bluuebunny/crossref_metadata_2025 huggingface dataset:
Endothelial progenitor cells and major adverse cardiovascular events in patients receiving elective coronary angiography
Authors: Liu Chung-Te , Guo Jiun-Yu , Chou Ruey-Hsing , Lu Ya-Wen , Tsai Yi-Lin , Kuo Chin-Sung , Chang Chun-Chin , Huang Po-Hsun , Chen Jaw-Wen , Lin Shing-Jong
Published: May 2023

Background and purpose:

The association of circulating endothelial progenitor cells (EPCs) with different cardiovascular diseases and their related major adverse cardiovascular events (MACE) remained inconclusive. We aimed to clarify associations between the circulating EPC levels and the risk of MACE concerning different atherosclerosis-related diseases.

Methods:

This prospective cohort study was conducted from December 2009 to March 2015. Patients who underwent non-emergent coronary angiography (CAG) were included. The circulating EPC levels were measured using flow cytometry prior to the CAG procedure. The study evaluation of circulating EPC levels among patients with obstructive coronary artery disease (CAD) and other comorbidities. Patients were then assigned to tertiles by circulating EPC levels to evaluate the predictive values of the development of MACEs.

Results:

The study enrolled 1099 patients, of whom, 736 (67%) were men, with a mean age of 66.7 ± 12.5 years old. Overall, 637 (58%) patients were diagnosed with obstructive CAD according to CAG. MACE occurred in 268 (24.4%) patients. Circulating EPC levels were lower in patients with peripheral artery disease (PAD) but not associated with the presence of obstructive CAD, atrial fibrillation, chronic kidney disease (CKD), heart failure, and diabetes mellitus. Higher circulating EPC levels are linked with higher MACE among patients with suspected CAD, regardless of the presence or absence of obstructive CAD or CKD. The association did not present in patients with PAD.

Conclusions:

Higher circulating EPC levels are associated with a greater risk of MACE, regardless of the presence of obstructive CAD or CKD. This association was not apparent in the patients with PAD, suggesting impaired endothelial repair in these patients.
Starting from scratch
Authors: Lai Alden Yuanhong , Larson Jeffrey D. , DePuccio Matthew J. , Hilligoss Brian
Published: May 2023

Background

Health care organizations are constantly creating new work to achieve evolving goals such as digitalization, equity, value, or well-being. However, scholars have paid less attention to how such work becomes “work” in the first place, despite implications for the design, quality, and experience of work and, consequently, employee and organizational outcomes.

Purpose

The aim of this study was to investigate how new work becomes enacted in health care organizations.

Methodology

A longitudinal, qualitative case study on the enactment of entrance screening—a new operation in response to COVID-19—in a multihospital academic medical center was performed.

Results

Entrance screening comprised four tasks, whose design was initially influenced by institutional guidelines (e.g., Centers for Disease Control and Prevention recommendations) and clinical experts. Organizational-level influences (e.g., resource availability) then became more prominent, necessitating multiple feedback–response loops to calibrate the performance of entrance screening. Finally, entrance screening was integrated into existing operations of the organization to ensure operational sustainability. The treatment of entrance screening as an operation changed over time—initially seen as infection control work, it eventually bifurcated into patient care and clerical work.

Conclusion

The enactment of new work is constrained by the fit between resources and its intended output. Furthermore, the schema of work influences how and when organizational actors calibrate this fit.

Practice Implications

Health care leaders and managers should continuously update their schemas of work so that they can develop more sufficient and accurate representations of the employee capabilities that are required for the performance of new work.
Diurnal Variation of Visual Acuity and Refraction in Fuchs Endothelial Corneal Dystrophy
Authors: Brandi-Dohrn Franziska , Jiang Jana , Grewing Viviane , Fritz Marianne , Zander Daniel , Lieberum Judith-Lisa , Kladny Anne-Marie , Siegel Helena , Bixler Stephanie , Müller Claudia , Reinhard Thomas , Wacker Katrin
Published: May 2023

Purpose:

Patients with advanced Fuchs endothelial corneal dystrophy frequently report poor vision in the morning, which improves as the day progresses. This study quantified the amount of variation in near and distance visual acuity and refraction over the course of a day.

Methods:

This was a prospective cohort study. Best-corrected distance visual acuity and near visual acuity were tested in participants with clinically advanced Fuchs dystrophy and in controls with healthy corneas. Subjective refraction and autorefraction were conducted in a presumed steady state in the afternoon. Measurements were repeated directly after eye opening in the hospital the next morning. In a subgroup, measurements were repeated every 30 minutes for up to 2 hours.

Results:

In Fuchs dystrophy, the mean distance visual acuity was worse by −3 letters (95% confidence interval, −4 to −1) directly after eye opening in the morning compared with late afternoon. No such difference was seen in healthy corneas. In Fuchs dystrophy, visual acuity improved over the course of the study. Visual acuity in the morning could be improved with fine tuning of refraction, and refractive changes were exclusive to Fuchs dystrophy (0.5–1.0 D in spherical equivalent in 30%, >1.0 D in 2% of eyes).

