ABSTRACT
PURPOSE: To evaluate reproducibility and interlobar agreement of intravoxel incoherent motion (IVIM) quantification in the liver across field strengths and MR scanners with different gradient hardware. METHODS: Cramer-Rao lower bound optimization was performed to determine optimized monopolar and motion-robust 2D (b-value and first-order motion moment [M1]) IVIM-DWI acquisitions. Eleven healthy volunteers underwent diffusion MRI of the liver, where each optimized acquisition was obtained five times across three MRI scanners. For each data set, IVIM estimates (diffusion coefficient (D), pseudo-diffusion coefficients ( d 1 * $$ {d}_1^{\ast } $$ and d 2 * $$ {d}_2^{\ast } $$ ), blood velocity SDs (Vb1 and Vb2), and perfusion fractions [f1 and f2]) were obtained in the right and left liver lobes using two signal models (pseudo-diffusion and M1-dependent physical) with and without T2 correction (fc1 and fc2) and three fitting techniques (tri-exponential region of interest-based full and segmented fitting and blood velocity SD distribution fitting). Reproducibility and interlobar agreement were compared across methods using within-subject and pairwise coefficients of variation (CVw and CVp), paired sample t-tests, and Bland-Altman analysis. RESULTS: Using a combination of motion-robust 2D (b-M1) data acquisition, M1-dependent physical signal modeling with T2 correction, and blood velocity SD distribution fitting, multiscanner reproducibility with median CVw = 5.09%, 11.3%, 9.20%, 14.2%, and 12.6% for D, Vb1, Vb2, fc1, and fc2, respectively, and interlobar agreement with CVp = 8.14%, 11.9%, 8.50%, 49.9%, and 42.0%, respectively, was achieved. CONCLUSION: Recently proposed advanced IVIM acquisition, signal modeling, and fitting techniques may facilitate reproducible IVIM quantification in the liver, as needed for establishment of IVIM-based quantitative biomarkers for detection, staging, and treatment monitoring of diseases.
ABSTRACT
Human cognitive capacities that enable flexible cooperation may have evolved in parallel with the expansion of frontoparietal cortical networks, particularly the default network. Conversely, human antisocial behavior and trait antagonism are broadly associated with reduced activity, impaired connectivity, and altered structure of the default network. Yet, behaviors like interpersonal manipulation and exploitation may require intact or even superior social cognition. Using a reinforcement learning model of decision-making on a modified trust game, we examined how individuals adjusted their cooperation rate based on a counterpart's cooperation and social reputation. We observed that learning signals in the default network updated the predicted utility of cooperation or defection and scaled with reciprocal cooperation. These signals were weaker in callous (vs. compassionate) individuals but stronger in those who were more exploitative (vs. honest and humble). Further, they accounted for associations between exploitativeness, callousness, and reciprocal cooperation. Separately, behavioral sensitivity to prior reputation was reduced in callous but not exploitative individuals and selectively scaled with responses of the medial temporal subsystem of the default network. Overall, callousness was characterized by blunted behavioral and default network sensitivity to cooperation incentives. Exploitativeness predicted heightened sensitivity to others' cooperation but not social reputation. We speculate that both compassion and exploitativeness may reflect cognitive adaptations to social living, enabled by expansion of the default network in anthropogenesis.
Subject(s)
Cooperative Behavior , Humans , Male , Female , Adult , Motivation/physiology , Decision Making/physiology , Trust/psychology , Young Adult , Nerve Net/physiology , Empathy/physiology , Brain/physiology , Brain/diagnostic imagingABSTRACT
Philanthropic donations are an increasingly important funding source for academic medical centers. Minimal published data is available about factors that influence alumni donations to residency programs. We performed a cross-sectional analysis of a single-site dermatology and combined internal medicine-dermatology residency programs to assess factors impacting alumni donations. Donors tended to have graduated less recently (only 20% graduating after 2010) and practice in the same region of their alma mater (50%). Respondents preferred funds be allocated to resident needs over needs of medical students. Strategically engaging senior alumni and offering fund allocation opportunities could increase philanthropy, with alumni perceptions of the residency program warranting further investigation for their impact on donation decisions.
