bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-Term Outcomes Following Elective Repair of Intact Abdominal Aortic Aneurysms
Authors: Garland Sarah K. , Falster Michael O. , Beiles C. Barry , Freeman Anthony J. , Jorm Louisa R. , Sedrakyan Art , Sotade Oluwadamisola , Varcoe Ramon L.
Published: October 2021

Objective:

Compare long-term mortality, secondary intervention and secondary rupture following elective endovascular aneurysm repair (EVAR) and open surgical repair (OSR).

Background:

EVAR has surpassed OSR as the most common procedure used to repair abdominal aortic aneurysm (AAA), but evidence regarding long-term outcomes is inconclusive.

Methods:

We included patients in linked clinical registry and administrative data undergoing EVAR or OSR for intact AAA between January 2010 and June 2019. We used an inverse probability of treatment-weighted survival analysis to compare all-cause mortality, cause-specific mortality, secondary interventions and secondary rupture, and evaluate the impact of secondary interventions and secondary rupture on all-cause mortality.

Results:

The study included 3460 EVAR and 427 OSR patients. Compared to OSR, the EVAR all-cause mortality rate was lower in the first 30 days [adjusted hazard ratio (HR) = 0.22, 95% confidence interval (CI) 0.140.33], but higher between 1 and 4 years (HR = 1.29, 95% CI 1.12–1.48) and after 4years (HR = 1.41, 95% CI 1.23–1.63). Secondary intervention rates were higher over the first 30 days (HR = 2.26, 95% CI 1.11–4.59), but lower between 1 and 4years (HR = 0.59, 95% CI 0.48–0.74). Secondary aortic intervention rates were higher across the entire follow-up period (HR = 2.52, 95% CI 2.06–3.07). Secondary rupture rates did not differ significantly (HR = 1.06, 95% CI 0.73–1.55). All-cause mortality beyond 1 year remained significantly higher for EVAR after adjusting for any secondary interventions, or secendary rupture

Conclusions:

EVAR has an early survival benefit compared to OSR. However, elevated long-term mortality and higher rates of secondary aortic interventions and subsequent aneurysm repair suggest that EVAR may be a less durable method of aortic aneurysm exclusion.
Electronic health record machine learning model predicts trauma inpatient mortality in real time: A validation study
Authors: Mou Zongyang , Godat Laura N. , El-Kareh Robert , Berndtson Allison E. , Doucet Jay J. , Costantini Todd W.
Published: October 2021

INTRODUCTION

Patient outcome prediction models are underused in clinical practice because of lack of integration with real-time patient data. The electronic health record (EHR) has the ability to use machine learning (ML) to develop predictive models. While an EHR ML model has been developed to predict clinical deterioration, it has yet to be validated for use in trauma. We hypothesized that the Epic Deterioration Index (EDI) would predict mortality and unplanned intensive care unit (ICU) admission in trauma patients.

METHODS

A retrospective analysis of a trauma registry was used to identify patients admitted to a level 1 trauma center for >24 hours from October 2019 to July 2020. We evaluated the performance of the EDI, which is constructed from 125 objective patient measures within the EHR, in predicting mortality and unplanned ICU admissions. We performed a 5 to 1 match on age because it is a major component of EDI, then examined the area under the receiver operating characteristic curve (AUROC), and benchmarked it against Injury Severity Score (ISS) and new injury severity score (NISS).

RESULTS

The study cohort consisted of 1,325 patients admitted with a mean age of 52.5 years and 91% following blunt injury. The in-hospital mortality rate was 2%, and unplanned ICU admission rate was 2.6%. In predicting mortality, the maximum EDI within 24 hours of admission had an AUROC of 0.98 compared with 0.89 of ISS and 0.91 of NISS. For unplanned ICU admission, the EDI slope within 24 hours of ICU admission had a modest performance with an AUROC of 0.66.

CONCLUSION

Epic Deterioration Index appears to perform strongly in predicting in-patient mortality similarly to ISS and NISS. In addition, it can be used to predict unplanned ICU admissions. This study helps validate the use of this real-time EHR ML-based tool, suggesting that EDI should be incorporated into the daily care of trauma patients.

LEVEL OF EVIDENCE

Prognostic, level III.
Improved identification of severely injured pediatric trauma patients using reverse shock index multiplied by Glasgow Coma Scale
Authors: Reppucci Marina L. , Acker Shannon N. , Cooper Emily , Meier Maxene , Stevens Jenny , Phillips Ryan , Moulton Steven L. , Bensard Denis D.
Published: October 2021

BACKGROUND

The shock index pediatric age-adjusted (SIPA) predicts the need for increased resources and mortality among pediatric trauma patients without incorporating neurological status. A new scoring tool, rSIG, which is the reverse shock index (rSI) multiplied by the Glasgow Coma Scale (GCS), has been proven superior at predicting outcomes in adult trauma patients and mortality in pediatric patients compared with traditional scoring systems. We sought to compare the accuracy of rSIG to Shock Index (SI) and SIPA in predicting the need for early interventions in civilian pediatric trauma patients.