Conclusions:

Distance and near visual acuity and refraction changes over the course of the day in patients with advanced Fuchs dystrophy. Although small changes in refraction may not usually require a second set of glasses for the first hours of the day, diurnal variation should be considered when determining disease severity in routine practice and in clinical trials.
Trailblazing New Paths to e-Learning Engagement
Authors: Fritz Elizabeth , Navales Edicarl , Talir Jaimie , Hayden Jennifer , Nordike Jeana , Keller Jessica , Maxwell Pam
Published: May 2023

E-learning modules are a common component of orientation and other education initiatives, but their usefulness can be limited by poor engagement. This article presents the results of an experimental cohort study testing interventions designed to improve learner engagement with e-learning modules.
Crush Injury and Simulated Flight Effects on Muscle Gene Expression in Female Mice
Authors: Schneider Barbara S. , Petereit Juli , Zhang Liyuan , Voss Joachim G.
Published: May 2023

Background

Aeromedical evacuation provides critical care during long-distance transport of injured victims between medical facilities. Often, these victims sustain muscle trauma related to mechanical insults, such as crush. Understanding the effects of flight on injured muscle is important because the aircraft cabin represents an external environment with mild hypoxia—the cabin’s altitude is 2,438 m instead of sea level. Because mild hypobaric hypoxia can alter gene expression in normal muscle and affect recovery patterns, it is beneficial to examine whether this type of hypoxia may also alter injury-related genes.

Objective

The objective of this study was to verify the hypothesis that differential gene expression occurs in response to mild hypobaric hypoxia exposure in crush-injured muscle during two early recovery (preregeneration stage) time points.

Methods

Twenty-four female mice were anesthetized, and the right gastrocnemius muscle underwent crush injury. Approximately 24 hours later, mice were exposed to normobaric normoxia or hypobaric hypoxia for 8–9 hours. After 32 or 48 hours of recovery, the mice were euthanized, and the right and left lateral gastrocnemius muscles were collected for microarray and bioinformatics analyses.

Results

The study hypothesis was verified. There were 353 highly upregulated, differentially expressed genes identified in the injured muscle compared to the uninjured muscle. Mid1 was upregulated in both pressure conditions regardless of injury status. There were 52 and 15 differentially expressed genes at 32 and 48 hours postinjury, respectively, in the hypobaric hypoxia-exposed, injured muscle compared to the normobaric normoxia-exposed, injured muscle. The macrophage gene Cd68 correlated with other leukocyte-related genes.

Discussion

These findings expand our understanding of the genetic changes that occur in muscle in response to a crush injury, including those related to the macrophage protein CD68. Nursing interventions addressing adequate functioning after crush muscle injury may need to consider the effects on Cd68 and its closely related genes. In addition, our results suggest a responsiveness of the gene Mid1 to flight-relevant hypobaric hypoxia. Changes in the expression of Mid1 may be appropriate in assessing the long-term health of flight crew members.
Patterns of Involvement of the Hand Joints in Classical Rheumatoid Arthritis
Authors: Anderson Ronald J. , Cui Jing , Weinblatt Michael E. , Solomon Daniel H. , Naik Chinmayi , Shadick Nancy A.
Published: May 2023

Background

Symmetrical involvement of the hand joints is described as characteristic of rheumatoid arthritis (RA). Quantitative data on specific patterns of involvement are lacking.

Objective

The Brigham Rheumatoid Arthritis Sequential Study was created for observational studies of patients with RA and afforded a unique opportunity to answer these questions.

Methods

Of 1598 subjects in the Brigham Rheumatoid Arthritis Sequential Study cohort, 535 met the following criteria: (1) disease duration of 7 years or greater, (2) seropositive, and (3) hand radiographs available. Patterns in specific hand joints based on physical examination and radiographic findings obtained at entry were identified. The level of symmetry of involvement of the metacarpophalangeal (MCP) and wrist joints was determined, as was the correlation between findings on physical examination and radiographic changes in the hand joints.

Results

The prevalence of joint space narrowing and/or erosions in each proximal interphalangeal (PIP) joints ranged between 11% and 18%. Joint space narrowing and/or erosions in the MCPs increased radially from the fifth to the second finger. Swelling and tenderness on physical examination of both the PIPs and MCPs also increased radially although the positive predictive value of physical examination as an indicator of joint damage decreased radially. The wrist was the most common joint involved both by physical examination (67%) and radiographically (70%). The right side was more involved radiographically. Analysis of radiographic changes in individual patients revealed that symmetrical findings in the wrists and MCPs occurred in only 67% of patients.