Subject(s)
Dermatology , Internship and Residency , Humans , Dermatology/education , Dermatology/statistics & numerical data , Internship and Residency/statistics & numerical data , Cross-Sectional Studies , Surveys and Questionnaires/statistics & numerical data , Students, Medical/statistics & numerical data , Female , Male , Internal Medicine/education , Internal Medicine/statistics & numerical data , Academic Medical Centers/statistics & numerical dataSubject(s)
Pathologists , Humans , Pathology, Clinical/methods , Pathology, Clinical/trends , Physician Assistants , PathologyABSTRACT
SMARCA4-deficient undifferentiated thoracic tumors are a rare phenomenon. A 40-year-old male was newly diagnosed with SMARCA4-deficient undifferentiated non-small cell lung cancer. He had a history of heavy smoking and job-related exposure to metal dust and melted nickel. CT imaging showed numerous right-sided pleural masses and soft tissue plaques, but no metastases. CT-guided biopsy of a pleural mass confirmed the diagnosis. He was prescribed six cycles of carboplatin paclitaxel, and follow-up imaging showed largely stable disease. Treatment was changed to nivolumab due to shortness of breath, and he received one cycle of nivolumab without considerable side effects. Unfortunately, during the second cycle of his nivolumab, the patient presented with new weakness. Imaging showed spinal cord metastasis and he underwent a laminectomy; he was subsequently followed up as an outpatient. The objective of this publication was to explore SMARCA4-deficient undifferentiated thoracic tumors, other related SMARCA4-deficient tumors, and their overall pattern of presentation. The genetic aberrations of this case are compared to recent publications that also discuss genetic aberrations commonly occurring with this disease process, with an ultimate goal of hastening detection and adding to the library of treatment results.
Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Sarcoma , Thoracic Neoplasms , Male , Humans , Adult , Nivolumab , Lung Neoplasms/genetics , Lung Neoplasms/diagnosis , Sarcoma/pathology , Thoracic Neoplasms/pathology , Biomarkers, Tumor/genetics , DNA Helicases/genetics , Nuclear Proteins/genetics , Transcription Factors/geneticsABSTRACT
Interferon Stimulated Gene (ISG) expression plays a key role in the control of viral replication and development of a robust adaptive response. Understanding this dynamic relationship between the pathogen and host is critical to our understanding of viral life-cycles and development of potential novel anti-viral strategies. Traditionally, plasmid based exogenous prompter driven expression of ISGs has been used to investigate anti-viral ISG function, however there are deficiencies in this approach. To overcome this, we investigated the utility of CRISPR activation (CRISPRa), which allows for targeted transcriptional activation of a gene from its endogenous promoter. Using the CRISPRa-SAM system to induce targeted expression of a panel of anti-viral ISGs we showed robust induction of mRNA and protein expression. We then employed our CRISPRa-SAM ISG panel in several antiviral screen formats to test for the ability of ISGs to prevent viral induced cytopathic cell death (CPE) and replication of Dengue Virus (DENV), Zika Virus (ZIKV), West Nile Virus Kunjin (WNVKUN), Hepatitis A Virus (HAV) and Human Coronavirus 229E (HCoV-229E). Our CRISPRa approach confirmed the anti-viral activity of ISGs like IFI6, IFNß and IFNλ2 that prevented viral induced CPE, which was supported by high-content immunofluorescence imaging analysis. This work highlights CRISPRa as a rapid, agile, and powerful methodology to identify and characterise ISGs and viral restriction factors.
