bluuebunny/crossref_metadata_2025 huggingface dataset:
Repeat Pediatric Trisomy 21 Radiographic Exam: Does Atlantoaxial Instability Develop Over Time?
Authors: Bauer Jennifer M. , Dhaliwal Virkamal K. , Browd Samuel R. , Krengel Walter F.
Published: June 2021

Background:

Atlantoaxial instability (AAI) is common in pediatric patients with Trisomy 21 and can lead to spinal cord injury during sports, trauma, or anesthetized neck manipulation. Children with Trisomy 21 therefore commonly undergo radiographic cervical spine screening, but recommendations on age and timing vary. The purpose of this study was to determine if instability develops over time.

Methods:

We performed a retrospective review for all pediatric Trisomy 21 patients receiving at least 2 cervical spine radiographic series between 2008 and 2020 at our institution. Atlantodens interval (ADI) and space available for the cord at C1 (SAC) were measured; bony abnormalities such as os odontoidium, and age and time between radiographs were noted. AAI was determined by ADI ≥6 mm or SAC ≤14 mm based on our groups’ prior study. Those who developed instability were compared with those who did not.

Results:

A total of 437 cervical spine radiographic series from 192 patients were evaluated, with 160 included. Mean age at first radiograph was 7.4±4.4 years, average ADI was 3.1 mm (±1.2), and SAC was 18.1 mm (±2.6). The average time between first and last radiographs was 4.3 years (±1.8), with average final ADI 3.2 mm (±1.4) and SAC 18.9 mm (±2.9). Seven patients (4%) had instability: 4 were unstable on their initial studies and 3 (1.6%) on subsequent imaging. Os odontoideum was found in 5 (71%) unstable spines and 3 (2%) stable spines (P<0.0001); only 1 patient that became unstable on subsequent radiograph did not have an os. There was no specific age cut-off or surveillance time period after which one could be determined no longer at risk.

Conclusions:

Trisomy 21 patients have a 4.4% overall rate of AAI in our series with a 1.6% rate of progression to instability over ∼4 years. Given this nearly 1 in 23 risk of instability, we recommend initial surveillance radiograph for all children over 3 years with Trisomy 21; repeat asymptomatic surveillance should continue in those with os odontoideum given their high instability risk.

Level of Evidence:

Level II—diagnostic study.
Generalization in Clinical Prediction Models: The Blessing and Curse of Measurement Indicator Variables
Authors: Futoma Joseph , Simons Morgan , Doshi-Velez Finale , Kamaleswaran Rishikesan
Published: June 2021

OBJECTIVE:

Specific factors affecting generalizability of clinical prediction models are poorly understood. Our main objective was to investigate how measurement indicator variables affect external validity in clinical prediction models for predicting onset of vasopressor therapy.

DESIGN:

We fit logistic regressions on retrospective cohorts to predict vasopressor onset using two classes of variables: seemingly objective clinical variables (vital signs and laboratory measurements) and more subjective variables denoting recency of measurements.

SETTING:

Three cohorts from two tertiary-care academic hospitals in geographically distinct regions, spanning general inpatient and critical care settings.

PATIENTS:

Each cohort consisted of adult patients (age greater than or equal to 18 yr at time of hospitalization), with lengths of stay between 6 and 600 hours, and who did not receive vasopressors in the first 6 hours of hospitalization or ICU admission. Models were developed on each of the three derivation cohorts and validated internally on the derivation cohort and externally on the other two cohorts.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

The prevalence of vasopressors was 0.9% in the general inpatient cohort and 12.4% and 11.5% in the two critical care cohorts. Models utilizing both classes of variables performed the best in-sample, with C-statistics for predicting vasopressor onset in 4 hours of 0.862 (95% CI, 0.844–0.879), 0.822 (95% CI, 0.793–0.852), and 0.889 (95% CI, 0.880–0.898). Models solely using the subjective variables denoting measurement recency had poor external validity. However, these practice-driven variables helped adjust for differences between the two hospitals and led to more generalizable models using clinical variables.

CONCLUSIONS:

We developed and externally validated models for predicting the onset of vasopressors. We found that practice-specific features denoting measurement recency improved local performance and also led to more generalizable models if they are adjusted for during model development but discarded at validation. The role of practice-specific features such as measurement indicators in clinical prediction modeling should be carefully considered if the goal is to develop generalizable models.
Systematic Approach for Management and Prevention of Boxy Breast
Authors: Abdelkader Rasha , El-Noamany Sameh , Raafat Sarah
Published: June 2021

Background:

Although a boxy breast is a common aesthetic problem following breast reduction and mastopexy, literature regarding this deformity is scarce. It is vaguely described as a definitive postreduction deformity. To address this complication, it is important to fully analyze the problem, understand and predict its causes, and then try to prevent it.

Methods:

This study included two groups. Group 1 included 14 patients presenting with boxy postoperative breasts. Revision surgeries were conducted for all patients, and the first algorithm was created for quantifying breast surgery in revision cases. Group 2 included 37 cases of primary mammaplasty reduction/mastopexy performed between 2016 and 2019. All the patients in this group were treated as per the study algorithm.

Results:

Patient satisfaction was measured on a scale of one to 10, with one being extremely dissatisfied and 10 being extremely satisfied. The results indicated overall satisfaction, with average scores of 9.5 and 9.1 in groups 1 and 2, respectively; the scores of surgeon satisfaction were 8.2 and 8.6, respectively.