Conclusions

The study describes the pattern of involvement of the hand joints in patients with long standing RA. Findings of interest include symmetrical involvement in only 67% of patients and a discordancy between physical findings and radiographic changes most marked in the more radial PIP joints
Isolated Superior Mesenteric Artery Vasculitis as a Cause of Abdominal Pain
Authors: Yamamoto Hirotaka , Taniguchi Yoshinori
Published: May 2023

This manuscript demonstrates that although isolated superior mesenteric artery vasculitis that also could be called as localized vasculitis of the gastrointestinal tract was rare entity, it is so significant as differential diagnosis of abdominal pain in addition to idiopathic dissection, infective arteritis, and lymphoma. This case should remind readers to consider isolated superior mesenteric artery vasculitis as a cause of (upper) abdominal pain.
Advanced Neuroimaging With Photon-Counting Detector CT
Authors: Abel Frederik , Schubert Tilman , Winklhofer Sebastian
Published: May 2023

Photon-counting detector computed tomography (PCD-CT) is an emerging technology and promises the next step in CT evolution. Photon-counting detectors count the number of individual incoming photons and assess the energy level of each of them. These mechanisms differ substantially from conventional energy-integrating detectors. The new technique has several advantages, including lower radiation exposure, higher spatial resolution, reconstruction of images with less beam-hardening artifacts, and advanced opportunities for spectral imaging. Research PCD-CT systems have already demonstrated promising results, and recently, the first whole-body full field-of-view PCD-CT scanners became clinically available. Based on published studies of preclinical systems and the first experience with clinically approved scanners, the performance can be translated to valuable neuroimaging applications, including brain imaging, intracranial and extracranial CT angiographies, or head and neck imaging with detailed assessment of the temporal bone. In this review, we will provide an overview of the current status in neuroimaging with upcoming and potential clinical applications.
Clinical Indications of Cultured Epithelial Autografts
Authors: Dhar Sarit , Chrisman Timothy , Simman Richard
Published: May 2023

Cultured epithelial autografts (CEAs) have been used for decades as a treatment for massive burn injuries. Cultured epithelial autografts allow for wounds to heal by taking a small sample and growing a patient's own epithelium in culture to create large, graftable sheets. This technique is especially useful in large wounds where donor sites are limited compared with conventional skin grafting. However, CEAs have a variety of uses in wound healing and reconstruction and have the potential to aid in the closure of several types of defects. Cultured epithelial autografts have shown applicability in large burns, chronic nonhealing wounds, ulcerating wounds of various etiologies, congenital defects, wounds requiring specialized epithelium to replace like by like, and wounds in critically ill patients. Several factors must be considered when using CEAs, such as time, cost, and outcomes. In this article, we detail the various clinical applications of CEAs and how they can be situationally advantageous outside of their original purpose.
Selective Denervation for the Thumb Carpometacarpal Joint
Authors: Lee Sang Ki , Kim Woo-suk , Baik Keun Ho , Choy Won Sik
Published: May 2023

Purpose

Various operative treatment options for advanced thumb carpometacarpal (CMC) joint arthritis have been presented without a definite surgical guideline. Selective denervation is a less invasive method for thumb CMC arthritis. However, it is unclear whether the clinical outcome varies with the stage of thumb CMC arthritis. This study aimed to evaluate the effectiveness of selective denervation on CMC arthritis for pain relief and functional outcome and to determine whether selective denervation depends on the stage of thumb CMC arthritis.

Methods

We evaluated 29 thumbs of 28 patients with thumb CMC arthritis treated with selective denervation. The disease stage was determined with the classification system described by Eaton. The denervation was performed in the articular branches of the palmar cutaneous branch of the median nerve, lateral antebrachial cutaneous nerve, and superficial branch of radial nerve. The clinical outcomes were evaluated using the visual analog scale (VAS) and Disabilities of the Arm, Shoulder, and Hand (DASH) scores, along with evaluation of the improvement in both postoperative range of motion and strength recovery.

Results

The mean duration of follow-up was 24 months (range, 18–48 months). The average VAS and DASH scores decreased from 6.1 to 1.3 and from 54.3 to 24.1, respectively. The range of motion during palmar abduction and opposition of the metacarpophalangeal joint improved with an increase in mean value from 44.1 to 53.7 degrees, and the Kapandji score increased from 7.2 to 9.2, respectively. The grip and key pinch strengths increased from mean preoperative values of 14.3 and 3.1 kg to 27.1 and 6.2 kg, respectively, as measured at the 12-month follow-up. The rate of change in the VAS and DASH scores was significantly higher in stages I to III than in stage IV (P = 0.01, P < 0.01, respectively).

Conclusion

The selective denervation for thumb CMC arthritis was effective in pain relief and functional recovery with several advantages, including less invasive procedure, quick recovery time, and regaining of strength. The clinical outcomes were more effective in the early-stage group (Eaton stages I and II) compared with the advance-stage group (Eaton stages III and IV).
Utility of continuous pulse CO-oximetry for hemoglobin monitoring in pediatric patients with solid organ injuries at level 1 trauma centers: A pilot study
Authors: Ryan Mark L. , Cairo Sarah B. , McLaughlin Cory , Herring Lela , Williams Regan F.
Published: May 2023

INTRODUCTION

Hemorrhage is a major cause of preventable death in injured children. Monitoring after admission often requires multiple blood draws, which have been shown to be stressful in pediatric patients. The Rainbow-7 device is a continuous pulse CO-oximeter that measures multiple wavelengths of light, permitting continuous estimation of the total hemoglobin (Hb) level. The purpose of this study was to evaluate the utility of the noninvasive Hb measurement for monitoring pediatric trauma patients admitted with solid organ injury.

