bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of CPT1A disrupts the maintenance and regenerative function of muscle stem cells
Authors: Qiu Jiamin , Yue Feng , Kim Kun Ho , Chen Xiyue , Khedr Mennatallah A. , Chen Jingjuan , Gu Lijie , Ren Junxiao , Ferreira Christina R. , Ellis Jessica , Kuang Shihuan
Published: October 2024

The skeletal muscle satellite cells (SCs) mediate regeneration of myofibers upon injury. As they switch from maintenance (quiescence) to regeneration, their relative reliance on glucose and fatty acid metabolism alters. To explore the contribution of mitochondrial fatty acid oxidation (FAO) pathway to SCs and myogenesis, we examined the role of carnitine palmitoyltransferase 1A (CPT1A), the rate‐limiting enzyme of FAO. CPT1A is highly expressed in quiescent SCs (QSCs) compared with activated and proliferating SCs, and its expression level decreases during myogenic differentiation. Myod1Cre‐driven overexpression (OE) of Cpt1a in embryonic myoblasts (Cpt1aMTG) reduces muscle weight, grip strength, and contractile force without affecting treadmill endurance of adult mice. Adult Cpt1aMTG mice have reduced number of SC, impairing muscle regeneration and promoting lipid infiltration. Similarly, Pax7CreER‐driven, tamoxifen‐inducible Cpt1a‐OE in QSCs of adult muscles (Cpt1aPTG) leads to depletion of SCs and compromises muscle regeneration. The reduced proliferation of Cpt1a‐OE SCs is associated with elevated level of acyl‐carnitine, and acyl‐carnitine treatment impedes proliferation of wildtype SCs. These findings indicate that aberrant level of CPT1A elevates acyl‐carnitine to impair the maintenance, proliferation and regenerative function of SCs.
Toddler’s fracture: an updated guide on evaluation and management
Authors: Noe McKenna C. , Jarka Dale E. , Sinclair Micah K. , Grote Caleb W.
Published: October 2024

Toddler’s fractures are commonly encountered in pediatric healthcare. These injuries are associated with little to no risk of fracture displacement or failure to heal, regardless of treatment modality. The standard treatment for these injuries has historically been several weeks of weightbearing restriction and immobilization in a circumferential cast or posterior splint. Over the last decade, numerous reports comparing clinical outcomes and iatrogenic complication rates between treatment modalities have emerged, revealing a concerning trend of higher rates of skin breakdown in patients treated with traditional management compared to those treated with removable walking boot immobilization or no immobilization. Current management practices for toddler’s fractures vary widely with respect to both initial and follow-up care, reflecting a need for additional guidance on this topic. This review provides an updated, evidence-based review of evaluation and management strategies for the toddler’s fracture.
Actuator Size of Magnetic Controlled Growth Rod (7 cm vs. 9 cm) is Not Predictive of Unplanned Return to the Operating Room: A Retrospective Multicenter Comparative Cohort Study
Authors: Garg Sumeet , Heffernan Michael , Feddema Tyler , Luhmann Scott , Sturm Peter , Vitale Michael , Andras Lindsay , White Klane ,   The Pediatric Spine Study Group, Carry Patrick
Published: October 2024

Background:

Magnetic controlled growth rods (MCGR) are the most common type of implant used for operative treatment of patients with early-onset scoliosis (EOS). Rods can have either a 7-cm actuator, allowing 2.8 cm of potential expansion, or a 9-cm actuator which allows 4.8 cm potential expansion. We hypothesized that the rate of unplanned return to the operating room (UPROR) will be increased when the 9-cm actuator is implanted in smaller patients. In addition, we aimed to identify a cutoff for spine length between planned upper and lower instrumented MCGR levels that best differentiated between patients having a high versus low risk of UPROR.

Methods:

We identified 167 patients from a prospectively collected registry of EOS patients who began MCGR treatment at 9 years of age or younger, with greater than 1 year of follow-up, and had adequate radiographs. Demographic, clinical, and surgical characteristics were analyzed for 7-cm and 9-cm actuator patients. Chi-square tests and Student t tests were used to test for differences between the 2 actuator rod groups. A predictive model for UPROR within 2 years was developed based on variables significantly predictive of UPROR.

Results:

The average follow-up was 2.6 years (range, 1 to 5 y) in both the 7 cm (n=74) and 9 cm (n=93) groups. Twenty-five complications in 14 patients led to UPROR within 2 years of MCGR insertion, 8% incidence (95% CI, 4%-13%). Device-related complications (n=15) were the most common reason for UPROR, followed by wound complications (n=4), pain-related complications (n=3), junctional kyphosis (n=2), and incarcerated umbilical hernia (n=1). After adjusting for age, spine height, number of spine anchors, sex, and diagnosis, there was no significant difference in UPROR rates between groups. Fewer proximal anchors, smaller T1-S1 height, and more caudal mid-point of primary coronal curvature were significantly associated with UPROR in the predictive model.

Conclusion:

MCGR actuator size is not a significant factor in predicted UPROR. Smaller height, fewer anchors, and caudal apex increased UPROR risk.