Conclusions:

The proposed algorithm, preoperative markings, intraoperative techniques, and postoperative orientation may help achieve optimal results and prevent undesired deformities or asymmetry. Applying a flexible and simplified algorithm provided a more objective plan, which enabled surgeons to attain more satisfactory results. Following a preset quantified plan supported and shortened learning curves and objectively addressed the common postoperative complication, breast boxing.
Estimating the Insertion Depth of a Peripherally Inserted Central Catheter in Newborns Using Weight and Gestational Age Measurements
Authors: Kim Dong-Yeon , Park Ho-Ran
Published: June 2021

The objective of this study was to estimate the peripherally inserted central catheter (PICC) insertion depth in newborns. We retrospectively reviewed the records of 790 neonates who underwent PICC insertion for intravenous injections administered for 6 days or more following neonatal intensive care unit admission at our institution between January 2011 and October 2015. We analyzed patients' electronic medical records and chest standard radiographs. PICC insertion depths were calculated using the following equation: Insertion depth = Section + (β1 × Body weight). The predicted equation was checked for accuracy using Bland-Altman plots. Of 835 included neonates, 790 (94.6%) had properly positioned PICCs. Forty-three of 45 unsuitable patients (5.4%) had catheters inserted into the cephalic veins. Of the 790 patients with correctly inserted catheter tips, regression equations and standard errors were calculated for the average insertion depth and timing of PICC insertion. The catheter depth increased with every 100 g of weight gain and week of gestational age. More than 90% of the 4 vessels incorporating PICCs were included within the standard deviation of ±2.0, indicating high predictive validity. This study established a standard for accurately measuring PICC insertion depths.
Case Report: A Novel Single Variant TJP2 Mutation in a Case of Benign Recurrent Intrahepatic Cholestasis
Authors: Kornitzer Gaël A. , Alvarez Fernando
Published: June 2021

Benign recurrent intrahepatic cholestasis (BRIC) is a disease on the spectrum of familial intrahepatic cholestasis caused by homozygous ABCB11 or ATP8B1 mutations. In recent years, genetic testing has allowed for discovery of a variety of homozygous or compound heterozygous TJP2 mutations associated with progressive familial intrahepatic cholestasis and intrahepatic cholestasis of pregnancy. To our knowledge, no cases of BRIC caused by a single variant mutation of TJP2 have been reported. We describe a 15-year-old female presenting with recurrent episodes of jaundice, vomiting, with intense pruritus, anorexia, and weight loss. Blood work revealed elevated serum conjugated bilirubin and liver enzymes but normal gamma-glutamyl transferase, consistent with BRIC. A genetic panel identified a not previously described single allele mutation in TJP2 of unknown functional significance. This is the first reported case of a clinical entity resembling BRIC with a heterozygous mutation in TJP2, without associated mutations in other cholestasis-related genes.
Effect of Perioperative Intravenous Iron Supplementation for Complex Cardiac Surgery on Transfusion Requirements
Authors: Song Jong Wook , Soh Sarah , Shim Jae-Kwang , Lee Sak , Lee Seung Hyun , Kim Hye Bin , Kim Min-Yu , Kwak Young Lan
Published: June 2021

Objectives:

We investigated whether routine perioperative intravenous iron replenishment reduces the requirement for packed erythrocytes (pRBC) transfusion.

Summary of Background Data:

Patients undergoing complex cardiac surgery are at high risk of developing postoperative iron deficiency anemia, thus requiring transfusion, which is associated with adverse outcomes.

Methods:

Patients were randomized to receive either ferric derisomaltose 20 mg/kg (n = 103) or placebo (n = 101) twice during the perioperative period: 3 days before and after the surgery. The primary endpoint was the proportion of patients who received pRBC transfusion until postoperative day (POD) 10. Hemoglobin, reticulocyte count, serum iron profile, hepcidin, and erythropoietin were serially measured.

Results:

pRBC was transfused in 60.4% and 57.2% of patients in the control and iron group, respectively (P = 0.651). Hemoglobin concentration at 3 weeks postoperatively was higher in the iron group than in the control group (11.6 ± 1.5 g/dL vs 10.9 ± 1.4 g/dL, P < 0.001). The iron group showed higher reticulocyte count [205 (150–267)×103/μL vs 164 (122–207)×103/μL, P = 0.003] at POD 10. Transferrin saturation and serum ferritin were significantly increased in the iron group than in the control group (P < 0.001). Serum hepcidin was higher in the iron group than in the control group at POD 3 [106.3 (42.9–115.9) ng/mL vs 39.3 (33.3–43.6) ng/mL, P < 0.001]. Erythropoietin concentration increased postoperatively in both groups (P = 0.003), with no between-group difference.

Conclusions:

Intravenous iron supplementation during index hospitalization for complex cardiac surgery did not minimize pRBC transfusion despite replenished iron store and augmented erythropoiesis, which may be attributed to enhanced hepcidin expression.
Financial Incentives to Improve Patient Follow-up and Weight Loss After Bariatric Surgery
Authors: Chao Grace F. , Kullgren Jeffrey T. , Ross Rachel , Bonham Aaron J. , Ghaferi Amir A.
Published: June 2021

Objective:

To examine effects of a financial incentives program on follow-up and weight loss after bariatric surgery.

