bluuebunny/crossref_metadata_2025 huggingface dataset:
Presentation, Management, and Hearing Outcomes of Labyrinthine Fistula Secondary to Cholesteatoma: A Systematic Review and Meta-analysis
Authors: Tomasoni Michele , Arcuri Mara , Dohin Isabelle , Zorzi Silvia , Borsetto Daniele , Piazza Cesare , Redaelli de Zinis Luca Oscar , Sorrentino Tommaso , Deganello Alberto
Published: October 2022

Objective

The current study systematically reviewed the literature to compare auditory outcomes of patients treated for labyrinthine fistula (LF) based on characteristics of disease and surgical management.

Databases Reviewed

PubMed, Scopus, Web of Science.

Methods

Original series (at least five cases) published from 2000 reporting management and hearing results of LF secondary to cholesteatoma were included. Proportion and odds-ratio (OR) meta-analyses were conducted through inverse variance random-effects models based on logit transformation.

Results

The prevalence of LF is estimated to be 7% (95% confidence interval [CI], 5–9%). Fistulae involving the lateral semicircular canal (90%; 95% CI, 87–93%) and larger than 2 mm (53%; 95% CI, 43–64%) were common, whereas membranous involvement was less frequent (20%; 95% CI, 12–30%). Complete removal of the cholesteatoma matrix overlying the LF was mostly applied. Bone conduction (BC) preservation was frequently achieved (81%; 95% CI, 76–85%); new-onset postoperative anacusis was rarely reported (5%; 95% CI, 4–8%). A higher chance of BC preservation was associated with sparing the perilymphatic space (OR, 4.67; 95% CI, 1.26–17.37) or membranous labyrinth (OR, 4.56; 95% CI, 2.33–8.93), exclusive lateral semicircular canal involvement (OR, 3.52; 95% CI, 1.32–9.38), smaller size (<2 mm; OR, 3.03; 95% CI, 1.24–7.40), and intravenous steroid infusion (OR, 7.87; 95% CI, 2.34–26.42).

Conclusion

LF occurs in a significant proportion of patients with cholesteatoma. In the past two decades, complete removal of the cholesteatoma matrix followed by immediate sealing has been favored, supported by the high proportion of BC preservation. Hearing preservation depends primarily on characteristics of the LF, and specific surgical strategies should be pursued. Intraoperative and postoperative intravenous steroid infusion is recommended.
Association of Baseline Frailty Status and Age With Postoperative Complications After Cochlear Implantation: A National Inpatient Sample Study
Authors: Cole Kyril L. , Babajanian Eric , Anderson Ryan , Gordon Steve , Patel Neil , Dicpinigaitis Alis J. , Kazim Syed Faraz , Bowers Christian A. , Gurgel Richard K.
Published: October 2022

Objective

To conduct a national registry-based evaluation of the independent associations of chronological age and frailty, as measured by 5- and 11-factor modified frailty index (mFI-5, mFI-11) score, on postoperative outcomes of participants undergoing cochlear implantation (CI).

Study Design

Cross-sectional analysis.

Setting

Multicenter national database.

Participants

Adults 18 years or older who underwent CI during 2001 to 2018.

Main Outcome Measures

Any postoperative complications (determined as the presence of major, minor, or implant-specific), extended hospital length of stay (eLOS) (≥75th percentile of study population), and nonhome discharge destination.

Results

There were 5,130 participants included with a median age of 60 years (interquartile range, 44–73 y) and slight female predominance (53.5%). Under mFI-5 scoring, there were 2,979 (58.1%) robust (mFI-5 = 0), 1710 (33.3%) prefrail (mFI-5 = 1), 362 (7.1%) frail (mFI-5 = 2), and 78 (1.5%) severely frail (mFI-5 ≥ 3) participants. Three hundred twenty-eight (6.49%) participants experienced a postoperative complication, with 320 (6.2%) discharged to a nonhome destination. Multivariate analysis showed no statistically significant correlation between increasing participant age or frailty status and postoperative complications; however, increasing baseline frailty tier showed an independent association with risk of eLOS (severely frail: odds ratio, 4..83; 95% confidence interval, 3.00–7.75; p < 0.001) and nonhome discharge (severely frail: odds ratio, 6.51; 95% confidence interval, 3.81–11.11; p < 0.001). The mFI-11 showed very similar trends.

