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2.
medRxiv ; 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-39040193

ABSTRACT

Long-standing hypertension (HTN) affects multiple organ systems and leads to pathologic arterial remodeling, which is driven largely by smooth muscle cell (SMC) plasticity. Although genome wide association studies (GWAS) have identified numerous variants associated with changes in blood pressure in humans, only a small percentage of these variants actually cause HTN. In order to identify relevant genes important in SMC function in HTN, we screened three separate human GWAS and Mendelian randomization studies to identify SNPs located within non-coding gene regions, focusing on genes encoding epigenetic enzymes, as these have been recently identified to control SMC fate in cardiovascular disease. We identified SNPs rs62059712 and rs74480102 in the promoter of the human JMJD3 gene and show that the minor C allele increases JMJD3 transcription in SMCs via increased SP1 binding to the JMJD3 promoter. Using our novel SMC-specific Jmjd3-deficient murine model ( Jmjd3 flox/flox Myh11 CreERT ), we show that loss of Jmjd3 in SMCs results in HTN, mechanistically, due to decreased EDNRB expression and a compensatory increase in EDNRA expression. As a translational corollary, through single cell RNA-sequencing (scRNA-seq) of human arteries, we found strong correlation between JMJD3 and EDNRB expression in SMCs. Further, we identified that JMJD3 is required for SMC-specific gene expression, and loss of JMJD3 in SMCs in the setting of HTN results in increased arterial remodeling by promoting the SMC synthetic phenotype. Our findings link a HTN-associated human DNA variant with regulation of SMC plasticity, revealing therapeutic targets that may be used in the screening and/or personalized treatment of HTN.

3.
JAMA Psychiatry ; 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-39018056

ABSTRACT

Importance: Suicide is the third-leading cause of death among US adolescents. Environmental and lifestyle factors influence suicidal behavior and can inform risk classification, yet quantifying and incorporating them in risk assessment presents a significant challenge for reproducibility and clinical translation. Objective: To quantify the aggregate contribution of environmental and lifestyle factors to youth suicide attempt risk classification. Design, Setting, and Participants: This was a cohort study in 3 youth samples: 2 national longitudinal cohorts from the US and the UK and 1 clinical cohort from a tertiary pediatric US hospital. An exposome-wide association study (ExWAS) approach was used to identify risk and protective factors and compute aggregate exposomic scores. Logistic regression models were applied to test associations and model fit of exposomic scores with suicide attempts in independent data. Youth from the Adolescent Brain Cognitive Development (ABCD) study, the UK Millennium Cohort Study (MCS), and the Children's Hospital of Philadelphia emergency department (CHOP-ED) were included in the study. Exposures: A single-weighted exposomic score that sums significant risk and protective environmental/lifestyle factors. Main Outcome and Measure: Self-reported suicide attempt. Results: A total of 40 364 youth were included in this analysis: 11 564 from the ABCD study (3 waves of assessment; mean [SD] age, 12.0 [0.7] years; 6034 male [52.2%]; 344 attempted suicide [3.0%]; 1154 environmental/lifestyle factors were included in the ABCD study), 9000 from the MCS cohort (mean [SD] age, 17.2 [0.3] years; 4593 female [51.0%]; 661 attempted suicide [7.3%]; 2864 environmental/lifestyle factors were included in the MCS cohort), and 19 800 from the CHOP-ED cohort (mean [SD] age, 15.3 [1.5] years; 12 937 female [65.3%]; 2051 attempted suicide [10.4%]; 36 environmental/lifestyle factors were included in the CHOP-ED cohort). In the ABCD discovery subsample, ExWAS identified 99 risk and protective exposures significantly associated with suicide attempt. A single weighted exposomic score that sums significant risk and protective exposures was associated with suicide attempt in an independent ABCD testing subsample (odds ratio [OR], 2.2; 95% CI, 2.0-2.6; P < .001) and explained 17.6% of the variance (based on regression pseudo-R2) in suicide attempt over and above that explained by age, sex, race, and ethnicity (2.8%) and by family history of suicide (6.3%). Findings were consistent in the MCS and CHOP-ED cohorts (explaining 22.6% and 19.3% of the variance in suicide attempt, respectively) despite clinical, demographic, and exposure differences. In all cohorts, compared with youth at the median quintile of the exposomic score, youth at the top fifth quintile were substantially more likely to have made a suicide attempt (OR, 4.3; 95% CI, 2.6-7.2 in the ABCD study; OR, 3.8; 95% CI, 2.7-5.3 in the MCS cohort; OR, 5.8; 95% CI, 4.7-7.1 in the CHOP-ED cohort). Conclusions and Relevance: Results suggest that exposomic scores of suicide attempt provided a generalizable method for risk classification that can be applied in diverse samples from clinical or population settings.