Summary Background Data:

Consistent follow-up may improve weight loss and other health outcomes after bariatric surgery. Yet, rates of follow-up after surgery are often low.

Methods:

Patients from 3 practices within a statewide collaborative were invited to participate in a 6-month financial incentives program. Participants received incentives for attending postoperative appointments at 1, 3, and 6 months which doubled when participants weighed less than their prior visit. Participants were matched with contemporary patients from control practices by demographics, starting body mass index and weight, surgery date, and procedure. Preintervention estimates used matched historic patients from the same program and control practices with the criteria listed above. Patients between the 2 historic groups were additionally matched on surgery date to ensure balance on matched variables. We conducted differ-ence-in-differences analyses to examine incentives program effects. Follow-up attendance and percent excess weight loss were measured postoperative months 1, 3, 6, and 12.

Results:

One hundred ten program participants from January 1, 2018 to July 31, 2019 were matched to 203 historic program practice patients (November 20 to December 27, 2017). The control group had 273 preinter-vention patients and 327 postintervention patients. In difference-in-differ-ences analyses, the intervention increased follow-up rates at 1 month (+14.8%, P<0.0001), 3months (+29.4%, P<0.0001), and 6 months (+16.4%, P<0.0001), but not at 12 months. There were no statistically significant differences in excess weight loss.

Conclusions:

A financial incentives program significantly increased follow-up after bariatric surgery for up to 6 months, but did not increase weight loss. Our study supports use of incentivized approaches as one way to improve postoperative follow-up, but may not translate into greater weight loss without additional supports.
Gender Bias in the Evaluation of Surgical Performance
Authors: Antonoff Mara B. , Feldman Hope , Luc Jessica G. Y. , Iaeger Paula I. , Rubin M. Laura , Li Liang , Vaporciyan Ara A.
Published: June 2021

Objective:

The study aims to determine the influence of trainee gender on assessments of coronary anastomosis performance.

Summary of Background Data:

Understanding the impact of gender bias on the evaluation of trainees may enable us to identify and utilize assessment tools that are less susceptible to potential bias.

Methods:

Cardiothoracic surgeons were randomized to review the video performance of trainees who were described by either male or female pronouns. All participants viewed the same video of a coronary anastomosis and were asked to grade technique using either a Checklist or Global Rating Scale (GRS). Effect of trainee gender on scores by respondent demographic was evaluated using regression analyses. Inter-rater reliability was assessed using the Cronbach’s alpha.

Results:

103 cardiothoracic surgeons completed the Checklist (trainee gender: male n=50, female n=53) and 112 completed the GRS (trainee gender: male n=56, female n=56). For the Checklist, male cardiothoracic surgeons who were in practice <10 years (P = 0.036) and involved in training residents (P = 0.049) were more likely to score male trainees higher than female trainees. The GRS demonstrated high inter-rater reliability across male and female trainees by years and scope of practice for the respondent (alpha >0.900) when compared to the Checklist assessment tool.

Conclusions:

Early career male surgeons may exhibit gender bias against women when evaluating trainee performance of coronary anastomoses. The GRS demonstrates higher interrater reliability and robustness against gender bias in the assessment of technical performance than the Checklist, and such scales should be emphasized in educational evaluations.
Robot-assisted Versus Conventional Minimally Invasive Esophagectomy for Resectable Esophageal Squamous Cell Carcinoma
Authors: Yang Yang , Li Bin , Yi Jun , Hua Rong , Chen Hezhong , Tan Lijie , Li Hecheng , He Yi , Guo Xufeng , Sun Yifeng , Yu Bentong , Li Zhigang
Published: June 2021

Objective:

To compare perioperative and long-term outcomes of robot-assisted minimally invasive esophagectomy (RAMIE) and conventional minimally invasive esophagectomy (MIE) in the treatment for patients with esophageal squamous cell carcinoma (ESCC).

Summary Background Data:

RAMIE has emerged as an alternative to traditional open or thoracoscopic approaches. Efficacy and safety of RAMIE and MIE in the surgical treatment for ESCC remains uncertain given the lack of high-level clinical evidence.

Methods:

The RAMIE trial was designed as a prospective, multicenter, randomized, controlled clinical trial that compares the efficacy and safety of RAMIE and MIE in the treatment of resectable ESCC. From August 2017 to December 2019, eligible patients were randomly assigned to receive either RAMIE or MIE performed by experienced thoracic surgeons from 6 high-volume centers in China. Intent-to-treat analysis was performed.

Results:

Significantly shorter operation time was taken in RAMIE (203.8 vs 244.9 min, P<0.001). Compared with MIE, RAMIE showed improved efficiency of thoracic lymph node dissection in patients who received neoadjuvant therapy (15 vs 12, P = 0.016), as well as higher achievement rate of lymph node dissection along the left recurrent laryngeal nerve (79.5% vs 67.6%, P = 0.001). No difference was found in blood loss, conversion rate, and R0 resection. The 90-day mortality was 0.6% in each group. Overall complications were similar in RAMIE (48.6%) compared with MIE (41.8%) (RR, 1.16; 95% CI, 0.92–1.46; P = 0.196). Besides, the rate of major complications (Clavien-Dindo classification ≥ III) was also comparable (12.2% vs 10.2%, P = 0.551). RAMIE showed similar incidences of pulmonary complications (13.8% vs 14.7%; P = 0.812), anastomotic leakage (12.2% vs 11.3%; P = 0.801), and vocal cord paralysis (32.6% vs 27.1%, P = 0.258) to MIE.

