PainPoints: A Framework for Language-based Detection of Chronic Pain and Expert-Collaborative Text-Summarization

Chronic pain is a pervasive disorder which is often very disabling and is associated with comorbidities such as depression and anxiety. Neuropathic Pain (NP) is a common sub-type which is often caused due to nerve damage and has a known pathophysiology. Another common sub-type is Fibromyalgia (FM) which is described as musculoskeletal, diffuse pain that is widespread through the body. The pathophysiology of FM is poorly understood, making it very hard to diagnose. Standard medications and treatments for FM and NP differ from one another and if misdiagnosed it can cause an increase in symptom severity. To overcome this difficulty, we propose a novel framework, PainPoints, which accurately detects the sub-type of pain and generates clinical notes via summarizing the patient interviews. Specifically, PainPoints makes use of large language models to perform sentence-level classification of the text obtained from interviews of FM and NP patients with a reliable AUC of 0.83. Using a sufficiency-based interpretability approach, we explain how the fine-tuned model accurately picks up on the nuances that patients use to describe their pain. Finally, we generate summaries of these interviews via expert interventions by introducing a novel facet-based approach. PainPoints thus enables practitioners to add/drop facets and generate a custom summary based on the notion of "facet-coverage" which is also introduced in this work

Gene expression links functional networks across cortex and striatum

The human brain is comprised of a complex web of functional networks that link anatomically distinct regions. However, the biological mechanisms supporting network organization remain elusive, particularly across cortical and subcortical territories with vastly divergent cellular and molecular properties. Here, using human and primate brain transcriptional atlases, we demonstrate that spatial patterns of gene expression show strong correspondence with limbic and somato/motor cortico-striatal functional networks. Network-associated expression is consistent across independent human datasets and evolutionarily conserved in non-human primates. Genes preferentially expressed within the limbic network (encompassing nucleus accumbens, orbital/ventromedial prefrontal cortex, and temporal pole) relate to risk for psychiatric illness, chloride channel complexes, and markers of somatostatin neurons. Somato/motor associated genes are enriched for oligodendrocytes and markers of parvalbumin neurons. These analyses indicate that parallel cortico-striatal processing channels possess dissociable genetic signatures that recapitulate distributed functional networks, and nominate molecular mechanisms supporting cortico-striatal circuitry in health and disease

Health-related quality of life and survival in liver transplant candidates.

Health-related quality of life (HRQOL) is an important measure of the effects of chronic liver disease in affected patients that helps guide interventions to improve well-being. However, the relationship between HRQOL and survival in liver transplant candidates remains unclear. We examined whether the Physical Component Summary (PCS) and Mental Component Summary (MCS) scores from the Short Form 36 (SF-36) Health Survey were associated with survival in liver transplant candidates. We administered the SF-36 questionnaire (version 2.0) to patients in the Pulmonary Vascular Complications of Liver Disease study, a multicenter prospective cohort of patients evaluated for liver transplantation in 7 academic centers in the United States between 2003 and 2006. Cox proportional hazards models were used with death as the primary outcome and adjustment for liver transplantation as a time-varying covariate. The mean age of the 252 participants was 54 +/- 10 years, 64% were male, and 94% were white. During the 422 person years of follow-up, 147 patients (58%) were listed, 75 patients (30%) underwent transplantation, 49 patients (19%) died, and 3 patients were lost to follow-up. Lower baseline PCS scores were associated with an increased mortality rate despite adjustments for age, gender, Model for End-Stage Liver Disease score, and liver transplantation (P for the trend = 0.0001). The MCS score was not associated with mortality (P for the trend = 0.53). In conclusion, PCS significantly predicts survival in liver transplant candidates, and interventions directed toward improving the physical status may be helpful in improving outcomes in liver transplant candidates

Risk factors and impact of chronic obstructive pulmonary disease in candidates for liver transplantation

Chronic obstructive pulmonary disease (COPD) may cause significant symptoms and have an impact on survival. Smoking is an important risk factor for COPD and is common in candidates for liver transplantation; however, the risk factors for and outcomes of COPD in this population are unknown. We performed a prospective cohort study of 373 patients being evaluated for liver transplantation at 7 academic centers in the United States. COPD was characterized by expiratory airflow obstruction and defined as follows: prebronchodilator forced expiratory volume in 1 second/forced vital capacity < 0.70. Patients completed the Liver Disease Quality of Life Questionnaire 1.0, which included the Short Form-36. The mean age of the study sample was 53 ± 9 years, and 234 (63%) were male. Sixty-seven patients (18%, 95% confidence interval 14%–22%) had COPD, and 224 (60%) had a history of smoking. Eighty percent of patients with airflow obstruction did not previously carry a diagnosis of COPD, and 27% were still actively smoking. Older age and any smoking (odds ratio = 3.74, 95% confidence interval 1.94–7.23, P < 0.001) were independent risk factors for COPD. Patients with COPD had worse New York Heart Association functional class and lower physical component summary scores on the 36-Item Short Form but had short-term survival similar to that of patients without COPD. In conclusion, COPD is common and often undiagnosed in candidates for liver transplantation. Older age and smoking are significant risk factors of COPD, which has adverse consequences on functional status and quality of life in these patients

Resting-state brain information flow predicts cognitive flexibility in humans.