Conclusion

Among those evaluated, this study demonstrates that CI is a low-risk procedure in participants of all ages. Increasing frailty does not predispose to postoperative complications. However, frail patients are at additional risk for an eLOS and nonhome discharge. Short follow-up time, hospital-coding errors, and selection bias of more robust patients may limit the true results of this study.
Characteristics and Predictors of Late Right Heart Failure After Left Ventricular Assist Device Implantation
Authors: Alkhunaizi Fatimah A. , Azih Nnamdi I. , Read Jacob M. , Goldberg Rachel L. , Gulati Arune A. , Scheel Paul J. , Muslem Rahatullah , Gilotra Nisha A. , Sharma Kavita , Kilic Ahmet , Houston Brian A. , Tedford Ryan J. , Hsu Steven
Published: October 2022

Late right heart failure (LRHF) following left ventricular assist device (LVAD) implantation remains poorly characterized and challenging to predict. We performed a multicenter retrospective study of LRHF in 237 consecutive adult LVAD patients, in which LRHF was defined according to the 2020 Mechanical Circulatory Support Academic Research Consortium guidelines. Clinical and hemodynamic variables were assessed pre- and post-implant. Competing-risk regression and Kaplan–Meier survival analysis were used to assess outcomes. LRHF prediction was assessed using multivariable logistic and Cox proportional hazards regression. Among 237 LVAD patients, 45 (19%) developed LRHF at a median of 133 days post-LVAD. LRHF patients had more frequent heart failure hospitalizations (p < 0.001) alongside other complications. LRHF patients did not experience reduced bridge-to-transplant rates but did suffer increased mortality (hazard ratio 1.95, 95% confidence interval [CI] 1.11–3.42; p = 0.02). Hemodynamically, LRHF patients demonstrated higher right atrial pressure, mean pulmonary arterial pressure, and pulmonary vascular resistance (PVR), but no difference in pulmonary arterial wedge pressure. History of early right heart failure, blood urea nitrogen (BUN) > 35 mg/dl at 1 month post-LVAD, and diuretic requirements at 1 month post-LVAD were each significant, independent predictors of LRHF in multivariable analysis. An LRHF prediction risk score incorporating these variables predicted LRHF with excellent discrimination (log-rank p < 0.0001). Overall, LRHF post-LVAD is more common than generally appreciated, with significant morbidity and mortality. Elevated PVR and precapillary pulmonary pressures may play a role. A risk score using early right heart failure, elevated BUN, and diuretic requirements 1 month post implant predicted the development of LRHF.
Processing of Positive Memories Technique
Authors: Banducci Anne N. , Fondren Alana , Bocanegra Ashley , Crespo Maria , Contractor Ateka A.
Published: October 2022

Although the majority of research and clinical interventions focused on posttraumatic stress disorder (PTSD) centers on traumatic memories, recent literature suggests the importance of considering emotionally laden memories more broadly among trauma-exposed individuals. Specifically, trauma-exposed individuals have difficulties retrieving positive and negative memories, and interventions focused on enhancing the retrieval of both traumatic and positive memories benefit overall well-being. These findings led to the development of a novel Processing of Positive Memories Technique (PPMT) for PTSD. As the next step in treatment development, PPMT was piloted among 12 trauma-exposed community members seeking therapeutic or assessment services at a university psychology clinic. In this study, we summarize participants' quantitative and qualitative feedback on the content, format, and feasibility of PPMT. Next, we outline proposed formative changes that are critical to the iterative refinement of PPMT, based on the obtained feedback to enhance its scalability, feasibility, and effectiveness. Within clinical practice, PPMT, as implemented in this study, may be feasible, and there may be potential benefits to incorporating positive memory processing using PPMT.
Being and Becoming: Narrative Records of Pediatric Critical Care Clinicians
Authors: Proulx Catherine , Min Kyung-Seo (Kay) , Mema Briseida
Published: October 2022

Medical humanities initiatives have been integrated in our Pediatric Critical Care program to help clinicians make meaning of key experiences in their professional and personal journeys. In particular, narrative medicine and clinicians’ writings illuminate and commemorate these journeys and increase our understanding of our profession in its full complexity. In this piece, we provide an example of a medical humanities curriculum and a selection of pieces written by several participants in it. These pieces form a collective narrative, portraying aspects of our individual and collective biography.
Lactate as a Screening Tool for Critical Illness in a Pediatric Emergency Department
Authors: Nygaard Ulrikka , Dungu Kia Hee Schultz , von Linstow Marie-Louise , Lundstrøm Kaare , Zhang He , Vissing Nadja Hawwa
Published: October 2022

Objectives

Lactate has in some pediatric emergency departments (PEDs) gained acceptance as a screening tool for critical illness, with cut-off values of 2.0 to 2.5 mmol/L. We aimed to investigate if lactate could predict the need of acute resuscitation in patients in a PED.

Patients and Methods

This retrospective observational cohort study included patients aged 0 to 17 years admitted to the PED at Copenhagen University Hospital in Denmark from January 1, 2019 to January 1, 2021. Patients were included if they had lactate measured as part of their routine blood sampling because of acute PED evaluation. Area under the receiver operating characteristic (ROC) curve (AUC) was calculated to assess the ability of lactate to predict the need of acute resuscitation. In patients without need of acute resuscitation, we calculated the lactate upper limit as the 95th percentile, and significant predictors were included in a multiple linear regression model.