METHODS

Patients (aged 1–18 years) in the 2014 to 2018 Pediatric Trauma Quality Improvement Program database with complete heart rate, systolic blood pressure, and total GCS were included. Optimal cut points of rSIG were calculated for predicting blood transfusion within 4 hours, intubation, intracranial pressure monitoring, and intensive care unit admission. From the optimal thresholds, sensitivity, specificity, and area under the curve were calculated from receiver operating characteristics analyses to predict each outcome and compared with SI and SIPA.

RESULTS

A total of 604,931 patients with a mean age of 11.1 years old were included. A minority of patients had a penetrating injury mechanism (5.6%) and the mean Injury Severity Score was 7.6. The mean SI and rSIG scores were 0.85 and 18.6, respectively. Reverse shock index multiplied by Glasgow Coma Scale performed better than SI and SIPA at predicting early trauma outcomes for the overall population, regardless of age.

CONCLUSION

Reverse shock index multiplied by Glasgow Coma Scale outperformed SI and SIPA in the early identification of traumatically injured children at risk for early interventions, such as blood transfusion within 4 hours, intubation, intracranial pressure monitoring, and intensive care unit admission. Reverse shock index multiplied by Glasgow Coma Scale adds neurological status in initial patient assessment and may be used as a bedside triage tool to rapidly identify pediatric patients who will likely require early intervention and higher levels of care.

LEVEL OF EVIDENCE

Prognostic, level III.
An estrogen (17α-ethinyl estradiol-3-sulfate) reduces mortality in a swine model of multiple injuries and hemorrhagic shock
Authors: Abdou Hossam , Morrison Jonathan J. , Edwards Joseph , Patel Neerav , Lang Eric , Richmond Michael J. , Elansary Noha , Gopalakrishnan Mathangi , Berman Jonathan , Hubbard William J. , Scalea Thomas M. , Chaudry Irshad H.
Published: October 2021

BACKGROUND

Although 17α-ethinyl estradiol-3-sulfate (EES) reduces mortality in animal models of controlled hemorrhage, its role in a clinically relevant injury model is unknown. We assessed the impact of EES in a swine model of multiple injuries and hemorrhage.

METHODS

The study was performed under Good Laboratory Practice, with 30 male uncastrated swine (25–50 kg) subjected to tibial fracture, pulmonary contusion, and 30% controlled hemorrhage for an hour. Animals were randomized to one of five EES doses: 0 (control), 0.3, 1, 3, and 5 mg/kg, administered postinjury. Subjects received no resuscitation and were observed for 6 hours or until death. Survival data were analyzed using Cox-proportional hazard regression. Left ventricular pressure-volume loops were used to derive preload recruitable stroke work as a measure of cardiac inotropy. Immediate postinjury preload recruitable stroke work values were compared with values at 1 hour post–drug administration.

RESULTS

Six-hour survival for the 0, 0.3, 1, 3, and 5 mg/kg groups was 0%, 50%, 33.3%, 16.7%, and 0%, respectively. Following Cox regression, the hazard (95% confidence interval) of death was significantly reduced in the 0.3 (0.22 [0.05–0.93]) and 1 (0.24 [0.06–0.89]) mg/kg groups but not the 3 (0.49 [0.15–1.64]) and 5 (0.46 [0.14–1.47]) mg/kg groups. Mean survival time was significantly extended in the 1 mg/kg group (246 minutes) versus the 0 mg/kg group (96 minutes) (p = 0.04, t test). At 1 hour post–drug administration, inotropy was significantly higher than postinjury values in the 0.3 and 1 mg/kg groups (p = 0.003 and p < 0.001, respectively). Inotropy was unchanged in the 3 and 5 mg/kg groups but significantly depressed in the control (p = 0.022).

