COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling.

Metabolism governs cell performance in biomanufacturing, as it fuels growth and productivity. However, even in well-controlled culture systems, metabolism is dynamic, with shifting objectives and resources, thus limiting the predictive capability of mechanistic models for process design and optimization. Here, we present Cellular Objectives and State Modulation In bioreaCtors (COSMIC)-dFBA, a hybrid multi-scale modeling paradigm that accurately predicts cell density, antibody titer, and bioreactor metabolite concentration profiles. Using machine-learning, COSMIC-dFBA decomposes the instantaneous metabolite uptake and secretion rates in a bioreactor into weighted contributions from each cell state (growth or antibody-producing state) and integrates these with a genome-scale metabolic model. A major strength of COSMIC-dFBA is that it can be parameterized with only metabolite concentrations from spent media, although constraining the metabolic model with other omics data can further improve its capabilities. Using COSMIC-dFBA, we can predict the final cell density and antibody titer to within 10% of the measured data, and compared to a standard dFBA model, we found the framework showed a 90% and 72% improvement in cell density and antibody titer prediction, respectively. Thus, we demonstrate our hybrid modeling framework effectively captures cellular metabolism and expands the applicability of dFBA to model the dynamic conditions in a bioreactor.

Factors affecting detection of bimodal sour-savory mixture and inter-individual umami taste perception.

While basic taste interactions have been the subject of many research studies, there is one combination where data is limited in the literature: sour and umami. This combination is universal in culinary preparations and of key interest to the food industry. Therefore, the primary goal of the present study is to assess how increasing concentrations of acidity (citric acid) affect, if at all, the intensity of a constant concentration of umami (monosodium glutamate, MSG). The secondary goal is to investigate other possible factors in umami taste perception. Here, a crowdsourced cohort of 734 individuals (age range 8-81) tasted and rated the intensity of 50 mM MSG alone, and in combination with citric acid at varying concentrations (1.25 mM, 6.25 mM, 31.25 mM). Participants were also genotyped for the single nucleotide polymorphism rs34160967 in the T1R1 gene. The results show a significant decrease in the intensity perception of umami as sour concentration increases (low: p = 0.005, medium: p < 0.001, high: p < 0.001). Situational factors such as participant hunger level and time since last eating also have a significant effect on umami intensity perception. Neither the biological factors of sex, age, and ancestry appear to play a role in umami perception, nor does variation in gene TAS1R1 at rs34160967. These new data contribute to the growing field of taste and sensory interaction by giving evidence that sour suppresses umami taste perception in bi-model samples.

Demonstration of the Pre-Emergency Use Authorization Path Using 3 Minor Groove Binder-Hydrolysis Probe Assays to Detect Escherichia coli O104:H4.

BACKGROUND: The Department of Defense (DoD) and the Food and Drug Administration (FDA) have collaboratively worked on a pre-Emergency Use Authorization (pre-EUA) process for in vitro diagnostic (IVD) devices, using FDA's regulatory flexibilities under the EUA authorities. The pre-EUA process enables FDA review of data in anticipation of a request for an EUA, advancing US government public health emergency preparedness efforts. METHODS: The IVD device developed to detect Escherichia coli O104:H4, for which an EUA has not been issued, serves as an example to illustrate that process. Specifically, DoD designed real-time PCR assays to target the virulent E. coli strain O104:H4 (etiological agent of the 2011 German outbreak) including: fliC (flagellin), Agg3C (AAF), and rfb (wbwC) on the basis of the published sequences. RESULTS: After development and optimization of these 3 specific assays, a defined protocol was followed to determine and document the sensitivity and specificity of each assay analytically. CONCLUSIONS: FDA reviewed these data and returned commentary on additional required experiments to complete the pre-EUA process and expedite the use of the device should there be an emergency need for an IVD device to detect this virulent E. coli strain before such a test is cleared by FDA.

Psychosis resulting from trimethoprim-sulfamethoxazole treatment for preseptal cellulitis.