METHODS

This is a prospective, dual-center, observational trial for patients younger than age 18 years admitted to a Level I pediatric trauma center. Following admission, blood was routinely measured as per current solid organ injury protocols. Noninvasive Hb monitoring was initiated after admission. Time-synced data for Hb levels were compared with that taken using blood draws. Data were evaluated using bivariate correlation, linear regression, and Bland-Altman analysis.

RESULTS

Over a 1-year period, 39 patients were enrolled. The mean ± SD age was 11 ± 3.8 years. Forty-six percent (n = 18) of patients were male. The mean ± SD Injury Severity Score was 19 ± 13. The average change in Hb levels between laboratory measurements was −0.34 ± 0.95 g/dL, and the average change in noninvasive Hb was −0.12 ± 1.0 g/dL per measurement. Noninvasive Hb values were significantly correlated with laboratory measurements (p < 0.001). Trends in laboratory Hb measurements were highly correlated with changes in noninvasive levels (p < 0.001). Bland-Altman analysis demonstrated similar deviation from the mean throughout the range of Hb values, but the differences between measurements were increased by anemia, African American race, and elevated shock index, pediatric age-adjusted score and Injury Severity Score.

CONCLUSION

Noninvasive Hb values demonstrated correlation with measured Hb concentration as isolated measurements and trends, although results were affected by skin pigmentation, shock, and injury severity. Given the rapid availability of results and the lack of requirement of venipuncture, noninvasive Hb monitoring may be a valuable adjunct for pediatric solid organ injury protocols. Further study is required to determine its role in management.

LEVEL OF EVIDENCE

Dianostic Test or Criteria; Level III.
Burden of unintentional pediatric firearm injury: An examination of the Nationwide Readmission Database
Authors: Lumbard Derek C. , Nygaard Rachel M. , Richardson Chad J. , Liao Lillian F. , Stewart Ronald M. , Eastridge Brian J. , Nicholson Susannah E.
Published: May 2023

BACKGROUND

Significant increases in firearm-related mortality in the US pediatric population drive an urgent need to study these injuries to drive prevention policies. The purpose of this study was (1) to characterize those with and without readmissions, (2) to identify risk factors for 90-day unplanned readmission, and (3) to examine reasons for hospital readmission.

METHODS

The 2016–2019 Nationwide Readmission Database of the Healthcare Cost and Utilization Project was used to identify hospital admissions with unintentional firearm injury in patients younger than 18 years. Ninety-day unplanned readmission characteristics were assessed and detailed. Multivariable regression analysis was used to assess factors associated with unplanned 90-day readmission.

RESULTS

Over 4 years, 1,264 unintentional firearm injury admissions resulted in 113 subsequent readmissions (8.9%). There were no significant differences in age or payor, but more women (14.7% vs. 23%) and older children (13–17 years [80.5%]) had readmissions. The mortality rate during primary hospitalization was 5.1%. Survivors of initial firearm injury were more frequently readmitted if they had a mental health diagnosis (22.1% vs. 13.8%; p = 0.017). Readmission diagnosis included complications (15%), mental health or drug/alcohol (9.7%), trauma (33.6%), a combination of the prior three (28.3%), and chronic disease (13.3%). More than a third (38.9%) of the trauma readmissions were for new traumatic injury. Female children, those with longer lengths of stay, and those with more severe injuries were more likely to have unplanned 90-day readmissions. Mental health and drug/alcohol abuse diagnoses were not an independent predictor for readmission.

CONCLUSION

This study provides insight into the characteristics of and risk factors for unplanned readmission in the pediatric unintentional firearm injury population. In addition to using prevention strategies, the utilization of trauma-informed care must be integrated into all aspects of care for this population to help minimize the long-term psychological impact of surviving firearm injury.

Level of Evidence

Prognostic and Epidemiological; Level IV.
Access to trauma center care: A statewide system-based approach
Authors: Medrano Nicolas W. , Villarreal Cynthia Lizette , Price Michelle A. , Bixby Pamela J. , Bulger Eileen M. , Eastridge Brian J. ,   MIMIC Study Group
Published: May 2023

BACKGROUND

Timely access to specialized trauma care is a vital element in patient outcome after severe and critical injury requiring the skills of trauma teams in levels I and II trauma centers to avoid preventable mortality. We used system-based models to estimate timely access to care.

METHODS

Trauma system models consisted of ground emergency medical services, helicopter emergency medical services, and designated levels I to V trauma centers were constructed for five states. These models incorporated geographic information systems along with traffic data and census block group data to estimate population access to trauma care within the “golden hour.” Trauma systems were further analyzed to identify the optimal location for an additional level I or II trauma center that would provide the greatest increase in access.

RESULTS

The population of the states studied totaled 23 million people, of which 20 million (87%) had access to a level I or II trauma center within 60 minutes. Statewide-specific access ranged from 60% to 100%. Including levels III to V trauma centers, access within 60 minutes increased to 22 million (96%), ranging from 95% to 100%. The addition of a levels I and II trauma center in an optimized location in each state would provide timely access to a higher trauma capability for an additional 1.1 million, increasing total access to approximately 21.1 million people (92%).

