bluuebunny/crossref_metadata_2025 huggingface dataset:
Parental Worrying, Family Functioning, and Quality of Life During the COVID-19 Pandemic
Authors: Taha Asma A. , Azar Najood Ghazi , Eisen Aaron M. , Abdul-Rahman Hana Q. , Hanes Douglas A.
Published: December 2021

Background

The 2019 novel coronavirus pandemic has affected many aspects of American life, with reported increases in parental anxiety and adverse health outcomes among children. However, it is unknown how family functioning and parental anxiety may be associated with child health outcomes during this pandemic.

Objectives

The aim of this study was to explore associations among parental worrying, family functioning, and the health-related quality of life (HRQoL) of middle and high school-aged children in the United States during the 2019 novel coronavirus pandemic.

Methods

Ninety-three parent–child dyads were recruited via snowball sampling through the WhatsApp messenger from December 2020 to February 2021 in this exploratory cross-sectional study. Each family completed a series of self-report measures, including the General Functioning Scale–Family Assessment Device and the Worry Domains Questionnaire for parent respondents and the KIDSCREEN-10 for child respondents. A hierarchical regression analysis was performed to examine effects of parental worrying and family functioning on the HRQoL of middle and high school-aged children.

Results

Lower levels of parental worrying and better family functioning predicted better child HRQoL, whereas parental worrying was associated with worse family functioning. The relationship between family functioning and child HRQoL did not differ by levels of parental worrying. Increased child age and parental education were associated with worse child HRQoL.

Discussion

The high socioeconomic status sample reported healthy family functioning during the 2019 novel coronavirus pandemic. Family functioning appears to improve child HRQoL consistently, even as parental worrying increases or decreases, although increased worrying would likely decrease family functioning and child HRQoL. The inverse relationships of parental educational attainment with family functioning and child HRQoL are surprising; they may be due to pandemic circumstances and the nature of the sample being high-socioeconomic status families with middle and high school-aged children.
Needs of chemotherapy regimen checks procedure: from the survey on chemotherapy regimen checks performed by pharmacists in hospitals other than designated cancer hospitals in Japan
Authors: Ohta Takahiro , Suzuki Shinya , Shinohara Akira , Ohashi Yasukata , Ueki Daisuke , Konuma Daisuke , Ryushima Yasuaki , Udagawa Ryoko , Kawasaki Toshikatsu , Yamaguchi Masakazu
Published: December 2021

Introduction:

Pharmacists perform regimen checks of physicians’ prescription orders in hospitals for providing appropriate chemotherapy. Details of these steps and procedures are confined to reports within individual facilities.

Methods:

In July 2016, a questionnaire was sent to the 33 pharmacists of the total 33 National Hospital Organization hospitals that were not cancer hospitals in Japan to survey the items checked in regimen checks and to assess whether the regimen checks are performed for oral anticancer drugs (OACDs) and injected anticancer drugs (IACDs) according to prescription category. The questionnaires included items on characteristics of respondents and their facilities and the 7 items related to regimen checks.

Results:

All facilities responded to the questionnaires, and 15 and 22 of the facilities performed chemotherapy regimen checks for OACDs and IACDs, respectively. Regimen checks for OACDs were performed for 80% (12/15) of internal and 27% (4/15) of external prescriptions for outpatient care and 93% (14/15) of prescriptions for inpatient care. Regimen checks for IACDs were performed for 91% (20/22) of prescriptions for outpatient care and 100% (22/22) of inpatient care.

Conclusions:

The surveyed facilities differed in terms of items checked, suggesting that procedures of regimen checks followed protocols unique to each facility. It is vital to establish an adequate procedure to perform safe chemotherapy.
Influence of Immune Cell Subtypes on Mitochondrial Measurements in Peripheral Blood Mononuclear Cells From Children with Sepsis
Authors: Weiss Scott L. , Henrickson Sarah E. , Lindell Robert B. , Sartori Laura F. , Zhang Donglan , Bush Jenny , Farooqi Sumera , Starr Jonathan , Deutschman Clifford S. , McGowan Francis X. , Becker Lance , Tuluc Florin , Wherry E. John , Picard Martin , Wallace Douglas C.
Published: December 2021

Introduction:

Peripheral blood mononuclear cells (PBMCs) are commonly used to compare mitochondrial function in patients with versus without sepsis, but how these measurements in this mixed cell population vary by composition of immune cell subtypes is not known, especially in children. We determined the effect of changing immune cell composition on PBMC mitochondrial respiration and content in children with and without sepsis.

Methods:

PBMC mitochondrial respiration and citrate synthase (CS) activity, a marker of mitochondrial content, were measured in 167 children with sepsis at three timepoints (day 1–2, 3–5, and 8–14) and once in 19 nonseptic controls. The proportion of lymphocytes and monocytes and T, B, and NK cells was measured using flow cytometry. More specific CD4+ and CD8+ T cell subsets were measured from 13 sepsis patients and 6 controls. Spearman's correlation and simple and mixed effects linear regression were used to determine the association of PBMC mitochondrial measures with proportion of immune cell subtypes.

Results:

PBMC mitochondrial respiration and CS activity were correlated with proportion of monocytes, lymphocytes, T B, and NK cells in controls, but not in sepsis patients. PBMC mitochondrial respiration was correlated with CD4+ and CD8+ T cell subsets in both groups. After controlling for differences in immune cell composition between groups using linear regression models, PBMC respiration and CS activity remained lower in sepsis patients than controls.