4.
bioRxiv ; 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38948807

ABSTRACT

Emerging antibiotic resistance requires continual improvement in the arsenal of antimicrobial drugs, especially the critical macrolide antibiotics. Formation of the macrolactone scaffold of these polyketide natural products is catalyzed by a modular polyketide synthase (PKS) thioesterase (TE). The TE accepts a linear polyketide substrate from the termina PKS acyl carrier protein to generate an acyl-enzyme adduct that is resolved by attack of a substrate hydroxyl group to form the macrolactone. Our limited mechanistic understanding of TE selectivity for a substrate nucleophile and/or water has hampered development of TEs as biocatalysts that accommodate a variety of natural and non-natural substrates. To understand how TEs direct the substrate nucleophile for macrolactone formation, acyl-enzyme intermediates were trapped as stable amides by substituting the natural serine OH with an amino group. Incorporation of the unnatural amino acid, 1,3-diaminopropionic acid (DAP), was tested with five PKS TEs. DAP-modified TEs (TE DAP ) from the pikromycin and erythromycin pathways were purified and tested with six full-length polyketide intermediates from three pathways. The erythromycin TE had permissive substrate selectivity, whereas the pikromycin TE was selective for its native hexaketide and heptaketide substrates. In a crystal structure of a native substrate trapped in pikromycin TE DAP , the linear heptaketide was curled in the active site with the nucleophilic hydroxyl group positioned 4 Å from the amide-enzyme linkage. The curled heptaketide displayed remarkable shape complementarity with the TE acyl cavity. The strikingly different shapes of acyl cavities in TEs of known structure, including those reported here for juvenimicin, tylosin and fluvirucin biosynthesis, provide new insights to facilitate TE engineering and optimization.

5.
Cancer Imaging ; 24(1): 89, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38972972

ABSTRACT

BACKGROUND: High b-value diffusion-weighted images (DWI) are used for detection of clinically significant prostate cancer (csPCa). This study qualitatively and quantitatively compares synthesized DWI (sDWI) to acquired (aDWI) for detection of csPCa. METHODS: One hundred fifty-one consecutive patients who underwent prostate MRI and biopsy were included in the study. Axial DWI with b = 0, 500, 1000, and 2000 s/mm2 using a 3T clinical scanner using a 32-channel phased-array body coil were acquired. We retrospectively synthesized DWI for b = 2000 s/mm2 via extrapolation based on mono-exponential decay, using b = 0 and b = 500 s/mm2 (sDWI500) and b = 0, b = 500 s/mm2, and b = 1000 s/mm2 (sDWI1000). Differences in signal intensity between sDWI and aDWI were evaluated within different regions of interest (prostate alone, prostate plus 5 mm, 30 mm and 70 mm margin and full field of view). The maximum DWI value within each ROI was evaluated for prediction of csPCa. Classification accuracy was compared to Restriction Spectrum Imaging restriction score (RSIrs), a previously validated biomarker based on multi-exponential DWI. Discrimination of csPCa was evaluated via area under the receiver operating characteristic curve (AUC). RESULTS: Within the prostate, mean ± standard deviation of percent mean differences between sDWI and aDWI signal were -46 ± 35% for sDWI1000 and -67 ± 24% for sDWI500. AUC for aDWI, sDWI500, sDWI1000, and RSIrs within the prostate 0.62[95% confidence interval: 0.53, 0.71], 0.63[0.54, 0.72], 0.65[0.56, 0.73] and 0.78[0.71, 0.86], respectively. CONCLUSION: sDWI is qualitatively comparable to aDWI within the prostate. However, hyperintense artifacts are introduced with sDWI in the surrounding pelvic tissue that interfere with quantitative cancer detection and might mask metastases. In the prostate, RSIrs yields superior quantitative csPCa detection than sDWI or aDWI.


