Biomedical discovery through the integrative biomedical knowledge hub (iBKH).

The abundance of biomedical knowledge gained from biological experiments and clinical practices is an invaluable resource for biomedicine. The emerging biomedical knowledge graphs (BKGs) provide an efficient and effective way to manage the abundant knowledge in biomedical and life science. In this study, we created a comprehensive BKG called the integrative Biomedical Knowledge Hub (iBKH) by harmonizing and integrating information from diverse biomedical resources. To make iBKH easily accessible for biomedical research, we developed a web-based, user-friendly graphical portal that allows fast and interactive knowledge retrieval. Additionally, we also implemented an efficient and scalable graph learning pipeline for discovering novel biomedical knowledge in iBKH. As a proof of concept, we performed our iBKH-based method for computational in-silico drug repurposing for Alzheimer's disease. The iBKH is publicly available.

Blocking ActRIIB and restoring appetite reverses cachexia and improves survival in mice with lung cancer.

Cancer cachexia is a common, debilitating condition with limited therapeutic options. Using an established mouse model of lung cancer, we find that cachexia is characterized by reduced food intake, spontaneous activity, and energy expenditure accompanied by muscle metabolic dysfunction and atrophy. We identify Activin A as a purported driver of cachexia and treat with ActRIIB-Fc, a decoy ligand for TGF-ß/activin family members, together with anamorelin (Ana), a ghrelin receptor agonist, to reverse muscle dysfunction and anorexia, respectively. Ana effectively increases food intake but only the combination of drugs increases lean mass, restores spontaneous activity, and improves overall survival. These beneficial effects are limited to female mice and are dependent on ovarian function. In agreement, high expression of Activin A in human lung adenocarcinoma correlates with unfavorable prognosis only in female patients, despite similar expression levels in both sexes. This study suggests that multimodal, sex-specific, therapies are needed to reverse cachexia.

Increased Comorbidity Burden Among Hip Fracture Patients During the COVID-19 Pandemic in New York City.

BACKGROUND: The coronavirus disease 19 (COVID-19) pandemic had a devastating effect on New York City in the spring of 2020. Several global reports suggested worse early outcomes among COVID-positive patients with hip fractures. However, there is limited data comparing baseline comorbidities among patients treated during the pandemic relative to those treated in non-pandemic conditions. MATERIALS AND METHODS: A multicenter retrospective cohort study was performed at two Level 1 Trauma centers and one orthopedic specialty hospital to assess demographics, comorbidities, and outcomes among 67 hip fracture patients treated (OTA/AO 31, 32.1) during the peak of the COVID-19 pandemic in New York City (March 20, 2020 to April 24, 2020), including 9 who were diagnosed with COVID-19. These patients were compared to a cohort of 76 hip fracture patients treated 1 year prior (March 20, 2019 to April 24, 2019). Baseline demographics, comorbidities, treatment characteristics, and respiratory symptomatology were evaluated. The primary outcome was inpatient mortality. RESULTS: Relative to patients treated in 2019, patients with hip fractures during the pandemic had worse Charlson Comorbidity Indices (median 5.0 vs 6.0, P = .03) and American Society of Anesthesiologists (ASA) scores (mean 2.4 vs 2.7, P = .04). Patients during the COVID-19 pandemic were more likely to have decreased ambulatory status (P<.01) and a smoking history (P = .04). Patients in 2020 had longer inpatient stays (median 5 vs 7 days, P = .01), and were more likely to be discharged home (61% vs 9%, P<.01). Inpatient mortality was significantly increased during the COVID-19 pandemic (12% vs 0%, P = .002). CONCLUSIONS: Patients with hip fractures during the COVID-19 pandemic had worse comorbidity profiles and decreased functional status compared to patients treated the year prior. This information may be relevant in negotiations regarding reimbursement for cost of care of hip fracture patients with COVID-19, as these patients may require more expensive care.

En route to single-step, two-phase purification of carbon nanotubes facilitated by high-throughput spectroscopy.