Conclusions:

Mitochondrial measurements from PBMCs varied with changes in immune cell composition in children with and without sepsis. However, differences in PBMC mitochondrial measurements between sepsis patients and controls were at least partially attributable to the effects of sepsis rather than solely an epiphenomena of variable immune cell composition.
Quality Improvement Initiative Using Blended In Situ Simulation Training on Procedural Sedation and Analgesia in a Pediatric Emergency Department
Authors: Nucci Alessia , Sforzi Idanna , Morley-Fletcher Alessio , Saffirio Claudia , Bussolin Leonardo , Masi Stefano , Weinstock Peter , De Luca Marco
Published: December 2021

Introduction

There is evidence in the literature for high-fidelity in situ simulation training programs being an effective modality for physicians training. This quality initiative focused on implementation of the procedural sedation and analgesia (PSA) in our pediatric emergency department (PED). The primary outcomes of this study were to evaluate the impact of blended in situ simulation training (BST) program on PSA for closed forearm fracture reduction in the PED and to assess its cost-effectiveness. The secondary outcomes were to estimate this change on PSA's clinical efficacy and safety.

Methods

Between 2014 and 2018, a single-center, quasi-experimental, uncontrolled before and after study on forearm fracture reduction management was conducted. To assess the impact of our BST-PSA course, both historical control and prospective analyses were performed. Statistical significance was based on Fisher exact test or Pearson χ2 test.

Results

Eight hundred eighty-five children met inclusion criteria. A significant difference in the number of PSAs performed in the PED, before and after BST, was found (37% vs. 85.3%, P < 0.001). Furthermore, a reduction in the number of hospitalizations for closed fracture reduction was measured (68.2% vs. 31.8%, P < 0.001). The overall cost savings from the BST-enabled increase in PSAs carried out in the PED was €370,714 ($440,838) with a return on investment of 64:1. No significant increase of PSA-related adverse events was found, and no serious adverse events occurred.

Conclusions

Findings provide evidence of the benefits of implementing BST to enable PSA use in the PED, with an improved patient flow and significant cost savings from avoiding unnecessary hospitalizations.
Diabetes Remission After Bariatric Surgery in Patients on Glucocorticoids: A Pilot Study
Authors: Vahibe Ahmet , Livia Christopher , Portela Ray , Shah Meera , McKenzie Travis , Kellogg Todd , Ghanem Omar M.
Published: December 2021

Background:

Diabetes mellitus type 2 (DM2) remission after bariatric surgery has long been reported in the medical literature. Glucocorticoid use is associated with weight gain and could theoretically affect diabetes remission post bariatric surgery.

Objectives:

The aim is to identify remission rates of DM2 among patients using glucocorticoids after bariatric surgery and assess long-term postsurgical follow-up.

Methods:

A retrospective analysis was performed on patients who used glucocorticoids and underwent bariatric surgery at the Mayo Clinic between 2008 and 2020. Data were analyzed for 3-month, 6-month, 1-year, 2-year, and 5-year intervals for factors indicative of diabetes remission.

Results:

Within our retrospective search, we identified 92 patients who were on any immunosuppressant medication before surgery. Of those, 22 patients had a diagnosis of DM2 while 18 of them were concurrently on glucocorticoids. Diabetes remission occurred in 11 of the 18 DM2 patients (61.11%). There was a statistically significant negative correlation between diabetes remission and combination therapy with glucocorticoids and tacrolimus (P=0.016); patients with a longer duration of DM2 diagnosis (P=0.024), and patients who used insulin three months after the procedure (P=0.001). However, percent total weight loss and the number of preoperative oral DM2 medications were not associated with worse outcomes.

Conclusions:

Patients who use systemic glucocorticoids are able to achieve diabetes remission after bariatric surgery. Concurrent therapy with tacrolimus is associated with worse remission outcomes.
Ictal Theta Power as an Electroconvulsive Therapy Safety Biomarker
Authors: Miller Jeremy , Jones Tom , Upston Joel , Deng Zhi-De , McClintock Shawn M. , Ryman Sephira , Quinn Davin , Abbott Christopher C.
Published: December 2021

Objective

Electroconvulsive therapy (ECT) remains the benchmark for treatment resistant depression, yet its cognitive adverse effects have a negative impact on treatment. A predictive safety biomarker early in ECT treatment is needed to identify patients at cognitive risk to maximize therapeutic outcomes and minimize adverse effects. We used ictal electroencephalography frequency analysis from suprathreshold treatments to assess the relationships between ECT dose, ictal power across different frequency domains, and cognitive outcomes.

Methods

Seventeen subjects with treatment resistant depression received right unilateral ECT. Structural magnetic resonance imaging was obtained pre-ECT for electric field modeling to assess ECT dose. Serial assessments with 24-lead electroencephalography captured ictal activity. Clinical and cognitive assessments were performed before and after ECT. The primary cognitive outcome was the change in Delis Kaplan Executive Function Verbal Fluency Letter Fluency.

Results

Ictal theta (4–8 Hz) power in the Fp1/Fp2 channels was associated with both whole-brain electric field strength (t
(2,12) = 19.5, P = 0.007)/(t
(2,10) = 21.85, P = 0.02) and Delis Kaplan Executive Function Verbal Fluency Letter Fluency scores (t
(2,12) = −2.05, P = 0.05)/(t
(2,10) = −2.20, P = 0.01). Other frequency bands (beta, alpha, delta, and gamma) did not demonstrate this relationship.