Subject(s)
Diffusion Magnetic Resonance Imaging , Prostatic Neoplasms , Humans , Male , Prostatic Neoplasms/diagnostic imaging , Prostatic Neoplasms/pathology , Diffusion Magnetic Resonance Imaging/methods , Aged , Retrospective Studies , Middle Aged , Aged, 80 and over , Prostate/diagnostic imaging , Prostate/pathology
6.
Respir Care ; 2024 Jul 16.
Article in English | MEDLINE | ID: mdl-39013570

ABSTRACT

BACKGROUND: Mechanical ventilation is a common life-saving procedure but can lead to serious complications, including ARDS and oxygen toxicity. Nonadherence to lung-protective ventilation guidelines is common. We hypothesized that a respiratory therapist-driven mechanical ventilation bundle could increase adherence to lung-protective ventilation and decrease the incidence of pulmonary complications in the ICU. METHODS: A respiratory therapist-driven protocol was implemented on August 1, 2018, in all adult ICUs of a Midwestern academic tertiary center. The protocol targeted low tidal volume, adequate PEEP, limiting oxygen, adequate breathing frequency, and head of the bed elevation. Adherence to lung-protective guidelines and clinical outcomes were retrospectively observed in adult subjects admitted to the ICU and on ventilation for ≥ 24 h between January 2011 and December 2019. RESULTS: We included 666 subjects; 68.5% were in the pre-intervention group and 31.5% were in the post-intervention group. After adjusting for body mass index and intubation indication, a significant increase in overall adherence to lung-protective ventilation guidelines was observed in the post-intervention period (adjusted odds ratio 2.48, 95% CI 1.73-3.56). Fewer subjects were diagnosed with ARDS in the post-intervention group (adjusted odds ratio 0.22, 95% CI 0.08-0.65) than in the pre-intervention group. There was no difference in the incidence of ventilator-associated pneumonia, ventilator-free days, ICU mortality, or death within 1 month of ICU discharge. CONCLUSIONS: A respiratory therapist-driven protocol increased adherence to lung-protective mechanical ventilation guidelines in the ICU and was associated with decreased ARDS incidence.

7.
JAMA Netw Open ; 7(7): e2420034, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38958976

ABSTRACT

Importance: Prostate cancer, a leading cause of cancer death among men, urgently requires new prevention strategies, which may involve targeting men with an underlying genetic susceptibility. Objective: To explore differences in risk of early prostate cancer death among men with higher vs lower genetic risk to inform prevention efforts. Design, Setting, and Participants: This cohort study used a combined analysis of genotyped men without prostate cancer at inclusion and with lifestyle data in 2 prospective cohort studies in Sweden and the US, the Malmö Diet and Cancer Study (MDCS) and the Health Professionals Follow-Up Study (HPFS), followed up from 1991 to 2019. Data were analyzed between April 2023 and April 2024. Exposures: Men were categorized according to modifiable lifestyle behaviors and genetic risk. A polygenic risk score above the median or a family history of cancer defined men at higher genetic risk (67% of the study population); the remaining men were categorized as being at lower genetic risk. Main Outcomes and Measures: Prostate cancer death analyzed using time-to-event analysis estimating hazard ratios (HR), absolute risks, and preventable deaths by age. Results: Among the 19 607 men included for analysis, the median (IQR) age at inclusion was 59.0 (53.0-64.7) years (MDCS) and 65.1 (58.0-71.8) years (HPFS). During follow-up, 107 early (by age 75 years) and 337 late (after age 75 years) prostate cancer deaths were observed. Compared with men at lower genetic risk, men at higher genetic risk had increased rates of both early (HR, 3.26; 95% CI, 1.82-5.84) and late (HR, 2.26; 95% CI, 1.70-3.01) prostate cancer death, and higher lifetime risks of prostate cancer death (3.1% vs 1.3% [MDCS] and 2.3% vs 0.6% [HPFS]). Men at higher genetic risk accounted for 94 of 107 early prostate cancer deaths (88%), of which 36% (95% CI, 12%-60%) were estimated to be preventable through adherence to behaviors associated with a healthy lifestyle (not smoking, healthy weight, high physical activity, and a healthy diet). Conclusions and Relevance: In this 20-year follow-up study, men with a genetic predisposition accounted for the vast majority of early prostate cancer deaths, of which one-third were estimated to be preventable. This suggests that men at increased genetic risk should be targeted in prostate cancer prevention strategies.