Subject(s)
Antiviral Agents , Interferons , Virus Replication , Humans , Interferons/metabolism , Interferons/genetics , Antiviral Agents/pharmacology , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , HEK293 Cells , Transcriptional Activation/genetics , AnimalsABSTRACT
Quantitative, empirical approaches to establishing the structure of psychopathology hold promise to improve on traditional psychiatric classification systems. The Hierarchical Taxonomy of Psychopathology (HiTOP) is a framework that summarizes the substantial and growing body of quantitative evidence on the structure of psychopathology. To achieve its aims, HiTOP must incorporate emerging research in a systematic, ongoing fashion. In this article, we describe the historical context and grounding of the principles and procedures for revising the HiTOP framework. Informed by strengths and shortcomings of previous classification systems, the proposed revisions protocol is a formalized system focused around three pillars: (a) prioritizing systematic evaluation of quantitative evidence by a set of transparent criteria and processes, (b) balancing stability with flexibility, and (c) promoting inclusion over gatekeeping in all aspects of the process. We detail how the revisions protocol will be applied in practice, including the scientific and administrative aspects of the process. Additionally, we describe areas of the HiTOP structure that will be a focus of early revisions and outline challenges for the revisions protocol moving forward. The proposed revisions protocol is designed to ensure that the HiTOP framework reflects the current state of scientific knowledge on the structure of psychopathology and fulfils its potential to advance clinical research and practice. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Subject(s)
Knowledge , Mental Disorders , Humans , Databases, Factual , Psychopathology , Research Design , Mental Disorders/diagnosisABSTRACT
Deep learning (DL) reconstruction techniques to improve MR image quality are becoming commercially available with the hope that they will be applicable to multiple imaging application sites and acquisition protocols. However, before clinical implementation, these methods must be validated for specific use cases. In this work, the quality of standard-of-care (SOC) T2w and a high-spatial-resolution (HR) imaging of the breast were assessed both with and without prototype DL reconstruction. Studies were performed using data collected from phantoms, 20 retrospectively collected SOC patient exams, and 56 prospectively acquired SOC and HR patient exams. Image quality was quantitatively assessed via signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and edge sharpness. Qualitatively, all in vivo images were scored by either two or four radiologist readers using 5-point Likert scales in the following categories: artifacts, perceived sharpness, perceived SNR, and overall quality. Differences in reader scores were tested for significance. Reader preference and perception of signal intensity changes were also assessed. Application of the DL resulted in higher average SNR (1.2-2.8 times), CNR (1.0-1.8 times), and image sharpness (1.2-1.7 times). Qualitatively, the SOC acquisition with DL resulted in significantly improved image quality scores in all categories compared to non-DL images. HR acquisition with DL significantly increased SNR, sharpness, and overall quality compared to both the non-DL SOC and the non-DL HR images. The acquisition time for the HR data only required a 20% increase compared to the SOC acquisition and readers typically preferred DL images over non-DL counterparts. Overall, the DL reconstruction demonstrated improved T2w image quality in clinical breast MRI.
Subject(s)
Deep Learning , Humans , Retrospective Studies , Magnetic Resonance Imaging/methods , Breast/diagnostic imaging , Signal-To-Noise RatioABSTRACT
The Hypoxia Inducible Factor (HIF) transcription factors are imperative for cell adaption to low oxygen conditions and development; however, they also contribute to ischaemic disease and cancer. To identify novel genetic regulators which target the HIF pathway or small molecules for therapeutic use, cell-based reporter systems are commonly used. Here, we present a new, highly sensitive and versatile reporter system, NanoFIRE: a NanoLuciferase and Fluorescent Integrated Reporter Element. Under the control of a Hypoxic Response Element (HRE-NanoFIRE), this system is a robust sensor of HIF activity within cells and potently responds to both hypoxia and chemical inducers of the HIF pathway in a highly reproducible and sensitive manner, consistently achieving 20 to 150-fold induction across different cell types and a Z' score > 0.5. We demonstrate that the NanoFIRE system is adaptable via substitution of the response element controlling NanoLuciferase and show that it can report on the activity of the transcriptional regulator Factor Inhibiting HIF, and an unrelated transcription factor, the Progesterone Receptor. Furthermore, the lentivirus-mediated stable integration of NanoFIRE highlights the versatility of this system across a wide range of cell types, including primary cells. Together, these findings demonstrate that NanoFIRE is a robust reporter system for the investigation of HIF and other transcription factor-mediated signalling pathways in cells, with applications in high throughput screening for the identification of novel small molecule and genetic regulators.