Results

A total of 1355 children were included. Fourteen (1%) children with a need of acute resuscitation had a median lactate of 1.7 mmol/L (interquartile range, 1.4–2.3) versus 1.6 mmol/L (interquartile range, 1.3–2.1) in children without need of resuscitation (P> 0.05). The AUC for lactate to predict acute resuscitation was 0.56 (95% confidence interval, 0.54–0.59). In children without need of acute resuscitation, the 95th percentile of lactate was 3.2 mmol/L, and 392 (29.8%) had lactate greater than 2.0 mmol/L. Increasing age and venous sampling were associated with lower lactate. Lactate was not associated with sex, pediatric early warning score, or duration of hospital admission. The 95th percentile of lactate after inhaled beta-2-agonists was 5.0 mmol/L.

Conclusions

In children evaluated in a PED, lactate achieved a low AUC, suggesting a poor ability of predicting acute resuscitation. In children without need of acute resuscitation, the 95th percentile for lactate was 3.2 mmol/L, higher than the generally accepted cut-off values. This is important to recognize to avoid concern in otherwise clinically stable children. Our data did not support the use of lactate as a screening tool for early recognition of critical illness in a PED.
Development of a Risk Prediction Model for Complications Following Forehead Flaps for Nasal and Periorbital Reconstruction
Authors: Wu Shannon S. , Patel Viren , Oladeji Temiloluwa , Knackstedt Rebecca , Gastman Brian
Published: October 2022

Background:

Forehead flaps are a workhorse for nasal reconstruction, but complications occur in up to 30% of patients and risk factors are not well characterized. This study aimed to identify risk factors for complications, and provide clinicians a method to stratify patient risk to facilitate shared decision-making.

Materials and Methods:

This retrospective study included patients who underwent forehead flaps between 2007 and 2020. Demographic and treatment characteristics were abstracted, in addition to clinical outcomes data. Multivariable regression was conducted, with step-wise variable elimination to determine inclusion in the final model. From the final regression, a risk-stratification scheme was developed.

Results:

One hundred ninety-seven patients underwent forehead flap reconstruction, with a mean age of 68.5 years. Mean follow-up time was 42 months. There were 50 (25.4%) patients who developed a complication, including impaired nasal function (18.8%), flap congestion (5.1%), infection (2.5%), poor donor site healing (2.5%) wound dehiscence (2.0%), and flap congestion (1.5%). On univariate analysis, female sex, immunosuppression, prior radiotherapy, and larger resection area were associated with complications (P<0.05). On multivariable analysis, female sex [odds ratio (OR): 3.89, P<0.001], hypoalbuminemia (OR: 3.70, P=0.01), and prior wide local excision (OR: 3.62, P=0.04) were predictors of complications. A clinical calculator was developed incorporating these risk factors, with a C-statistic of 0.85, indicating strong predictive value.

Conclusions:

We conducted the most comprehensive review of risk factors for the development of complications after forehead flap reconstruction. From this analysis, a novel, implementable, risk-stratification scheme was developed to equip surgeons with the ability to provide individualized risk assessment to patients and address preoperative comorbidities to optimize outcomes.
Changes in Transcriptome-Associated Co-Expression Profile of Embryonic External Ear Development After Prkra Gene Mutation
Authors: Liu Wei , Lin Lin , Yang Qinghua , Jin Shengyang , Jiang Haiyue
Published: October 2022

The aim was to understand the changes in gene expression during the mouse external ear embryonic development in the full transcriptomes of mice with a point mutation in the Prkra gene, the outer ear tissues of mouse embryos were developed to embryonic day (E)15.5 and E17.5, and a Prkra Little-ear mouse model was obtained. The purpose of this study was to perform a whole transcriptome association analysis of the Prkra Little-ear mouse model during external ear embryonic development using advanced sequencing techniques. The association analysis of the full transcriptome mainly included lncRNA and mRNA association analysis, lncRNA and miRNA association analysis, miRNA and mRNA association analysis, circRNA and mRNA association analysis, circRNA, miRNA, and mRNA association analysis, and lncRNA, miRNA, and mRNA association analysis. The results of the correlation analysis showed that in the Prkra Little-ear mouse embryo development of the external ear was regulated by whole transcriptome and that these changes were different in wild-type mice. This study provides a new concept for elucidating the mechanism of the regulation of mouse external ear development.
Antibody-mediated Rejection Without Detectable Donor-specific Antibody Releases Donor-derived Cell-free DNA: Results From the Trifecta Study
Authors: Halloran Philip F. , Reeve Jeff , Madill-Thomsen Katelynn S. , Demko Zachary , Prewett Adam , Gauthier Philippe , Billings Paul , Lawrence Christopher , Lowe Dave , Hidalgo Luis G.
Published: October 2022

Background.

Trifecta (ClinicalTrials.gov #NCT04239703) is a prospective trial defining relationships between donor-derived cell-free DNA (dd-cfDNA), donor-specific antibody (DSA), and molecular findings in kidney transplant biopsies. Previous analyses of double results showed dd-cfDNA was strongly associated with rejection-associated molecules in the biopsy. The present study analyzed the triple results in 280 biopsies, focusing on the question of dd-cfDNA levels in DSA-negative antibody-mediated rejection (AMR).