Conclusions

This pilot data identify ictal theta power as a potential safety biomarker in ECT and is related to the strength of the ECT dose. Ictal theta power could prove to be a convenient and powerful tool for clinicians to identify those patients most susceptible to cognitive impairment early in the treatment series. Additional studies are needed to assess the role of longitudinal changes in ictal theta power throughout the ECT series.
A Clinical Case Series of Acute and Maintenance Home Administered Transcranial Direct Current Stimulation in Treatment-Resistant Depression
Authors: Le Brandon , Alonzo Angelo , Bull Michael , Kabourakis Michael , Martin Donel , Loo Colleen
Published: December 2021

Objectives

Transcranial direct current stimulation (tDCS) is a noninvasive neurostimulation technique being translated clinically for the treatment of depression. There is limited research documenting the longer-term effectiveness and safety of tDCS treatment. This case series is the first report of remotely supervised, home-administered tDCS (HA-tDCS) for depression in a clinical setting.

Methods

We report clinical, cognitive, and safety outcomes from 16 depressed patients who received acute and/or maintenance HA-tDCS. We retrospectively examined clinical data from up to 2.5 years of treatment. Descriptive statistics are reported to document patient outcomes.

Results

Twelve patients received acute treatment for a current depressive episode and 4 commenced tDCS maintenance therapy after responding to ECT or repetitive transcranial magnetic stimulation (rTMS). The cohort was highly treatment-resistant wherein 15 of 16 patients failed 3 trials or more of antidepressant medication in the current episode, and 6 patients failed to gain significant benefit from prior ECT or rTMS. Five of 12 patients responded to acute tDCS within 6 weeks, and 9 patients who received tDCS for more than 12 weeks maintained improvements over several months. Cognitive tests showed no evidence of impairments in cognitive outcomes after up to 2 years of treatment. Two patients were withdrawn from treatment because of blurred vision or exacerbation of tinnitus. Transcranial direct current stimulation was otherwise safe and well tolerated.

Conclusions

Transcranial direct current stimulation given for at least 6 weeks may be of clinical benefit even in treatment-resistant depression. Results provide support for long-term effectiveness, safety, and feasibility of remotely supervised HA-tDCS and suggest a role for maintenance tDCS after acute treatment with tDCS, rTMS, or ECT.
The Effect of Electroconvulsive Therapy on Positive Affect and Hedonism in Patients With Depression
Authors: Crauwels Bo , Vansteelandt Kristof , Obbels Jasmien , Lambrichts Simon , Pilato Eva , Demyttenaere Koen , Sienaert Pascal
Published: December 2021

Objectives

The outcome of antidepressant treatments is generally assessed with standardized symptom scales such as the Quick Inventory of Depressive Symptomatology–Clinician Rating (QIDS-C). These scales, however, might not reflect patients' expectations for treatment, including a recovery of positive affect (PA) and hedonism. The Leuven Affect and Pleasure Scale (LAPS) was developed to better reflect patients' expectations for treatment. We used the LAPS to investigate changes in PA and hedonism alongside depressive symptoms during electroconvulsive therapy (ECT) and over 12 weeks after treatment.

Methods

Fifty-three patients with a Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, depressive episode, referred for ECT, were included in this prospective study. The LAPS and QIDS-C were administered before and 1 and 12 weeks after the ECT course. LAPS normative levels were obtained in 149 healthy controls.

Results

Pearson correlations revealed only moderate overlap of the QIDS-C with PA and hedonism. Piecewise linear mixed models indicated significant improvements in depressive symptoms (QIDS-C and LAPS negative affect), PA, and hedonism during ECT. In the 12 weeks after ECT treatment, negative affect and QIDS-C further improved, but PA and hedonism plateaued. Exploratory analyses indicated that only fully remitted patients (QIDS-C) attained normative levels on PA and hedonism at 12 weeks after ECT.

Conclusions

Standardized symptom scales (QIDS-C) may incompletely reflect clinical change in ECT treatment for depression. Although ECT improved depressive symptoms, PA, and hedonism in patients with depression, only fully remitted patients attained normative levels of PA and hedonism, due to plateaus in improvement. These plateaus were not observed for depressive symptoms, which further improved after ECT discontinuation.
First Acute-Course Electroconvulsive Therapy for Moderate-to-Severe Depression Benefits Patients With or Without Accompanying Baseline Cognitive Impairment
Authors: Copersino Marc L. , Long Marina P. , Bolton Paula , Ressler Kerry J. , Seiner Stephen J. , Yip Agustin G.
Published: December 2021

Background

Researchers are increasingly investigating therapeutic response associated with new patient subgroups as a way to improve electroconvulsive therapy (ECT) treatment outcomes and reduce adverse events. This study is the first to examine baseline cognitive impairment status as a predictor of clinical outcome in first acute-course ECT patients.

Methods

Baseline cognitive function at various thresholds and serial depressive symptom severity data from first-time ECT patients were examined using generalized linear mixed-effects models.

Results

Of 1345 patients who met the inclusion criteria, 617 had available data at their third assessment visit (~15th treatment visit). There was a robust improvement in depression symptoms over time (P < 0.0001), and cognitive function was not associated with baseline levels of depressive symptoms or serially measured change in self-reported symptom severity during acute-phase ECT.