Trimethoprim-sulfamethoxazole (TMP-SMX) is a commonly used antimicrobial agent because of its low cost, diverse antimicrobial profile, and minimal severe adverse effects. A rare side effect is psychosis, a complication that has not been published in the ophthalmology literature. A 53-year-old female presented to the ophthalmology office with left upper eyelid erythema, focal tenderness, and discharge. She was diagnosed with preseptal cellulitis of the left upper lid and started on TMP-SMX. The next day, the patient's condition improved with reduced swelling and no discharge. However, 2 days later, she experienced visual hallucinations whereby worms were growing out of her left eye accompanied by theme-congruent tactile hallucinations. TMP-SMX was discontinued and substituted for clindamycin, and she reported resolution of her symptoms 8 h later. TMP-SMX has extensive cerebrospinal fluid penetration and causes a folic acid deficiency, which may explain the rare occurrence of neuropsychiatric side effects. This patient had a substance-induced psychosis, in which visual and tactile hallucinations began 3 days after taking TMP-SMX and resolved 8 h after discontinuation, a timeline consistent with the literature. Central nervous system toxicity is rare in nonelderly immunocompetent patients, with only three such cases reported in the literature. While visual and auditory hallucinations have been described previously, this is the first reported case of TMP-SMX-induced tactile hallucinations and unilateral visual hallucinations. Moreover, because TMP-SMX is a first-line agent commonly used to treat orbital and preseptal cellulitis, it is important for ophthalmologists to be aware of this atypical side effect, as it can be life threatening.

The Biomedical Research Hub: a federated platform for patient research data.

OBJECTIVE: The objective was to develop and operate a cloud-based federated system for managing, analyzing, and sharing patient data for research purposes, while allowing each resource sharing patient data to operate their component based upon their own governance rules. The federated system is called the Biomedical Research Hub (BRH). MATERIALS AND METHODS: The BRH is a cloud-based federated system built over a core set of software services called framework services. BRH framework services include authentication and authorization, services for generating and assessing findable, accessible, interoperable, and reusable (FAIR) data, and services for importing and exporting bulk clinical data. The BRH includes data resources providing data operated by different entities and workspaces that can access and analyze data from one or more of the data resources in the BRH. RESULTS: The BRH contains multiple data commons that in aggregate provide access to over 6 PB of research data from over 400 000 research participants. DISCUSSION AND CONCLUSION: With the growing acceptance of using public cloud computing platforms for biomedical research, and the growing use of opaque persistent digital identifiers for datasets, data objects, and other entities, there is now a foundation for systems that federate data from multiple independently operated data resources that expose FAIR application programming interfaces, each using a separate data model. Applications can be built that access data from one or more of the data resources.

Clinical and laboratory characteristics of patients with novel coronavirus disease-2019 infection and deep venous thrombosis.

OBJECTIVE: Early reports suggest that patients with novel coronavirus disease-2019 (COVID-19) infection carry a significant risk of altered coagulation with an increased risk for venous thromboembolic events. This report investigates the relationship of significant COVID-19 infection and deep venous thrombosis (DVT) as reflected in the patient clinical and laboratory characteristics. METHODS: We reviewed the demographics, clinical presentation, laboratory and radiologic evaluations, results of venous duplex imaging and mortality of COVID-19-positive patients (18-89 years) admitted to the Indiana University Academic Health Center. Using oxygen saturation, radiologic findings, and need for advanced respiratory therapies, patients were classified into mild, moderate, or severe categories of COVID-19 infection. A descriptive analysis was performed using univariate and bivariate Fisher's exact and Wilcoxon rank-sum tests to examine the distribution of patient characteristics and compare the DVT outcomes. A multivariable logistic regression model was used to estimate the adjusted odds ratio of experiencing DVT and a receiver operating curve analysis to identify the optimal cutoff for d-dimer to predict DVT in this COVID-19 cohort. Time to the diagnosis of DVT from admission was analyzed using log-rank test and Kaplan-Meier plots. RESULTS: Our study included 71 unique COVID-19-positive patients (mean age, 61 years) categorized as having 3% mild, 14% moderate, and 83% severe infection and evaluated with 107 venous duplex studies. DVT was identified in 47.8% of patients (37% of examinations) at an average of 5.9 days after admission. Patients with DVT were predominantly male (67%; P = .032) with proximal venous involvement (29% upper and 39% in the lower extremities with 55% of the latter demonstrating bilateral involvement). Patients with DVT had a significantly higher mean d-dimer of 5447 ± 7032 ng/mL (P = .0101), and alkaline phosphatase of 110 IU/L (P = .0095) than those without DVT. On multivariable analysis, elevated d-dimer (P = .038) and alkaline phosphatase (P = .021) were associated with risk for DVT, whereas age, sex, elevated C-reactive protein, and ferritin levels were not. A receiver operating curve analysis suggests an optimal d-dimer value of 2450 ng/mL cutoff with 70% sensitivity, 59.5% specificity, and 61% positive predictive value, and 68.8% negative predictive value. CONCLUSIONS: This study suggests that males with severe COVID-19 infection requiring hospitalization are at highest risk for developing DVT. Elevated d-dimers and alkaline phosphatase along with our multivariable model can alert the clinician to the increased risk of DVT requiring early evaluation and aggressive treatment.

