis, the type of access and anticoagulation used as well as the size of the circuit used.
Gastrostomy and Tracheostomy After Complete Repair of Tetralogy of Fallot in Children With 22q11.2 Deletion Syndrome
Authors: Herington Danielle M. , Tang Xinyu , Spray Beverly J. , Reemtsen Brian L. , Prodhan Parthak , Richter Gresham T. , Kyle William B. , Bolin Elijah H.
Published: March 2020

Objectives:

Caring for a child with gastrostomy and/or tracheostomy can cause measurable parental stress. It is generally known that children with 22q11.2 deletion syndrome are at greater risk of requiring gastrostomy or tracheostomy after heart surgery, although the magnitude of that risk after complete repair of tetralogy of Fallot has not been described. We sought to determine the degree to which 22q11.2 deletion is associated with postoperative gastrostomy and/or tracheostomy after repair of tetralogy of Fallot.

Design:

Retrospective cohort study.

Setting:

Pediatric Health Information System.

Patients:

Children undergoing complete repair of tetralogy of Fallot (ventricular septal defect closure and relief of right ventricular outflow tract obstruction) from 2003 to 2016. Patients were excluded if they had pulmonary atresia, other congenital heart defects, and/or genetic diagnoses other than 22q11.2 deletion.

Measurements and Main Results:

Two groups were formed on the basis of 22q11.2 deletion status. Outcomes were postoperative tracheostomy and postoperative gastrostomy. Bivariate analysis and Kaplan-Meier analysis at 150 days postoperatively were performed. There were 4,800 patients, of which 317 (7%) had a code for 22q11.2 deletion. There were no significant differences between groups for age at surgery or sex. Patients with 22q11.2 deletion had significantly higher rates of gastrostomy (18% vs 5%; p < 0.001) and higher rates of tracheostomy (7% vs 1%; p < 0.001); there was no difference for mortality. Kaplan-Meier analyses also showed higher rates of gastrostomy (p = 0.024) and tracheostomy (p = 0.037).

Conclusions:

The present study establishes rates of postoperative gastrostomy and tracheostomy in children with 22q11.2 deletion after complete repair of tetralogy of Fallot. These data are useful to clinicians for providing families with preoperative counseling.
Deep Convolutional Neural Network–Based Diagnosis of Anterior Cruciate Ligament Tears
Authors: Germann Christoph , Marbach Giuseppe , Civardi Francesco , Fucentese Sandro F. , Fritz Jan , Sutter Reto , Pfirrmann Christian W.A. , Fritz Benjamin
Published: March 2020

Objectives

The aim of this study was to clinically validate a Deep Convolutional Neural Network (DCNN) for the detection of surgically proven anterior cruciate ligament (ACL) tears in a large patient cohort and to analyze the effect of magnetic resonance examinations from different institutions, varying protocols, and field strengths.

Materials and Methods

After ethics committee approval, this retrospective analysis of prospectively collected data was performed on 512 consecutive subjects, who underwent knee magnetic resonance imaging (MRI) in a total of 59 different institutions followed by arthroscopic knee surgery at our institution. The DCNN and 3 fellowship-trained full-time academic musculoskeletal radiologists evaluated the MRI examinations for full-thickness ACL tears independently. Surgical reports served as the reference standard. Statistics included diagnostic performance metrics, including sensitivity, specificity, area under the receiver operating curve (“AUC ROC”), and kappa statistics. P values less than 0.05 were considered to represent statistical significance.

Results

Anterior cruciate ligament tears were present in 45.7% (234/512) and absent in 54.3% (278/512) of the subjects. The DCNN had a sensitivity of 96.1%, which was not significantly different from the readers (97.5%–97.9%; all P ≥ 0.118), but significantly lower specificity of 93.1% (readers, 99.6%–100%; all P < 0.001) and “AUC ROC” of 0.935 (readers, 0.989–0.991; all P < 0.001) for the entire cohort. Subgroup analysis showed a significantly lower sensitivity, specificity, and “AUC ROC” of the DCNN for outside MRI (92.5%, 87.1%, and 0.898, respectively) than in-house MRI (99.0%, 94.4%, and 0.967, respectively) examinations (P = 0.026, P = 0.043, and P < 0.05, respectively). There were no significant differences in DCNN performance for 1.5-T and 3-T MRI examinations (all P ≥ 0.753, respectively).