Methods.

Molecular Microscope Diagnostic System biopsy testing was performed at Alberta Transplant Applied Genomics Centre, dd-cfDNA testing at Natera, Inc, and central HLA antibody testing at One Lambda Inc. Local DSA and histologic diagnoses were assigned per center standard-of-care.

Results.

DSA was frequently negative in both molecular (56%) and histologic (51%) AMR. DSA-negative AMR had slightly less molecular AMR activity and histologic peritubular capillaritis than DSA-positive AMR. However, all AMRs—DSA-positive or -negative—showed elevated %dd-cfDNA. There was no association between dd-cfDNA and DSA in biopsies without rejection. In AMR, %dd-cfDNA ≥1.0 was more frequent (75%) than DSA positivity (44%). In logistic regression, dd-cfDNA percent (area under the curve [AUC] 0.85) or quantity (AUC 0.86) predicted molecular AMR better than DSA (AUC 0.66). However, the best predictions incorporated both dd-cfDNA and DSA, plus time posttransplant (AUC 0.88).

Conclusions.

DSA-negative AMR has moderately decreased mean molecular and histologic AMR-associated features compared with DSA-positive AMR, though similarly elevated dd-cfDNA levels. In predicting AMR at the time of indication biopsies in this population, dd-cfDNA is superior to DSA, reflecting the prevalence of DSA-negative AMR, but the optimal predictions incorporated both dd-cfDNA and DSA.
Intravesical BCG and Incidence of Alzheimer Disease in Patients With Bladder Cancer
Authors: Makrakis Dimitrios , Holt Sarah K. , Bernick Charles , Grivas Petros , Gore John L. , Wright Jonathan L.
Published: October 2022

Introduction:

Alzheimer disease (AD) is a common neurodegenerative disease, and immunomodulation offers treatment opportunities. Preclinical data suggest that intravesical Bacillus Calmette-Guerin (BCG) treatment could delay AD development. We investigated this relationship in a population-based cancer database.

Sample and Methods:

We queried the Surveillance, Epidemiology, and End Results-Medicare database for patients with high-risk nonmuscle-invasive bladder cancer (hrNMIBC). BCG dosage and subsequent Alzheimer diagnosis were collected through ICD-9/10 codes. Multivariable Cox regression was performed to assess the association between BCG therapy and subsequent Alzheimer diagnosis.

Results:

We identified 26,584 hrNMIBC patients; 51% received BCG and 8.3% were diagnosed with Alzheimer. BCG exposure was significantly associated with lower Alzheimer occurrence (hazard ratio: 0.73, P<0.05), which was dose-dependent. Increasing age, female sex, Black race, and increasing comorbidity index were significantly associated with a greater risk of subsequent Alzheimer diagnosis.

Discussion:

Treatment with intravesical BCG among patients with hrNMIBC was associated with a significantly lower risk for subsequent Alzheimer diagnosis, which seemed dose-dependent.
Three-dimensional visualization of the cardiac ryanodine receptor clusters and the molecular-scale fraying of dyads
Authors: Sheard Thomas M. D. , Hurley Miriam E. , Smith Andrew J. , Colyer John , White Ed , Jayasinghe Izzy
Published: October 2022

Clusters of ryanodine receptor calcium channels (RyRs) form the primary molecular machinery of intracellular calcium signalling in cardiomyocytes. While a range of optical super-resolution microscopy techniques have revealed the nanoscale structure of these clusters, the three-dimensional (3D) nanoscale topologies of the clusters have remained mostly unresolved. In this paper, we demonstrate the exploitation of molecular-scale resolution in enhanced expansion microscopy (EExM) along with various 2D and 3D visualization strategies to observe the topological complexities, geometries and molecular sub-domains within the RyR clusters. Notably, we observed sub-domains containing RyR-binding protein junctophilin-2 (JPH2) occupying the central regions of RyR clusters in the deeper interior of the myocytes (including dyads), while the poles were typically devoid of JPH2, lending to a looser RyR arrangement. By contrast, peripheral RyR clusters exhibited variable co-clustering patterns and ratios between RyR and JPH2. EExM images of dyadic RyR clusters in right ventricular (RV) myocytes isolated from rats with monocrotaline-induced RV failure revealed hallmarks of RyR cluster fragmentation accompanied by breaches in the JPH2 sub-domains. Frayed RyR patterns observed adjacent to these constitute new evidence that the destabilization of the RyR arrays inside the JPH2 sub-domains may seed the primordial foci of dyad remodelling observed in heart failure.