CONCLUSION

Administration of EES even in the absence of fluid resuscitation reduces mortality and improves cardiac inotropy in a clinically relevant swine model of multiple injuries and hemorrhage. These findings support the need for a clinical trial in human trauma patients.
Impact of rheological properties on bacterial streamer formation
Authors: Kitamura Hiroki , Omori Toshihiro , Ishikawa Takuji
Published: October 2021

Bacterial biofilms, which can be found wherever there is water and a substrate, can cause chronic infections and clogging of industrial flow systems. Despite intensive investigation of the dynamics and rheological properties of biofilms, the impact of their rheological properties on streamer growth remains unknown. We numerically simulated biofilm growth in a pillar-flow and investigated the effects of rheological properties of a filamentous flow-shaped biofilm, called a ‘streamer’, on its formation by varying the viscoelasticity. The flow-field is assumed to be a Stokes flow and is solved by a boundary element method. A Maxwell model is used for extracellular matrix-mediated streamer growth to express the fluidity of streamer formations. Both high elastic modulus and viscosity are needed for streamer formation, and high viscosity promotes streamer growth at low cell concentrations. Our findings are consistent with experimental observations and can explain the relationship between the cell concentrations and viscosity at which streamers form.
Phase transitions in biology: from bird flocks to population dynamics
Authors: Heffern Elleard F. W. , Huelskamp Holly , Bahar Sonya , Inglis R. Fredrik
Published: October 2021

Phase transitions are an important and extensively studied concept in physics. The insights derived from understanding phase transitions in physics have recently and successfully been applied to a number of different phenomena in biological systems. Here, we provide a brief review of phase transitions and their role in explaining biological processes ranging from collective behaviour in animal flocks to neuronal firing. We also highlight a new and exciting area where phase transition theory is particularly applicable: population collapse and extinction. We discuss how phase transition theory can give insight into a range of extinction events such as population decline due to climate change or microbial responses to stressors such as antibiotic treatment.
Molecular pathology of a cystic fibrosis mutation is explained by loss of a hydrogen bond
Authors: Simon Márton A. , Csanády László
Published: October 2021

The phosphorylation-activated anion channel CFTR is gated by an ATP hydrolysis cycle at its two cytosolic nucleotide binding domains, and is essential for epithelial salt-water transport. A large number of CFTR mutations cause cystic fibrosis. Since recent breakthrough in targeted pharmacotherapy, CFTR mutants with impaired gating are candidates for stimulation by potentiator drugs. Thus, understanding the molecular pathology of individual mutations has become important. The relatively common R117H mutation affects an extracellular loop, but nevertheless causes a strong gating defect. Here we identify a hydrogen bond between the side chain of arginine 117 and the backbone carbonyl group of glutamate 1124 in the cryo-electronmicroscopic structure of phosphorylated, ATP-bound CFTR. We address the functional relevance of that interaction for CFTR gating using macroscopic and microscopic inside-out patch-clamp recordings. Employing thermodynamic double-mutant cycles, we systematically track gating-state dependent changes in the strength of the R117-E1124 interaction. We find that the H-bond is formed only in the open state, but neither in the short-lived “flickery” nor in the long-lived “interburst” closed state. Loss of this H-bond explains the entire gating phenotype of the R117H mutant, including robustly shortened burst durations and strongly reduced intraburst open probability. The findings may help targeted potentiator design.
Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations
Authors: Thirimanne H. Nayanga , Wu Feinan , Janssens Derek H , Swanger Jherek , Feldman Heather M , Amezquita Robert A , Gottardo Raphael , Paddison Patrick J , Henikoff Steven , Clurman Bruce E
Published: October 2021

Fbw7 is a ubiquitin ligase substrate receptor that targets proteins for proteasomal degradation. Most known Fbw7 substrates are transcription factors (TFs) and many are also oncoproteins (e.g., c-Myc, c-Jun, Notch). Fbw7 is an important tumor suppressor andFBXW7mutations drive tumorigenesis through activation of oncogenic Fbw7 substrates. Defining the mechanisms of Fbw7-associated tumorigenesis is critical for developing targeted therapies. We thus determined the transcriptional consequences of oncogenic Fbw7 mutations by studying isogenic colorectal cancer cell lines with engineeredFBXW7null and heterozygous missense mutations. We used an integrated approach employing RNA-Seq and high-resolution mapping (CUT&RUN) of histone modifications and TF occupancy (c-Jun and c-Myc) to examine the combinatorial effects of mis-regulated Fbw7 substrates. Fbw7 mutations caused widespread transcriptional changes associated with active chromatin and altered TF occupancy at distal regulatory regions. Some regulatory changes were common to bothFBXW7-mutant cell lines whereas others wereFBXW7mutation-specific. By comparing c-Jun and c-Myc binding sites, we also identified co-regulated elements, suggesting that Fbw7 substrates may have synergistic effects. One co-regulated gene was CIITA, a master regulator of MHC Class II gene expression, and Fbw7 loss increased CIITA and MHC Class II gene expression in colorectal cancer cells. Fbw7 mutations were also correlated with increased CIITA expression in TCGA colorectal tumors and cell lines, which may have immunologic implications for progression and treatment of Fbw7-associated cancers. This integrative analysis provides a framework for understanding normal and neoplastic context-specific Fbw7 functions.
Coral settlement and recruitment are negatively related to reef fish trait diversity
Authors: Chow Cher F Y , Bolton Caitlin , Boutros Nader , Brambilla Viviana , Fontoura Luisa , Hoey Andrew S , Madin Joshua S , Pizarro Oscar , Torres-Pulliza Damaris , Woods Rachael M , Zawada Kyle J A , Barbosa Miguel , Dornelas Maria
Published: October 2021