Conclusions

Deep Convolutional Neural Network performance of ACL tear diagnosis can approach performance levels similar to fellowship-trained full-time academic musculoskeletal radiologists at 1.5 T and 3 T; however, the performance may decrease with increasing MRI examination heterogeneity.
Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing
Authors: Ferretti Luca , Wymant Chris , Kendall Michelle , Zhao Lele , Nurtay Anel , Abeler-Dörner Lucie , Parker Michael , Bonsall David , Fraser Christophe
Published: March 2020

The newly emergent human virus SARS-CoV-2 is resulting in high fatality rates and incapacitated health systems. Preventing further transmission is a priority. We analysed key parameters of epidemic spread to estimate the contribution of different transmission routes and determine requirements for case isolation and contact-tracing needed to stop the epidemic. We conclude that viral spread is too fast to be contained by manual contact tracing, but could be controlled if this process was faster, more efficient and happened at scale. A contact-tracing App which builds a memory of proximity contacts and immediately notifies contacts of positive cases can achieve epidemic control if used by enough people. By targeting recommendations to only those at risk, epidemics could be contained without need for mass quarantines (‘lock-downs’) that are harmful to society. We discuss the ethical requirements for an intervention of this kind.
Retrospective Analysis of Clinical Features in 101 Death Cases with COVID-19
Authors: Fan Hua , Zhang Lin , Huang Bin , Zhu Muxin , Zhou Yong , Zhang Huan , Tao Xiaogen , Cheng Shaohui , Yu Wenhu , Zhu Liping , Chen Jian
Published: March 2020

Background

In December 2019, viral pneumonia outbreaks caused by the novel coronavirus occurred in Wuhan, China, and spread rapidly worldwide, the illness progress of coronavirus disease 2019(COVID-19) in partial patients is rapid and the mortality rate is relatively high. The present study aims to describe the clinical features in the death cases with COVID-19.

Methods

In this single center and observational study, we recruited 101 death cases with COVID-19 from Dec 30, 2019 to Feb 16, 2020 in Intensive Care Unit (ICU) of Wuhan Jinyintan Hospital. Demographics, underlying diseases, X-ray/CT images, possible therapy strategies and test results were collected and analyzed on patients admission to the ICU and 48 hours before deaths.

Findings

Of 101 COVID-19 dead cases, 47 patients went directly to the ICU because of critical condition, and 54 patients were transferred to ICU with aggravated condition. Over fifty six percent (56.4%) of patients were laboratory confirmed by RT-PCR, and 43.6% were consistent with clinical diagnostic criteria.Among them, 64 were males and 37 were females, with average age of 65.46 years (SD 9.74). Interestingly, all deaths shwed significant difference in blood type distribution, with 44.44% of type A, 29.29% of type B, 8.08% of type AB, and 18.19% of type O.The clinical manifestations of the novel coronavirus pneumonia are non-specific,the common symptoms included fever (91,,90.10%), cough (69,68.32%) and dyspnea (75,74.26%). Neutrophils, procalcitonin(PCT),C-reactive protein(CRP),and interleukin-6(IL-6), D-dimer gradually increased with progress of the disease. Myocardial enzymes were abnormal in most patients at admission, myocardial damage indicators were significantly increased. Sixty one (60.40%) patients were given antiviral drugs, 59(58.42%),received glucocorticoids, 63.37% were given intravenous immunoglobulins, and 44.55% were treated with thymosin preparations. All patients received antibiotic treatment, 63(62.38%) were given restricted antibiotics, 23(22.78%) were administrated to antifungal drugs. Non-invasive ventilator or high-flow oxygen therapy were given in 84(83.17%) patients, and invasive mechanical ventilation was used in 76.24% patients. The median time from acute respiratory distress syndrome(ARDS) to invasive mechanical ventilation was 3.00 days(IQR 0.00-6.00). The duration of invasive mechanical ventilation was 5 days (IQR2.00-8.00).