This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Inositol 1,4,5-trisphosphate receptors in cardiomyocyte physiology and disease
Authors: Demydenko Kateryna , Ekhteraei-Tousi Samaneh , Roderick H. Llewelyn
Published: October 2022

The contraction of cardiac muscle underlying the pumping action of the heart is mediated by the process of excitation-contraction coupling (ECC). While triggered by Ca
2+
entry across the sarcolemma during the action potential, it is the release of Ca
2+
from the sarcoplasmic reticulum (SR) intracellular Ca
2+
store via ryanodine receptors (RyRs) that plays the major role in induction of contraction. Ca
2+
also acts as a key intracellular messenger regulating transcription underlying hypertrophic growth. Although Ca
2+
release via RyRs is by far the greatest contributor to the generation of Ca
2+
transients in the cardiomyocyte, Ca
2+
is also released from the SR via inositol 1,4,5-trisphosphate (InsP
3
) receptors (InsP
3
Rs). This InsP
3
-induced Ca
2+
release modifies Ca
2+
transients during ECC, participates in directing Ca
2+
to the mitochondria, and stimulates the transcription of genes underlying hypertrophic growth. Central to these specific actions of InsP
3
Rs is their localization to responsible signalling microdomains, the dyad, the SR-mitochondrial interface and the nucleus. In this review, the various roles of InsP
3
R in cardiac (patho)physiology and the mechanisms by which InsP
3
signalling selectively influences the different cardiomyocyte cell processes in which it is involved will be presented.

This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Ontogeny of cardiomyocytes: ultrastructure optimization to meet the demand for tight communication in excitation–contraction coupling and energy transfer
Authors: Birkedal Rikke , Laasmaa Martin , Branovets Jelena , Vendelin Marko
Published: October 2022

The ontogeny of the heart describes its development from the fetal to the adult stage. In newborn mammals, blood pressure and thus cardiac performance are relatively low. The cardiomyocytes are thin, and with a central core of mitochondria surrounded by a ring of myofilaments, while the sarcoplasmic reticulum (SR) is sparse. During development, as blood pressure and performance increase, the cardiomyocytes become more packed with structures involved in excitation–contraction (e-c) coupling (SR and myofilaments) and the generation of ATP (mitochondria) to fuel the contraction. In parallel, the e-c coupling relies increasingly on calcium fluxes through the SR, while metabolism relies increasingly on fatty acid oxidation. The development of transverse tubules and SR brings channels and transporters interacting via calcium closer to each other and is crucial for e-c coupling. However, for energy transfer, it may seem counterintuitive that the increased structural density restricts the overall ATP/ADP diffusion. In this review, we discuss how this is because of the organization of all these structures forming modules. Although the overall diffusion across modules is more restricted, the energy transfer within modules is fast. A few studies suggest that in failing hearts this modular design is disrupted, and this may compromise intracellular energy transfer.

This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Serial block face scanning electron microscopy reveals region-dependent remodelling of transverse tubules post-myocardial infarction
Authors: Perera Tharushi , Pius Charlene , Niort Barbara , Radcliffe Emma J. , Dibb Katharine M. , Trafford Andrew W. , Pinali Christian
Published: October 2022

The highly organized transverse tubule (t-tubule) network facilitates cardiac excitation–contraction coupling and synchronous cardiac myocyte contraction. In cardiac failure secondary to myocardial infarction (MI), changes in the structure and organization of t-tubules result in impaired cardiac contractility. However, there is still little knowledge on the regional variation of t-tubule remodelling in cardiac failure post-MI. Here, we investigate post-MI t-tubule remodelling in infarct border and remote regions, using serial block face scanning electron microscopy (SBF-SEM) applied to a translationally relevant sheep ischaemia reperfusion MI model and matched controls. We performed minimally invasive coronary angioplasty of the left anterior descending artery, followed by reperfusion after 90 min to establish the MI model. Left ventricular tissues obtained from control and MI hearts eight weeks post-MI were imaged using SBF-SEM. Image analysis generated three-dimensional reconstructions of the t-tubular network in control, MI border and remote regions. Quantitative analysis revealed that the MI border region was characterized by t-tubule depletion and fragmentation, dilation of surviving t-tubules and t-tubule elongation. This study highlights region-dependent remodelling of the tubular network post-MI and may provide novel localized therapeutic targets aimed at preservation or restoration of the t-tubules to manage cardiac contractility post-MI.

This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease’.
Co-infection of SARS-CoV-2 with other respiratory pathogens in patients with liver disease
Authors: Samal Jasmine , Agarwal Reshu , Soni Anushka , Pandey Amit , Thapar Shalini , Gupta Ekta
Published: October 2022

Respiratory illness caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was first documented in Wuhan, China, in December 2019, followed by its rapid spread across the globe. Accumulating evidence has demonstrated viral/bacterial co-infection in the respiratory tract could modulate disease severity and its outcome in COVID-19 infection. In this retrospective study, 300 chronic liver disease patients with radiologically confirmed lower respiratory tract infection were enrolled from September 2020 to December 2021. In all of them, along with SARS-CoV-2, other respiratory viral/bacterial pathogens were studied. In total, 23.7 % (n=71) patients were positive for SARS-CoV-2. Among the positive patients, 23.9 % (n=17) had co-infection with other respiratory pathogens, bacterial co-infections being dominant. The SARS-CoV-2 negative cohort had 39.7  % positivity (n=91) for other respiratory pathogens, the most common being those of the rhinovirus/enterovirus family. Ground glass opacity (GGO) with consolidation was found to be the most common radiological finding among SARS-CoV-2 positive co-infected patients, as compared to only GGO among SARS-CoV-2 mono-infected patients. Accurate diagnosis of co-infections, especially during pandemics including COVID-19, can ameliorate the treatment and management of suspected cases.
Fast and Automated Protein-DNA/RNA Macromolecular Complex Modeling from Cryo-EM Maps
Authors: Nakamura Andrew , Meng Hanze , Zhao Minglei , Wang Fengbin , Hou Jie , Cao Renzhi , Si Dong
Published: October 2022

Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fit residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/.
Reduction ofParaoxonaseexpression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization
Authors: Graham Allie M , Jamison Jerrica M , Bustos Marisol , Cournoyer Charlotte , Michaels Alexa , Presnell Jason S , Richter Rebecca , Crocker Daniel E. , Fustukjian Ari , Hunter Margaret E. , Rea Lorrie D. , Marsillach Judit , Furlong Clement E , Meyer Wynn K , Clark Nathan L
Published: October 2022

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of theParaoxonase 1(Pon1) gene among aquatic mammal lineages -Pon1became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studyingPon1sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression ofPon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding level pseudogenization events inPon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss ofPon1function in aquatic/semiaquatic lineages is consistent with a benefit toPon1functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces ofPon1functional loss. We find that loss is best correlated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.
Stacked binding of a small molecule PET tracer to Alzheimer’s tau paired helical filaments
Authors: Merz Gregory E. , Chalkley Matthew J. , Tan Sophia , Tse Eric , Lee Joanne , Prusiner Stanley B. , Paras Nick A. , DeGrado William F. , Southworth Daniel R.
Published: October 2022

Neurodegenerative diseases (NDs) are characterized by the formation of amyloid filaments that adopt disease-specific conformations in the brain. Recently developed small molecules hold promise as diagnostics and possible therapeutics for NDs, but their binding mechanisms to amyloid filaments remain unknown. Here, we used cryo–electron microscopy (cryo-EM) to determine a 2.7 Å structure of Alzheimer’s disease patient-derived tau paired-helical filaments incubated with the GTP-1 PET probe. GTP-1 is bound stoichiometrically along an exposed cleft of each protofilament in a stacked arrangement that matches the fibril’s symmetry. Multiscale modeling revealed favorable pi-pi aromatic stacking interactions between GTP-1 molecules that, together with small molecule–protein contacts, result in high affinity binding. This binding mode offers new insight into designing compounds for diagnosis and treatment of specific NDs.

One Sentence Summary

Cryo-EM structure reveals a novel stacked arrangement of the GTP-1 PET ligand bound to Alzheimer’s disease tau filaments.
Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal
Authors: Rancilhac Loïs , Miralles Aurélien , Geniez Philippe , Mendez-Aranda Daniel , Beddek Menad , Brito José Carlos , Leblois Raphaël , Crochet Pierre-André
Published: October 2022

Aim

Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting.

Location

Morocco

Taxon

Spiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae

Methods

Using 325 samples from 40 localities, we identified genetic discontinuities withinA. erythrurusbased on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks).

Result

A. erythrurusis characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases.

Main conclusions

The genetic diversity ofA. erythrurusoriginates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations withinA. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.
Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: comparison of experiments and computation
Authors: Pacheco-Garcia Juan Luis , Cagiada Matteo , Tienne-Matos Kelly , Salido Eduardo , Lindorff-Larsen Kresten , Pey Angel L.
Published: October 2022

Recent advances in DNA sequencing technologies are revealing a large variability in the human genome. Our capacity to establish genotype-phenotype correlations in such large-scale is, however, limited. This task is particularly challenging due to the multifunctional nature of proteins. Here we describe an extensive analysis of the stability and function of naturally-occurring variants (found in the COSMIC and gnomAD databases) of the cancer-associated human NAD(P)H: quinone oxidoreductase 1 (NQO1). First, we performed in silico saturation mutagenesis studies (>5000 substitutions) aimed to identify regions in NQO1 important for stability and function. We then experimentally characterized twenty-two naturally-occurring variants in terms of protein levels during bacterial expression, solubility, thermal stability and coenzyme binding. These studies showed a good overall correlation between experimental analysis and computational predictions; also the magnitude of the effects of the substitutions are similarly distributed in variants from the COSMIC and gnomAD databases. Outliers in these experimental-computational genotype-phenotype correlations remain, and we discuss these on the grounds and limitations of our approaches. Our work represents a further step to characterize the mutational landscape of NQO1 in the human genome and may help to improve high-throughput in silico tools for genotype-phenotype correlations in multifunctional proteins associated with disease.
CNHplus: the chromosomal copy number heterogeneity which respects biological constraints
Authors: Grendár Marian , Martínek Petr , Loderer Dušan , Ondič Ondrej
Published: October 2022

Motivation

Intra-Tumor Heterogeneity (ITH) is a hallmark of cancer. ITH influences evolution of tumors and hence also affects patients survival. There are several methods for quantifying ITH. Recently, van Dijk et al. (Nat. Commun. 12(1):1-12, 2021) introduced Copy Number Heterogeneity (CNH) method for quantifying ITH from a single tumor sample, based on a copy number profile. The authors demonstrated capability of CNH to stratify patients for survival, across cancers. We aimed to reproduce the authors’ study.