Level of Evidence:

This is a retrospective, multicenter comparative cohort study (Level III therapeutic).
VITRECTOMY COMBINED WITH INVERTED INTERNAL LIMITING MEMBRANE FLAP INSERTION OR SINGLE-LAYERED FLAP COVERING TECHNIQUE FOR HIGHLY MYOPIC MACULAR HOLES WITH MACULAR RETINOSCHISIS
Authors: Jia Qinlang , Zhang Ke , Qi Biying , Yang Xiaohan , Wu Xijin , Wang Xinbo , Feng Xiao , Liu Wu
Published: October 2024

Purpose:

To investigate the anatomical and visual outcomes of inverted internal limiting membrane flap insertion versus single-layered i-internal limiting membrane flap covering in highly myopic macular holes associated with macular retinoschisis.

Methods:

A retrospective study compared 23 G vitrectomy with inverted-internal limiting membrane flap insertion (30 eyes) or covering (31 eyes) in highly myopic macular holes patients. Pre- and postoperative optical coherence tomography images and best-corrected visual acuity (BCVA) were evaluated. Macular hole schisis was classified into three types based on the extent of outer layer schisis. Regression analysis identified predictors of closure rate and postoperative BCVA.

Results:

The baseline data of the two groups were matched, including BCVA, axial length, and minimum linear diameter, except for a higher hole height in insertion group (P = 0.038). After a mean follow-up of 11.7 months, type I closure rates were 83.3% (25/30) in the insertion group and 90.3% (28/31) in the covering group (P = 0.335), respectively. The intact external limiting membrane in the covering group (7/28) was higher compared with the insertion group (1/28) finally (P = 0.026). Final BCVA improved significantly in both groups (P < 0.001); the BCVA was better in closed highly myopic macular holes in the covering group (P = 0.011). Multivariate linear regression analysis revealed that preoperative BCVA (β = 0.386, P = 0.001) and Macular hole schisis stage (β = 0.309, P = 0.004) were independent predictive factors for the final BCVA.

Conclusion:

The single-layered inverted-internal limiting membrane flap covering favored foveal structure recovery and provided a better visual prognosis in closed highly myopic macular holes compared with insertion. The preoperative BCVA and macular hole schisis stage were independent predictors of visual outcomes in patients with highly myopic macular holes.
Finger-controlled nonultrasonic lens extractor
Authors: Beniz Luiz A.F. , Chatzea Marina S. , Zarei-Ghanavati Siamak , Jammal Alessandro A. , Yoo Sonia H.
Published: October 2024

Purpose:

To report initial surgical experience and learning curve with a new finger-controlled, ultrasoundless lens extractor device and provide insights for future surgical endeavors.

Setting:

Bascom Palmer Eye Institute, Miami, Florida.

Design:

Single-center, noncomparative, retrospective, consecutive case series.

Methods:

61 eyes of 51 individuals with cataract. All surgeries were performed with the miCOR 700 lens extractor by a single experienced physician. Nuclear density was graded preoperatively. Corrected distance visual acuity (CDVA), intraocular pressure (IOP), and pachymetry were evaluated preoperatively and postoperatively. Surgical videos were reviewed to collect data on time for each surgical step and complications. Regression analyses assessed the learning curve, performance improvement, and effects of nuclear density on surgical time and postoperative pachymetric variation.

Results:

Patients had a mean age of 72.2 ± 7.6 years. Increased surgical experience significantly reduced procedure time (P < .001), nuclear removal time (P = .018), and cortex removal time (P = .002). Higher nuclear density resulted in a longer procedure (P < .001) and nuclear removal time (P < .001). One posterior capsular rent occurred, not attributed to the lens extractor. No thermal damage to the corneal wound was observed. Postoperative CDVA improved significantly (P < .001 for eyes without ocular comorbidities, P = .016 for eyes with ocular comorbidities). All cases of corneal edema and IOP spikes resolved within a month.

Conclusions:

The miCOR 700 lens extractor offers an innovative, cost-effective approach to cataract surgery. Further research is needed to compare it with conventional phacoemulsification techniques.
NaV1.8/NaV1.9 double deletion mildly affects acute pain responses in mice
Authors: Alves-Simões Marta , Teege Laura , Tomni Cecilia , Lürkens Martha , Schmidt Annika , Iseppon Federico , Millet Queensta , Kühs Samuel , Katona Istvan , Weis Joachim , Heinemann Stefan H. , Hübner Christian A. , Wood John , Leipold Enrico , Kurth Ingo , Haag Natja
Published: October 2024

The 2 tetrodotoxin-resistant (TTXr) voltage-gated sodium channel subtypes NaV1.8 and NaV1.9 are important for peripheral pain signaling. As determinants of sensory neuron excitability, they are essential for the initial transduction of sensory stimuli, the electrogenesis of the action potential, and the release of neurotransmitters from sensory neuron terminals. NaV1.8 and NaV1.9, which are encoded by SCN10A and SCN11A, respectively, are predominantly expressed in pain-sensitive (nociceptive) neurons localized in the dorsal root ganglia (DRG) along the spinal cord and in the trigeminal ganglia. Mutations in these genes cause various pain disorders in humans. Gain-of-function missense variants in SCN10A result in small fiber neuropathy, while distinct SCN11A mutations cause, i. a., congenital insensitivity to pain, episodic pain, painful neuropathy, and cold-induced pain. To determine the impact of loss-of-function of both channels, we generated NaV1.8/NaV1.9 double knockout (DKO) mice using clustered regularly interspaced short palindromic repeats/Cas-mediated gene editing to achieve simultaneous gene disruption. Successful knockout of both channels was verified by whole-cell recordings demonstrating the absence of NaV1.8- and NaV1.9-mediated Na+ currents in NaV1.8/NaV1.9 DKO DRG neurons. Global RNA sequencing identified significant deregulation of C-LTMR marker genes as well as of pain-modulating neuropeptides in NaV1.8/NaV1.9 DKO DRG neurons, which fits to the overall only moderately impaired acute pain behavior observed in DKO mice. Besides addressing the function of both sodium channels in pain perception, we further demonstrate that the null-background is a very valuable tool for investigations on the functional properties of individual human disease-causing variants in NaV1.8 or NaV1.9 in their native physiological environment.
Increasing Diabetic Retinopathy Screening in Resident-Run Clinic Through Partnership With Ophthalmology Clinic: A Pilot Study
Authors: Mahoney Catherine , Toomey Caitlin
Published: October 2024