Conclusions:

Early results demonstrate that both RAMIE and MIE are safe and feasible for the treatment of ESCC. RAMIE can achieve shorter operative duration and better lymph node dissection in patients who received neoadjuvant therapy. Long-term results are pending for further follow-up investigations.

Trial Registration:

ClinicalTrial.gov Identifier: NCT03094351.
Detection and partial characterization of extracellular inducers of persistence in Staphylococcus epidermidis and Staphylococcus aureus
Authors: Curry Elyse C. , Hart Ryan G. , Habtu Danni Y. , Chamberlain Neal R.
Published: June 2021

Introduction. This study describes the identification and partial characterization of persistence-inducing factors (PIFs) from staphylococci.

Hypothesis/Gap Statement. Increases in persisters during mid-log phase growth indicate that quorum-sensing factors might be produced by staphylococci.

Aim. To identify and partially characterize PIFs from

Staphylococcus epidermidis

RP62A and

Staphylococcus aureus

SH1000.

Methodology. Others have demonstrated a significant increase in persister numbers during mid-log phase. Inducers of this mid-log increase have yet to be identified in staphylococci. Optical density at 600 nm (OD600) was used instead of time to determine when persister numbers increased during logarithmic growth. Concentrated culture filtrates (CCFs) from

S. epidermidis

and

S. aureus

were obtained at various OD600s and following incubation at 16 h. The CCFs were used to develop a PIF assay. The PIF assay was used to partially characterize PIF from

S. epidermidis

and

S. aureus

for sizing of PIF activity, temperature and protease sensitivity and inter-species communications.

Results. The optimal OD600s for

S. epidermidis

and

S. aureus

PIF assays were 2.0 and 0.5, respectively. The highest PIF activity for both species was from CCF following incubation overnight (16 h).

S. epidermidis

’ PIF activity was decreased by storage at 4 oC but not at 20 oC (16 h), 37 oC (1 h) or 100 oC (15 min).

S. aureus

’ PIF activity was decreased following storage at 4 oC (2 weeks) and after boiling at 100 oC for 5 min but not after incubation at 37 oC (1 h). PIF activity from both species went through a 3000 molecular weight cutoff ultrafilter. Proteinase K treatment of

S. aureus

PIF decreased activity but did not decrease the PIF activity of

S. epidermidis

. PIF from

S. epidermidis

did not increase persisters when used to treat

S. aureus

cells and nor did PIF from

S. aureus

increase persisters when used to treat

S. epidermidis

cells.

Conclusions. Attempts to discover PIFs for staphylococci were unsuccessful due to the time-based means used to identify mid-log. Both staphylococcal species produce extracellular, low-molecular-weight inducers of persistence when assayed using an OD600 -based PIF assay.
Minority potassium-uptake system Trk2 has a crucial role in yeast survival of glucose-induced cell death
Authors: Dušková Michala , Cmunt Denis , Papoušková Klára , Masaryk Jakub , Sychrová Hana
Published: June 2021

The existence of programmed cell death in Saccharomyces cerevisiae has been reported for many years. Glucose induces the death of S. cerevisiae in the absence of additional nutrients within a few hours, and the absence of active potassium uptake makes cells highly sensitive to this process. S. cerevisiae cells possess two transporters, Trk1 and Trk2, which ensure a high intracellular concentration of potassium, necessary for many physiological processes. Trk1 is the major system responsible for potassium acquisition in growing and dividing cells. The contribution of Trk2 to potassium uptake in growing cells is almost negligible, but Trk2 becomes crucial for stationary cells for their survival of some stresses, e.g. anhydrobiosis. As a new finding, we show that both Trk systems contribute to the relative thermotolerance of S. cerevisiae BY4741. Our results also demonstrate that Trk2 is much more important for the cell survival of glucose-induced cell death than Trk1, and that stationary cells deficient in active potassium uptake lose their ATP stocks more rapidly than cells with functional Trk systems. This is probably due to the upregulated activity of plasma-membrane Pma1 H+-ATPase, and consequently, it is the reason why these cells die earlier than cells with functional active potassium uptake.
Burden of COVID-19 and Case Fatality Rate in Pune India: An Analysis of First and Second Wave of the Pandemic
Authors: Bogam Prasad , Joshi Aparna , Nagarkar Sanket , Jain Divyashri , Gupte Nikhil , Shashidhara LS , Monteiro Joy Merwin , Mave Vidya
Published: June 2021

Background

The recent second wave in India in April-May 2021 placed an unprecedented burden on the Indian health systems. However, limited data exist on the epidemiology of the COVID-19 pandemic from the first wave through the second wave in India. With detailed epidemiologic data, we aimed to assess trends in incident cases and case fatality, its risk between pandemic waves in Pune, an epicenter of COVID-19 cases in India, a country with the second-largest absolute burden worldwide.

Methods

Programmatic COVID-19 data from Pune city between the first wave (March 09th 2020-October 31st, 2020), maintenance phase (November 01st 2020-February 14th, 2021), the second wave (February 15th, 2021-May 31st, 2021) were assessed for trends of incident cases, time-to-death, and case fatality rate (CFR). In addition, Poisson regression models adjusted for age and gender were used to determine the independent effect of pandemic waves on mortality.