CONCLUSION

This analysis demonstrates that nearly universal access to trauma care is present in these states when including levels I to V trauma centers. However, concerning gaps remain in timely access to levels I and II trauma centers. This study provides an approach to determine more robust statewide estimates of access to care. It highlights the need for a national trauma system, one in which all components of state-managed trauma systems are assembled in a national data set to accurately identify gaps in care.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level IV.
Technical Outcomes of Porto-Mesenteric Venous Reconstruction in Pancreatic Resection Using Autologous Left Renal Vein Graft as Conduit
Authors: Fogliati Alessandro , Fiorentini Guido , Alva-Ruiz Roberto , Abdelrahman Amro M , Zironda Andrea , Lynch Isaac T , Smoot Rory L , Starlinger Patrick P , Cleary Sean P , Kendrick Michael L , Truty Mark J
Published: May 2023

Background:

Porto or superior mesenteric vein (PV-SMV) resection and reconstruction is sometimes required during pancreatic tumor resection. In patients requiring segmental venous resection with interposition grafting the left renal vein (LRV) is an accessible autologous solution. However, long-term patency outcomes of the LRV as an interposition conduit in this setting have not been analyzed.

Study design:

We conducted a retrospective analysis of patients undergoing pancreatic resection with PV-SMV reconstruction using LRV between 2002 and 2022. The primary outcome was PV-SMV patency at last follow up, assessed with postoperative CT scans and analyzed using Kaplan-Meier survival methods that account for variation in follow up duration. Development of any postoperative acute kidney injury (AKI) within 7 days of surgery and morbidity were secondary outcomes.

Results:

The study cohort includes 65 patients who underwent LRV harvest, 60 (92%) ultimately underwent successful reconstruction with harvested LRV graft. Kaplan-Meier 2-year estimated patency rate of the LRV graft was 88%, with no cases of complete occlusion. Six (10%) patients experienced graft stenosis. Nine of 61 (15%) patients experienced grade II or III AKI, 6 of 9 returning to normal renal function before discharge. No difference in median serum creatinine was observed at baseline, 6 and 12 months from surgery. Left renal vein remnant thrombosis was seen in 7/65 (11%) patients. Only 3 of 61 (5%) patients had persistent AKI caused by complications unrelated to LRV harvesting.

Conclusion:

Autologous LRV graft was a reliable conduit for segmental PV-SMV reconstruction, resulting in a high patency rate, and marginal impact on renal function. LRV harvest is a safe and potentially ideal surgical option for PV-SMV reconstruction in pancreatic surgery.
Verifiable biology
Authors: Konur Savas , Gheorghe Marian , Krasnogor Natalio
Published: May 2023

The formalization of biological systems using computational modelling approaches as an alternative to mathematical-based methods has recently received much interest because computational models provide a deeper mechanistic understanding of biological systems. In particular, formal verification, complementary approach to standard computational techniques such as simulation, is used to validate the system correctness and obtain critical information about system behaviour. In this study, we survey the most frequently used computational modelling approaches and formal verification techniques for computational biology. We compare a number of verification tools and software suites used to analyse biological systems and biochemical networks, and to verify a wide range of biological properties. For users who have no expertise in formal verification, we present a novel methodology that allows them to easily apply formal verification techniques to analyse their biological or biochemical system of interest.
Semiclassical theory predicts stochastic ghosts scaling
Authors: Tomás Lázaro J. , Alarcón, Tomás , Garay Carlos P. , Sardanyés Josep
Published: May 2023

Slowing down occurs in dynamical systems close to bifurcations or phase transitions. The time length (

τ

) of ghost transients close to a saddle-node bifurcation in deterministic systems follows

τ
∼

|

ϵ
−

ϵ
c

|

−
1

/

2

,

ϵ

being the bifurcation parameter and

ϵ
c

its critical value. Recently, we numerically investigated how intrinsic noise affected the deterministic picture, finding a more complicated scaling law. We here provide a theoretical basis for this new law with two models of cooperation using a Wentzel–Kramers–Brillouin asymptotic approximation of the Master Equation. A study of the phase space of the Hamiltonian derived from the Hamilton–Jacobi equation shows that the statistically significant orbits (paths) reproduce the scaling function observed in the stochastic simulations. The flight times tied to these orbits underpin the scaling law of the stochastic system, and the same properties should extend in a universal way to all stochasticsystems whose associated Hamiltonian exhibits the same behaviour. Our approach allows to make useful theoretical predictions of transient times in stochastic systems close to a bifurcation.
The Taxonomy Dictionary: a resource for correct spelling of taxa
Authors: Bagge Kristian
Published: May 2023