Subject(s)
Genetic Predisposition to Disease , Prostatic Neoplasms , Humans , Male , Prostatic Neoplasms/genetics , Prostatic Neoplasms/mortality , Middle Aged , Aged , Sweden/epidemiology , Prospective Studies , Risk Factors , United States/epidemiology , Life Style , Cohort Studies
8.
Front Mol Neurosci ; 17: 1376128, 2024.
Article in English | MEDLINE | ID: mdl-38952419

ABSTRACT

Deafness-causing deficiencies in otoferlin (OTOF) have been addressed preclinically using dual adeno-associated virus (AAV)-based approaches. However, timing of transduction, recombination of mRNA, and protein expression with dual hybrid AAV methods methods have not previously been characterized. Here, we have established an ex vivo assay to determine the kinetics of dual-AAV mediated expression of OTOF in hair cells of the mouse utricle. We utilized two different recombinant vectors that comprise DB-OTO, one containing the 5' portion of OTOF under the control of the hair cell-specific Myo15 promoter, and the other the 3' portion of OTOF. We explored specificity of the Myo15 promoter in hair cells of the mouse utricle, established dose response characteristics of DB-OTO ex vivo in an OTOF-deficient mouse model, and demonstrated tolerability of AAV1 in utricular hair cells. Furthermore, we established deviations from a one-to-one ratio of 5' to 3' vectors with little impact on recombined OTOF. Finally, we established a plateau in quantity of recombined OTOF mRNA and protein expression by 14 to 21 days ex vivo with comparable recovery timing to that in vivo model. These findings demonstrate the utility of an ex vivo model system for exploring expression kinetics and establish in vivo and ex vivo recovery timing of dual AAV-mediated OTOF expression.

9.
Nat Commun ; 15(1): 6343, 2024 Jul 27.
Article in English | MEDLINE | ID: mdl-39068174

ABSTRACT

Clinical success with poly (ADP-ribose) polymerase inhibitors (PARPi) is impeded by inevitable resistance and associated cytotoxicity. Depletion of Amplified in Liver Cancer 1 (ALC1), a chromatin-remodeling enzyme, can overcome these limitations by hypersensitizing BReast CAncer genes 1/2 (BRCA1/2) mutant cells to PARPi. Here, we demonstrate that PARPi hypersensitivity upon ALC1 loss is reliant on its role in promoting the repair of chromatin buried abasic sites. We show that ALC1 enhances the ability of the abasic site processing enzyme, Apurinic/Apyrimidinic endonuclease 1 (APE1) to cleave nucleosome-occluded abasic sites. However, unrepaired abasic sites in ALC1-deficient cells are readily accessed by APE1 at the nucleosome-free replication forks. APE1 cleavage leads to fork breakage and trapping of PARP1/2 upon PARPi treatment, resulting in hypersensitivity. Collectively, our studies reveal how cells overcome the chromatin barrier to repair abasic lesions and uncover cleavage of abasic sites as a mechanism to overcome limitations of PARPi.