Interpretation

Critical COVID-19 can cause fatal respiratory distress syndrome and multiple organ failure with high mortality. The blood group distribution of the deaths remarkably differred from that of Han population in Wuhan.Heart may be the earliest damaged organ except the lungs. Hospital-acquired pneumonia(HAP) in the later period is worthy of attention.

Funding

Supported by “the Fundamental Research Funds for the Central Universities (WK9110000037)”.
Development of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assays Targeting SARS-CoV-2
Authors: Park Gun-Soo , Ku Keunbon , Baek Seung-Hwa , Kim Seong Jun , Kim Seung Il , Kim Bum-Tae , Maeng Jin-Soo
Published: March 2020

Epidemics of Coronavirus Disease 2019 (COVID-19) now have more than 100,000 confirmed cases worldwide. Diagnosis of COVID-19 is currently performed by RT-qPCR methods, but the capacity of RT-qPCR methods is limited by its requirement of high-level facilities and instruments. Here, we developed and evaluated RT-LAMP assays to detect genomic RNA of SARS-CoV-2, the causative virus of COVID-19. RT-LAMP assays in this study can detect as low as 100 copies of SARS-CoV-2 RNA. Cross-reactivity of RT-LAMP assays to other human Coronaviruses was not observed. We also adapted a colorimetric detection method for our RT-LAMP assay so that the tests potentially performed in higher throughput.
Comprehensive valuation of the ecosystem services of the Arctic National Wildlife Refuge
Authors: Turner Adam C. , Young Margaret A. , McClung Maureen R. , Moran Matthew D.
Published: March 2020

Ecosystem services (ES) have been well studied in most biomes, but the Arctic tundra has received little attention, despite covering over 10% of terrestrial Earth. Using established ES methodologies, we calculated values for the United States Arctic National Wildlife Refuge, a region virtually undisturbed by humans, but slated for future oil and gas drilling. We estimated the Refuge is worth about 1,709 USD/hectare/year, equal to over 13 billion USD annually.

Globally important services, such as climate regulation (e.g., carbon storage) and non-use services (e.g., aesthetic information), contributed the most value and were similar to valuations from more productive ecosystems. Local services made smaller contributions to the total, but they remain vitally important to local indigenous cultures. Strikingly, a contingent valuation survey of U.S. residents found that, after neutral educational information, willingness-to-pay to maintain the Refuge in its current state exceeded estimated values of the oil and gas deposits.

Our study shows that citizens may value Arctic habitats beyond their traditional economic development potential. Our comprehensive ecosystem services valuation suggests that maintaining the Refuge in its current condition (i.e.,de factowilderness) with its full range of ES is more valuable to humanity compared to development for oil and gas.
SFRP1 shapes astrocyte to microglia cross-talk in acute and chronic neuroinflammation
Authors: Rueda-Carrasco Javier , Mateo María Inés , Borroto Aldo , Martin-Bermejo María Jesús , Kummer Markus P. , Schwartz Stephanie , López-Atalaya José P. , Alarcon Balbino , Heneka Michael T. , Esteve Pilar , Bovolenta Paola
Published: March 2020