This article describes ‘The Taxonomy Dictionary’, a resource that can enhance the spelling engine of a text editor such as Word, so that it can correctly spell every taxon described and listed in the largest taxonomy databases. It contains around 1.4 million unique words, and once installed an incorrectly spelled taxon will be marked by the spelling engine and it will suggest possible correct spellings. Installation instructions for Firefox, LibreOffice and Microsoft Word can be found on the GitHub repository. The software is licensed with a GPL3 licence.
Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization
Authors: Scelfo Andrea , Barra Viviana , Abdennur Nezar , Spracklin George , Busato Florence , Salinas-Luypaert Catalina , Bonaiti Elena , Velasco Guillaume , Chipont Anna , Guérin Coralie , Tijhuis Andréa E. , Spierings Diana C.J. , Francastel Claire , Foijer Floris , Tost Jorg , Mirny Leonid , Fachinetti D.
Published: May 2023

DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present untransformed and cancer cell models that allow inducible and reversible global modulation of DNAme through DNMT1 depletion. By dynamically assessing the effects of induced passive demethylation through cell divisions at both the whole genome and locus-specific level, we reveal a cooperative activity between DNMT1 and DNMT3B to maintain and control DNAme. Moreover, we show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin abundance, compartmentalization, and peripheral localization. DNA methylation loss coincided with a gradual reduction of cell fitness due to G1 arrest, but with minor level of mitotic failure. Altogether, this powerful system allows DNMT and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNA methylation dysfunction and human disease.
Analysis of intracellular transport dynamics using quantitative phase imaging and FRET-based calcium sensors
Authors: Highland Robert E , Rancu Albert , Price Hillel , Parker Steven M , Reynolds Meghan , Hoffman Brenton D. , Wax Adam
Published: May 2023

Understanding cellular responses to mechanical environmental stimuli is an essential goal of cellular mechanotransduction studies and remains a target for microscopy technique development. While fluorescence microscopy has been advanced for this purpose - its molecular sensitivity, the ability of quantitative phase imaging to visualize subcellular structure has yet to be widely applied, perhaps due to its limited specificity. Here we seek to combine Quantitative Phase Imaging (QPI) with a molecularly sensitive Förster resonance energy transfer (FRET) construct for cell mechanotransduction studies. The multimodal imaging instrument is applied to examine cellular response to hypo-osmotic stimulus by observing the influx of calcium ions using a FRET based sensor coupled with mapping of the redistribution of intracellular mass using QPI. The combined imaging modality enables discrimination of cell response by localized region and reveals distinct behavior for each. The analysis shows cell flattening and oscillatory mass transport in response to the stimulus. With the broad array of FRET sensors under development, the combination with QPI offers new avenues for studying cell response to environmental stimuli.
A novel proteomics-based plasma test for early detection of multiple cancers in the general population
Authors: Budnik Bogdan , Amirkhani Hossein , Forouzanfar Mohammad H. , Afshin Ashkan
Published: May 2023

Background

Early detection of cancer is crucial for reducing the global burden of cancer and saving lives, but effective screening tests for many cancers do not exist. Genomics-based liquid biopsy tests for screening multiple cancers at once have been developed, but they have low sensitivity for early-stage cancers and are expensive. Recent advancements in measuring protein abundances in plasma offer new opportunities for developing multi-cancer screening tests.

Methods

We collected plasma samples from 440 individuals, healthy and diagnosed with 18 various types of early-stage solid tumours. Using Proximity Extension Assay, we measured more than 3000 high and low-abundance proteins in each sample. Then, using a multi-step statistical approach, we identified a limited set of proteins that could detect early-stage cancers and their tissue of origin with high diagnostic accuracy.

Findings

Our sex-specific cancer detection consisting of 10 proteins showed high accuracy for both males (AUC: 0.98) and females ((AUC: 0.983). At stage I and at the specificity of 99%, our detection panels were able to identify 89% of cancers among males and 75% of cancers among females.

Our sex-specific localization panels consisted of 150 proteins and were able to identify the tissue of origin of most cancers in more than 80% of cases. The analysis of the plasma concentrations of proteins selected showed that almost all the proteins were in the low-concentration part of the human plasma proteome.

Interpretation

The proteome-based screening test showed promising performance compared with other technologies and could be a starting point for developing a new generation of screening tests for the early detection of cancer and potentially other chronic diseases. This new approach may provide a more accessible and cost-effective alternative to existing methods for cancer detection and may help reduce cancer mortality rates globally.
Towards a human brain EV atlas: Characteristics of EVs from different brain regions, including small RNA and protein profiles
Authors: Huang Yiyao , Arab Tanina , Russell Ashley E. , Mallick Emily R. , Nagaraj Rajini , Gizzie Evan , Redding-Ochoa Javier , Troncoso Juan C. , Pletnikova Olga , Turchinovich Andrey , Routenberg David A. , Witwer Kenneth W.
Published: May 2023