The process of coral recruitment is crucial to the functioning of coral reef ecosystems, as well as recovery of coral assemblages following disturbances. Fishes can be key mediators of this process by removing benthic competitors like algae, but their foraging impacts are capable of being facilitative or harmful to coral recruits depending on species traits. Reef fish assemblages are highly diverse in foraging strategies and the relationship between this diversity with coral settlement and recruitment success remains poorly understood. Here, we investigate how foraging trait diversity of reef fish assemblages covaries with coral settlement and recruitment success across multiple sites at Lizard Island, Great Barrier Reef. Using a multi-model inference approach incorporating six metrics of fish assemblage foraging diversity (foraging rates, trait richness, trait evenness, trait divergence, herbivore abundance, and sessile invertivore abundance), we found that herbivore abundance was positively related to both coral settlement and recruitment success. However, the correlation with herbivore abundance was not as strong in comparison with foraging trait diversity metrics. Coral settlement and recruitment exhibited a negative relationship with foraging trait diversity, especially with trait divergence and richness in settlement. Our findings provide further evidence that fish play a role in making benthic habitats more conducive for coral settlement and recruitment. Because of their ability to shape the reef benthos, the variation of fish biodiversity is likely to contribute to spatially uneven patterns of coral recruitment and reef recovery.
Immortalization and Functional Screening of Natively Paired Human T Cell Receptor Repertoires
Authors: Fahad Ahmed S. , Chung Cheng Yu , Lopez Acevedo Sheila N. , Boyle Nicoleen , Madan Bharat , Gutiérrez-González Matias F. , Matus-Nicodemos Rodrigo , Laflin Amy D. , Ladi Rukmini R. , Zhou John , Wolfe Jacy , Llewellyn-Lacey Sian , Douek Daniel C. , Balfour Henry H. , Price David A. , DeKosky Brandon J.
Published: October 2021

Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. Here we developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale. To exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen-specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of human TCRs against diverse antigen targets associated with health, vaccination, or disease.
Phospho-regulation accommodates Type III secretion and assembly of a tether of ER-Chlamydia inclusion membrane contact sites
Authors: Murray Rebecca L. , Ende Rachel J. , D’Spain Samantha K. , Derré Isabelle
Published: October 2021

Membrane contact sites (MCS) are crucial for non-vesicular trafficking-based inter-organelle communication. ER-organelle tethering occurs in part through the interaction of the ER resident protein VAP with FFAT-motif containing proteins. FFAT motifs are characterized by a seven amino acidic core surrounded by acid tracks. We have previously shown that the human intracellular bacterial pathogen Chlamydia trachomatis establishes MCS between its vacuole (the inclusion) and the ER through expression of a bacterial tether, IncV, displaying molecular mimicry of eukaryotic FFAT motif cores. Here, we show that multiple layers of host cell kinase-mediated phosphorylation events govern the assembly of the IncV-VAP tethering complex. CK2-mediated phosphorylation of a C-terminal region of IncV enables IncV hyperphosphorylation of a phospho- FFAT motif core and serine-rich tracts immediately upstream of IncV FFAT motif cores. Phosphorylatable serine tracts, rather than genetically-encoded acidic tracts, accommodate Type III-mediated translocation of IncV to the inclusion membrane, while achieving full mimicry of FFAT motifs. Thus, regulatory components and post-translational modifications are integral to MCS biology, and intracellular pathogens such as C. trachomatis have evolved complex molecular mimicry of these eukaryotic features.
Multireader Evaluation of Radiologist Performance for COVID-19 Detection on Emergency Department Chest Radiographs
Authors: Gichoya Judy W. , Sinha Priyanshu , Davis Melissa , Dunkle Jeffrey W. , Hamlin Scott A. , Herr Keith D. , Hoff Carrie N. , Letter Haley P. , McAdams Christopher R. , Puthoff Gregory D. , Smith Kevin L. , Steenburg Scott D. , Banerjee Imon , Trivedi Hari
Published: October 2021

Background

Chest radiographs (CXR) are frequently used as a screening tool for patients with suspected COVID-19 infection pending reverse transcriptase polymerase chain reaction (RT-PCR) results, despite recommendations against this. We evaluated radiologist performance for COVID-19 diagnosis on CXR at the time of patient presentation in the Emergency Department (ED).