Subject(s)
BRCA1 Protein , BRCA2 Protein , DNA Repair , DNA-(Apurinic or Apyrimidinic Site) Lyase , Poly(ADP-ribose) Polymerase Inhibitors , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Humans , Cell Line, Tumor , BRCA1 Protein/metabolism , BRCA1 Protein/genetics , BRCA1 Protein/deficiency , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , BRCA2 Protein/metabolism , BRCA2 Protein/genetics , BRCA2 Protein/deficiency , DNA Repair/drug effects , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly (ADP-Ribose) Polymerase-1/genetics , Female , Chromatin/metabolism , Mutation , DNA Damage/drug effects , Breast Neoplasms/genetics , Breast Neoplasms/drug therapy , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , DNA Replication/drug effects , Nucleosomes/metabolism , DNA Helicases , DNA-Binding Proteins
10.
Orthop Nurs ; 43(4): 218-222, 2024.
Article in English | MEDLINE | ID: mdl-39047274

ABSTRACT

Total knee arthroplasty (TKA) is an orthopaedic operation that improves quality of life and reduces pain in patients with disabling arthritis of the knee. One commonly recognized complication is flexion contracture of the knee. Early physical therapy helps prevent flexion contracture and improve range of motion (ROM) postoperatively. This study evaluated postoperative sleeping position and its effect on terminal knee extension and ROM following primary TKA. We hypothesized that patients who slept in the supine position would achieve earlier knee extension and greater ROM when compared to those in the lateral recumbent position. A total of 150 consecutive primary TKAs were performed by a single surgeon (J.M.C.) from April 2014 to December 2014. The data were collected prospectively to determine preoperative ROM, postoperative ROM, and sleeping position. Mean postoperative terminal extension ROM at 1 month was 2.9 degrees in the supine group versus 6.0 degrees (p< .001) in the lateral group. No significant demographic differences between the two groups at baseline were found. Our results demonstrate that sleeping position affects initial postoperative terminal extension, however, not overall ROM. We found a statistically significant difference in extension when comparing patients in the supine versus lateral group. Patients who slept in the lateral position lacked 6 degrees of extension which is greater than the 5 degrees needed for normal gait mechanics. Those in the supine group lacked 2.9 degrees of extension, allowing for normal gait mechanics. This study identifies an easy, effective means of increasing patients initial ability to achieve knee extension and satisfaction following TKA.


Subject(s)
Arthroplasty, Replacement, Knee , Range of Motion, Articular , Sleep , Humans , Arthroplasty, Replacement, Knee/methods , Arthroplasty, Replacement, Knee/adverse effects , Female , Male , Aged , Sleep/physiology , Prospective Studies , Middle Aged , Knee Joint/physiopathology , Knee Joint/surgery , Postoperative Period , Quality of Life , Posture/physiology
11.
Am J Gastroenterol ; 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38976379

ABSTRACT

INTRODUCTION: Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is frequently used to risk-stratify pancreatic cystic lesions (PCLs). Rising PCL incidence and developments in tissue acquisition and specimen analysis necessitate updated appraisal of EUS-FNA safety, particularly the risk of postprocedure pancreatitis, the most common EUS-FNA-related adverse event. Our systematic review aims to accurately quantify the risk of EUS-FNA-related pancreatitis to best inform decisions regarding EUS-FNA's optimal role in PCL workup. METHODS: We performed systematic searches in 4 databases from inception to April 2024 for original English-language studies investigating EUS-FNA-related pancreatitis. We extracted data on demographics and EUS-FNA-related pancreatitis risk, severity, and risk factors. These were meta-analyzed through the DerSimonian Laird Method using a random-effects model. Meta-regression of pancreatitis risk was performed to delineate associations with clinical and procedural characteristics. RESULTS: Sixty-four studies comprised 8,086 patients and reported 110 EUS-FNA-related pancreatitis events. Pooled risk of EUS-FNA-related pancreatitis was 1.4% (95% confidence intervals, -0.8% to 3.5%; I2 = 0.00), which was predominantly of mild severity (67%) and uniformly nonfatal. Pancreatitis risk lacked significant association with sample size, age, sex, cyst size, needle caliber, or passes, although we noted trends toward higher risk in studies published after 2015, those using higher gauge needles (19 G vs 22 G/25 G), and those performing EUS-guided through-the-needle biopsy. DISCUSSION: We note with high certainty that pancreatitis after EUS-FNA of PCLs is infrequent and mild in severity with no mortality in the included cohort. EUS-guided through-the-needle biopsy may serve as a significant risk factor for EUS-FNA-related pancreatitis risk; however, further studies are needed to delineate other predisposing characteristics.