Conclusions

These results indicate that an acute course of ECT for the treatment of moderate-to-severe depression benefits patients with or without accompanying baseline cognitive impairment. These findings may be useful in informing shared decision-making discussions about ECT risks and expected benefits.
A preliminary study of commercially available general-purpose chest radiography artificial intelligence-based software for detecting airspace opacity lesions in COVID-19 patients
Authors: Suzuki Munemura , Niimura Aruta , Nakamura Yusuke , Otsuka Yujiro
Published: December 2021

Purpose

To validate commercially available general-purpose artificial intelligence (AI)-based software for detecting airspace opacity in chest radiographs (CXRs) of COVID-19 patients.

Materials and Methods

We used the ieee8023-covid-chestxray-dataset to validate commercial AI software capable of detecting “Nodule/Mass” and “Airspace opacity” as regions of interest with probability scores. From this dataset, we excluded computed tomography images and CXR images taken using an anteroposterior spine view and analyzed CXR images tagged with “Pneumonia/Viral/COVID-19” and “no findings.” A radiologist then reviewed the images and rated them on a 3-point opacity score for the presence of airspace opacity. The maximum probability score of airspace opacity for each image was calculated using this software. The difference in each maximum probability for each opacity score was evaluated using Wilcoxon’s rank sum test. The threshold of the probability score was determined by receiver operator characteristic curve analysis for the presence or absence of COVID-19, and the true positive rate (TPR) and false positive rate (FPR) were determined for the individual and overall opacity scores.

Results

Images from 342 patients with COVID-19 and 15 normal images were included. Opacity scores of 1, 2, and 3 were observed in 44, 70, and 243 images, respectively, of which 33 (75%), 66 (94.2%), and 243 (100%), respectively, were from COVID-19 patients. The overall TPR and FPR were 0.82 and 0.13, respectively, at an area under the curve of 0.88 and a threshold of 0.06, while the FPR for opacity score 1 was 0.18 and the TPR for score 3 was 0.97.

Conclusion

Using a public database containing CXR images of COVID-19 patients, commercial AI software was shown to be able to detect airspace opacity in severe pneumonia.

Commercially available AI software was capable of detecting airspace opacity in CXR images of COVID-19 patients in a public database.
Multi-Analyte Liquid Biopsies for Molecular Pathway Guided Personalized Treatment Selection in Advanced Refractory Cancers: A Clinical Utility Pilot Study
Authors: Patil Darshana , Akolkar Dadasaheb , Nagarkar Rajnish , Srivastava Navin , Datta Vineet , Patil Sanket , Apurwa Sachin , Srinivasan Ajay , Datar Rajan
Published: December 2021

Purpose

The selection of safe and efficacious anticancer regimens for treatment of broadly refractory patients with metastatic cancers remains a clinical challenge. Such patients are often fatigued by toxicities of prior failed treatments and may have no further viable standard of care treatment options. Liquid Biopsy-based multi-analyte profiling in peripheral blood can identify a majority of drug targets that can guide the selection of efficacious combination regimens.

Patients and Methods

LIQUID IMPACT was a pilot clinical study where patients with advanced refractory cancers received combination anticancer treatment regimens based on multi-analyte liquid biopsy (MLB) profiling of circulating tumor biomarkers; this study design was based on the findings of prior feasibility analysis to determine the abundance of targetable variants in blood specimens from 1299 real-world cases of advanced refractory cancers.

Results

Among the 29 patients in the intent to treat (ITT) cohort of the trial, 26 were finally evaluable as per study criteria out of whom 12 patients showed Partial Response (PR) indicating an Objective Response Rate (ORR) of 46.2% and 11 patients showed Stable Disease (SD) indicating the Disease Control Rate (DCR) to be 88.5%. The median Progression-Free Survival (mPFS) and median Overall Survival (mOS) were 4.3 months (95% CI: 3.0 – 5.6 months) and 8.8 months (95% CI: 7.0 – 10.7 months), respectively. Toxicities were manageable and there were no treatment-related deaths.

Conclusion

The study findings suggest that MLB could be used to assist treatment selection in heavily pretreated patients with advanced refractory cancers.
Seroprevalence, waning, and correlates of anti-SARS-CoV-2 IgG antibodies in Tyrol, Austria: Large-scale study of 35,193 blood donors conducted between June 2020 and September 2021
Authors: Siller Anita , Seekircher Lisa , Wachter Gregor A. , Astl Manfred , Tschiderer Lena , Pfeifer Bernhard , Gaber Manfred , Schennach Harald , Willeit Peter
Published: December 2021

Background

There is uncertainty about the seroprevalence of anti-SARS-CoV-2 antibodies in the general population of Austria, and about the extent to which antibodies elicited by vaccination or infection wane over time.

Aim

To estimate seroprevalence, waning, and correlates of anti-SARS-CoV-2 IgG antibodies in the Federal State of Tyrol, Austria.

Methods

We conducted a seroepidemiological study between June 2020 and September 2021, enrolling blood donors aged 18-70 years across Tyrol, Austria (participation rate 84.0%). We analysed serum samples for antibodies against spike or nucleocapsid proteins of SARS-CoV-2 with Abbott SARS-CoV-2 IgG assays.