Materials and Methods

We extracted RT-PCR results, clinical history, and CXRs of all patients from a single institution between March and June 2020. 984 RT-PCR positive and 1043 RT-PCR negative radiographs were reviewed by 10 emergency radiologists from 4 academic centers. 100 cases were read by all radiologists and 1927 cases by 2 radiologists. Each radiologist chose the single best label per case: Normal, COVID-19, Other – Infectious, Other – Noninfectious, Non-diagnostic, and Endotracheal Tube. Cases labeled with endotracheal tube or non-diagnostic were excluded. Remaining cases were analyzed for label distribution, clinical history, and inter-reader agreement.

Results

1727 radiographs (732 RT-PCR positive, 995 RT-PCR negative) were included from 1,594 patients (51.2% male, 48.8% female, age 59 ± 19 years). For 89 cases read by all readers, there was poor agreement for RT-PCR positive (Fleiss Score 0.36) and negative (Fleiss Score 0.46) exams. Agreement between two readers on 1,638 cases was 54.2% (373/688) for RT-PCR positive cases and 71.4% (679/950) for negative cases. Agreement was highest for RT-PCR negative cases labeled as Normal (50.4%, n= 479). Reader performance did not improve with clinical history or time between CXR and RT-PCR result.

Conclusion

At the time of presentation to the emergency department, emergency radiologist performance is non-specific for diagnosing COVID-19.
Food Security Impacts of the COVID-19 Pandemic: Following a Cohort of Vermonters During the First Year
Authors: McCarthy Ashley C. , Belarmino Emily H. , Bertmann Farryl , Niles Meredith T.
Published: October 2021

Objective

This study assessed changes in household food insecurity throughout the first year of the COVID-19 pandemic in a cohort of Vermonters and examined the socio-demographic characteristics associated with increased odds of experiencing food insecurity during the pandemic.

Design

We conducted three online surveys with a cohort of Vermonters between March 2020 and March 2021 to collect longitudinal data on food security, food access, and job disruptions during the COVID-19 pandemic. Food security was measured using the USDA six-item module. We used t-tests and chi-square tests to determine statistically significant differences between groups and multivariate logistic regression models to determine the factors correlated with food insecurity.

Participants

441 adults (18 years and older)

Setting

Vermont, United States

Results

Food insecurity rates increased significantly during the pandemic and remained above pre-pandemic levels a year after the start of the pandemic. Nearly a third (31.6%) of respondents experienced food insecurity at some point during the first year of the pandemic. Certain demographic groups were at significantly higher odds of experiencing food insecurity during the first year of the COVID-19 pandemic including households with children (OR 5.1, p < 0.01), women (OR 7.3, p < 0.05), BIPOC/Hispanic respondents (OR 10.4, p < 0.05), and households experiencing a job disruption (OR 4.6, p <0.01).

Conclusion

The prevalence of food insecurity increased during the first year of the COVID-19 pandemic and remained higher than pre-pandemic levels a year after the pandemic began. Odds of experiencing food insecurity during the pandemic vary based on socio-demographic factors.
Combinatorial tumor suppressor inactivation efficiently initiates lung adenocarcinoma with therapeutic vulnerabilities
Authors: Yousefi Maryam , Boross Gábor , Weiss Carly , Murray Christopher W. , Hebert Jess D. , Cai Hongchen , Ashkin Emily L. , Karmakar Saswati , Andrejka Laura , Chen Leo , Wang Minwei , Tsai Min K. , Lin Wen-Yang , Li Chuan , Yakhchalian Pegah , Colón Caterina I. , Chew Su- Kit , Chu Pauline , Swanton Charles , Kunder Christian A. , Petrov Dmitri A. , Winslow Monte M.
Published: October 2021

Lung cancer is the leading cause of cancer death worldwide, with lung adenocarcinoma being the most common subtype. Many oncogenes and tumor suppressor genes are altered in this cancer type and the discovery of oncogene mutations has led to the development of targeted therapies that have improved clinical outcomes. However, a large fraction of lung adenocarcinomas lacks mutations in known oncogenes, and the genesis and treatment of these oncogene-negative tumors remain enigmatic. Here, we perform iterative in vivo functional screens using quantitative autochthonous mouse model systems to uncover the genetic and biochemical changes that enable efficient lung tumor initiation in the absence of oncogene alterations. Through the generation of hundreds of diverse combinations of tumor suppressor alterations, we demonstrate that the inactivation of suppressors of the RAS and PI3K pathways drive the development of oncogene-negative lung adenocarcinoma. Human genomic data and histology identified RAS/MAPK and PI3K pathway activation as a common event in oncogene- negative human lung adenocarcinomas. We demonstrate that these Onc-negativeRAS/PI3K tumors and related cell lines are vulnerable to pharmacological inhibition of these signaling axes. These results transform our understanding of this prevalent yet understudied subtype of lung adenocarcinoma.
REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats
Authors: Dolzhenko Egor , Weisburd Ben , Garikano Kristina Ibanez , Rajan Babu Indhu Shree , Bennett Mark F , Billingsley Kimberley , Carroll Ashley , Danzi Matt C. , Deshpande Viraj , Ding Jinhui , Fazal Sarah , Halman Andreas , Jadhav Bharati , Qiu Yunjiang , Richmond Phillip , Scheffler Konrad , van Vugt Joke J.F.A , Zwamborn Ramona R.A.J. ,   Genomics England Research Consortium, Chong Samuel S. , Friedman Jan M. , Tucci Arianna , Rehm Heidi L. , Eberle Michael A
Published: October 2021