Neuroinflammation is a common feature of many neurodegenerative diseases, which fosters a dysfunctional neuron-microglia-astrocyte crosstalk that, in turn, maintains microglial cells into a perniciously reactive state that often enhance neuronal damage. The molecular components that mediate this critical communication are however not fully explored. Here, we have asked whether Secreted-Frizzled-Related-Protein-1 (SFRP1), a multifunctional regulator of cell-to-cell communication, is part of the cellular crosstalk underlying neuroinflammation. We show that in mouse models of acute and chronic neuroinflammation, astrocyte-derived SFRP1 is sufficient to promote and sustain microglial activation, and thus a chronic inflammatory state. SFRP1 allows the upregulation of components of Hypoxia Induced Factors-dependent inflammatory pathway and, to a lower extent, of those downstream of the Nuclear Factor-kappaB. We thus propose that SFRP1 acts as a critical astrocyte to microglia amplifier of neuroinflammation, representing a potential valuable therapeutic target for counteracting the harmful effect of chronic inflammation present in several neurodegenerative diseases.
rePROBE: Workflow for Revised Probe Assignment and Updated Probe-Set Annotation in Microarrays
Authors: Hadlich Frieder , Reyer Henry , Oster Michael , Trakooljul Nares , Muráni Eduard , Ponsuksili Siriluck , Wimmers Klaus
Published: March 2020

Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns, but require the integration of the latest genomic information. This study provides a comprehensive workflow implemented in an R package (rePROBE) to assign the entire probes and to annotate the probe sets based on up-to-date genomic and transcriptomic information. The rePROBE R package is freely available athttps://github.com/friederhadlich/rePROBE. It can be applied to available gene expression microarray platforms and addresses both public and custom databases. The revised probe assignment and updated probe-set annotation were applied to commercial microarrays available for different livestock species,i.e.ChiGene-1_0-st (Gallus gallus, 443,579 probes;18,530 probe sets), PorGene-1_1-st (Sus scrofa, 592,005;25,779) and BovGene-1_0-st (Bos taurus, 530,717;24,759) as well as human (Homo sapiens, HuGene-1_0-st) and mouse (Mus musculus, HT_MG-430_PM) microarrays. Using current specie-specific transcriptomic information (RefSeq, Ensembl and partially non-redundant nucleotide sequences) and genomic information, the applied workflow revealed 297,574 probes for chickens (pig: 384,715; cattle: 363,077; human: 481,168; mouse: 324,942) assigned to 15,689 probe sets (pig: 21,673; cattle: 21,238; human: 23,495; mouse: 32,494). These are representative of 12,641 unique genes that were both annotated and positioned (pig: 15,758; cattle: 18,046; human: 20,167; mouse: 16,335). Additionally, the workflow collects information on the number of single nucleotide polymorphisms (SNPs) within respective targeted genomic regions and thus provides a detailed basis for comprehensive analyses such as quantitative trait locus (eQTL) expression studies to identify quantitative and functional traits.
Integrated Metabolomics, Transcriptomics, and Signal Protein Profile Define the Effector Function and Associated Metabotype of Five Polarized Macrophage Phenotypes
Authors: Anders Catherine B. , Lawton Tyler M.W. , Smith Hannah L. , Garret Jamie , Doucette Margaret M. , Ammons Mary Cloud B.
Published: March 2020

Macrophages (MΦs) display remarkable plasticity and the ability to activate diverse responses to a host of intracellular and external stimuli. Despite extensive characterization of M1 MΦs and a broad set of M2 MΦs, comprehensive characterization of metabolic shifts driving MΦ activation remains. Herein, we utilized anex vivomodel to produce six MΦ functional phenotypes. Isolated CD14+ PBMCs were differentiated into resting M0 MΦs, and then polarized into M1 (IFN-γ/LPS), M2a (IL-4/IL-13), M2b (IC/LPS), M2c (IL-10), and M2d (IL-6/LIF) MΦs. The MΦs were profiled using a bioanalyte matrix of four cell surface markers, ∼50 secreted proteins, ∼800 expressed myeloid genes, and ∼450 identified metabolites relative to M0 MΦs. Signal protein and expressed gene profiles grouped the MΦs into inflammatory (M1 and M2b) and wound resolution (M2a, M2c, and M2d) phenotypes; however, each had a unique metabolic profile. While both M1 and M2b MΦs shared metabotype profiles consistent with an inflammatory signature; key differences were observed in the TCA cycle, FAO and OXPHOS. Additionally, M2a, M2c and M2d MΦs all profiled as tissue repair MΦs; however, metabotype differences were observed in multiple pathways including hexosamine, polyamine, and fatty acid metabolism. These metabolic and other key functional distinctions suggest phagocytic and proliferative functions for M2a MΦs, and angiogenesis and ECM assembly capabilities for M2b, M2c and M2d MΦs. By integrating metabolomics into a systems analysis of MΦ phenotypes, we provide the most comprehensive map of MΦ diversity to date, along with the global metabolic shifts driving MΦ functional plasticity in these phenotypes.