12.
Langmuir ; 2024 Jul 27.
Article in English | MEDLINE | ID: mdl-39067033

ABSTRACT

The use of nanoparticle surface chemistry to direct metal deposition has been well-studied in the modification of metal nanoparticle substrates but is not yet well-established for metal chalcogenide particle substrates, although integration of these particles into nanoheterostructures is of high interest. In this report, we investigate the effect of Cu2-xSe surface chemistry on the morphology of metal deposition on these plasmonic semiconductor nanoparticles. Specifically, we functionalize Cu2-xSe nanoparticles with a suite of 12 different ligands and investigate how different aspects of the ligand structure do or do not impact the morphology and extent of subsequent metal deposition on the Cu2-xSe surface. Surprisingly, our results indicate that the morphology of the resulting metal deposits and the extent of metal deposition onto the existing Cu2-xSe particle substrate are indistinguishable for the majority of ligands tested. An exception to these findings is observed for particles functionalized by quaternary alkylammonium bromides, which exhibit statistically distinct metal deposition patterns compared to all other ligands tested. We hypothesize that this unique behavior is due to a cooperative binding mechanism of the quaternary alkylammonium bromides to the surface of copper selenide. Taken together, these results yield both new strategies for controlling postsynthetic modification of copper selenide nanoparticles and also reveal limitations of surface chemistry-based approaches for this system.

13.
Prim Care ; 51(3): 523-533, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39067976

ABSTRACT

Sports endocrinology holds a unique importance in understanding and optimizing an active and healthy lifestyle. Active patients with diabetes will need to consider modifying medications, especially insulin. The use of the dual energy x-ray absorptiometry and Fracture Risk Assessment Tool scores is important as both initiate and monitor bone health treatment. Menstrual disorders and energy imbalances are some special concerns when treating female athletes, calling for a multidisciplinary treatment team. Performance agents are popular and have made their way into recreational sports.


Subject(s)
Sports Medicine , Humans , Female , Sports , Endocrinology/organization & administration , Absorptiometry, Photon , Bone Density , Fractures, Bone/therapy , Osteoporosis/therapy
14.
Orthopedics ; : 1-6, 2024 Jul 31.
Article in English | MEDLINE | ID: mdl-39073045

ABSTRACT

BACKGROUND: Patients undergoing total joint arthroplasty (TJA) may receive unexpected medical bills. Such "surprise" bills may cause financial hardship for patients, which prompted policymakers to pass the No Surprises Act. The purpose of this study was to determine the incidence of surprise bills for patients undergoing TJA and the effect of surprise billing on patient satisfaction. MATERIALS AND METHODS: This was a retrospective study of patients who underwent a primary total hip arthroplasty (THA) or total knee arthroplasty (TKA) at a large multi-state institution. Patients completed a questionnaire regarding the incidence of surprise bills after their surgery, details of those bills, and how the bills affected their surgical satisfaction. Independent predictors for receiving a surprise bill were assessed through a multivariate regression analysis. RESULTS: Twelve percent of participants received at least one surprise bill after their TJA. The most common surprise bill came from the surgical facility (48%), followed by anesthesia (36%). Multivariate logistic regression analysis identified older age and Black race to be independent predictors of surprise billing. Furthermore, surgery occurring after the No Surprises Act bill enforcement on January 1, 2022, was found to increase a patient's likelihood of receiving a surprise bill (P=.039, effect size=0.18). Patients who received a surprise bill reported being significantly less satisfied with their surgery (P=.002, effect size=0.45). Forty-nine percent of patients with a surprise bill felt their billing negatively affected their surgical satisfaction. CONCLUSION: Surprise billing continues to occur after TJA and can negatively affect patient satisfaction. Although surgeons may be unable to limit the amount of bills patients receive postoperatively, increased communication and education regarding the perioperative billing process may prove to be beneficial for both patient satisfaction and the physician-patient relationship. [Orthopedics. 20XX;4X(X):XXX-XXX.].