Results

A deficiency in CNH is pointed out. The absolute copy number (ACN) profile obtained by solving the CNH optimization problem may contain negative number of copies. For a large portion of samples from The Cancer Genome Atlas (TCGA) studies considered by the authors the CNH-recovered ACN profiles are faulty. CNHplus corrects the flaw by imposing the non-negativity constraint. CNHplus is applied to survival stratification of patients from the TCGA studies. Also, it is discussed which other biological constraints should be incorporated into CNHplus. CNHplus estimates of the tumor purity, tumor ploidy are compared with those of the ABSOLUTE method.

Availability and implementation

R library CNHplus can be accessed here:https://github.com/grendar/CNHplus
Intermediately Synchronised Brain States optimise trade-off between Subject Identifiability and Predictive Capacity
Authors: Sasse Leonard , Larabi Daouia I. , Omidvarnia Amir , Jung Kyesam , Hoffstaedter Felix , Jocham Gerhard , Eickhoff Simon B. , Patil Kaustubh R.
Published: October 2022

Functional connectivity (FC) refers to the statistical dependencies between activity of distinct brain areas. To study temporal fluctuations in FC within the duration of a functional magnetic resonance imaging (fMRI) scanning session, researchers have proposed the computation of an edge time series (ETS) and their derivatives. Evidence suggests that FC is driven by a few time points of high-amplitude co-fluctuation (HACF) in the ETS, which may also contribute disproportionately to interindividual differences. However, it remains unclear to what degree different time points actually contribute to brain-behaviour associations. Here, we systematically evaluate this question by assessing the predictive utility of FC estimates at different levels of co-fluctuation using machine learning (ML) approaches. We demonstrate that time points of lower and intermediate co-fluctuation levels provide overall highest subject specificity as well as highest predictive capacity of individual-level phenotypes.
Notes on the data quality of bibliographic records from the MEDLINE database
Authors: Bramley Robin , Howe Stephen , Marmanis Haralambos
Published: October 2022

The US National Library of Medicine has created and maintains the PubMed®database, a collection of over 33.8 million records that contain citations and abstracts from the biomedical and life sciences literature. That database is an important resource for researchers and information service providers alike. As part of our work related to the creation of an author graph for coronaviruses, we encountered several data quality issues with records from a curated subset of the PubMed database called MEDLINE. We provide a data quality assessment for records selected from the MEDLINE database and report on several issues ranging from parsing issues (e.g., character encodings and schema definition weaknesses) to low scores against several data quality metrics (e.g., identifier completeness, validity, and uniqueness).
A single-cell multi-omic atlas spanning the adult rhesus macaque brain
Authors: Chiou Kenneth L. , Huang Xingfan , Bohlen Martin O. , Tremblay Sébastien , O’Day Diana R. , Spurrell Cailyn H. , Gogate Aishwarya A. , Zintel Trisha M. ,   Cayo Biobank Research Unit, Andrews Madeline G. , Martínez Melween I. , Starita Lea M. , Montague Michael J. , Platt Michael L. , Shendure Jay , Snyder-Mackler Noah
Published: October 2022

Cataloging the diverse cellular architecture of the primate brain is crucial for understanding cognition, behavior and disease in humans. Here, we generated a brain-wide single-cell multimodal molecular atlas of the rhesus macaque brain. Altogether, we profiled 2.58M transcriptomes and 1.59M epigenomes from single nuclei sampled from 30 regions across the adult brain. Cell composition differed extensively across the brain, revealing cellular signatures of region-specific functions. We also identified 1.19M candidate regulatory elements, many novel, allowing us to explore the landscape ofcis-regulatory grammar and neurological disease risk in a cell-type-specific manner. Together, this multi-omic atlas provides an open resource for investigating the evolution of the human brain and identifying novel targets for disease interventions.
Pro-tumor and prothrombotic activities of hepsin in colorectal cancer cells and suppression by venetoclax
Authors: Rodenas Maria Carmen , Peñas-Martínez Julia , Pardo-Sánchez Irene , Zaragoza-Huesca David , Ortega-Sabater Carmen , Peña-García Jorge , Espín Salvador , Ricote Guillermo , Montenegro Sofía , de la Peña Francisco Ayala , Luengo-Gil Ginés , Nieto Andrés , García-Molina Francisco , Vicente Vicente , Bernardi Francesco , Lozano Maria Luisa , Mulero Victoriano , Pérez-Sánchez Horacio , Carmona-Bayonas Alberto , Martínez-Martínez Irene
Published: October 2022