Subject(s)
Gene Expression Regulation , Transcription Factors , Humans , Transcription Factors/genetics , Response Elements , Nuclear Proteins/genetics , Hypoxia/genetics , Cell Hypoxia/geneticsABSTRACT
Cerebritis may present with encephalopathy, seizures, localizing neurologic deficits, or death. Topical betadine has a high iodine content and application to open scalp wounds may cause sterile cerebritis.
ABSTRACT
Episodic memory-based decision-making requires top-down medial prefrontal cortex and hippocampal interactions. This integrated prefrontal-hippocampal memory state is thought to be organized by synchronized network oscillations and mediated by connectivity with the thalamic nucleus reuniens (RE). Whether and how the RE synchronizes prefrontal-hippocampal networks in memory, however, remains unknown. Here, we recorded local field potentials from the prefrontal-RE-hippocampal network while rats engaged in a nonspatial sequence memory task, thereby isolating memory-related activity from running-related oscillations. We found that synchronous prefrontal-hippocampal beta bursts (15-30 Hz) dominated during memory trials, whereas synchronous theta activity (6-12 Hz) dominated during non-memory-related running. Moreover, RE beta activity appeared first, followed by prefrontal and hippocampal synchronized beta, suggesting that prefrontal-hippocampal beta could be driven by the RE. To test whether the RE is capable of driving prefrontal-hippocampal beta synchrony, we used an optogenetic approach (retroAAV-ChR2). RE activation induced prefrontal-hippocampal beta coherence and reduced theta coherence, matching the observed memory-driven network state in the sequence task. These findings are the first to demonstrate that the RE contributes to memory by driving transient synchronized beta in the prefrontal-hippocampal system, thereby facilitating interactions that underlie memory-based decision-making.
Subject(s)
Midline Thalamic Nuclei , Prefrontal Cortex , Rats , Animals , Midline Thalamic Nuclei/physiology , Prefrontal Cortex/physiology , Hippocampus/physiology , Thalamic Nuclei , Neural Pathways/physiologyABSTRACT
The evolution of human social cognitive capacities such as mentalizing was associated with the expansion of frontoparietal cortical networks, particularly the default network. Mentalizing supports prosocial behaviors, but recent evidence indicates it may also serve a darker side of human social behavior. Using a computational reinforcement learning model of decision-making on a social exchange task, we examined how individuals optimized their approach to social interactions based on a counterpart's behavior and prior reputation. We found that learning signals encoded in the default network scaled with reciprocal cooperation and were stronger in individuals who were more exploitative and manipulative, but weaker in those who were more callous and less empathic. These learning signals, which help to update predictions about others' behavior, accounted for associations between exploitativeness, callousness, and social reciprocity. Separately, we found that callousness, but not exploitativeness, was associated with a behavioral insensitivity to prior reputation effects. While the entire default network was involved in reciprocal cooperation, sensitivity to reputation was selectively related to the activity of the medial temporal subsystem. Overall, our findings suggest that the emergence of social cognitive capacities associated with the expansion of the default network likely enabled humans to not only cooperate effectively with others, but to exploit and manipulate others as well.
ABSTRACT
Graphically prescribed patient-specific imaging volumes and local pre-scan volumes are routinely placed by MRI technologists to optimize image quality. However, manual placement of these volumes by MR technologists is time-consuming, tedious, and subject to intra- and inter-operator variability. Resolving these bottlenecks is critical with the rise in abbreviated breast MRI exams for screening purposes. This work proposes an automated approach for the placement of scan and pre-scan volumes for breast MRI. Anatomic 3-plane scout image series and associated scan volumes were retrospectively collected from 333 clinical breast exams acquired on 10 individual MRI scanners. Bilateral pre-scan volumes were also generated and reviewed in consensus by three MR physicists. A deep convolutional neural network was trained to predict both the scan and pre-scan volumes from the 3-plane scout images. The agreement between the network-predicted volumes and the clinical scan volumes or physicist-placed pre-scan volumes was evaluated using the intersection over union, the absolute distance between volume centers, and the difference in volume sizes. The scan volume model achieved a median 3D intersection over union of 0.69. The median error in scan volume location was 2.7 cm and the median size error was 2%. The median 3D intersection over union for the pre-scan placement was 0.68 with no significant difference in mean value between the left and right pre-scan volumes. The median error in the pre-scan volume location was 1.3 cm and the median size error was -2%. The average estimated uncertainty in positioning or volume size for both models ranged from 0.2 to 3.4 cm. Overall, this work demonstrates the feasibility of an automated approach for the placement of scan and pre-scan volumes based on a neural network model.
