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There is much evidence indicating that human leukemic cells and monocytes/macrophages synthesize, and secrete, several matrix metalloproteinases (MMPs), and participate in the degradation of extracellular matrix components in tissue lesions. In this study, we investigated the effects and mechanisms of andrographolide, extracted from the herb Andrographis paniculata, on human monocytic MMPs expression and activation. Andrographolide (1-50 μM) exhibited concentration-dependent inhibition of MMP-9 activation, induced by either tumor necrosis factor-α (TNF-α), or lipopolysaccharide (LPS), in THP-1cells. In addition, andrographolide did not present an inhibitory effect on MMP-9 enzymatic activity at a concentration of 50 μM. By contrast, enzyme-linked immunosorbent assay (ELISA) showed that andrographolide partially affect TIMP-1 levels. Western blot analysis showed that both TNF-α, and LPS stimulators attenuated MMP-9 protein expression in a concentration-dependent manner. Using reverse transcription polymerase chain reaction (RT-PCR), we found that andrographolide suppressed expression of MMP-9 messenger RNA. Furthermore, we also found that andrographolide could significantly inhibit the degradation of inhibitor-κB-α (IκB-α) induced by TNF-α. We used electrophoretic mobility shift assay and reporter gene detection to show that andrographolide also markedly inhibited NF-κB signaling, anti-translocation and anti-activation. In conclusion, we demonstrate that andrographolide attenuates MMP-9 expression, and its main mechanism might involve the NF-κB signal pathway. These results provide new opportunities for the development of new anti-inflammatory and leukemic therapies. [ABSTRACT FROM AUTHOR]

Objective: Interleukin (IL)-22 is a potential therapeutic protein for the treatment of metabolic diseases such as obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease due to its involvement in multiple cellular pathways and observed hepatoprotective effects. The short serum half-life of IL-22 has previously limited its use in clinical applications; however, the development of mRNA-lipid nanoparticle (LNP) technology offers a novel therapeutic approach that uses a host-generated IL-22 fusion protein. In the present study, the effects of administration of an mRNA-LNP encoding IL-22 on metabolic disease parameters was investigated in various mouse models., Methods: C57BL/6NCrl mice were used to confirm mouse serum albumin (MSA)-IL-22 protein expression prior to assessments in C57BL/6NTac and CETP/ApoB transgenic mouse models of metabolic disease. Mice were fed either regular chow or a modified amylin liver nonalcoholic steatohepatitis-inducing diet prior to receiving either LNP-encapsulated MSA-IL-22 or MSA mRNA via intravenous or intramuscular injection. Metabolic markers were monitored for the duration of the experiments, and postmortem histology assessment and analysis of metabolic gene expression pathways were performed., Results: MSA-IL-22 was detectable for ≥8 days following administration. Improvements in body weight, lipid metabolism, glucose metabolism, and lipogenic and fibrotic marker gene expression in the liver were observed in the MSA-IL-22-treated mice, and these effects were shown to be durable., Conclusions: These results support the application of mRNA-encoded IL-22 as a promising treatment strategy for metabolic syndrome and associated comorbidities in human populations., Competing Interests: Declaration of competing interest At the time of this analysis, all authors were employees of Moderna, Inc. and may hold stock/stock options in the company., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Background: People living with multiple chronic conditions (MCCs) face substantial challenges in planning and coordinating increasingly complex care. Family caregivers provide important assistance for people with MCCs but lack sufficient support. Caregiver apps have the potential to help by enhancing care coordination and planning among the health care team, including patients, caregivers, and clinicians., Objective: We aim to conduct a scoping review to assess the evidence on the development and use of caregiver apps that support care planning and coordination, as well as to identify key factors (ie, needs, barriers, and facilitators) related to their use and desired caregiver app functionalities., Methods: Papers intersecting 2 major domains, mobile health (mHealth) apps and caregivers, that were in English and published from 2015 to 2021 were included in the initial search from 6 databases and gray literature and ancestry searches. As per JBI (Joanna Briggs Institute) Scoping Review guidelines and PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews), 2 authors independently screened full texts with disagreements resolved by a third author. Working in pairs, the authors extracted data using a pilot-tested JBI extraction table and compared results for consensus., Results: We identified 34 papers representing 25 individual studies, including 18 (53%) pilot and feasibility studies, 13 (38%) qualitative studies, and 2 experimental or quasi-experimental studies. None of the identified studies assessed an intervention of a caregiver app for care planning and coordination for people with MCCs. We identified important caregiver needs in terms of information, support, and care coordination related to both caregiving and self-care. We compiled desired functionalities and features enabling apps to meet the care planning and care coordination needs of caregivers, in particular, the integration of caregiver roles into the electronic health record., Conclusions: Caregiver needs identified through this study can inform developers and researchers in the design and implementation of mHealth apps that integrate with the electronic health record to link caregivers, patients, and clinicians to support coordinated care for people with MCCs. In addition, this study highlights the need for more rigorous research on the use of mHealth apps to support caregivers in care planning and coordination., (©Marjorie M Kelley, Tia Powell, Djibril Camara, Neha Shah, Jenna M Norton, Chelsea Deitelzweig, Nivedha Vaidy, Chun-Ju Hsiao, Jing Wang, Arlene S Bierman. Originally published in the Journal of Medical Internet Research (https://www.jmir.org), 23.05.2024.)