Transcatheter Aortic Valve Replacement in Low-Risk Patients With Symptomatic Severe Bicuspid Aortic Valve Stenosis.

OBJECTIVES: The aim of this study was to evaluate clinical outcomes and transcatheter heart valve hemodynamic parameters after transcatheter aortic valve replacement (TAVR) in low-risk patients with bicuspid aortic stenosis (AS). BACKGROUND: TAVR is approved for low-risk patients in the United States. However, patients with bicuspid AS were excluded from the randomized cohorts of the pivotal low-risk trials. METHODS: The LRT (Low Risk TAVR) trial was an investigator-initiated, prospective, multicenter study and was the first and only U.S. Food and Drug Administration-approved investigational device exemption trial to evaluate the feasibility of TAVR with either balloon-expandable or self-expanding valves in low-risk patients with bicuspid AS. The primary endpoint was all-cause mortality at 30 days. Baseline and follow-up echocardiography and computed tomography to detect leaflet thickening were analyzed in an independent core laboratory. RESULTS: Sixty-one low-risk patients with symptomatic, severe AS and bicuspid aortic valves (78.3% Sievers type 1 morphology) underwent TAVR at 6 centers from 2016 to 2019. The mean age was 68.6 years, and 42.6% were men. At 30 days, there was zero mortality and no disabling strokes. The rate of new permanent pacemaker implantation was 13.1%; just 1 patient had a moderate paravalvular leak at 30 days. Hypoattenuated leaflet thickening was observed in 10% of patients at 30 days. CONCLUSIONS: TAVR appears to be safe in patients with bicuspid AS, with short length of hospital stay, zero mortality, and no disabling strokes at 30 days. Subclinical leaflet thrombosis was observed in a minority of patients at 30 days but did not appear to be associated with clinical events.

A tablet-based task for assessing environmental preferences in children and adults.

To assess environmental preferences in a wide age range of children, a tablet-based task was developed which can be used with children as young as 4-years-old. The current method uses images which have been rated on aesthetic preference in a separate adult sample to ensure that the nature and urban images shown are matched on aesthetics, allowing for a true evaluation of environmental preferences (without any confound of general aesthetics). However, the app is customizable and can evaluate preference for any set of 10 images researchers may be interested in (i.e. is not limited to environmental preferences or these specific images). •This task runs as an Android tablet app•The app allows for up to 10 pictures at a time and uses a ranking of 4 images on each trial (from frowny to happy face) where each image is compared with every other image at least once•The app was successfully employed with a sample of 4-to-11-year-old children and their parents/guardians.

Spontaneous Iliac Vein Rupture Due to May-Thurner Syndrome and Its Staged Management.