Despite the importance of early detection of diabetic retinopathy, many diabetic patients fail to receive the recommended screening. The objective of this quality-improvement initiative was to increase diabetic retinopathy screening through a partnership between primary care and ophthalmology, where primary care clinic staff may schedule patients directly for screening appointments at point of referral. To our knowledge, this intervention is the first described to use an interspecialty partnership to increase screening. We implemented the intervention at a resident-run primary care clinic with a medically underserved patient population. The pilot intervention took place over a 6-month time frame. The completion rate of diabetic retinopathy screening examinations was compared before and after intervention and was found to increase in a statistically significant manner from 34.7% to 40.5% (p = .01). The no-show rate did improve from 66.7% preintervention to 46.0% postintervention; however, this change was not statistically significant (p = .44). During this pilot, the intervention was able to increase diabetic retinopathy screening completion rate; however, further efforts should be aimed at addressing no-shows. Overall, this initiative was a positive step toward the goal of every diabetic patient undergoing the appropriate screening examinations.
Use of calculated free testosterone in men: advantages and limitations
Authors: Nyamaah Jennifer Afrakoma , Narinx Nick , Antonio Leen , Vanderschueren Dirk
Published: October 2024

Purpose of review

Due to technical requirements and high cost, equilibrium dialysis-free testosterone (T) measurements are not commonly available in clinical practice. Clinicians rely on calculated free T (cFT) as a proxy. This review discusses using free T as a second-line assessment, highlighting its relevance in preventing misdiagnosis and overtreatment of male hypogonadism.

Recent findings

While there is consensus on measuring total T – comprising sex hormone-binding globulin (SHBG)-bound, albumin-bound, and free T – as a first step in diagnosing male hypogonadism, evidence confirms that aging and conditions like obesity influence both total T and SHBG levels. Furthermore, low free T has been associated with symptoms of androgen deficiency, even in men with normal total T. Clinicians should, however, be aware of limitations of free T calculations, particularly the lack of standardization. Recent developments include establishing age-stratified free T reference ranges measured by equilibrium dialysis.

Free T remains a subject of longstanding controversy. Factors such as age and obesity can alter total T and SHBG levels. Free T serves as a second-line indicator of androgen exposure, taking SHBG fluctuations into account. Given that commonly used free T calculators only provide approximations of free T, there is a need to further standardize free T calculators.
Fibro-osseous lesions of the sinonasal tract: a contemporary review
Authors: Motwani Kartik , Adelman Avraham E. , Chapurin Nikita
Published: October 2024

Purpose of review

Fibro-osseous lesions (FOL) are benign, slow-growing lesions that are often incidentally discovered in the sinonasal cavity. They may necessitate surgical resection in patients with postobstructive sinusitis, or in cases of cranial nerve and orbital compression. We examine the recent advancements in otolaryngology relating to diagnostic characteristics and treatments for FOL, with emphasis on new technologies to improve outcomes and reduce recurrence.

Recent findings

We discuss distinguishing characteristics across FOL subtypes, including osteomas, fibrous dysplasia, and ossifying fibroma. Recent literature encompasses clinical case series and animal model studies examining mechanistic, diagnostic, and therapeutic findings in FOL. Recent advancements include emerging pharmacological therapies, development of imaging guidance for surgical planning, and focus on the importance of complete surgical resection for improved outcomes.

Management of most FOL may be approached by endoscopic techniques, harnessing recent improvements in image guidance and surgical innovation. Improved diagnostic imaging, including the use of 3-D surgical planning, has been shown to enhance treatment outcomes. Improved understanding of the genetic and pathophysiological characteristics of FOL could further reveal targeted therapies, reducing recurrence and improving patient quality of life.
Emerging Artificial Intelligence-Based Pedagogies in Didactic Nursing Education
Authors: Gerdes Michele , Bayne Andrew , Henry Kristina , Ludwig Barbara , Stephenson Leigh , Vance Allison , Wessol Jennifer , Winston Sarah
Published: October 2024

Background:

Artificial intelligence pedagogies are increasingly commonplace in health care education, and limited information guides their application in didactic nursing environments.

Purpose:

To examine the current state of artificial intelligence–based pedagogies used in didactic nursing education.

Design:

The review was conducted using Arksey and O’Malley’s scoping review framework and the Joanna Briggs Institute’s System for the Unified Management, Assessment, and Review of Information platform. Literature is reported using the Preferred Reporting Items for Systematic Reviews Extension for Scoping Reviews.

Methods:

The review included articles published between January 1, 2013, and July 23, 2024, in MEDLINE (via PubMed), Cumulative Index to Nursing and Allied Health Literature, Education Resources Information Center, World Science, and Google Scholar. Two reviewers independently assessed all articles.

Results:

Themes for the 16 included articles were generative artificial intelligence and pairing artificial intelligence with other pedagogical strategies.