Subject(s)
Image Processing, Computer-Assisted , Neural Networks, Computer , Humans , Image Processing, Computer-Assisted/methods , Retrospective Studies , Breast/diagnostic imaging , Magnetic Resonance Imaging/methodsABSTRACT
Cognitive behavioral therapy (CBT) is often recommended as a first-line treatment in depression. However, access to CBT remains limited, and up to 50% of patients do not benefit from this therapy. Identifying biomarkers that can predict which patients will respond to CBT may assist in designing optimal treatment allocation strategies. In a Canadian Biomarker Integration Network for Depression (CAN-BIND) study, forty-one adults with depression were recruited to undergo a 16-week course of CBT with thirty having resting-state electroencephalography (EEG) recorded at baseline and week 2 of therapy. Successful clinical response to CBT was defined as a 50% or greater reduction in Montgomery-Åsberg Depression Rating Scale (MADRS) score from baseline to post-treatment completion. EEG relative power spectral measures were analyzed at baseline, week 2, and as early changes from baseline to week 2. At baseline, lower relative delta (0.5-4 Hz) power was observed in responders. This difference was predictive of successful clinical response to CBT. Furthermore, responders exhibited an early increase in relative delta power and a decrease in relative alpha (8-12 Hz) power compared to non-responders. These changes were also found to be good predictors of response to the therapy. These findings showed the potential utility of resting-state EEG in predicting CBT outcomes. They also further reinforce the promise of an EEG-based clinical decision-making tool to support treatment decisions for each patient.
Subject(s)
Cognitive Behavioral Therapy , Depression , Adult , Humans , Canada , Depression/therapy , Biomarkers , ElectroencephalographyABSTRACT
BACKGROUND: Molecular testing can detect actionable genomic alterations and tumor cell surface proteins in patients with non-small cell lung cancer (NSCLC). However, utilization remains suboptimal, representing missed treatment opportunities. This study aimed to identify challenges and potential solutions to obtaining percutaneous lung needle biopsy specimens for successful molecular testing in patients with advanced NSCLC. METHODS: This interdisciplinary qualitative study included ten radiologists and four pathologists from academic and community settings across the United States who routinely perform and analyze percutaneous lung needle biopsies. Participants underwent semi-structured one-on-one interviews (Phase 1). Interview questionnaires were constructed based on a literature review of key lines of inquiry and conducted by professional market researchers using the theoretical domains framework. Primary barriers to molecular testing were identified using thematic analysis. Subsequently, multidisciplinary focus groups were convened to identify potential solutions (Phase 2). RESULTS: Four themes emerged as barriers to molecular testing and were matched to the clinical workflow: (1) biopsy request, (2) biopsy procedure, (3) specimen analysis, and (4) communication. The nineteen potential solutions included adding a "checkbox" to indicate molecular testing in the biopsy request, leveraging pre-procedural imaging to guide biopsies, conserving tissue through appropriate allocation strategies and next generation sequencing panels instead of sequential single-gene assays, instituting reflex-molecular testing upon NSCLC diagnosis, tracking and communicating biopsy outcomes at multidisciplinary tumor boards, and improving integration of radiologists and pathologists into oncology care teams. CONCLUSIONS: Potential solutions exist to increase successful molecular testing of lung needle biopsy specimens in patients with advanced NSCLC.
Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , United States , Carcinoma, Non-Small-Cell Lung/diagnosis , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Biopsy, Needle , Biopsy , Molecular Diagnostic TechniquesABSTRACT
The midline thalamus is critical for flexible cognition, memory, and stress regulation in humans and its dysfunction is associated with several neurological and psychiatric disorders, including Alzheimer's disease, schizophrenia, and depression. Despite the pervasive role of the midline thalamus in cognition and disease, there is a limited understanding of its function in humans, likely due to the absence of a rigorous noninvasive neuroimaging methodology to identify its location. Here, we introduce a new method for identifying the midline thalamus in vivo using probabilistic tractography and k-means clustering with diffusion weighted imaging data. This approach clusters thalamic voxels based on data-driven cortical and subcortical connectivity profiles and then segments the midline thalamus according to anatomical connectivity tracer studies in rodents and macaques. Results from two different diffusion weighted imaging sets, including adult data (22-35 years) from the Human Connectome Project (n = 127) and adolescent data (9-14 years) collected at Florida International University (n = 34) showed that this approach reliably classifies midline thalamic clusters. As expected, these clusters were most evident along the dorsal/ventral extent of the third ventricle and were primarily connected to the agranular medial prefrontal cortex (e.g., anterior cingulate cortex), nucleus accumbens, and medial temporal lobe regions. The midline thalamus was then bisected based on a human brain atlas into a dorsal midline thalamic cluster (paraventricular and paratenial nuclei) and a ventral midline thalamic cluster (rhomboid and reuniens nuclei). This anatomical connectivity-based identification of the midline thalamus offers the opportunity for necessary investigation of this region in vivo in the human brain and how it relates to cognitive functions in humans, and to psychiatric and neurological disorders.
Subject(s)
Midline Thalamic Nuclei , Thalamus , Adult , Humans , Adolescent , Thalamus/diagnostic imaging , Thalamus/physiology , Midline Thalamic Nuclei/physiology , Nucleus Accumbens/physiology , Brain/diagnostic imaging , Cognition , Neural Pathways/diagnostic imaging , Neural Pathways/physiologyABSTRACT
Small molecule targeting of RNA has emerged as a new frontier in medicinal chemistry, but compared to the protein targeting literature our understanding of chemical matter that binds to RNA is limited. In this study, we reported Repository Of BInders to Nucleic acids (ROBIN), a new library of nucleic acid binders identified by small molecule microarray (SMM) screening. The complete results of 36 individual nucleic acid SMM screens against a library of 24 572 small molecules were reported (including a total of 1 627 072 interactions assayed). A set of 2 003 RNA-binding small molecules was identified, representing the largest fully public, experimentally derived library of its kind to date. Machine learning was used to develop highly predictive and interpretable models to characterize RNA-binding molecules. This work demonstrates that machine learning algorithms applied to experimentally derived sets of RNA binders are a powerful method to inform RNA-targeted chemical space.
Subject(s)
Machine Learning , RNA , RNA/chemistry , Gene Library , Biological Assay , Microarray AnalysisABSTRACT
BACKGROUND: Major depressive disorder (MDD) is associated with various cognitive impairments, including response inhibition. Deficits in response inhibition may also underlie poor antidepressant treatment response. Recent studies revealed that the neurobiological correlates of response inhibition can predict response to pharmacological treatments. However, the generalizability of this finding to first-line nonpharmacological treatments, particularly cognitive behavioral therapy, remains to be investigated. METHODS: Data from two independent treatment protocols were combined, one in which 65 patients with MDD underwent treatment with escitalopram, and the other in which 41 patients with MDD underwent a course of cognitive behavioral therapy. A total of 25 healthy control subjects were also recruited. Neural correlates of response inhibition were captured by participants completing a Go/NoGo task during electroencephalography recording. Response inhibition-related measures of interest included the amplitudes of the N2 and P3 event-related potentials. RESULTS: Pretreatment P3 amplitude, which has been linked to both the motor and cognitive aspects of response inhibition, was a significant predictor of change in depressive symptoms following escitalopram and cognitive behavioral therapy treatment. A greater pretreatment P3 amplitude was associated with a greater reduction in depressive severity. In addition, the pretreatment P3 amplitude was found to be significantly greater at baseline in remitters than in nonremitters and healthy control subjects. CONCLUSIONS: The integrity of response inhibition may be critical for a successful course of pharmacological or psychological treatment for MDD. Electrophysiological correlates of response inhibition may have utility as a general prognostic marker of treatment response in MDD. Future studies may investigate the benefit of preceding first-line treatments with interventions that improve response inhibition in MDD.