Summary Sentence

Macrophage functional plasticity of six macrophage phenotypes correlates with unique distinctions in cell-surface marker expression, signal protein secretion, transcriptomics profiles, and metabolic processes.
Model-based identification of the crosstalks and feedbacks that determine the doxorubicin response dynamics of the JNK-p38-p53 network
Authors: Tuffery Laura , Halasz Melinda , Fey Dirk
Published: March 2020

Cellular responses to perturbations and drugs are determined by interconnected networks, rather than linear pathways. Individually, the JNK, p38 and p53 stress and DNA-damage response networks are well understood and regulate critical cell-fate decisions, such as apoptosis, in response to many chemotherapeutical agents, such as doxorubicin. To better understand how interactions between these pathways determine the dynamic behaviour of the entire network, we constructed a data-driven mathematical model. This model contains mechanistic details about the kinase cascades that activate JNK, p38, AKT and p53, and free parameters that describe possible interactions between these pathways. Fitting this model to experimental time-course perturbation data (five time-courses with six time-points under five different conditions), identified specific network interactions that can explain the observed network responses. JNK emerged as an important control node. JNK exhibited a positive feedback loop, was tightly controlled by negative feedback and crosstalk from p38 and AKT, respectively, and was the strongest activator of p53. Compared to static network reconstruction methods, such as modular response analysis, the model-based approach identifies biochemical mechanisms and explains the dynamic control of cell signalling.
Effect of thermal and high-pressure processing on the thermo-rheological and functional properties of common bean (Phaseolus vulgarisL.) flours
Authors: Lin Tiantian , Fernández-Fraguas Cristina
Published: March 2020

The effect of hydrothermal (HT) (boiling for 15 or 120min) and high-hydrostatic pressure (HHP) (150, 300, 450, and 600MPa for 5, 10 or 15min) processing on the rheological, pasting, thermal and functional properties of bean flours was investigated. HT and HHP treatments differently affected these properties. HT120 led to maximum values of elastic and viscous moduli (G′,G″), and gel strength of bean flours. HHP enhancedG′,G″ and gel strength as the pressure and holding time increased. The viscoelastic properties of HT120 and HHP600/5-treated bean flours correlated with the increased viscosity of these samples. The pasting profiles and thermograms indicated a full, partial, and limited starch gelatinization in HT120, HHP600/5 and HHP ≤ 450MPa samples, respectively. Enthalpy values showed that HT120 caused a higher degree of protein denaturation than HHP, with protein denaturation increasing as pressurization and time increased. This had an impact on protein solubility and emulsifying activity of flours which were significantly diminished by HT15/HT120, but maintained or slightly decreased by HHP. Nevertheless, HHP-treated samples showed enhanced emulsifying stability with increased pressure and holding time. These results demonstrate that HHP has the technological potential to manufacture bean flours with a range of functionalities into diverse food products.
Detecting chromatin interactions along and between sister chromatids with SisterC
Authors: Oomen Marlies E. , Hedger Adam K. , Watts Jonathan K. , Dekker Job
Published: March 2020