Conclusions:

More research is needed to examine artificial intelligence–based pedagogies in didactic nursing education.
Innovative and best models of palliative and end-of-life care – with focus on rural and remote communities
Authors: Mogan Caroline , Davies Nathan , Dening Karen Harrison , Lloyd-Williams Mari
Published: October 2024

Purpose of review

The review aims to synthesize the most recent innovative models of palliative care being delivered in rural and remote locations.

Recent findings

Worldwide, as the ageing population grows, more people will require palliative care. However, equal availability of high-quality palliative care services remains a significant challenge, particularly in rural and remote communities. Innovative models of palliative care have been developed to address the projected need of people in rural and remote areas. Models that leverage the use of digital healthcare (such as telecare and Artificial Intelligence), the non-specialized palliative care workforce (such as GPs, pharmacists, and family carers), and community driven approaches have demonstrated success in achieving positive palliative care outcomes, such as reduced physical and emotional distress, and family carers feeling more supported.

There is a need to support people to remain within their rural and remote communities towards the end-of-life (EOL). While some models of care have been identified to help with this, there continues to be significant difficulties in access to health and social care in rural and remote areas. It is important we build on this research to understand more broadly the models of support for those living in remote and rural communities at the EOL.
The association between peripheral neuropathy and daily-life gait quality characteristics in people with diabetes
Authors: Hulshof Chantal M , van der Leeden Marike , van Netten Jaap J , Gijssel Maarten , Evers Jordi , Bus Sicco A , Pijnappels Mirjam
Published: October 2024

0.

Background

Peripheral neuropathy is a common complication of diabetes and increases the risk of falls, possibly through gait (quality) impairments in daily life. Characteristics of gait quality have been associated with peripheral neuropathy in a laboratory setting, but little is known about the more relevant association with gait quality in daily life.

Research question

What is the association between peripheral neuropathy and gait quality characteristics in daily life in people with diabetes?

Methods

Data from two cross-sectional studies were combined in an exploratory analysis, including a total of 98 participants with diabetes (mean age: 68 (SD 7) years, 32 females), of which 68 with peripheral neuropathy. Participants wore a tri-axial accelerometer for seven consecutive days. Walking episodes ≥5 seconds were identified and analysed to determine various gait quality characteristics. Associations were assessed using linear regression analyses, adjusted for walking speed and other potential confounders.

Results

Peripheral neuropathy was significantly associated with a lower walking speed (people with neuropathy: 0.81 vs without neuropathy: 0.88 m/s; β (95% confidence interval (CI)): -0.114 (−0.202 to -0.026)), a lower stride frequency (0.81 vs 0.85 strides/s; β (95% CI): -0.030 (−0.057 to -0.003)), lower gait intensity (i.e. lower root mean square) in vertical direction (1.38 vs 1.63 m/s2; β (95% CI): -0.074 (−0.143 to -0.006)), and less gait symmetry (i.e. lower harmonic ratio) in vertical direction (1.82 vs 2.27; β (95% CI): -0.322 (−0.474 to -0.170)). People with peripheral neuropathy had non-significantly poorer gait quality for most of the other 21 gait quality characteristics.

Significance

Peripheral neuropathy seems to negatively affect several gait quality characteristics measured in daily life. These results need to be replicated in future studies and may help to develop targeted gait training to improve gait quality and potentially reduce fall risk in people with diabetes and peripheral neuropathy.
Circadian clock features define novel breast cancer subtypes and shape drug sensitivity
Authors: Ector Carolin , Didier Jeff , Landtsheer Sébastien De , Nordentoft Malthe S. , Schmal Christoph , Keilholz Ulrich , Herzel Hanspeter , Kramer Achim , Sauter Thomas , Granada Adrián E.
Published: October 2024

The circadian clock regulates key physiological processes, including cellular responses to DNA damage. Circadian-based therapeutic strategies optimize treatment timing to enhance drug efficacy and minimize side effects, offering potential for precision cancer treatment. However, applying these strategies in cancer remains limited due to limited understanding of the clock’s function across cancer types and incomplete insights into how the circadian clock affects drug responses. To address this, we conducted deep circadian phenotyping across a panel of breast cancer cell lines using two complementary reporters. Observing diverse circadian dynamics, we developed metrics to assess circadian rhythm strength and stability. This led to the identification of four distinct circadian-based phenotypes in breast cancer: functional, weak, unstable, and dysfunctional clocks. Furthermore, we demonstrate that the circadian clock plays a critical role in shaping pharmacological responses to various anti-cancer drugs and identify circadian features that accurately predict drug sensitivity. Collectively, our findings establish a foundation for advancing the use of chronotherapeutic strategies in breast cancer treatment, expanding their potential application to improve therapeutic outcomes in breast cancer.
Regulating IL-2 immune signaling function via a core allosteric structural network
Authors: Woodward Claire H. , Solieva Shahlo O. , Hwang Daniel , De Paula Viviane S. , Fabilane Charina S. , Young Michael C. , Trent Tony , Teeley Ella C. , Majumdar Ananya , Spangler Jamie B. , Bowman Gregory R. , Sgourakis Nikolaos G.
Published: October 2024