Chirality purification of single-walled carbon nanotubes (SWCNTs) is desirable for applications in many fields, but general utility is currently hampered by low throughput. We discovered a method to obtain single-chirality SWCNT enrichment by the aqueous two-phase extraction (ATPE) method in a single step. To achieve appropriate resolution, a biphasic system of non-ionic tri-block copolymer surfactant is varied with an ionic surfactant. A nearly-monochiral fraction of SWCNTs can then be harvested from the top phase. We also found, via high-throughput, near-infrared excitation-emission photoluminescence spectroscopy, that the parameter space of ATPE can be mapped to probe the mechanics of the separation process. Finally, we found that optimized conditions can be used for sorting of SWCNTs wrapped with ssDNA as well. Elimination of the need for surfactant exchange and simplicity of the separation process make the approach promising for high-yield generation of purified single-chirality SWCNT preparations.

Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.

Age-related macular degeneration (AMD) is the leading cause of vision loss. Some patients experience vision loss over a delayed timeframe, others at a rapid pace. Physicians analyze time-of-visit fundus photographs to predict patient risk of developing late-AMD, the most severe form of AMD. Our study hypothesizes that 1) incorporating historical data improves predictive strength of developing late-AMD and 2) state-of-the-art deep-learning techniques extract more predictive image features than clinicians do. We incorporate longitudinal data from the Age-Related Eye Disease Studies and deep-learning extracted image features in survival settings to predict development of late- AMD. To extract image features, we used multi-task learning frameworks to train convolutional neural networks. Our findings show 1) incorporating longitudinal data improves prediction of late-AMD for clinical standard features, but only the current visit is informative when using complex features and 2) "deep-features" are more informative than clinician derived features. We make codes publicly available at https://github.com/bionlplab/AMD_prognosis_amia2021.

Universal Testing for COVID-19 in Essential Orthopaedic Surgery Reveals a High Percentage of Asymptomatic Infections.

BACKGROUND: The long incubation period and asymptomatic spread of COVID-19 present considerable challenges for health-care institutions. The identification of infected individuals is vital to prevent the spread of illness to staff and other patients as well as to identify those who may be at risk for disease-related complications. This is particularly relevant with the resumption of elective orthopaedic surgery around the world. We report the results of a universal testing protocol for COVID-19 in patients undergoing orthopaedic surgery during the coronavirus pandemic and to describe the postoperative course of asymptomatic patients who were positive for COVID-19. METHODS: A retrospective review of adult operative cases between March 25, 2020, and April 24, 2020, at an orthopaedic specialty hospital in New York City was performed. Initially, a screening questionnaire consisting of relevant signs and symptoms (e.g., fever, cough, shortness of breath) or exposure dictated the need for nasopharyngeal swab real-time quantitative polymerase chain reaction (RT-PCR) testing for all admitted patients. An institutional policy change occurred on April 5, 2020, that indicated nasopharyngeal swab RT-PCR testing for all orthopaedic admissions. Screening and testing data for COVID-19 as well as relevant imaging, laboratory values, and postoperative complications were reviewed for all patients. RESULTS: From April 5, 2020, to April 24, 2020, 99 patients underwent routine nasopharyngeal swab testing for COVID-19 prior to their planned orthopaedic surgical procedure. Of the 12.1% of patients who tested positive for COVID-19, 58.3% were asymptomatic. Three asymptomatic patients developed postoperative hypoxia, with 2 requiring intubation. The negative predictive value of using the signs and symptoms of disease to predict a negative test result was 91.4% (95% confidence interval [CI], 81.0% to 97.1%). Including a positive chest radiographic finding as a screening criterion did not improve the negative predictive value of screening (92.5% [95% CI, 81.8% to 97.9%]). CONCLUSIONS: A protocol for universal testing of all orthopaedic surgery admissions at 1 hospital in New York City during a 3-week period revealed a high rate of COVID-19 infections. Importantly, the majority of these patients were asymptomatic. Using chest radiography did not significantly improve the negative predictive value of screening. These results have important implications as hospitals anticipate the resumption of elective surgical procedures. LEVEL OF EVIDENCE: Diagnostic Level IV. See Instructions for Authors for a complete description of levels of evidence.

Hip Fracture Outcomes During the COVID-19 Pandemic: Early Results From New York.