Results

Of 465,192 COVID-19 cases, 162,182 (35%) were reported in the first wave, and 4,146 (2.5%) died among them; Maintenance period registered 27,517 (6%) cases with 590 (2.1%) deaths; Second wave reported 275,493 (59%) cases and 3184 (1.1%) deaths (p<0.01). The overall CFR was 1.16 per 1000 person-days (PD), which declined from 1.80 per 1000 PD during the first wave to 0.77 per 1000 PD in the second wave. The risk of death was 1.49 times higher during the first wave (adjusted case fatality rate ratio-aCFRR,1.49; 95% CI: 1.37–1.62) and 35% lower in the second wave (aCFRR, 0.65; 95% CI: 0.59 – 0.70), compared to the maintenance phase.

Interpretation

The absolute burden of COVID-19 cases and deaths were more significant in the second wave in Pune, India; however, the CFR declined as the pandemic progressed. Nevertheless, investigating newer therapies and implementing mass vaccinations against COVID-19 are urgently needed.
Dietary practices, physical activity and social determinants of non-communicable diseases in Nepal: a systemic analysis
Authors: Sharma Sudesh Raj , Matheson Anna , Lambrick Danielle , Faulkner James , Lounsbury David W. , Vaidya Abhinav , Page Rachel
Published: June 2021

Background

The objective of this paper was to describe the role of dietary practices and physical activity in the interaction of the social determinants of non-communicable diseases (NCDs) in Nepal.

Method

The study was a qualitative study design guided by systemic intervention methodology. Qualitative data were collected through key informant interviews (n=63) and focus group discussions (n= 12), and case study-based thematic analysis was carried out. Causal loop diagram was utilised to illustrate the dynamic interactions of the social determinants based on the themes. The study also involved sense-making sessions with policy level and local stakeholders.

Findings

Four key interacting themes emerged from the study. Dietary and physical activity practices have shifted significantly at community level contributing to increased risk of NCDs. The practice of healthy and locally produced meals was gradually being displaced by junk food and linked to junk food availability and declining agricultural activities. Health system was ineffective in preventing unhealthy practices. Gender and social economic factors were driving the poor dietary practices and physical inactivity.

Conclusion

While the current dietary and physical activity-related practices within communities were poor, the broader determinants such as socio-economic circumstances and gender further fuelled such practices. The health system has potential to play an effective role in the prevention of the behavioural and social determinants of NCDs.
MONITORING SARS-COV-2 TRANSMISSION AND PREVALENCE IN POPULATIONS UNDER REPEATED TESTING
Authors: Wascher Matthew , Schnell Patrick M. , Khudabukhsh Wasiur R. , Quam Mikkel , Tien Joseph H. , Rempała Grzegorz A.
Published: June 2021

We describe a repeat SARS-CoV-2 testing model for monitoring and containing outbreaks in a residential community. The analysis is motivated by the Ohio State University (OSU)’s approach to monitoring disease at its Columbus, Ohio campus during the COVID-19 epidemic in autumn 2020. The model is simple, yet flexible enough to accommodate changes in behavior over time and to eliminate bias due to a nonrandom testing scheme. Model parameters are estimated from individual results of weekly SARS-CoV-2 testing of residents. Model output serves several purposes, including estimating the effective reproduction number and monitoring prevalence to help inform isolation and quarantine bed capacity. An extended version of the model is also considered where the residential population (on-campus students) is assumed to interact with another population for whom the testing regime is more relaxed and possibly less frequent (off-campus students or instructional faculty and staff). To illustrate the model application, we analyze both the synthetic data as well as the actual student SARS-CoV-2 testing data collected at OSU Columbus campus.
Development of quantitative high-throughput screening methods for identification of antifungal biocontrol strains
Authors: Kjeldgaard Bodil , Neves Ana Rute , Fonseca César , Kovács Ákos T. , Domínguez- Cuevas Patricia
Published: June 2021

Large screens of bacterial strain collections to identify potential biocontrol agents are often time consuming, costly, and fail to provide quantitative results. In this study, we present two quantitative and high-throughput methods to assess the inhibitory capacity of bacterial biocontrol candidates against fungal phytopathogens. One method measures the inhibitory effect of bacterial culture supernatant components on the fungal growth, while the other accounts for direct interaction between growing bacteria and the fungus by co-cultivating the two organisms. The antagonistic supernatant method quantifies the culture components’ antifungal activity by calculating the cumulative impact of supernatant addition relative to a non-treated fungal control, while the antagonistic co-cultivation method identifies the minimal bacterial cell concentration required to inhibit fungal growth by co-inoculating fungal spores with bacterial culture dilution series. Thereby, both methods provide quantitative measures of biocontrol efficiency and allow prominent fungal inhibitors to be distinguished from less effective strains. The combination of the two methods shed light on the type of inhibition mechanisms and provide the basis for further mode of action studies. We demonstrate the efficacy of the methods usingBacillus spp. with different levels of antifungal activities as model antagonists and quantify their inhibitory potency against classic plant pathogens.