Results

We performed 47,363 serological tests among 35,193 individuals (median age 43.1 years [IQR: 29.3-53.7], 45.3% women, 10.0% with prior SARS-CoV-2 infection). Seroprevalence increased from 3.4% (95% CI: 2.8-4.2%) in June 2020 to 82.7% (95% CI: 81.4-83.8%) in September 2021, largely due to vaccination. Anti-spike IgG seroprevalence was 99.6% (99.4-99.7%) among fully vaccinated individuals, 90.4% (88.8-91.7%) among unvaccinated with prior infection, and 11.5% (10.8-12.3%) among unvaccinated without known prior infection. Anti-spike IgG levels were reduced by 44.0% (34.9-51.7%) at 5-6 months compared to 0-3 months after infection. In fully vaccinated individuals, they decreased by 31.7% (29.4-33.9%) per month. In multivariable adjusted analyses, both seropositivity among unvaccinated and antibody levels among fully vaccinated individuals were higher at young age (<25 years), higher with a known prior infection, and lower in current smokers.

Conclusion

Seroprevalence in Tyrol increased to 82.7% in September 2021, with the bulk of seropositivity stemming from vaccination. Antibody levels substantially and gradually declined after vaccination or infection.
Aberrant paracrine signalling for bone remodelling underlies the mutant histone-driven giant cell tumour of bone
Authors: Cottone Lucia , Ligammari Lorena , Knowles Helen J. , Lee Hang-Mao , Henderson Stephen , Bianco Sara , Davies Christopher , Strauss Sandra , Amary Fernanda , Leite Ana Paula , Tirabosco Roberto , Haendler Kristian , Schultze Joachim L. , Herrero Javier , O’Donnell Paul , Grigoriadis Agamemnon E. , Salomoni Paolo , Flanagan Adrienne M.
Published: December 2021

Oncohistones represent compelling evidence for a causative role of epigenetic perturbations in cancer. Giant cell tumours of bone (GCTs) are characterised by a mutated histone H3.3 as the sole genetic driver present in bone-forming osteoprogenitor cells but absent from abnormally large bone-resorbing osteoclasts which represent the hallmark of these neoplasms. While these striking features imply a pathogenic interaction between mesenchymal and myelomonocytic lineages during GCT development, the underlying mechanisms remain unknown.

We show that the changes in the transcriptome and epigenome in the mesenchymal cells caused by the H3.3-G34W mutation contribute to increase osteoclast recruitment in part via reduced expression of the TGFβ-like soluble factor, SCUBE3. In turn, osteoclasts secrete unregulated amounts of SEMA4D enhancing proliferation of mutated osteoprogenitors and arresting their maturation. These findings provide a mechanism by which GCTs undergo differentiation upon denosumab treatment, a drug that depletes osteoclasts. In contrast, gain of hTERT activity, commonly found in malignant GCT, makes neoplastic cells insensitive to osteoclasts, predicting the unresponsiveness to denosumab.

We provide a mechanism for GCT initiation and its response to current treatment, the basis of which is dysfunctional cross-talk between bone-forming and bone-resorbing cells, emphasising the importance of tumor/microenvironment bidirectional interactions in tumorigenesis.
Functional heterogeneity of cell populations increases robustness of pacemaker function in a numerical model of the sinoatrial node tissue
Authors: Maltsev Alexander V. , Stern Michael D. , Lakatta Edward G , Maltsev Victor A.
Published: December 2021

Each heartbeat is initiated by specialized pacemaker cells operating within the sinoatrial node (SAN). While individual cells within SAN tissue exhibit substantial heterogeneity of their electrophysiological parameters and Ca cycling, the role of this heterogeneity for cardiac pacemaker function remains mainly unknown. Here we investigated the problem numerically in a 25×25 square grid of coupled-clock Maltsev-Lakatta cell models and tested the hypothesis that functional heterogeneity of cell populations increases robustness of SAN function. The tissue models were populated by cells with different degree of heterogeneity of the two key model parameters of the coupled-clock system, maximum L-type Ca current conductance (gCaL) and sarcoplasmic reticulum Ca pumping rate (Pup). Our simulations showed that in the areas of Pup-gCaL parametric space at the edge of the system stability where action potential (AP) firing was absent or dysrhythmic in tissues populated by identical cells, rhythmic AP generation was rescued in tissues populated by cells with uniformly random distributions of gCaL or Pup (but keeping the same average values). This effect to increase robust AP generation was synergistic with respect to heterogeneity in both gCaL and Pup and was further strengthened by clustering of cells with higher gCaL or Pup. The effect of functional heterogeneity was not due to a simple summation of activity of intrinsically firing cells naturally present in SAN; rather AP firing cells locally and critically interacted with non-firing/dormant cells. When firing cells prevailed, they recruited many dormant cells to fire, strongly enhancing overall SAN function. And vice versa, prevailing dormant cells suppressed AP firing in cells with intrinsic automaticity and halted SAN automaticity.
A miRNAs Based Exploration of promising Biomarkers in Cervical Cancer using Bioinformatic Methods
Authors: Elumalai Elakkiya , Malarvizhi A. , Sri Shyla T. , Aruna devi OM. , Gupta Krishna Kant
Published: December 2021