15.
Nature ; 632(8023): 166-173, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39020176

ABSTRACT

Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Protein Domains , Transcription Factors , Transcriptional Activation , Arabidopsis/genetics , Arabidopsis/metabolism , Transcriptional Activation/genetics , Transcription Factors/metabolism , Transcription Factors/chemistry , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/chemistry , Gene Expression Regulation, Plant , Indoleacetic Acids/metabolism , Proteome/metabolism , Proteome/genetics , Molecular Sequence Annotation , Conserved Sequence
16.
BJUI Compass ; 5(6): 593-601, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38873351

ABSTRACT

Introduction: Although prostate magnetic resonance imaging (MRI) is commonly used in the diagnosis, staging and active surveillance of prostate cancer, little is known about patient perspectives on MRI. Methods: We performed a qualitative study consisting of in-depth, semi-structured interviews of patients with low- and intermediate-risk prostate cancer managed with active surveillance. Interviews focused on experiences with and knowledge of prostate MRI and MRI-ultrasound fusion biopsy during active surveillance. We purposively sampled patients who received prostate MRI as part of their clinical care, conducted interviews until reaching thematic saturation and performed conventional content analysis to analyse data. Results: Twenty patients aged 51-79 years (mean = 68 years) participated in the study. At diagnosis, 17 (85%) had a Gleason grade group 1, and three (15%) had a grade group 2 tumour. Overall, participants viewed prostate MRI as a valuable tool that accurately localizes and monitors prostate cancer over time, and they considered prostate MRI central to active surveillance monitoring. We identified five thematic categories related to MRI use: (1) the experiential aspects of undergoing an MRI scan; (2) the experience of visualizing one's own prostate and prostate cancer; (3) adequacy of provider explanations of MRI results; (4) confidence in prostate MRI in decision-making; and (5) the role of prostate MRI in longitudinal follow-up, including an interest in using MRI to modify the timing of, or replace, prostate biopsy. Conclusion: Patients value prostate MRI as a tool that enhances their confidence in the initial diagnosis and monitoring of prostate cancer. This work can inform future studies to optimize patient experience, education and counselling during active surveillance for prostate cancer.

17.
bioRxiv ; 2024 May 29.
Article in English | MEDLINE | ID: mdl-38854152

ABSTRACT

Precise control of morphogen signaling levels is essential for proper development. An outstanding question is: what mechanisms ensure proper morphogen activity and correct cellular responses? Previous work has identified Semaphorin (SEMA) receptors, Neuropilins (NRPs) and Plexins (PLXNs), as positive regulators of the Hedgehog (HH) signaling pathway. Here, we provide evidence that NRPs and PLXNs antagonize Wnt signaling in both fibroblasts and epithelial cells. Further, Nrp1/2 deletion in fibroblasts results in elevated baseline Wnt pathway activity and increased maximal responses to Wnt stimulation. Notably, and in contrast to HH signaling, SEMA receptor-mediated Wnt antagonism is independent of primary cilia. Mechanistically, PLXNs and NRPs act downstream of Dishevelled (DVL) to destabilize ß-catenin (CTNNB1) in a proteosome-dependent manner. Further, NRPs, but not PLXNs, act in a GSK3ß/CK1-dependent fashion to antagonize Wnt signaling, suggesting distinct repressive mechanisms for these SEMA receptors. Overall, this study identifies SEMA receptors as novel Wnt pathway antagonists that may also play larger roles integrating signals from multiple inputs.