OBJECTIVE: To evaluate inpatient outcomes among patients with hip fracture treated during the COVID-19 pandemic in New York City. DESIGN: Multicenter retrospective cohort study. SETTING: One Level 1 trauma center and one orthopaedic specialty hospital in New York City. PATIENTS/PARTICIPANTS: Fifty-nine consecutive patients (average age 85 years, range: 65-100 years) treated for a hip fracture (OTA/AO 31, 32.1) over a 5-week period, March 20, 2020, to April 24, 2020, during the height of the COVID-19 crisis. MAIN OUTCOME MEASUREMENTS: COVID-19 infection status was used to stratify patients. The primary outcome was inpatient mortality. Secondary outcomes were admission to the intensive care unit, unexpected intubation, pneumonia, deep vein thrombosis, pulmonary embolus, myocardial infarction, cerebrovascular accident, urinary tract infection, and transfusion. Baseline demographics, comorbidities, treatment characteristics, and COVID-related symptomatology were also evaluated. RESULTS: Ten patients (15%) tested positive for COVID-19 (COVID+) (n = 9; 7 preoperatively and 2 postoperatively) or were presumed positive (n = 1), 40 (68%) patients tested negative, and 9 (15%) patients were not tested in the primary hospitalization. American Society of Anesthesiologists' scores were higher in the COVID+ group (d = -0.83; P = 0.04); however, the Charlson Comorbidity Index was similar between the study groups (d = -0.17; P = 0.63). Inpatient mortality was significantly increased in the COVID+ cohort (56% vs. 4%; odds ratio 30.0, 95% confidence interval 4.3-207; P = 0.001). Including the one presumed positive case in the COVID+ cohort increased this difference (60% vs. 2%; odds ratio 72.0, 95% confidence interval 7.9-754; P < 0.001). CONCLUSIONS: Hip fracture patients with concomitant COVID-19 infection had worse American Society of Anesthesiologists' scores but similar baseline comorbidities with significantly higher rates of inpatient mortality compared with those without concomitant COVID-19 infection. LEVEL OF EVIDENCE: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.

Widespread diversity in the transcriptomes of functionally divergent limb tendons.

KEY POINTS: Tendon is a hypocellular, matrix-rich tissue that has been excluded from comparative transcriptional atlases. These atlases have provided important knowledge about biological heterogeneity between tissues, and our study addresses this important gap. We performed measures on four of the most studied tendons, the Achilles, forepaw flexor, patellar and supraspinatus tendons of both mice and rats. These tendons are functionally distinct and are also among the most commonly injured, and therefore of important translational interest. Approximately one-third of the filtered transcriptome was differentially regulated between Achilles, forepaw flexor, patellar and supraspinatus tendons within either mice or rats. Nearly two-thirds of the transcripts that are expressed in anatomically similar tendons were different between mice and rats. The overall findings from this study identified that although tendons across the body share a common anatomical definition based on their physical location between skeletal muscle and bone, tendon is a surprisingly genetically heterogeneous tissue. ABSTRACT: Tendon is a functionally important connective tissue that transmits force between skeletal muscle and bone. Previous studies have evaluated the architectural designs and mechanical properties of different tendons throughout the body. However, less is known about the underlying transcriptional differences between tendons that may dictate their designs and properties. Therefore, our objective was to develop a comprehensive atlas of the transcriptome of limb tendons in adult mice and rats using systems biology techniques. We selected the Achilles, forepaw digit flexor, patellar, and supraspinatus tendons due to their divergent functions and high rates of injury and tendinopathies in patients. Using RNA sequencing data, we generated the Comparative Tendon Transcriptional Database (CTTDb) that identified substantial diversity in the transcriptomes of tendons both within and across species. Approximately 30% of filtered transcripts were differentially regulated between tendons of a given species, and nearly 60% of the filtered transcripts present in anatomically similar tendons were different between species. Many of the genes that differed between tendons and across species are important in tissue specification and limb morphogenesis, tendon cell biology and tenogenesis, growth factor signalling, and production and maintenance of the extracellular matrix. This study indicates that tendon is a surprisingly heterogenous tissue with substantial genetic variation based on anatomical location and species.