Cervical Cancer (CC) is a gynecologic cancer. In this cancer early detection is incredibly tough because most of the patients are not have any specific symptoms that results in suspending the proper identification. In this work, we selected TCGA CESC datasets and miRNA Seq analysis was done. The expression profiles of miRNAs in cervical cancer datasets were investigated using bioinformatics tools. The expression profiles of miRNA in Normal tissue, primary tumor and metastatic samples were analyzed. Based on p-value, principal component analysis and comparative literature survey, we reported 6 over-expressed (5X) miRNA at metastatic stage namely, hsa-mir-363, hsa-mir-429, hsa-mir-141, hsa-mir-93, hsa-mir-203b and hsa-mir-18a. Expression profiles were compared in heatmap. The target genes for the selected miRNAs were investigated for interaction and pathway details. The identification of two hub proteins (PTEN and MYC) in Protein-Protein Interaction Network was followed by pathway analysis. Our results indicate thathsa-mir-363,hsa-mir-429, hsa-mir-141, hsa-mir-93, hsa-mir-203b and hsa-mir-18acould be a potential diagnostic biomarkers for early-stage CESC and serve as prognostic predictors for patients with CESC.
Evolution of synchronous bilateral breast cancers provide insights into interactions between host, tumor and immunity
Authors: Hamy Anne-Sophie , Abecassis Judith , Darrigues Lauren , Laurent Cecile , Zaccarini François , Sadacca Benjamin , Delomenie Myriam , Laas Enora , Mariani Odette , Lam Thanh , Grandal Beatriz , Lae Marick , Bieche Ivan , Vacher Sophie , Pierga Jean-Yves , Brain Etienne , Vallot Celine , Hotton Judicael , Richer Wilfrid , Waterfall Joshua , Reyal Fabien
Published: December 2021

Synchronous bilateral breast cancer (sBBC) occurs after both breasts have been affected by the same germline genetics, reproductive life factors and environmental exposures for decades. It represents an opportunity to decipher the complex interplay between host, tumor, immune system and response to neoadjuvant chemotherapy (NAC). On a cohort of 17575 BCs treated between 2005 and 2012, sBBCs (n=404) were associated with less aggressive proliferative patterns and higher rates of luminal breast cancers (BCs) when compared with unilateral BCs (n=17171). The left and right tumors were concordant for the majority of clinical and pathological features. Tumor pairs of concordant BC subtype were more frequent than pairs of discordant BC subtype, with notably a particularly high frequency of pairs of luminal BCs. Intriguingly, both the levels of tumor infiltrating lymphocytes (TILs) and the response to NAC were modified by the subtype of the contralateral tumors. Whole exome sequencing and RNAseq analyses revealed that left and right tumors were independent from a somatic mutation and transcriptomic point of view, while primary tumors (PT) before NAC and specimens with residual disease (RD) after NAC were more closely related. The analysis of the TCR repertoire identified very little overlap between patients, while common clones were shared in bilateral tumors within each patient. After NAC, the TCR repertoire of RD was enriched and expanded with clones edited by the contralateral PT.
Increased persuadability and credulity in people with corpus callosum dysgenesis
Authors: Barnby JM , Dean R. , Burgess H , Kim J , Teunisse A.K. , Mackenzie L , Robinson G , Dayan P , Richards LJ.
Published: December 2021

Corpus callosum dysgenesis is one of the most common congenital neurological malformations. Despite being a clear and identifiable structural alteration of the brain’s white matter connectivity, the impact of corpus callosum dysgenesis on cognition and behaviour has remained unclear. Here we build upon past clinical observations in the literature to define the clinical phenotype of corpus callosum dysgenesis better using unadjusted and adjusted group differences compared with a neurotypical sample on a range of social and cognitive measures that have been previously reported to be impacted by a corpus callosum dysgenesis diagnosis. Those with a diagnosis of corpus callosum dysgenesis (n = 22) demonstrated significantly higher persuadability, credulity, and insensitivity to social trickery than neurotypical (n = 86) participants, after controlling for age, sex, education, autistic-like traits, social intelligence, and general cognition. To explore this further, machine learning, utilising a set neurotypical sample for training the normative covariance structure of our psychometric variables, was used to test whether these dimensions possessed the capability to discriminate between a test-set of neurotypical and corpus callosum dysgenesis participants. We found that participants with a diagnosis of corpus callosum dysgenesis were best classed within dimension space along the same axis as persuadability, credulity, and insensitivity to social trickery after controlling for age and sex, with Leave-One-Out-Cross-Validation across 250 training-set permutations providing a mean accuracy of 71.7%. These results have wide- reaching implications for a) the characterisation of corpus callosum dysgenesis, and b) the role of the corpus callosum in social inference.
Clathrin-mediated Endocytosis Facilitates Internalization ofMagnaporthe oryzaeEffectors into Rice Cells
Authors: Oliveira-Garcia Ely , Tamang Tej Man , Park Jungeun , Dalby Melinda , Martin-Urdiroz Magdalena , Herrero Clara Rodriguez , Vu An Hong , Park Sunghun , Talbot Nicholas J. , Valent Barbara
Published: December 2021