The human brain is a dynamic system, where communication between spatially distinct areas facilitates complex cognitive functions and behaviors. How information transfers between brain regions and how it gives rise to human cognition, however, are unclear. In this article, using resting-state functional magnetic resonance imaging (fMRI) data from 783 healthy adults in the Human Connectome Project (HCP) dataset, we map the brain's directed information flow architecture through a Granger-Geweke causality prism. We demonstrate that the information flow profiles in the general population primarily involve local exchanges within specialized functional systems, long-distance exchanges from the dorsal brain to the ventral brain, and top-down exchanges from the higher-order systems to the primary systems. Using an information flow map discovered from 550 subjects, the individual directed information flow profiles can significantly predict cognitive flexibility scores in 233 novel individuals. Our results provide evidence for directed information network architecture in the cerebral cortex, and suggest that features of the information flow configuration during rest underpin cognitive ability in humans

Identifying neural signatures mediating behavioral symptoms and psychosis onset: High-dimensional whole brain functional mediation analysis.

Along the pathway from behavioral symptoms to the development of psychotic disorders sits the multivariate mediating brain. The functional organization and structural topography of large-scale multivariate neural mediators among patients with brain disorders, however, are not well understood. Here, we design a high-dimensional brain-wide functional mediation framework to investigate brain regions that intermediate between baseline behavioral symptoms and future conversion to full psychosis among individuals at clinical high risk (CHR). Using resting-state functional magnetic resonance imaging (fMRI) data from 263 CHR subjects, we extract an α brain atlas and a β brain atlas: the former underlines brain areas associated with prodromal symptoms and the latter highlights brain areas associated with disease onset. In parallel, we identify and separate mediators that potentially positively and negatively mediate symptoms and psychosis, respectively, and quantify the effect of each neural mediator on disease development. Taken together, these results paint a brain-wide picture of neural markers that are potentially mediating behavioral symptoms and the development of psychotic disorders; additionally, they underscore a statistical framework that is useful to uncover large-scale intermediating variables in a regulatory biological system

Identifying neural signatures mediating behavioral symptoms and psychosis onset: High-dimensional whole brain functional mediation analysis.

Along the pathway from behavioral symptoms to the development of psychotic disorders sits the multivariate mediating brain. The functional organization and structural topography of large-scale multivariate neural mediators among patients with brain disorders, however, are not well understood. Here, we design a high-dimensional brain-wide functional mediation framework to investigate brain regions that intermediate between baseline behavioral symptoms and future conversion to full psychosis among individuals at clinical high risk (CHR). Using resting-state functional magnetic resonance imaging (fMRI) data from 263 CHR subjects, we extract an α brain atlas and a β brain atlas: the former underlines brain areas associated with prodromal symptoms and the latter highlights brain areas associated with disease onset. In parallel, we identify and separate mediators that potentially positively and negatively mediate symptoms and psychosis, respectively, and quantify the effect of each neural mediator on disease development. Taken together, these results paint a brain-wide picture of neural markers that are potentially mediating behavioral symptoms and the development of psychotic disorders; additionally, they underscore a statistical framework that is useful to uncover large-scale intermediating variables in a regulatory biological system

The human cortex possesses a reconfigurable dynamic network architecture that is disrupted in psychosis

Higher-order cognition emerges through the flexible interactions of large-scale brain networks, an aspect of temporal coordination that may be impaired in psychosis. Here, we map the dynamic functional architecture of the cerebral cortex in healthy young adults, leveraging this atlas of transient network configurations (states), to identify state- and network-specific disruptions in patients with schizophrenia and psychotic bipolar disorder. We demonstrate that dynamic connectivity profiles are reliable within participants, and can act as a fingerprint, identifying specific individuals within a larger group. Patients with psychotic illness exhibit intermittent disruptions within cortical networks previously associated with the disease, and the individual connectivity profiles within specific brain states predict the presence of active psychotic symptoms. Taken together, these results provide evidence for a reconfigurable dynamic architecture in the general population and suggest that prior reports of network disruptions in psychosis may reflect symptom-relevant transient abnormalities, rather than a time-invariant global deficit

The Roles, Challenges, and Merits of the p Value.

Since the 18th century, the p value has been an important part of hypothesis-based scientific investigation. As statistical and data science engines accelerate, questions emerge: to what extent are scientific discoveries based on p values reliable and reproducible? Should one adjust the significance level or find alternatives for the p value? Inspired by these questions and everlasting attempts to address them, here, we provide a systematic examination of the p value from its roles and merits to its misuses and misinterpretations. For the latter, we summarize modest recommendations to handle them. In parallel, we present the Bayesian alternatives for seeking evidence and discuss the pooling of p values from multiple studies and datasets. Overall, we argue that the p value and hypothesis testing form a useful probabilistic decision-making mechanism, facilitating causal inference, feature selection, and predictive modeling, but that the interpretation of the p value must be contextual, considering the scientific question, experimental design, and statistical principles