Human interleukin-2 (IL-2) is a crucial cytokine for T cell regulation, with therapeutic potential in cancer and autoimmune diseases. However, IL-2’s pleiotropic effects across different immune cell types often lead to toxicity and limited efficacy. Previous efforts to enhance IL-2’s therapeutic profile have focused on modifying its receptor binding sites. Yet, the underlying dynamics and intramolecular networks contributing to IL-2 receptor recognition remain unexplored. This study presents a detailed characterization of IL-2 dynamics compared to two engineered IL-2 mutants, “superkines” S15 and S1, which exhibit biased signaling towards effector T cells. Using NMR spectroscopy and molecular dynamics simulations, we demonstrate significant variations in core dynamic pathways and conformational exchange rates across these three IL-2 variants. We identify distinct allosteric networks and excited state conformations in the superkines, despite their structural similarity to wild-type IL-2. Furthermore, we rationally design a mutation (L56A) in the S1 superkine’s core network, which partially reverts its dynamics, receptor binding affinity, and T cell signaling behavior towards that of wild-type IL-2. Our results reveal that IL-2 superkine core dynamics play a critical role in their enhanced receptor binding and function, suggesting that modulating IL-2 dynamics and core allostery represents an untapped approach for designing immunotherapies with improved immune cell selectivity profiles.

Highlights

NMR and molecular dynamics simulations revealed distinct conformational dynamics and allosteric networks in computationally re-designed IL-2 superkines compared to wild-type IL-2, despite their similar crystal structures.

The superkines S1 and S15 exhibit altered sampling of excited state conformations at an intermediate timescale, with slower conformational exchange rates compared to wild-type IL-2.

A rationally designed mutation (L56A) in the S1 superkine’s core allosteric network partially reverted its dynamics, receptor binding affinity, and T cell signaling behavior towards that of wild-type IL-2.

Our study demonstrates that IL-2 core dynamics play a critical role in receptor binding and signaling function, providing a foundation for engineering more selective IL-2-based immunotherapies.

Graphical Abstract
Comprehensive identification of coronary artery disease-associated variants regulating vascular smooth muscle cell gene expression
Authors: Barbera Nicolas , Wallace Lexi , Perry Noah , Lei Lily , den Ruijter Hester M , Civelek Mete
Published: October 2024

Coronary artery disease (CAD) is a complex disorder with genetic and environmental influences. Genome-wide association studies (GWAS) have identified over 300 genomic loci associated with disease risk. However, identifying the functional variants within these loci has been limited in large part due to linkage disequilibrium. This represents a critical step in understanding the molecular mechanisms underlying disease risk. To identify and prioritize candidate causal CAD-associated variants, we performed lentivirus-based massively parallel reporter assays (lentiMPRAs) in primary vascular smooth muscle cells (SMCs), which play significant roles in atherosclerosis, the underlying cause of CAD. We tested 25892 CAD-associated variants for their allele-specific enhancer activity in quiescent and proliferative SMCs, modeling healthy and disease conditions. We identified 122 candidate variants showing significant enhancer activity and differences in reporter gene expression between risk and non-risk alleles. We also identified 23 variants showing condition-biased allelic imbalance and 41 variants showing sex-biased allelic imbalance. We further functionally characterized 25892 variants by performing CUT&RUN assays to identify variants in enhancer and promoter regions of SMCs. By integrating the results of these experiments, we identified a credible set of 49 CAD-associated variants in functionally relevant regions. Furthermore, by comparing these identified variants with our previously obtained expression quantitative trait loci (eQTL) data, 27 of these 49 variants were associated with SMC gene expression levels. Finally, we performed CRISPRi experiments on 8 variants comprising 9 variant-gene pairs, rs35976034 (MAP1S), rs4888409 (CFDP1), rs73193808 (MAP3K7CL), rs67631072 (INPP5B/FHL3), rs1651285 (SNHG18), rs17293632 (SMAD3), rs2238792 (ARVCF), rs4627080 (NRIP3), to confirm their regulatory potential of nearby gene expression. Taken together, our results comprehensively fine-map the causal variants that confer increased risk of CAD through their effects on vascular smooth muscle cells.
Effect of Ventilator Mode on Ventilator-Free Days in Critically Ill Adults: A Randomized Trial
Authors: Seitz Kevin P. , Lloyd Bradley D. , Wang Li , Shotwell Matthew S. , Qian Edward T. , Muhs Amelia L. , Richardson Roger K. , Rooks J. Craig , Hennings-Williams Vanessa , Sandoval Claire E. , Richardson Whitney D. , Morgan Tracy L. , Thompson Amber N. , Hastings Pamela G. , Ring Terry P. , Stollings Joanna L. , Talbot Erica M. , Krasinski David J. , DeCoursey Bailey R. , Marvi Tanya K. , DeMasi Stephanie C. , Gibbs Kevin W. , Self Wesley H. , Mixon Amanda S. , Rice Todd W. , Semler Matthew W. , Casey Jonathan D. ,   the Pragmatic Critical Care Research Group
Published: October 2024

Rationale

For critically ill adults receiving invasive mechanical ventilation, the ventilator mode determines how breaths are delivered. Whether the choice of ventilator mode affects outcomes for critically ill patients is unknown. To compare the effects of three common ventilator modes (volume control, pressure control, and adaptive pressure control) on death and duration of mechanical ventilation.

Methods

We conducted a pragmatic, cluster-randomized, crossover trial among adults receiving invasive mechanical ventilation in a medical ICU between November 1, 2022 and July 31, 2023. Each month, patients in the participating unit were assigned to receive volume control, pressure control, or adaptive pressure control during continuous mandatory ventilation. The primary outcome was ventilator-free days through 28 days.