Fungi and oomycetes deliver effectors into living plant cells to suppress defenses and control plant processes needed for infection. Little is known about the mechanism by which these pathogens translocate effector proteins across the plasma membrane into the plant cytoplasm. The blast fungusMagnaporthe oryzaesecretes cytoplasmic effectors into a specialized biotrophic interfacial complex (BIC) before translocation. Here we show that cytoplasmic effectors within BICs are packaged into vesicles that are occasionally observed in the host cytoplasm. Live cell imaging with fluorescently-labeled rice showed that effector vesicles colocalize with plant plasma membrane and with clathrin light chain-1, a marker for clathrin-mediated endocytosis (CME). Inhibition of CME using Virus-Induced Gene Silencing (VIGS) and chemical treatments results in cytoplasmic effectors in swollen BICs lacking vesicles. In contrast, fluorescent marker co-localization, VIGS and chemical inhibitor studies failed to support a major role for clathrin-independent endocytosis in effector vesicle formation. Localization studies of two novel effectors, and of known effectors after CME inhibition, indicate that cytoplasmic effector translocation occurs underneath appressoria before invasive hyphal growth. Taken together, this study provides evidence that cytoplasmic effector translocation is mediated by clathrin-mediated endocytosis in BICs and suggests a role forM. oryzaeeffectors in co-opting plant endocytosis.
Assessment of chimeric antigen receptor T (CAR-T) cytotoxicity by droplet microfluidics in vitro
Authors: Wong Kuan Un , Shi Jingxuan , Li Peng , Wang Haitao , Jia Yanwei , Deng Chuxia , Jang Lianmei , Wong Ada Hang-Heng
Published: December 2021

Chimeric antigen receptor T (CAR-T) cells are cytotoxic T cells engineered to specifically kill cancer cells expressing specific target receptor(s). Prior CAR-T efficacy tests include CAR expression analysis by qPCR or ELISA, in vitro measurement of interferon-γ (IFNγ) or interleukin-2 (IL-2), and xenograft models. However, the in vitro measurements did not reflect CAR-T cytotoxicity, whereas xenograft models are low throughput and costly. Here we presented a robust in vitro droplet microfluidic assay for CAR-T cytotoxicity assessment. This method not only enabled assessment of CAR-T cytotoxic activity under different fluid viscosity conditions, but also facilitated measurement of CAR-T expansion and dissection of mechanism of action via phenotype analysis in vitro. Furthermore, our data suggested that label-free cytotoxicity analysis is feasible by acquiring data before and after treatment. Hence, this study presented a novel in vitro method for assessment of cellular cytotoxicity that could potentially be applied to any cell-kill-cell experiment with varying solvent composition.
Identifying challenges and opportunities for histone peptides in protein engineering platforms
Authors: Meanor Jenna N , Keung Albert J , Rao Balaji M
Published: December 2021

Histone post-translational modifications are small chemical changes to histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET based systems. High throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet published studies on their use with histones have been noticeably sparse. Here we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.
Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign
Authors: Aggarwal Tushar , Hansen William A. , Hong Jonathan , Ganguly Abir , York Darrin M. , Khare Sagar D. , Izgu Enver Cagri
Published: December 2021

DNA polymerases have evolved to feature a highly conserved activity across the tree of life: formation of, without exception, phosphodiester linkages that create the repeating sugarphosphate backbone of DNA. Can this linkage selectivity observed in nature be overcome by design to produce non-natural nucleic acids? Here, we report that structure-guided redesign of an archaeal DNA polymerase (9°N) enables a new polymerase activity that is undetectable in the wild type enzyme: catalyzing the formation of N3’→P5’ phosphoramidate linkages in the presence of 3’-amino-2’,3’-dideoxynucleoside 5’-triphosphate (3’-NH2-ddNTP) building blocks. Replacing a highly conserved metal-binding aspartate in the 9°N active site (Asp-404) with asparagine was key to the emergence of this unnatural enzyme activity. Molecular dynamics simulations provided insights into how a single substitution could enhance the productive positioning of the 3’-amino nucleophile in the active site. Further remodeling of the protein-nucleic acid interface with substitutions in the finger subdomain led to a quadruple-mutant variant (9°N-NRQS) that incorporated 3’-NH2-ddNTPs into a 3’-amino-primer on various DNA templates. This work presents the first example of an active-site substitution of a metal-binding residue that leads to a novel activity in a DNA polymerase, and sheds light on the molecular basis of substrate fidelity and latent promiscuity in enzymes.
VRK1 is required in VRK2-methylated cancers of the nervous system
Authors: So Jonathan , Mabe Nathaniel W. , Englinger Bernhard , Moyer Sydney M. , Trissal Maria C. , Marques Joana G. , Kwon Jason , Shim Brian , Panditharatna Eshini , Jeong Daeun , Mayhew David , Hwang Justin , Stegmaier Kimberly , Filbin Mariella G. , Hahn William C.
Published: December 2021

Collateral lethality occurs when loss of one paralog renders cancer cells dependent on the remaining paralog. Combining genome scale CRISPR/Cas9 screens coupled with RNA-sequencing in over 900 cancer cell lines, we found that cancers of nervous system lineage, including adult and pediatric gliomas and neuroblastomas, required the nuclear kinase Vaccinia-Related Kinase 1 (VRK1) for their survival. VRK1 dependency was inversely correlated with expression of its paralog VRK2. VRK2 knockout (KO) sensitized cells to VRK1 suppression, and conversely, VRK2 overexpression increased cell fitness in the setting of VRK1 suppression. DNA methylation of the VRK2 promoter was associated with low VRK2 expression in human neuroblastomas, and adult and pediatric gliomas. Mechanistically, depletion of VRK1 reduced Barrier-to-Autointegration Factor (BAF) phosphorylation during mitosis, resulting in DNA damage and apoptosis. Together, these studies identify VRK1 as a synthetic lethal target in VRK2 promoter-methylated adult and pediatric gliomas and neuroblastomas.