Background

Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely-recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads.

Results

We implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in STR research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically-relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR.

Conclusions

Read pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions.
Cryo-EM structures of pentameric autoinducer-2 exporter from E. coli reveal its transport mechanism
Authors: Khera Radhika , Mehdipour Ahmad Reza , Bolla Jani R , Kahnt Joerg , Welsch Sonja , Ermler Ulrich , Muenke Cornelia , Robinson Carol V , Hummer Gerhard , Xie Hao , Michel Hartmut
Published: October 2021

Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from E. coli, which belongs to a large underexplored membrane transporter family, the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism. This study emphasizes the structural distinctiveness of this family of pentameric transporters and provides fundamental insights for the ensuing studies.
Yn-situ: a robust single RNA molecule in situ detection method
Authors: Wu Yunming , Xu Wenjing , Ma Limei , Yu Zulin , Wang Yongfu , Yu C. Ron
Published: October 2021

We describe a cost-effective, highly sensitive, and quantitative method for in situ detection of single RNA molecules in tissue sections. This method, dubbed Yn situ, standing for Y-branched probe in situ hybridization, uses a single-strand DNA preamplifier with multiple initiation sites that trigger hybridization chain reaction (HCR) to detect polynucleotide. We characterized the performance of this method and compared it to other approaches in the postnatal mouse olfactory epithelia. We find that the Yn situ method, in conjunction with an improved fixation step, is sensitive enough to allow detection of single molecules using a single pair of probes targeting a short nucleotide sequence. A set of 5-probes can produce quantitative results with smaller puncta and higher signal-to-noise ratio than the 20-probe sets commonly required for HCR and RNA-Scope. We show that the high sensitivity and wide dynamic range allow quantification of genes expressed at different levels in the olfactory sensory neurons. We describe key steps of this method to enable broad utility by individual laboratories.
Structural Basis for the Inhibition of IAPP Fibril Formation by the Hsp60 Co-Chaperonin Prefoldin
Authors: Törner Ricarda , Kupreichyk Tatsiana , Gremer Lothar , Debled Elisa Colas , Fenel Daphna , Gans Pierre , Willbold Dieter , Schoehn Guy , Hoyer Wolfgang , Boisbouvier Jerome
Published: October 2021

Chaperones, as modulators of protein conformational states, are key cellular actors to prevent the accumulation of fibrillar aggregates. Here, we integrated kinetic investigations with structural studies to elucidate how the ubiquitous co-chaperonin prefoldin (PFD) inhibits diabetes associated islet amyloid polypeptide (IAPP) fibril formation. We demonstrated that both human and archaeal PFD interfere similarly with the IAPP fibril elongation and secondary nucleation pathways. Using archaeal prefoldin model, we combined NMR spectroscopy with EM to establish that the inhibition of fibril formation is mediated by the binding of prefoldin’s coiled-coil helices to the flexible IAPP N-terminal segment accessible on the fibril surface and fibril ends. AFM demonstrates that binding of prefoldin to IAPP leads to the formation of lower amounts of aggregates, composed of shorter fibrils, clustered together. Linking structural models with observed fibrillation inhibition processes opens new perspectives for understanding the interference between natural chaperones and formation of disease-associated amyloids.
A Network-based Deep Learning Framework Catalyzes GWAS and Multi-Omics Findings to Biology and Drug Repurposing for Alzheimer’s Disease
Authors: Xu Jielin , Hou Yuan , Zhou Yadi , Hu Ming , Cheng Feixiong
Published: October 2021