Results

Among 566 patients included in the primary analysis, the median number of ventilator-free days was 23 [IQR, 0-26] in the volume control group, 22 [0-26] in the pressure control group, and 24 [0-26] in the adaptive pressure control group (P=0.60). The median tidal volume was similar in the three groups, but the percentage of breaths larger than 8mL/kg of predicted body weight differed between volume control (median, 4.0%; IQR, 0.0-14.1), pressure control (10.6%; 0.0-31.5), and adaptive pressure control (4.7%; 0.0-19.2). Incidences of hypoxemia, acidemia, and barotrauma were similar in the three groups.

Conclusions

Among critically ill adults receiving invasive mechanical ventilation, the use of volume control, pressure control, or adaptive pressure control did not affect the number of ventilator-free days, however, confidence intervals included differences that may be clinically meaningful.
Analysis of Eligibility Criteria Clusters Based on Large Language Models for Clinical Trial Design
Authors: Bornet Alban , Khlebnikov Philipp , Meer Florian , Haas Quentin , Yazdani Anthony , Zhang Boya , Amini Poorya , Teodoro Douglas
Published: October 2024

Objectives

Clinical trials (CTs) are essential for improving patient care by evaluating new treatments’ safety and efficacy. A key component in CT protocols is the study population defined by the eligibility criteria. This study aims to evaluate the effectiveness of large language models (LLMs) in encoding eligibility criterion information to support CT protocol design.

Materials and Methods

We extracted eligibility criterion sections, phases, conditions, and interventions from CT protocols available in theClinicalTrials.govregistry. Eligibility sections were split into individual rules using a criterion tokenizer and embedded using LLMs. The obtained representations were clustered. The quality and relevance of the clusters for protocol design was evaluated through 3 experiments: intrinsic alignment with protocol information and human expert cluster coherence assessment, extrinsic evaluation through CT-level classification tasks, and eligibility section generation.

Results

Sentence embeddings fine-tuned using biomedical corpora produce clusters with the highest alignment to CT-level information. Human expert evaluation confirms that clusters are well-structured and coherent. Despite the high information compression, clusters retain significant CT information, up to 97% of the classification performance obtained with raw embeddings. Finally, eligibility sections automatically generated using clusters achieve 95% of the ROUGE scores obtained with a generative LLM.

Conclusions

We show that clusters derived from sentence-level LLM embeddings are effective in summarizing complex eligibility criterion data while retaining relevant CT protocol details. Clustering-based approaches provide a scalable enhancement in CT design that balances information compression with accuracy.
Characterization of cell states in biliary tract cancers identifies mechanisms of therapeutic resistance in a phase II trial of DKN-01/nivolumab
Authors: Park Ryan J , Parikh Milan , Pappas Leon , Sade-Feldman Moshe , Kulkarni Anupriya S. , Bi Lynn , LaSalle Thomas J. , Galway Aralee , Kuhlman Caroline , Blaszkowsky Lawrence S , Meyerhardt Jeffrey A. , Enzinger Peter C , Biller Leah , Allen Jill N , Kagey Michael H. , Baum Jason , Sirard Cynthia , Duda Dan G. , Zhu Andrew X. , Abrams Thomas A. , Hacohen Nir , Ting David T. , Mehta Arnav , Goyal Lipika
Published: October 2024

Biliary tract cancers demonstrate profound therapeutic resistance, and broadly effective therapies for refractory disease are lacking. We conducted a single-arm, second-line phase II trial combining DKN-01, a humanized monoclonal antibody targeting Dickkopf-1 (DKK-1), and nivolumab to treat patients with advanced biliary tract cancer (NCT04057365). No objective responses were seen. To identify mechanisms of treatment failure, we analyzed paired pre-treatment and on-treatment biopsies using scRNA-seq and constructed a detailed molecular classification of malignant and immune cells. We annotated five biliary tract cancer malignant cell states: classical, basal, mesenchymal, neural-like, and endothelial-like. Neural-like and endothelial-like states, which drive therapeutic resistance in other cancers, have not previously been described in BTC. Malignant cell states co-varied with distinct immune cell states, revealing diverse mechanisms of myeloid and T-cell mediated immune suppression, including M2 myeloid and terminally exhausted T cell programs that were induced by DKN-01/nivolumab. Here, we provide the first systematic classification of functionally annotated cell states in biliary tract cancer and provide new insight into resistance mechanisms to an immunotherapy combination that can inform the next generation of trials.
Insulin moderates the effects of early life adversity on executive functioning in a sex-specific manner
Authors: Batra Aashita , Pokhvisneva Irina , Elgbeili Guillaume , Ruge Olivia , Fitzgerald Eamon , Patel Sachin , Czamara Darina , Meaney Michael J , Binder Elisabeth B. , Silveira Patricia P
Published: October 2024

Background

Early life adversity (ELA) is associated with altered insulin signaling and altered EF behaviors, in a potentially sex-specific manner. Considering the high co-morbidity between altered metabolism and executive function (EF) problems, we hypothesized that the genetic background associated with altered fasting insulin (FI) and EF could be shared