Statement of Significance

We credential VRK1 as a target in adult and pediatric gliomas, and neuroblastomas with VRK2 promoter methylation. This demonstrates the utility of paralog-driven synthetic lethal interactions for biomarker-linked, targeted therapeutics.
The P2Y2 Nucleotide Receptor Mediates Monocyte Tissue Factor Expression and Endotoxemia Death in Mice
Authors: Peng Qianman , Qian Shenqi , Alqahtani Saud , Panizzi Peter , Shen Jianzhong
Published: December 2021

Recently we reported that in human coronary artery endothelial cells, activation of the P2Y2 receptor (P2Y2R) induces up-regulation of tissue factor (TF), a vital initiator of the coagulation cascade. However, others have shown that monocyte TF is more critical than endothelial TF in provoking a pro-thrombotic state. Thus, we aimed to study whether monocytes express the P2Y2R, its role in controlling TF expression, and its relevance in vivo. RT-PCR and receptor activity assays revealed that among the eight P2Y nucleotide receptors, the P2Y2 subtype was selectively and functionally expressed in human monocytic THP-1 cells and primary monocytes. Stimulation of the cells by ATP or UTP dramatically increased TF protein expression, which was abolished by AR-C118925, a selective P2Y2R antagonist, or by siRNA silencing the P2Y2R. In addition, UTP or ATP treatment induced a rapid accumulation of TF mRNA preceded with an increased TF pre-mRNA, indicating enhanced TF gene transcription. In addition, stimulation of the monocyte P2Y2R significantly activated ERK1/2, JNK, p38, and Akt, along with their downstream transcription factors including c-Jun, c-Fos, and ATF-2, whereas blocking these pathways respectively, all significantly suppressed P2Y2R-mediated TF expression. Furthermore, we found that LPS triggered ATP release and TF expression, the latter of which was suppressed by apyrase or P2Y2R blockage. Importantly, P2Y2R-null mice were more resistant than wild-type mice in response to a lethal dose of LPS, accompanied by much less TF expression in bone marrow cells. These findings demonstrate for the first time that the P2Y2R mediates TF expression in human monocytes through mechanisms involving ERK1/2, JNK, p38, and AKT, and that P2Y2R deletion protects the mice from endotoxemia-induced TF expression and death, highlighting monocyte P2Y2R may be a new drug target for the prevention and/or treatment of relevant thrombotic disease.
Comparative analysis of Lysine and Arginine biosynthesis pathway in Deinococcus genomes
Authors: Mahesh Sankar , Sethi Deepa , Priyadarshini Richa , Yennamalli Ragothaman M.
Published: December 2021

The members of the Deinococcaceae family have the ability to survive extreme environmental conditions. Deinococcus species have a complex cell envelope composed of L-ornithine containing peptidoglycan. Anabolism of L-ornithine is intrinsically linked to L-lysine and L-arginine biosynthetic pathways. To understand these two pathways, we analyzed the L-lysine and L-arginine pathways using 23 Deinococcus genomes, including D. indicus. We used BLAST-P based ortholog identification using D. radiodurans’ genes as the query. We identified some BLAST-P hits that shared the same functional annotation. We analyzed three (class I aminotransferase, acetyl-lysine deacetylase, and acetyl glutamate/acetyl aminoadipate kinase) from L-lysine biosynthesis pathway and three (bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase protein, nitric oxide synthase-like protein, and Acetyl-lysine deacetylase) from L-arginine biosynthesis pathway. Two proteins showed certain structural variations. Specifically, [LysW]-lysine hydrolase protein’s sequence and structure level changes indicated changes in oligomeric conformation, which could likely be a result of divergent evolution. And, bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase had its active site pocket positions shifted at the structural level and we hypothesize that it may not perform at the optimal level. Thus, we were able to compare and contrast different Deinococcus species indicating some genes occurring because of divergent evolution.
A Programmable Ontology Encompassing the Functional Logic of the Drosophila Brain
Authors: Lazar Aurel A. , Turkcan Mehmet Kerem , Zhou Yiyin
Published: December 2021

The Drosophila brain has only a fraction of the number of neurons of higher organisms such as mice and humans. Yet the sheer complexity of its neural circuits recently revealed by large connectomics datasets suggests that computationally modeling the function of fruit fly brain circuits at this scale posits significant challenges.

To address these challenges, we present here a programmable ontology that expands the scope of the current Drosophila brain anatomy ontologies to encompass the functional logic of the fly brain. The programmable ontology provides a language not only for modeling circuit motifs but also for programmatically exploring their functional logic. To achieve this goal, we tightly integrated the programmable ontology with the workflow of the interactive FlyBrainLab computing platform. As part of the programmable ontology, we developed NeuroNLP++, a web application that supports free-form English queries for constructing functional brain circuits fully anchored on the available connectome/synaptome datasets, and the published worldwide literature.

In addition, we present a methodology for including a model of the space of odorants into the programmable ontology, and for modeling olfactory sensory circuits of the antenna of the fruit fly brain that detect odorant sources. Furthermore, we describe a methodology for modeling the functional logic of the antennal lobe circuit consisting of massive local feedback loops, a characteristic feature observed across Drosophila brain regions. Finally, using a circuit library, we demonstrate the power of our methodology for interactively exploring the functional logic of the massive number of feedback loops in the antennal lobe.