We present a case of a 58-year-old otherwise healthy women who presented with left lower extremity deep venous thrombosis and was found to have pulmonary embolism along with a ruptured left internal iliac vein. Our patient was hemodynamically stable upon presentation; therefore, a staged approach was undertaken. Initially, an inferior vena cava filter was placed and the patient was slowly advanced to therapeutic anticoagulation and subsequently discharged. She then returned 2 weeks after discharge for venogram, mechanical thrombectomy, and stenting. At 1-year follow-up in clinic, she was found to have patent stents and resolution of symptoms.

Pavlik Harness initiation on Barlow positive hips: Can we wait?

We investigated if infants with a Barlow positive hip(s) have natural hip stabilization and can thus avoid Pavlik Harness (PH) treatment. We conducted a chart review for infants who presented within two weeks of life, had a Barlow positive hip, and were deferred treatment. Of the thirty infants, eighteen were treated with PH at 4-6 weeks or 12 weeks due to persistent dysplasia. Twelve infants avoided PH entirely. There were zero cases of PH failure. Parents can be counseled that deferring treatment until at least 4-6 weeks of age might avoid treatment altogether without an increased risk of harness failure.

The effects of oral ondansetron disintegrating tablets for prevention of at-home emesis in pediatric patients after ear-nose-throat surgery.

BACKGROUND: Tonsillectomy and adenoidectomy are associated with a frequent incidence of vomiting, both in the hospital and at home. We evaluated the effects of oral ondansetron disintegrating tablets (ODT) on the incidence of at-home emesis in children undergoing tonsillectomy with and without adenoidectomy and with and without bilateral myringotomy and tube insertion. METHODS: All patients underwent inhaled mask induction with nitrous oxide, oxygen, and sevoflurane. Morphine, dexamethasone, and ondansetron were administered to all patients intraoperatively. Postoperative pain was treated with fentanyl or acetaminophen with codeine. Rescue antiemetics in the postanesthesia care unit or same day surgery unit were administered for three emetic episodes within 15 min, or upon patient or parent request. Patients were randomized for at-home administration of five doses of either ondansetron ODT or a placebo. All patients were followed for the first 3 days after surgery. At-home emesis was the primary outcome variable. RESULTS: Two hundred and twenty-one patients were entered into the study, yielding 200 evaluable subjects. At-home emesis occurred in 15 (14.5%) of the 103 children who received ODT, and 31 (32%) of the 97 children in the placebo group, P = 0.004. Subgroup analysis demonstrated efficacy in patients who did not require rescue medication for nausea and vomiting while in the hospital, but did not demonstrate efficacy for patients who required rescue medication. CONCLUSIONS: At-home use of ODT may prevent emesis in children during the first 3 days after tonsillectomy in children. Patients who require rescue after prophylactic treatment for nausea and vomiting in the hospital may not respond to prophylactic ondansatron ODT at home.

Drs2p-dependent formation of exocytic clathrin-coated vesicles in vivo.

The small GTP binding protein ARF has been implicated in budding clathrin-coated vesicles (CCVs) from Golgi and endosomal membranes. An arf1 synthetic lethal screen identified DRS2/SWA3 along with a clathrin heavy-chain conditional allele (chc1-5/swa5-1) and SWA2, encoding the yeast auxilin-like protein involved in uncoating CCVs. Drs2p/Swa3p is a P-type ATPase and a potential aminophospholipid translocase that localizes to the trans-Golgi network (TGN) in yeast. Genetic and phenotypic analyses of drs2Delta mutants suggested that Drs2p was required for clathrin function. To address a potential role for Drs2p in CCV formation from the TGN in vivo, we have performed epistasis analyses between drs2 and mutations that cause accumulation of distinct populations of post-Golgi vesicles. We find that Drs2p is required to form a specific class of secretory vesicles that accumulate when the actin cytoskeleton is disrupted. Accumulation of these vesicles also requires clathrin and is perturbed by mutation of AP-1, but not AP-2, AP-3, or GGA adaptins. Most of the accumulated vesicles are uncoated; however, clathrin coats can be partially stabilized on these vesicles by deletion of SWA2. These data provide the first in vivo evidence for an integral membrane protein requirement in forming CCVs.

Evaluation of ViroCyt® Virus Counter for rapid filovirus quantitation.