Extracellular vesicles (EVs) are released from different cell types in the central nervous system (CNS) and play roles in regulating physiological and pathological functions. Although brain-derived EVs (bdEVs) have been successfully collected from brain tissue, there is not yet a “bdEV atlas” of EVs from different brain regions. To address this gap, we separated EVs from eight anatomical brain regions of a single individual and subsequently characterized them by count, size, morphology, and protein and RNA content. The greatest particle yield was from cerebellum, while the fewest particles were recovered from the orbitofrontal, postcentral gyrus, and thalamus regions. EV surface phenotyping indicated that CD81 and CD9 were more abundant than CD63 for all regions. Cell-enriched surface markers varied between brain regions. For example, putative neuronal markers NCAM, CD271, and NRCAM were more abundant in medulla, cerebellum, and occipital regions, respectively. These findings, while restricted to tissues from a single individual, suggest that additional studies are merited to lend more insight into the links between EV heterogeneity and function in the CNS.
An intrinsically disordered kinetochore protein coordinates mechanical regulation of chromosome segregation by dynein
Authors: McGory Jessica M. , Barcelos Dylan M. , Verma Vikash , Maresca Thomas J.
Published: May 2023

Kinetochores connect chromosomes and spindle microtubules to maintain genomic integrity through cell division. Crosstalk between the minus-end directed motor dynein and kinetochore-microtubule attachment factors promotes accurate chromosome segregation through a poorly understood pathway. Here we identify a physical linkage between the intrinsically disordered protein Spc105 (KNL1 orthologue) and dynein using an optogenetic oligomerization assay. Core pools of the checkpoint protein BubR1 and the adaptor complex RZZ mediate the connection of Spc105 to dynein. Furthermore, a minimal segment of Spc105 that contains regions with a propensity to multimerize and binding motifs for Bub1 and BubR1 is sufficient to functionally link Spc105 to RZZ and dynein. Deletion of the minimal region from Spc105 reduces recruitment of its binding partners to bioriented kinetochores and causes chromosome mis-segregation. Restoration of normal chromosome segregation and localization of BubR1 and RZZ requires both protein binding motifs and higher-order oligomerization of Spc105. Together, our results reveal that higher-order multimerization of Spc105 is required to recruit a core pool of RZZ that modulates microtubule attachment stability to promote accurate chromosome segregation.
CRISPRi Gene Modulation and All-Optical Electrophysiology in Post-Differentiated Human iPSC-Cardiomyocytes
Authors: Han Julie L. , Heinson Yuli W. , Chua Christianne J. , Liu Wei , Entcheva Emilia
Published: May 2023

Uncovering gene-phenotype relationships can be enabled by precise gene modulation in human induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CMs) and follow up phenotyping using scalable all- optical electrophysiology platforms. Such efforts towards human functional genomics can be aided by recent CRISPR-derived technologies for reversible gene inhibition or activation (CRISPRi/a). We set out to characterize the performance of CRISPRi in post-differentiated iPSC-CMs, targeting key cardiac ion channel genes, KCNH2, KCNJ2, and GJA1, and providing a multiparametric quantification of the effects on cardiac repolarization, stability of the resting membrane potential and conduction properties using all- optical tools. More potent CRISPRi effectors, e.g. Zim3, and optimized viral delivery led to improved performance on par with the use of CRISPRi iPSC lines. Confirmed mild yet specific phenotype changes when CRISPRi is deployed in non-dividing differentiated heart cells is an important step towards more holistic pre-clinical cardiotoxicity testing and for future therapeutic use in vivo.
Lipidome unsaturation affects the morphology and proteome of theDrosophilaeye
Authors: Kumar Mukesh , Has Canan , Lam-Kamath Khanh , Ayciriex Sophie , Dewett Deepshe , Bashir Mhamed , Poupault Clara , Schuhmann Kai , Knittelfelder Oskar , Raghuraman Bharath Kumar , Ahrends Robert , Rister Jens , Shevchenko Andrej
Published: May 2023

While the proteome of an organism is largely determined by the genome, the lipidome is shaped by a poorly understood interplay of environmental factors and metabolic processes. To gain insights into the underlying mechanisms, we analyzed the impacts of dietary lipid manipulations on the ocular proteome ofDrosophila melanogaster. We manipulated the lipidome with synthetic food media that differed in the supplementation of an equal amount of saturated or polyunsaturated triacylglycerols. This allowed us to generate flies whose eyes had a highly contrasting length and unsaturation of glycerophospholipids, the major lipid class of biological membranes, while the abundance of other membrane lipid classes remained unchanged. By bioinformatically comparing the resulting ocular proteomic trends and contrasting them with the impacts of vitamin A deficiency, we identified ocular proteins whose abundances are differentially affected by lipid saturation and unsaturation. For instance, we unexpectedly identified a group of proteins that have muscle-related functions and increase their abundances in the eye upon lipidome unsaturation but are unaffected by lipidome saturation. Moreover, we identified two differentially lipid-responsive proteins involved in stress responses, Turandot A and Smg5, whose abundances decrease with lipid unsaturation. Lastly, we discovered that the ocular lipid class composition is robust to dietary changes and propose that this may be a general homeostatic feature of the organization of eukaryotic tissues, while the length and unsaturation of fatty acid moieties is more variable to compensate environmental challenges. We anticipate that these insights into the molecular responses of theDrosophilaeye proteome to specific lipid manipulations will guide the genetic dissection of the mechanisms that maintain visual function when the eye is exposed to dietary challenges.
Scoping Review: Differences between the risk factors of indigenous and non-indigenous latin american and caribbean children younger than 5 years old
Authors: Rodriguez Romero Daniel David , Rojas Gómez Ana María , Cuadrado Guzmán Jesús David
Published: May 2023

Objective

To map the existing literature on the difference in risk factors for undernutrition between indigenous and non-indigenous children younger than 5 years old of Latin America and caribbean.