18.
Article in English | MEDLINE | ID: mdl-38837187

ABSTRACT

BACKGROUND: The mean wait time for new patient appointments has been growing across specialties, including obstetrics and gynecology, in recent years. This study aimed to assess the impact of insurance type (Medicaid versus commercial insurance) on new patient appointment wait times in general obstetrics and gynecology practices. METHODS: A cross-sectional study used covert mystery calls to general obstetrician gynecologists. Physicians were selected from the American College of Obstetricians and Gynecologists directory and stratified by districts to ensure nationwide representation. Wait times for new patient appointments were collected and analyzed. RESULTS: Regardless of insurance type, the mean wait time for all obstetrician gynecologists was 29.9 business days. Medicaid patients experienced a marginally longer wait time of 4.8% (Ratio: 1.048). While no statistically significant difference in wait times based on insurance type was observed (P=0.39), the data revealed other impactful factors. Younger physicians and those in university-based practices had longer wait times. The gender of the physician also influenced wait times, with female physicians having a mean wait time of 34.7 days compared to 22.7 days for male physicians (P=0.03). Additionally, geographical variations were noted, with physicians in American College of Obstetricians and Gynecologists District I (Atlantic Provinces, CT, ME, MA, NH, RI, VT) having the longest mean wait times and those in District III (DE, NJ, PA) the shortest. CONCLUSIONS: While the type of insurance did not significantly influence the wait times for general obstetrics and gynecology appointments, physician demographic and geographic factors did.

19.
Psychol Med ; : 1-11, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38828712

ABSTRACT

BACKGROUND: Neurocognitive dysfunction is a transdiagnostic finding in psychopathology, but relationships among cognitive domains and general and specific psychopathology dimensions remain unclear. This study aimed to examine associations between cognition and psychopathology dimensions in a large youth cohort. METHOD: The sample (N = 9350; age 8-21 years) was drawn from the Philadelphia Neurodevelopmental Cohort. Data from structured clinical interviews were modeled using bifactor confirmatory factor analysis (CFA), resulting in an overall psychopathology ('p') factor score and six orthogonal psychopathology dimensions: dysphoria/distress, obsessive-compulsive, behavioral/externalizing, attention-deficit/hyperactivity, phobias, and psychosis. Neurocognitive data were aggregated using correlated-traits CFA into five factors: executive functioning, memory, complex cognition, social cognition, and sensorimotor speed. We examined relationships among specific and general psychopathology dimensions and neurocognitive factors. RESULTS: The final model showed both overall and specific associations between cognitive functioning and psychopathology, with acceptable fit (CFI = 0.91; TLI = 0.90; RMSEA = 0.024; SRMR = 0.054). Overall psychopathology and most psychopathology dimensions were negatively associated with neurocognitive functioning (phobias [p < 0.0005], behavioral/externalizing [p < 0.0005], attention-deficit/hyperactivity [p < 0.0005], psychosis [p < 0.0005 to p < 0.05]), except for dysphoria/distress and obsessive-compulsive symptoms, which were positively associated with complex cognition (p < 0.05 and p < 0.01, respectively). CONCLUSION: By modeling a broad range of cognitive and psychopathology domains in a large, diverse sample of youth, we found aspects of neurocognitive functioning shared across clinical phenotypes, as well as domain-specific patterns. Findings support transdiagnostic examination of cognitive performance to parse variability in the link between neurocognitive functioning and clinical phenotypes.

20.
Article in English | MEDLINE | ID: mdl-38869751

ABSTRACT

Accumulating evidence supports the presence of a general psychopathology dimension, the p factor ('p'). Despite growing interest in the p factor, questions remain about how p is assessed. Although multi-informant assessment of psychopathology is commonplace in clinical research and practice with children and adolescents, almost no research has taken a multi-informant approach to studying youth p or has examined the degree of concordance between parent and youth reports. Further, estimating p requires assessment of a large number of symptoms, resulting in high reporter burden that may not be feasible in many clinical and research settings. In the present study, we used bifactor multidimensional item response theory models to estimate parent- and adolescent-reported p in a large community sample of youth (11-17 years) and parents (N = 5,060 dyads). We examined agreement between parent and youth p scores and associations with assessor-rated youth global functioning. We also applied computerized adaptive testing (CAT) simulations to parent and youth reports to determine whether adaptive testing substantially alters agreement on p or associations with youth global functioning. Parent-youth agreement on p was moderate (r =.44) and both reports were negatively associated with youth global functioning. Notably, 7 out of 10 of the highest loading items were common across reporters. CAT reduced the average number of items administered by 57%. Agreement between CAT-derived p scores was similar to the full form (r =.40) and CAT scores were negatively correlated with youth functioning. These novel results highlight the promise and potential clinical utility of a multi-informant p factor approach.

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