Importance

Fungal phytopathogens are responsible for tremendous agricultural losses on annual basis. While microbial biocontrol agents represent a promising solution to the problem, there is a growing need for high-throughput methods to evaluate and quantify inhibitory properties of new potential biocontrol agents for agricultural application. In this study, we present two high-throughput and quantitative fungal inhibition methods that are suitable for commercial biocontrol screening.
Viral detection and identification in 20 minutes by rapid single-particle fluorescence in-situ hybridization of viral RNA
Authors: Hepp Christof , Shiaelis Nicolas , Robb Nicole C. , Kapanidis Achillefs N
Published: June 2021

The increasing risk from viral outbreaks such as the ongoing COVID-19 pandemic exacerbates the need for rapid, affordable and sensitive methods for virus detection, identification and quantification; however, existing methods for detecting virus particles in biological samples usually depend on multistep protocols that take considerable time to yield a result. Here, we introduce a rapid fluorescence in situ hybridization (FISH) protocol capable of detecting influenza virus, avian infectious bronchitis virus and SARS-CoV-2 specifically and quantitatively in approximately 20 minutes, in both virus cultures and combined throat and nasal swabs without previous purification. This fast and facile workflow is applicable to a wide range of enveloped viruses and can be adapted both as a lab technique and a future diagnostic tool.
Pulmonary thromboembolism in patients after COVID-19 - predictive indicators for correct diagnosis
Authors: Yakova-Hristova D. , Simova I. , Pavlov P. , Hristov M. , Kundurzhiev T. , Dimitrov N. , Vekov T.
Published: June 2021

Introduction

Infection caused by SARS-CoV-2 has been shown to lead to significant procoagulant events, in some cases involving life-threatening pulmonary thromboembolism (PE). Additional conditions complicating the diagnosis are the presence of risk factors for PE in almost all patients with COVID-19, as well as the overlap of the clinical presentation between PE and COVID-19. Materials and Methods: Тherefore we conducted a single-center study at the Heart and Brain Hospital, Pleven in the period December 2020-February 2021. It included 27 consecutively hospitalized patients with recent pneumonia caused by Covid-19 and clinical presentation referring to PE. The cohort was divided into two groups - with and without a definitive diagnosis of PE, proven by CT pulmoangiography. The aim was to find the indicators that predict the presence of PE in patients with acute or Post-acute COVID-19 conditions. Results: Our results show that part of the ECG criteria - S-wave over 1.5 mm in I lead and aVL (p = 0.007), Q-wave in III and aVF (p = 0.020), as well as the D-dimer as quantitative variable (p = 0.025) proved to be independent predictors of PE. The RV/ LV diameter ratios ≥1.0 as well as right ventricular dysfunction showed sensitivity 62.5%, specificity 100%, positive predictive value 100% and negative such 86.4% to verify the PE diagnosisЛ We suggest that the cut-off value of D-dimer of 1032 ng/ml has an optimal sensitivity (Se) of 87.5%, specificity (Sp) 57.9%, positive a predictive value (PPV) 46.7% and negative predictive value (NPV) of 91.7% for the diagnosis of PE (p = 0.021). Conclusion: Against the background of acute and Post-acute COVID-19 conditions ECG and EchoCG criteria remain predictive of PE. We suggest that a higher D-dimer cut-off value should be applied in COVID-19 and post-COVID-19 patients in order to confirm/dismiss the diagnosis PE.
Long-term course of humoral and cellular immune responses in outpatients after SARS-CoV-2 infection
Authors: Schiffner Julia , Backhaus Insa , Rimmele Jens , Schulz Sören , Möhlenkamp Till , Klemens Julia Maria , Zapf Dorinja , Solbach Werner , Mischnik Alexander
Published: June 2021

Characterisation of the naturally acquired B and T cell immune responses to SARS-CoV-2 is important for the development of public health and vaccination strategies to manage the burden of COVID-19 disease. We conducted a prospective, longitudinal analysis in COVID-19 recovered patients at various time points over a 10-month period in order to determine how circulating antibody levels and interferon-gamma (IFN-γ) release by peripheral blood cells change over time following natural infection.

From March 2020 till January 2021, we enrolled 412 adults mostly with mild or moderate disease course. At each study visit, subjects donated peripheral blood for testing of anti-SARS-CoV-2 IgG antibodies and IFN-γ release after SARS-CoV-2 S-protein stimulation. Anti-SARS-CoV-2 IgG antibodies were identified in 316/412 (76.7%) of the patients and 215/412 (52.2%) had positive neutralizing antibody levels. Likewise, in 274/412 (66.5 %) positive IFN-γ release and IgG antibodies were detected. With respect to time after infection, both IgG antibody levels and IFN-γ concentrations decreased by about half within three hundred days. Statistically, IgG and IFN-γ production were closely associated, but on an individual basis we observed patients with high antibody titres but low IFN-γ levels and vice versa.