Introduction

Compared to non-indigenous children, Indigenous children have a higher risk for undernutrition, however, there are not systematic or scoping reviews identifying this difference through the risk factors.

Inclusion criteria

Every paper designed to assess directly or indirectly associations between undernutrition and risk factors, also, it must show results where indigenous people had not been aggregated to other races. We excluded every paper that didn’t have a covariate different to ethnicity.

Methods

This scoping review will use the JBI methodology to search several databases, trial registries, and gray literature for both published and unpublished studies related to malnutrition. Two or more independent reviewers will screen titles and abstracts for inclusion criteria, assess full texts, and extract data using a data extraction tool. Results will be presented as a narrative synthesis with key findings, knowledge gaps, and recommendations. A PRISMA-ScR flow diagram will be included in the final report.
HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers
Authors: Morozov Viacheslav M. , Riva Alberto , Sarwar Sadia , Kim WanJu , Li Jianping , Zhou Lei , Licht Jonathan D. , Daaka Yehia , Ishov Alexander M.
Published: May 2023

Incorporation of histone variant H3.3 comprises active territories of chromatin. Exploring the function of H3.3 in prostate cancer (PC), we found that knockout (KO) of H3.3 chaperone HIRA suppresses PC growthin vitroand in xenograft settings, deregulates androgen-induced gene expression and alters androgen receptor (AR) binding within enhancers of target genes. H3.3 affects transcription in multiple ways, including activation of p300 by phosphorylated H3.3 at Ser-31 (H3.3S31Ph), which results in H3K27 acetylation (H3K27Ac) at enhancers. In turn, H3K27Ac recruits bromodomain protein BRD4 for enhancer-promoter interaction and transcription activation. We observed that HIRA KO reduces H3.3 incorporation, diminishes H3.3S31Ph and H3K27Ac, modifies recruitment of BRD4. These results suggest that H3.3-enriched enhancer chromatin serves as a platform for H3K27Ac-mediated BRD4 recruitment, which interacts with and retains AR at enhancers, resulting in transcription reprogramming. AR KO reduced levels of H3.3 at enhancers, indicating feedback mechanism. In addition, HIRA KO deregulates glucocorticoid-driven transcription, suggesting a common H3.3/HIRA-dependent mechanism of nuclear receptors function. Expression of HIRA complex proteins is increased in PC compared with normal prostate tissue, especially in high-risk PC groups, and is associated with a negative prognosis. Collectively, our results demonstrate function of HIRA-dependent H3.3 pathway in regulation of nuclear receptors activity.

Key points

*H3.3 at enhancers promotes acetylation of H3K27Ac and retention of AR/BRD4 complex for transcription regulation

*Knockout of H3.3 chaperone HIRA suppresses PC cells growth and deregulates androgen-induced transcription

*H3.3/HIRA pathway regulates both AR and GR, suggesting a common HIRA/H3.3 mechanism of nuclear receptors function
Heterologous expression, purification and structural features of nativeDictyostelium discoideumdye-decolorizing peroxidase bound to a natively incorporated heme
Authors: Kalkan Özlem , Kantamneni Sravya , Brings Lea , Han Huijong , Mancuso Adrian P. , Koua Faisal H.M.
Published: May 2023

TheDictyostelium discoideumdye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily.DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism ofDdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a hemein vitroreconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing theDdDyP peroxidase in 2×YT enriched medium at low temperature (20 °C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure ofDdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of nativeDdDyP active site and its implication on DyP catalysis.
The depletion of TRAIP results in the retention of PCNA on chromatin during mitosis, leads to inhibiting DNA replication initiation
Authors: Shiomi Yasushi , Hayashi Akiyo , Saito Yuichiro , Kanemaki Masato T. , Nishitani Hideo
Published: May 2023

Loading PCNA onto chromatin is a pivotal step in DNA replication, cell cycle progression, and genome integrity. Conversely, unloading PCNA from chromatin is equally crucial for maintaining genome stability. Cells deficient in the PCNA unloader ATAD5-RFC exhibit elevated levels of chromatin-bound PCNA during S phase, but still show dissociation of PCNA from chromatin in mitosis. In this study, we found that depletion of TRAIP, an E3 ubiquitin ligase, results in the retention of PCNA on chromatin during mitosis. Although TRAIP-depleted cells with chromatin-bound PCNA during mitosis progressed into the subsequent G1 phase, they displayed reduced levels of Cdt1, a key replication licensing factor, and impaired S phase entry. In addition, TRAIP-depleted cells exhibited delayed S phase progression. These results suggest that TRAIP functions independently of ATAD5-RFC in removing PCNA from chromatin. Furthermore, TRAIP appears to be essential for precise pre-replication complexes (pre-RCs) formation necessary for faithful initiation of DNA replication and S phase progression.