Methods

Our study used conjunctional false discovery rate (ConjFDR) to identify the shared genetic architecture between FI and two EFs: impulsivity and attention deficit-hyperactivity disorder (ADHD). We identified the polygenic risk score (PRS) threshold from a FI genome-wide association study (GWAS) that best predicted insulin levels in male and female ALSPAC children [Nmales=1,901, Nfemales=1,834; pt-intial-males= 0.05 (11,121 SNPs), pt-intial-females= 0.15 (27,202 SNPs)], further refining it to only include SNPs significantly associated with insulin levels in children [NSNP-males= 635 SNPs, NSNP-females= 1,449 SNPs]. A phenome-wide association study (PheWAS) was also run to identify EFs associated with the interaction between the refined PRS (rPRS) and early adversity. To investigate the presence of a direct causal relationship between FI and impulsivity in the presence of adversity, we applied mendelian randomization (MR)

Results

ConjFDR suggested that environmental factors could be involved in the association between insulin and EFs, as there was no shared genetic background. PheWAS highlighted impulsivity and attention-related outcomes in interaction models between FI rPRS and early adversity. Finally, two-sample MR suggested a causal association between higher fasting insulin levels and impulsive behavior, specifically in females exposed to adversity (p < 0.001). Overall, a sex-specific impulsivity GWAS demonstrated thatMYT1LandTSSC1, genes that are associated with motor impulsivity, were enriched only in females.

Conclusions

Our study solidifies the evidence that the relationship between high FI and EF is not direct, but rather interacting with ELA exposure, especially in females.

Key points

Early life adversity is associated with alterations in insulin signaling and executive functioning behaviors.

We report a causal association between high fasting insulin and increased impulsivity in females exposed to adversity.

Our findings also support the idea that fasting insulin moderates the long-term effects of early life adversity on executive functions in females.

This research provides insights into the mechanisms by which insulin moderates the effects of early life adversity on executive function disorders and informs the development of potential interventions.
Mechanisms of cortical microtubule organization in epidermal keratinocytes
Authors: Guo Keying , Merdes Andreas
Published: October 2024

Microtubules in many differentiated cell types are reorganized from a radial, centrosome-bound array into a cell type-specific, non-centrosomal network. In epidermal keratinocytes, cortical microtubules are organized from desmosomes (Lechler, T., and Fuchs, E. 2007. J. Cell Biol. 176:147-154). Details of this organization are poorly understood. We used immunofluorescence expansion microscopy to visualize directly the contact between cortical microtubules and desmosomes in murine skin tissue. Microtubule bound laterally to desmosomes, or with their ends at mixed polarity. Experiments including time-lapse microscopy of EB3-GFP, microtubule regrowth after depolymerization, and expression of ectopic ninein that was sequestered to the plasma membrane with a CAAX sequence motif, indicated that limited nucleation of microtubules can occur at the cortex, but mostly, cortical microtubules may accumulate by translocation from non-cortical sites and anchorage to desmosomes.
Two temperature-responsive RNAs act in concert: The small RNA CyaR and the mRNAompX
Authors: Guanzon David A. , Pienkoß Stephan , Brandenburg Vivian B. , Röder Jennifer , Dietze Alisa , Wimbert Andrea , Twittenhoff Christian , Narberhaus Franz
Published: October 2024

Bacterial pathogens, such as inYersinia pseudotuberculosis, encounter temperature fluctuations during host infection and upon return to the environment. These temperature shifts impact RNA structures globally. While previous transcriptome-wide studies have focused on RNA thermometers in the 5’-untranslated region of virulence-related mRNAs, our investigation revealed temperature-driven structural rearrangements in the small RNA (sRNA) CyaR. At 25°C, CyaR primarily adopts a conformation that occludes its seed region, but transitions to a liberated state at 37°C. By RNA-sequencing and in-line probing experiments, we identified the Shine-Dalgarno sequence ofompXas a direct target of CyaR. Interestingly, theompXtranscript itself exhibits RNA thermometer-like properties, facilitating CyaR base pairing at elevated temperatures. This interaction impedes ribosome binding toompXand accelerates degradation of theompXtranscript. Furthermore, we observed induced proteolytic turnover of the OmpX protein at higher temperatures. Collectively, our study uncovered multi-layered posttranscriptional mechanisms governingompXexpression, resulting in lower OmpX levels at 37°C compared to 25°C. We propose that CyaR remains mostly passive at 25°C but becomes primed to repressompXat 37°C, thereby expediting outer membrane remodelling in anticipation of pathogenesis.
Synonymous mutations in AAV Rep enhance genome packaging in a library selection
Authors: Azim Tasfia , Myerscough Dru , Silberg Jonathan
Published: October 2024

When producing Adeno-Associated Virus (AAV) gene therapies, a significant fraction of capsids can lack the desired DNA cargo. In AAV, Rep proteins mediate DNA packaging and virus assembly, suggesting that changes in Rep activity, expression, or DNA binding might affect genome packaging. To understand how mutations in the Rep gene affect activity, we selected a library of Rep mutants for their ability to produce active virions. By sequencing the Rep gene following the purification of viruses that package AAV genomes, we identified Rep mutants having non-synonymous mutations with a range of cellular activities. Surprisingly, synonymous mutations within the p19 promoter were enriched to the greatest extent, increasing in abundance by 102to 104fold. When the most highly enriched mutant was used to package a synthetic DNA cargo into the AAV capsid, the packaging efficiency could not be differentiated from native Rep. These findings suggest that these synonymous mutations enhance AAV genome packaging into capsids by affecting Rep-DNA interactions. They also suggest that silent sequence changes in the DNA cargo packaged by Rep can be used to tune packaging DNA packaging efficiency.
Polybacterial Intracellular Macromolecules Shape Single-Cell Epikine Profiles in Upper Airway Mucosa
Authors: Easter Quinn T , Alvarado-Martinez Zabdiel , Kunz Meik , Matuck Bruno , Rupp Brittany , Weaver Theresa , Ren Zhi , Tata Aleksandra T , Caballero-Perez Juan , Oscarson Nick , Hasuike Akira , Ghodke Ameer , Kimple Adam , Tata Purushothama Rao , Randell Scott H , Koo Hyun , Ko Kang I , Byrd Kevin Matthew
Published: October 2024