Our data suggest that immunological reaction is acquired in most individuals after infection with SARS-CoV-2 and is sustained in the majority of patients for at least 10 months after infection. Since no robust marker for protection against COVID-19 exists so far, we recommend utilizing both, IgG and IFN-γ release for an individual assessment of immunity status.
Efficacy of recombinant NP-M1 and NP-M1-CRT DNA vaccines against Influenza A viruses in mice C57/BL6
Authors: Attaran Hamidreza , He Wen , Wang Wei
Published: June 2021

Effective vaccination against the influenza virus remains a challenge because of antigenic shift and drift in influenza viruses. Conservation is an important feature of the Nucleoprotein (NP) and Matrix protein 1(M1) qualifying them as potential candidates for developing a universal vaccine against the influenza A virus. Carliticulin (CRT), a member of heat shock protein (HSP) family, are conserved and widely distributed in many microorganisms and mammalian cells. In this study, a plasmid vector encoding the NP-M1-CRT sequence was constructed and compared with the NP-M1 sequence with respect to immunogenicity and protective efficacy in a murine model. The potency of the created construct for provoking humoral, cellular immune responses, and its protective immunity against the lethal influenza virus infection were then compared with commercial split vaccine and then evaluated in a murine model system. NP-M1-CRT as a DNA vaccine combined with in vivo electroporation could significantly improve the immunogenicity of constructed vectors. Serological evaluations demonstrated the potency of our approach to provoke strong anti-NP specific antibody responses. Furthermore, our strategy of immunization in prime-boost groups were able to provide protection against lethal viral challenge using H1N1 subtype. The ease of production of these types of vectors and the fact that they would not require annual updating and manufacturing may provide an alternative cost-effective approach to limit the spread of potential pandemic influenza viruses.
Distinct modes of action of IAPP oligomers on membranes
Authors: Sepehri Aliasghar , Nepal Binod , Lazaridis Themis
Published: June 2021

Islet Amyloid Polypeptide (IAPP, also known as amylin) is a peptide hormone which is co-secreted with insulin by pancreatic β-cells and forms amyloid aggregates in type II diabetes. Various lines of evidence indicate that oligomers of this peptide may induce toxicity by disrupting or forming pores in cell membranes but the structures of these pores are unknown. Here we create models of pores for both helical and β-structured peptides using implicit membrane modeling and test their stability using multimicrosecond all-atom simulations. We find that the helical peptides behave similarly to antimicrobial peptides; they remain stably inserted in a highly tilted or partially unfolded configuration creating a narrow water channel. Parallel helix orientation creates a somewhat larger pore. An octameric β barrel of parallel β-hairpins is highly stable in the membrane, whereas the corresponding barrel made of antiparallel hairpins is not. We propose that certain experiments probe the helical pore state while others probe the β-structured pore state; this provides a possible explanation for lack of correlation that is sometimes observed between in vivo toxicity and in vitro liposome permeabilization experiments.
Phylourny: Predicting the Knock-out-phase of Tournaments via Phylogenetic Methods by example of the UEFA EURO 2020
Authors: Bettisworth Ben , Stamatakis Alexandros
Published: June 2021

The prediction of knock-out tournaments represents an area of large public interest and active academic as well as industrial research. Here, we leverage the computational analogies between calculating the so-called phylogenetic likelihood score used in the area of molecular evolution and efficiently calculating, instead of approximating via simulations, the exact per-team winning probabilities, given a pairwise win probability matrix P. We implement and make available our method as open-source code and deploy it to calculate the winning probabilities for all teams participating at the knock-out phase of the UEFA EURO 2020 football tournament. We use three different P matrices to conduct predictions, two inferred via our own simple method and one computed by experts in the field. According to this expert P matrix which we trust most, we find that the most probable final is France versus England and that England has a slightly higher probability to win the title. The ability to efficiently and exactly compute winning probabilities, apart from improving and accelerating predictions, might allow for the development of novel methods to compute P.
Two evolutionary distinct effectors from a nematode and virus target RanGAP1 and 2 via the WPP domain to promote disease
Authors: Sukarta Octavina C. A , Diaz-Granados Amalia , Slootweg Erik J , Overmars Hein , van Schaik Casper , Pokhare Somnath , Roosien Jan , Pomp Rikus , Elashry Abdelnaser , Smant Geert , Goverse Aska
Published: June 2021

The Gpa2 and Rx1 intracellular immune receptors are canonical CC-NB-LRR proteins belonging to the same R gene cluster in potato. Despite sharing high sequence homology, they have evolved to provide defence against unrelated pathogens. Gpa2 detects Gp-RBP-1 effectors secreted by the potato cyst nematode Globodera pallida whereas Rx1 recognizes the viral coat protein (CP) of Potato Virus X (PVX). How Gpa2 and Rx1 perceive their matching effectors remains unknown. Using a combination of in planta Co-Immunoprecipitation and cellular imaging, we show that both Gp-RBP-1 and PVX-CP physically interact with RanGAP2 and RanGAP1 in the cytoplasm of plant cells. Interestingly, this was also demonstrated for the eliciting variants of Gp-RBP-1 and PVX-CP indicating a role for RanGAP1 and RanGAP2 in pathogenicity independent from Gpa2 and Rx1 recognition. Indeed, knocking down both RanGAP homologs reduce cyst nematode and PVX infection. These findings show that RanGAP1/2 act as common host targets of evolutionary distinct effectors from two plant pathogens with different lifestyles. The involvement of RanGAP1/2 to pathogen virulence is a novel role not yet reported for these key host cell components and as such, their possible role in cyst nematode parasitism and viral pathogenicity are discussed. Moreover, from these findings a model emerges for their possible role as co-factor in pathogen recognition by the potato immune receptors Gpa2/Rx1.
A Robust and Scalable Graph Neural Network for Accurate Single Cell Classification
Authors: Zeng Yuansong , Zhou Xiang , Pan Zixiang , Lu Yutong , Yang Yuedong
Published: June 2021

Motivation

Single-cell RNA sequencing (scRNA-seq) techniques provide high-resolution data on cellular heterogeneity in diverse tissues, and a critical step for the data analysis is cell type identification. Traditional methods usually cluster the cells and manually identify cell clusters through marker genes, which is time-consuming and subjective. With the launch of several large-scale single-cell projects, millions of sequenced cells have been annotated and it is promising to transfer labels from the annotated datasets to newly generated datasets. One powerful way for the transferring is to learn cell relations through the graph neural network (GNN), while vanilla GNN is difficult to process millions of cells due to the expensive costs of the message-passing procedure at each training epoch.