Human genome sequencing studies have identified numerous loci associated with complex diseases, including Alzheimer’s disease (AD). Translating human genetic findings (i.e., genome-wide association studies [GWAS]) to pathobiology and therapeutic discovery, however, remains a major challenge. To address this critical problem, we present anetworktopology-based deep learning framework to identify disease-associatedgenes (NETTAG). NETTAG is capable of integrating multigenomics data along with the protein-protein interactome to infer putative risk genes and drug targets impacted by GWAS loci. Specifically, we leverage non-coding GWAS loci effects on expression quantitative trait loci (eQTLs), histone-QTLs, and transcription factor binding-QTLs, enhancers and CpG islands, promoter regions, open chromatin, and promoter flanking regions. The key premises of NETTAG are that the disease risk genes exhibit distinct functional characteristics compared to non-risk genes and therefore can be distinguished by their aggregated genomic features under the human protein interactome. Applying NETTAG to the latest AD GWAS data, we identified 156 putative AD-risk genes (i.e.,APOE,BIN1,GSK3B,MARK4, andPICALM). We showed that predicted risk genes are: 1) significantly enriched in AD-related pathobiological pathways, 2) more likely to be differentially expressed regarding transcriptome and proteome of AD brains, and 3) enriched in druggable targets with approved medicines (i.e., choline and ibudilast). In summary, our findings suggest that understanding of human pathobiology and therapeutic development could benefit from a network-based deep learning methodology that utilizes GWAS findings under the multimodal genomic analyses.
Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells
Authors: Robinson Philip S. , Thomas Laura E. , Abascal Federico , Jung Hyunchul , Harvey Luke M.R. , West Hannah D. , Olafsson Sigurgeir , Lee Bernard C. H. , Coorens Tim H.H. , Lee-Six Henry , Butlin Laura , Lander Nicola , Sanders Mathijs A. , Lensing Stefanie V. , Buczacki Simon J.A. , ten Hoopen Rogier , Coleman Nicholas , Brunton-Sim Roxanne , Rushbrook Simon , Saeb-Parsy Kourosh , Lalloo Fiona , Campbell Peter J. , Martincorena Iñigo , Sampson Julian R. , Stratton Michael R.
Published: October 2021

Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequenced normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 5-fold in all individuals, except for one showing a 33-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C>A changes. Different mutation rates and signatures between individuals were likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.

Summary
CRISPR-Cas9 mediated knockout of SagD gene for overexpression of streptokinase in Streptococcus equisimilis
Authors: Chaudhari Armi M. , Vyas Sachin , Patel Amrutlal , Singh Vijai , Joshi Chaitanya G. , Joshi Madhvi
Published: October 2021

Streptokinase is an enzyme that can break down the blood clots in some cases of myocardial infarction (Heart attack), pulmonary embolism, and arterial thromboembolism. Demand for streptokinase is high globally than the production due to increased incidences of various heart conditions. The main source of streptokinase is from various strains of Streptococcus. Expression of streptokinase in native strain Streptococcus equisimilis is limited due to the SagD inhibitor gene for production of streptokinase that needs to be knocked out in order to increase it expression. However, FasX is a small RNA (sRNA) present in group A Streptococcus species which is responsible for post-transcriptional regulation of streptokinase (ska) gene by binding at the 5’ end of ska mRNA. S. equisimilis is a β-hemolysin producing streptococcus bacterium (group C) containing the orthologue of FasX and natively expresses a clinically important thrombolytic streptokinase. In order to improve the stability of mRNA and increasing the expression of streptokinase which is inhibited by SagD. We used CRISPR-Cas9 to successfully knock-out of SagD gene and observed a 13.58-fold relative quantification of streptokinase expression in the mutant strain as compared to wild type. We have also demonstrated the successful target gene knockout using CRISPR-Cas9 in S. equisimilis that engineered strain can be used further for overexpression of streptokinase for therapeutic applications.

Graphical Abstract
Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex
Authors: Greenrod Samuel T. E. , Stoycheva Martina , Elphinstone John , Friman Ville-Petri
Published: October 2021

Ralstonia solanacearum is a destructive plant pathogenic bacterium and the causative agent of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, its virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape R. solanacearum virulence, the global diversity, distribution, and wider functional gene content of R. solanacearum prophages is unknown. In this study, prophages were identified in a diverse collection of 192 R. solanacearum draft genome assemblies originating from six continents. Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distribution was characterised using metadata on R. solanacearum geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 343 intact prophages were identified, forming ten genetically distinct clusters. These included five prophage clusters belonging to the Inoviridae, Myoviridae, and Siphoviridae phage families, and five uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distribution being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained a myriad of auxiliary genes involved in metabolism and virulence of both phage and bacteria. Our results show that while R. solanacearum prophages are highly diverse globally, they make lineage-specific contributions to the R. solanacearum accessory genome, which could have resulted from shared coevolutionary history.
Cholesterol biosynthetic pathway induces cellular senescence through ERRα
Authors: Ziegler Dorian V. , Vernier Mathieu , Czarnecka-Herok Joanna , Scholtes Charlotte , Machon Christelle , Guitton Jérôme , Rieusset Jennifer , Giguère Vincent , Martin Nadine , Bernard David
Published: October 2021