Hepsin is a type II transmembrane serine protease whose expression has been linked to greater tumorigenicity and worse prognosis in different tumors such as prostate and gastric cancer. Recently, our group described hepsin expression in the primary biopsy as a potential biomarker of thrombosis and metastasis in localized colorectal cancer patients. Here we explored the role of hepsin in this tumor. Hepsin overexpression increased Caco-2 cell migration and invasion, higher phosphorylation of Erk1/2 and STAT3 and led to more thrombin generation in plasma. Indeed, our study revealed higher plasma levels of hepsin in metastatic colorectal cancer patients, which was associated with a greater tendency toward thrombosis. By virtual screening of a FDA-approved drug library, we identified venetoclax as a potent hepsin inhibitor, reducing the metastatic and prothrombotic phenotype of Caco-2 cells, but not of other colorectal cancer cells without hepsin expression. Interestingly, pre-treating Caco-2 cells overexpressing hepsin with venetoclax reduced its in vivo invasiveness. Taken together, our results demonstrate that elevated hepsin levels correlate with a more aggressive and prothrombotic tumor phenotype. Likewise, they evidence an antitumor role for venetoclax as a hepsin inhibitor. This lays the groundwork for molecular targeted therapy for colorectal cancer.
Biophysical analysis of Gaussia Luciferase bioluminescence mechanisms using a non-oxidizable coelenterazine
Authors: Takatsu Kyoko , Kobayashi Naohiro , Wu Nan , Janin Yves L. , Yamazaki Toshio , Kuroda Yutaka
Published: October 2022

Gaussia luciferase (GLuc 18.2kDa; 168 residues) is a marine copepod luciferase that emits a bright blue light when oxidizing coelenterazine (CTZ). It is a helical protein where two homologous sequential repeats form two anti-parallel bundles, each made of four helices. We previously identified a hydrophobic cavity as a prime candidate for the catalytic site, but Gluc’s fast bioluminescence reaction hampered a detailed analysis. Here, we used azacoelenterazine, a non-oxidizable coelenterazine analog, as a probe to investigate its binding mode to GLuc. Interestingly, the biochemical studies of GLuc inhibition by azacoelenterazine also led us to find that salt, and monovalent anions, are required for GLuc’s bioluminescence, which seems reasonable for a sea-dwelling creature. The NMR-based investigation, using chemical shift perturbations monitored by 15NH-HSQC, suggested that CTZ binds to residue in or near the hydrophobic cavity. Of note is that these NMR data are in line with a recent structural prediction of GLuc, hypothesizing that large structural changes occur in regions remote from the hydrophobic cavity upon the addition of CTZ. Interestingly, these results point toward a unique mode of catalysis to achieve CTZ oxidative decarboxylation.
Functional characterization of enhancer activity during a long terminal repeat's evolution
Authors: Du Alan Y. , Zhuo Xiaoyu , Sundaram Vasavi , Jensen Nicholas O. , Chaudhari Hemangi G. , Saccone Nancy L. , Cohen Barak A. , Wang Ting
Published: October 2022

Many transposable elements (TEs) contain transcription factor binding sites and are implicated as potential regulatory elements. However, TEs are rarely functionally tested for regulatory activity, which in turn limits our understanding of how TE regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1- and CEBP-related binding motifs as drivers of enhancer activity. Functional analysis of evolutionarily reconstructed ancestral sequences revealed that LTR18A elements have generally lost regulatory activity over time through sequence changes, with the largest effects occurring owing to mutations in the AP-1 and CEBP motifs. We observed that the two motifs are conserved at higher rates than expected based on neutral evolution. Finally, we identified LTR18A elements as potential enhancers in the human genome, primarily in epithelial cells. Together, our results provide a model for the origin, evolution, and co-option of TE-derived regulatory elements.
Model predictive control using LPV approach for trajectory tracking of quadrotor UAV with external disturbances
Authors: Singh Brajesh Kumar , Kumar Awadhesh
Published: October 2022

Purpose

The rotorcraft technology is very interesting area since last few decades due to variety of applications. One of the rotorcrafts is the quadrotor unmanned aerial vehicle (QUAV), which contains four rotors mounted on an airframe with an onboard controller. The QUAV is a highly nonlinear system and underactuated. Its controller design is very challenging task, and the need of controller is to make it autonomous based on mission planning. The purpose of this study is to design a controller for quadrotor UAV for attitude stabilization and trajectory tracking problem in presence of external environmental disturbances such as wind gust.

Design/methodology/approach

To address this problem, the model predictive control has been designed for attitude control and feedback linearization control for the position control using the linear parameter varying (LPV) approach. The trajectory tracking problem has been addressed using the circular trajectory and helical trajectory.

Findings

The simulation results show the efficient performance with good trajectory tracking even in presence of external disturbances in both the scenarios considered, one for circular trajectory tracking and other for helical trajectory tracking.

Originality/value

The novelty of the work came from using the LPV approach in controller design, which increases the robustness of the controller in presence of external disturbances.