Accurate chromosome segregation requires chromosome compaction with concordant disentanglement of the two sister chromatids. This process has been studied extensively by microscopy but has remained a challenge for genomic methods, such as Hi-C, because sister chromatids have identical DNA sequences. Here we describe SisterC, a chromosome conformation capture assay that can distinguish interactions between and within sister chromatids. The assay is based on BrdU incorporation during S-phase, which labels the newly replicated strands of the sister chromatids. This is followed by Hi-C, e.g. during different stages of mitosis, and the selective destruction of BrdU containing strands by UV/Hoechst treatment. After PCR amplification and sequencing of the remaining intact strands, this allows for the assignment of Hi-C products as inter- and intra-sister interactions by read orientation. We performed SisterC on mitotically arrestedS. cerevisiaecells. As expected, we find prominent interactions and alignment of sister chromatids at their centromeres. Along the arms, sister chromatids are less precisely aligned with inter-sister connections every ~35kb. In many instances, inter-sister interactions do not involve the interaction of two identical loci but occur between cohesin binding sites that can be offset by 5 to 25kb. Along sister chromatids, extruding cohesin forms loops up to 50kb. Combined, SisterC allows the observation of the complex interplay between sister chromatid compaction and sister chromatid segregation as the cell transitions from late S-phase to mitosis. SisterC should be applicable to study mitotic events in a wide range of organisms and cell types.
Gamma activity accelerates during prefrontal development
Authors: Bitzenhofer Sebastian H. , Pöpplau Jastyn A. , Hanganu-Opatz Ileana L.
Published: March 2020

Gamma oscillations are a prominent activity pattern in the cerebral cortex. While gamma rhythms have been extensively studied in the adult prefrontal cortex in the context of cognitive (dys)functions, little is known about their development. We addressed this issue by using extracellular recordings and optogenetic stimulations in mice across postnatal development. We show that fast rhythmic activity in the prefrontal cortex becomes prominent during the second postnatal week. While initially at about 15 Hz, fast oscillatory activity progressively accelerates with age and stabilizes within gamma frequency range (30-80 Hz) during the fourth postnatal week. Activation of layer 2/3 pyramidal neurons drives fast oscillations throughout development, yet the acceleration of their frequency follows similar temporal dynamics as the maturation of fast-spiking interneurons. These findings uncover the development of prefrontal gamma activity and provide a framework to examine the origin of abnormal gamma activity in neurodevelopmental disorders.
The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor
Authors: Brielle Esther S. , Schneidman-Duhovny Dina , Linial Michal
Published: March 2020

The COVID-19 disease has plagued over 110 countries and has resulted in over 4,000 deaths within 10 weeks. We compare the interaction between the human ACE2 receptor and the SARS-CoV-2 spike protein with that of other pathogenic coronaviruses using molecular dynamics simulations. SARS-CoV, SARS-CoV-2, and HCoV-NL63 recognize ACE2 as the natural receptor but present a distinct binding interface to ACE2 and a different network of residue-residue contacts. SARS-CoV and SARS-CoV-2 have comparable binding affinities achieved by balancing energetics and dynamics. The SARS-CoV-2–ACE2 complex contains a higher number of contacts, a larger interface area, and decreased interface residue fluctuations relative to SARS-CoV. These findings expose an exceptional evolutionary exploration exerted by coronaviruses toward host recognition. We postulate that the versatility of cell receptor binding strategies has immediate implications on therapeutic strategies.

One Sentence Summary

Molecular dynamics simulations reveal a temporal dimension of coronaviruses interactions with the host receptor.
Rational design of novel fluorescent enzyme biosensors for direct detection of strigolactones
Authors: Chesterfield Rebecca J , Whitfield Jason H , Pouvreau Benjamin , Cao Da , Beveridge Christine A , Vickers Claudia E
Published: March 2020