Cellular senescence is a cell program induced by various stresses that leads to a stable proliferation arrest and to a senescence-associated secretory phenotype. Accumulation of senescent cells during age-related diseases participates in these pathologies and regulates healthy lifespan. Recent evidences point out a global dysregulated intracellular metabolism associated to senescence phenotype. Nonetheless, the functional contribution of metabolic homeostasis in regulating senescence is barely understood. In this work, we describe how the mevalonate pathway, an anabolic pathway leading to the endogenous biosynthesis of poly-isoprenoids, such as cholesterol, acts as a positive regulator of cellular senescence in normal human cells. Mechanistically, this mevalonate-induced senescence is partly mediated by the downstream cholesterol biosynthetic pathway. This pathway promotes transcriptional activity of ERRα leading to dysfunctional mitochondria, ROS production, DNA damage and a p53-dependent senescence. Supporting the relevance of these observations, increase of senescence in liver due to a high-fat diet regimen is abrogated in ERRα knockout mouse. Overall, this work unravels the role of cholesterol biosynthesis in the induction of an ERRα-dependent mitochondrial program leading to cellular senescence and related pathological alterations.
A Tissue-Bioengineering Strategy for Modeling Rare Human Kidney Diseases In Vivo
Authors: Hernandez J.O.R. , Wang X. , Vazquez-Segoviano M. , Sobral-Reyes M.F. , Moran-Horowich A. , Sundberg M. , Lopez-Marfil M. , Lopez-Cantu D.O. , Probst C.K. , Ruiz-Esparza G.U , Giannikou K. , Henske E.P. , Kwiatkowski D.J. , Sahin M. , Lemos D.R.
Published: October 2021

The lack of animal models for certain human diseases precludes our understanding of disease mechanisms and our ability to test new therapies in vivo. Here we generated kidney organoids from Tuberous Sclerosis Complex (TSC) patient-derived-hiPSCs to recapitulate a rare kidney tumor called angiomylipoma (AML). Organoids derived from TSC2-/- hiPSCs but not from isogenic TSC2+/- or TSC2+/+ hiPSCs shared a common transcriptional signature and a myomelanocytic cell phenotype with kidney AMLs, and developed epithelial cysts, replicating two major TSC-associated kidney lesions driven by genetic mechanisms that cannot be robustly and consistently recapitulated with transgenic mice. Transplantation of multiple TSC2-/- kidney organoids into the kidneys of immunodeficient rats allowed us to recapitulate AML and cystic kidney disease in vivo, in a scalable fashion and with fidelity, and to test the efficiency of rapamycin-loaded nanoparticles as a novel approach to ablate AMLs by inducing apoptosis triggered by mTOR-inhibition. Collectively, these methods represent a novel tissue-bioengineering strategy for rare disease modeling in vivo.
Persistent synaptic inhibition of the subthalamic nucleus by high frequency stimulation
Authors: Steiner Leon A , Kühn Andrea A , Geiger Jörg RP , Alle Henrik , Popovic Milos R , Kalia Suneil K , Hodaie Mojgan , Lozano Andres M , Hutchison William D , Milosevic Luka
Published: October 2021

Background

Deep brain stimulation (DBS) provides symptomatic relief in a growing number of neurological indications, but local synaptic dynamics in response to electrical stimulation that may relate to its mechanism of action have not been fully characterized.

Objective

The objectives of this study were to (1) study local synaptic dynamics during high frequency extracellular stimulation of the subthalamic nucleus (STN), and (2) compare STN synaptic dynamics with those of the neighboring substantia nigra pars reticulata (SNr).

Methods

Two microelectrodes were advanced into the STN and SNr of patients undergoing DBS surgery for PD. Neuronal firing and evoked field potentials (fEPs) were recorded with one microelectrode during stimulation from an adjacent microelectrode.

Results

Excitatory and inhibitory fEPs could be discerned within the STN and their amplitudes predicted bidirectional effects on neuronal firing (p = .007). There were no differences between STN and SNr inhibitory fEP dynamics at low stimulation frequencies (p > .999). However, inhibitory neuronal responses were sustained over time in STN during high frequency stimulation, but not SNr (p < .001) where depression of inhibitory input was coupled with a return of neuronal firing (p = .003).

Interpretation

Persistent inhibitory input to the STN suggests a local synaptic mechanism for the suppression of subthalamic firing during high frequency stimulation. Moreover, differences in the resiliency versus vulnerability of inhibitory inputs to the STN and SNr suggest a projection source- and frequency-specificity for this mechanism. The feasibility of targeting electrophysiologically-identified neural structures may provide insight into how DBS achieves frequency-specific modulation of neuronal projections.