Development and evaluation of medical countermeasures for diagnostics, vaccines, and therapeutics requires production of standardized, reproducible, and well characterized virus preparations. For filoviruses this includes plaque assay for quantitation of infectious virus, transmission electron microscopy (TEM) for morphology and quantitation of virus particles, and real-time reverse transcription PCR for quantitation of viral RNA (qRT-PCR). The ViroCyt® Virus Counter (VC) 2100 (ViroCyt, Boulder, CO, USA) is a flow-based instrument capable of quantifying virus particles in solution. Using a proprietary combination of fluorescent dyes that stain both nucleic acid and protein in a single 30 min step, rapid, reproducible, and cost-effective quantification of filovirus particles was demonstrated. Using a seed stock of Ebola virus variant Kikwit, the linear range of the instrument was determined to be 2.8E+06 to 1.0E+09 virus particles per mL with coefficient of variation ranging from 9.4% to 31.5% for samples tested in triplicate. VC particle counts for various filovirus stocks were within one log of TEM particle counts. A linear relationship was established between the plaque assay, qRT-PCR, and the VC. VC results significantly correlated with both plaque assay and qRT-PCR. These results demonstrated that the VC is an easy, fast, and consistent method to quantify filoviruses in stock preparations.

Practice patterns of academic general thoracic and adult cardiac surgeons.

OBJECTIVE: We hypothesized that academic adult cardiac surgeons (CSs) and general thoracic surgeons (GTSs) would have distinct practice patterns of, not just case-mix, but also time devoted to outpatient care, involvement in critical care, and work relative value unit (wRVU) generation for the procedures they perform. METHODS: We queried the University Health System Consortium-Association of American Medical Colleges Faculty Practice Solution Center database for fiscal years 2007-2008, 2008-2009, and 2009-2010 for the frequency of inpatient and outpatient current procedural terminology coding and wRVU data of academic GTSs and CSs. The Faculty Practice Solution Center database is a compilation of productivity and payer data from 86 academic institutions. RESULTS: The greatest wRVU generating current procedural terminology codes for CSs were, in order, coronary artery bypass grafting, aortic valve replacement, and mitral valve replacement. In contrast, open lobectomy, video-assisted thoracic surgery wedge, and video-assisted thoracic surgery lobectomy were greatest for GTSs. The 10 greatest wRVU-generating procedures for CSs generated more wRVUs than those for GTSs (P<.001). Although CSs generated significantly more hospital inpatient evaluation and management (E & M) wRVUs than did GTSs (P<.001), only 2.5% of the total wRVUs generated by CSs were from E & M codes versus 18.8% for GTSs. Critical care codes were 1.5% of total evaluation and management billing for both CSs and GTSs. CONCLUSIONS: Academic CSs and GTSs have distinct practice patterns. CSs receive greater reimbursement for services because of the greater wRVUs of the procedures performed compared with GTSs, and evaluation and management coding is a more important wRVU generator for GTSs. The results of our study could guide academic CS and GTS practice structure and time prioritization.

Therapeutic intervention of Ebola virus infection in rhesus macaques with the MB-003 monoclonal antibody cocktail.

Ebola virus (EBOV) remains one of the most lethal transmissible infections and is responsible for high fatality rates and substantial morbidity during sporadic outbreaks. With increasing human incursions into endemic regions and the reported possibility of airborne transmission, EBOV is a high-priority public health threat for which no preventive or therapeutic options are currently available. Recent studies have demonstrated that cocktails of monoclonal antibodies are effective at preventing morbidity and mortality in nonhuman primates (NHPs) when administered as a post-exposure prophylactic within 1 or 2 days of challenge. To test whether one of these cocktails (MB-003) demonstrates efficacy as a therapeutic (after the onset of symptoms), we challenged NHPs with EBOV and initiated treatment upon confirmation of infection according to a diagnostic protocol for U.S. Food and Drug Administration Emergency Use Authorization and observation of a documented fever. Of the treated animals, 43% survived challenge, whereas both the controls and all historical controls with the same challenge stock succumbed to infection. These results represent successful therapy of EBOV infection in NHPs.