Strigolactones are plant hormones and rhizosphere signalling molecules with key roles in plant development, mycorrhizal fungal symbioses, and plant parasitism. Currently, sensitive, specific, and high-throughput methods of detecting strigolactones are limited. Here, we developed genetically encoded fluorescent strigolactone biosensors based on the strigolactone receptors DAD2 from Petunia hybrida, and HTL7 from Striga hermonthica via domain insertion of circularly permuted GFP. The DAD2 biosensor exhibited loss of cpGFP fluorescence in vitro upon treatment with the strigolactones 5-deoxystrigol and orobanchol, or the strigolactone analogue GR24. The biosensor likewise responded to strigolactones in an in vivo protoplast system, and retained strigolactone hydrolysis activity. The ShHTL7 biosensor exhibited loss of cpGFP fluorescence upon GR24 treatment in vitro, and responded to a specific inhibitor of ShHTL7 but not DAD2, indicating that the biosensors retained the specificity of their parent receptors. These biosensors have applications in high-throughput screening, and may also have utility for studying strigolactone biology.
Machine Learning to Identify Flexibility Signatures of Class A GPCR Inhibition
Authors: Bemister-Buffington Joseph , Wolf Alex J. , Raschka Sebastian , Kuhn Leslie A.
Published: March 2020

We show that machine learning can pinpoint features distinguishing inactive from active states in proteins, in particular identifying key ligand binding site flexibility transitions in GPCRs that are triggered by biologically active ligands. Our analysis was performed on the helical segments and loops in 18 inactive and 9 active class A GPCRs. These 3-dimensional structures were determined in complex with ligands. However, considering the flexible versus rigid state identified by graph-theoretic ProFlex rigidity analysis for each helix and loop segment with the ligand removed, followed by feature selection and k-nearest neighbor classification, was sufficient to identify four segments surrounding the ligand binding site whose flexibility/rigidity accurately predicts whether a GPCR is in an active or inactive state. GPCRs bound to inhibitors were similar in their pattern of flexible versus rigid regions, whereas agonist-bound GPCRs were more flexible and diverse. This new ligand-proximal flexibility signature of GPCR activity was identified without knowledge of the ligand binding mode or previously defined switch regions, while being adjacent to the known transmission switch. Following this proof of concept, the ProFlex flexibility analysis coupled with pattern recognition and activity classification may be useful for predicting whether newly designed ligands behave as activators or inhibitors, based on the pattern of flexibility they induce in the protein.
Methods for Extraction and Detection of Bacteriophage DNA from the Sputum of Patients with Cystic Fibrosis
Authors: Burgener Elizabeth B , Secor Patrick R , Tracy Michael C , Sweere Johanna M , Bik Elisabeth M , Milla Carlos E , Bollyky Paul L
Published: March 2020

There is increasing interest in the pulmonary microbiome’s bacterial and viral communities, particularly in the context of chronic airway infections in cystic fibrosis (CF). However, the isolation of microbial DNA from the sputum from patients with CF is technically challenging and the optimal protocols for the analysis of viral species, including bacteriophage, from clinical samples remains challenging. Here, we evaluate a set of methods developed for processing and analyzing sputum from patients with CF with a particular emphasis on detecting bacteriophage viron-derived nucleic acid. We evaluate the impact of bead-beating, deoxyribonuclease digestion, and heating steps in these protocols focusing on the quantitative assessment ofPseudomonas aeruginosaand Pf bacteriophage in sputum as a proof of concept. Based on these comparative data, we describe an optimized protocol for processing sputum from patients with CF and isolating DNA for PCR or sequencing-based studies. These studies will facilitate future assessments of bacteriophage and bacteria in sputum from patients with CF.

Author Summary

Patients with cystic fibrosis (CF) have thickened secretions and develop chronic infections in their airways. While we culture bacterial pathogens from expectorated sputum this method favors detection of certain organisms. There is greater understanding that the microbiome with in the airway of patients with cystic fibrosis is varied and contains more than just the bacteria that we selectively culture. Processing sputum is difficult as it is very thick. There are many different ways to process sputum depending on what aspect of the sputum is to be studied. We have an interest in a specific bacteriophage, or a virus that infects bacteria. We sought to find the best method to take sputum from a CF patient and extract DNA so that we could detect both bacteria and bacteriophage DNA. We compared different methods that included different combinations of heat, mechanical homogenization, chemical lysis and DNA extraction by commercially available kits. We describe the method we found easiest to execute and produced the best yield for detection of both bacteria and bacteriophage. Our purpose of publishing this method in detail is to facilitate further study of viral and bacterial communities in the sputum of patients with CF.