The upper airway, particularly the nasal and oral mucosal epithelium, serves as a primary barrier for microbial interactions throughout life. Specialized niches like the anterior nares and the tooth are especially susceptible to dysbiosis and chronic inflammatory diseases. To investigate host-microbial interactions in mucosal epithelial cell types, we reanalyzed our single-cell RNA sequencing atlas of human oral mucosa, identifying polybacterial signatures (20% Gram-positive, 80% Gram-negative) within both epithelial- and stromal-resident cells. This analysis revealed unique responses of bacterial-associated epithelia when compared to two inflammatory disease states of mucosa. Single-cell RNA sequencing, in situ hybridization, and immunohistochemistry detected numerous persistent macromolecules from Gram-positive and Gram-negative bacteria within human oral keratinocytes (HOKs), including bacterial rRNA, mRNA and glycolipids. Epithelial cells with higher concentrations of 16S rRNA and glycolipids exhibited enhanced receptor-ligand signaling in vivo. HOKs with a spectrum of polybacterial intracellular macromolecular (PIM) concentrations were challenged with purified exogenous lipopolysaccharide, resulting in the synergistic upregulation of select innate (CXCL8, TNFSF15) and adaptive (CXCL17, CCL28) epikines. Notably, endogenous lipoteichoic acid, rather than lipopolysaccharide, directly correlated with epikine expression in vitro and in vivo. Application of the Drug2Cell algorithm to health and inflammatory disease data suggested altered drug efficacy predictions based on PIM detection. Our findings demonstrate that PIMs persist within mucosal epithelial cells at variable concentrations, linearly driving single-cell effector cytokine expression and influencing drug responses, underscoring the importance of understanding host-microbe interactions and the implications of PIMs on cell behavior in health and disease at single-cell resolution.
Leveraging HILIC/ERLIC Separations for Online Nanoscale LC-MS/MS Analysis of Phosphopeptide Isoforms from RNA Polymerase II C-terminal Domain
Authors: Ficarro Scott B. , Kothiwal Deepash , Bae Hyun Jin , Tavares Isidoro , Giordano Gabriela , Buratowski Stephen , Marto Jarrod A.
Published: October 2024

The eukaryotic RNA polymerase II (Pol II) multi-protein complex transcribes mRNA and coordinates several steps of co-transcriptional mRNA processing and chromatin modification. The largest Pol II subunit, Rpb1, has a C-terminal domain (CTD) comprising dozens of repeated heptad sequences (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), each containing five phospho-accepting amino acids. The CTD heptads are dynamically phosphorylated, creating specific patterns correlated with steps of transcription initiation, elongation, and termination. This CTD phosphorylation ‘code’ choreographs dynamic recruitment of important co-regulatory proteins during gene transcription. Genetic tools were used to engineer protease cleavage sites across the CTD (msCTD), creating tryptic peptides with unique sequences amenable to mass spectrometry analysis. However, phosphorylation isoforms within each msCTD sequence are difficult to resolve by standard reversed phase chromatography typically used for LC-MS/MS applications. Here, we use a panel of synthetic CTD phosphopeptides to explore the potential of hydrophilic interaction and electrostatic repulsion hydrophilic interaction (HILIC and ERLIC) chromatography as alternatives to reversed phase separation for CTD phosphopeptide analysis. Our results demonstrate that ERLIC provides improved performance for separation of singly- and doubly-phosphorylated CTD peptides for sequence analysis by LC-MS/MS. Analysis of native yeast msCTD confirms that phosphorylation on Ser5 and Ser2 represents the major endogenous phosphoisoforms. We expect this methodology will be especially useful in the investigation of pathways where multiple protein phosphorylation events converge in close proximity.
Motifs of human hippocampal and cortical high frequency oscillations structure processing and memory of naturalistic stimuli
Authors: Mishra Akash , Tostaeva Gelana , Nentwich Maximilian , Espinal Elizabeth , Markowitz Noah , Winfield Jalen , Freund Elizabeth , Gherman Sabina , Mehta Ashesh D. , Bickel Stephan
Published: October 2024

The discrete events of our narrative experience are organized by the neural substrate that underlies episodic memory. This narrative process is segmented into discrete units by event boundaries. This permits a replay process that acts to consolidate each event into a narrative memory. High frequency oscillations (HFOs) are a potential mechanism for synchronizing neural activity during these processes. Here, we use intracranial recordings from participants viewing and freely recalling a naturalistic stimulus. We show that hippocampal HFOs increase following event boundaries and that coincident hippocampal-cortical HFOs (co-HFOs) occur in cortical regions previously shown to underlie event segmentation (inferior parietal, precuneus, lateral occipital, inferior frontal cortices). We also show that event-specific patterns of co-HFOs that occur during event viewing re-occur following the subsequent three event boundaries (in decaying fashion) and also during recall. This is consistent with models that support replay as a mechanism for memory consolidation. Hence, HFOs may coordinate activity across brain regions serving widespread event segmentation, encode naturalistic memory, and bind representations to assemble memory of a coherent, continuous experience.