Results

Here, we have developed a robust and scalable GNN-based method for accurate single cell classification (GraphCS), where the graph is constructed to connect similar cells within and between labelled and unlabelled scRNA-seq datasets for propagation of shared information. To overcome the slow information propagation of GNN at each training epoch, the diffused information is pre-calculated via the approximate Generalized PageRank algorithm, enabling sublinear complexity for a high speed and scalability on millions of cells. Compared with existing methods, GraphCS demonstrates better performance on simulated, cross-platform, and cross-species scRNA-seq datasets. More importantly, our model can achieve superior performance on a large dataset with one million cells within 50 minutes.
Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness
Authors: Jin Xin , Lee Ji-Eun , Schaefer Charley , Luo Xinwei , Wollman Adam J. M. , Tian Tian , Zhang Xiaowei , Chen Xiao , Li Yingxing , McLeish Tom C. B. , Leake Mark C. , Bai Fan
Published: June 2021

Liquid-liquid phase separation is emerging as a crucial phenomenon in several fundamental cell processes. A range of eukaryotic systems exhibit liquid condensates. However, their function in bacteria, which in general lack membrane-bound compartments, remains less clear. Here, we used high-resolution optical microscopy to observe single bacterial aggresomes, nanostructured intracellular assemblies of proteins, to undercover their role in cell stress. We find that proteins inside aggresomes are mobile and undergo dynamic turnover, consistent with a liquid state. Our observations are in quantitative agreement with phase-separated liquid droplet formation driven by interacting proteins under thermal equilibrium that nucleate following diffusive collisions in the cytoplasm. We have discovered aggresomes in multiple species of bacteria, and show that these emergent, metastable liquid-structured protein assemblies increase bacterial fitness by enabling cells to tolerate environmental stresses.

One Sentence Summary

Bacteria use subcellular proteinaceous liquid droplets to survive stress
Rational engineering of an erythropoietin fusion protein to treat hypoxia
Authors: Lee Jungmin , Vernet Andyna , Gruber Nathalie G. , Kready Kasia M. , Burrill Devin R. , Way Jeffrey C. , Silver Pamela A.
Published: June 2021

Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia.
Evolution of innate behavioral strategies through competitive population dynamics
Authors: Liang Tong , Brinkman Braden A. W.
Published: June 2021

Many organism behaviors are innate or instinctual and have been “hard-coded” through evolution. Current approaches to understanding these behaviors model evolution as an optimization problem in which the traits of organisms are assumed to optimize an objective function representing evolutionary fitness. Here, we use a mechanistic birth-death dynamics approach to study the evolution of innate behavioral strategies in a population of organismsin silico. In particular, we performed agent-based stochastic simulations and mean-field analyses of organisms exploring random environments and competing with each other to find locations with plentiful resources. We find that when organism density is low, the mean-field model allows us to derive an effective objective function, predicting how the most competitive phenotypes depend on the exploration-exploitation trade-off between the scarcity of high-resource sites and the increase in birth rate those sites offer organisms. However, increasing organism density alters the most competitive behavioral strategies and precludes the existence of a well-defined objective function. Moreover, there exists a range of densities for which the coexistence of many phenotypes persists for evolutionarily long times.
Pyrimidine biosynthesis inhibitors synergize with nucleoside analogs to block SARS-CoV-2 infection
Authors: Schultz David C. , Johnson Robert M. , Ayyanathan Kasirajan , Miller Jesse , Whig Kanupriya , Kamalia Brinda , Dittmar Mark , Weston Stuart , Hammond Holly L. , Dillen Carly , Castellana Lauren , Lee Jae Seung , Li Minghua , Lee Emily , Constant Samuel , Ferrer Marc , Thaiss Christoph A. , Frieman Matthew B. , Cherry Sara
Published: June 2021

The ongoing COVID-19 pandemic has highlighted the dearth of approved drugs to treat viral infections, with only ∼90 FDA approved drugs against human viral pathogens. To identify drugs that can block SARS-CoV-2 replication, extensive drug screening to repurpose approved drugs is underway. Here, we screened ∼18,000 drugs for antiviral activity using live virus infection in human respiratory cells. Dose-response studies validate 122 drugs with antiviral activity and selectivity against SARS-CoV-2. Amongst these drug candidates are 16 nucleoside analogs, the largest category of clinically used antivirals. This included the antiviral Remdesivir approved for use in COVID-19, and the nucleoside Molnupirivir, which is undergoing clinical trials. RNA viruses rely on a high supply of nucleoside triphosphates from the host to efficiently replicate, and we identified a panel of host nucleoside biosynthesis inhibitors as antiviral, and we found that combining pyrimidine biosynthesis inhibitors with antiviral nucleoside analogs synergistically inhibits SARS-CoV-2 infection in vitro and in vivo suggesting a clinical path forward.