Developing an effective mRNA therapeutic often requires maximizing protein output per delivered mRNA molecule. We previously found that coding sequence (CDS) design can substantially affect protein output, with mRNA variants containing more optimal codons and higher secondary structure yielding the highest protein outputs due to their slow rates of mRNA decay. Here, we demonstrate that CDS-dependent differences in translation initiation and elongation rates lead to differences in translation- and deadenylation-dependent mRNA decay rates, thus explaining the effect of CDS on mRNA half-life. Surprisingly, the most stable and highest-expressing mRNAs in our test set have modest initiation/elongation rates and ribosome loads, leading to minimal translation-dependent mRNA decay. These findings are of potential interest for optimization of protein output from therapeutic mRNAs, which may be achieved by attenuating rather than maximizing ribosome load., Competing Interests: Declaration of interests D.W.R., A.A.B., M.C.L., A.K.J., Y.M.C., M.L., C.J.H., R.J., E.A.A., M.M., and B.R.F. are employees of Moderna, Inc., and hold stock/stock options in the company. C.K. and C.S.P. are former employees of Moderna, Inc., and hold stock/stock options in the company. M.J.M. is a former employee of Moderna, Inc., and a current consultant, and holds stock/stock options in the company., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Messenger RNA (mRNA)-based therapeutics have emerged as a promising modality for various clinical applications, necessitating robust methods for mRNA quantification. This biodistribution study compares the performance of branched DNA and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assays for measuring lipid nanoparticle-encapsulated mRNA. Following intravenous administration of nascent peptide imaging luciferase mRNA (1 mg/kg) to rats, mRNA levels in various tissues and serum were quantified using both assays. Statistical analyses, including Bland-Altman, Deming regression and Passing-Bablok regression, were employed to assess method comparability and reproducibility. The results indicated that mRNA pharmacokinetics measured by branched DNA and RT-qPCR were largely consistent across tissues, with RT-qPCR showing greater reproducibility across multiple laboratories. RT-qPCR also demonstrated a wider dynamic range and higher sensitivity, making it a more versatile option for large-scale studies. Despite some differences in data due to tissue types and timepoints, both methods provided comparable pharmacokinetic profiles for mRNA quantification. This study underscores the importance of selecting an appropriate quantification method based on study requirements and highlights RT-qPCR's adaptability for multisite research, especially for the clinical development of mRNA-based therapeutics.

Prenatal maternal stress has a negative impact on child health but the mechanisms through which maternal stress affects child health are unclear. Epigenetic variation, such as DNA methylation, is a likely mechanistic candidate as DNA methylation is sensitive to environmental insults and can regulate long-term changes in gene expression. We recruited 155 mother-newborn dyads in the Democratic Republic of Congo to investigate the effects of maternal stress on DNA methylation in mothers and newborns. We used four measures of maternal stress to capture a range of stressful experiences: general trauma, sexual trauma, war trauma, and chronic stress. We identified differentially methylated positions (DMPs) associated with general trauma, sexual trauma, and war trauma in both mothers and newborns. No DMPs were associated with chronic stress. Sexual trauma was positively associated with epigenetic age acceleration across several epigenetic clocks in mothers. General trauma and war trauma were positively associated with newborn epigenetic age acceleration using the extrinsic epigenetic age clock. We tested the top DMPs for enrichment of DNase I hypersensitive sites (DHS) and found no enrichment in mothers. In newborns, top DMPs associated with war trauma were enriched for DHS in embryonic and foetal cell types. Finally, one of the top DMPs associated with war trauma in newborns also predicted birthweight, completing the cycle from maternal stress to DNA methylation to newborn health outcome. Our results indicate that maternal stress is associated with site-specific changes in DNAm and epigenetic age acceleration in both mothers and newborns.

Colonization of the gut and airways by pathogenic bacteria can lead to local tissue destruction and life-threatening systemic infections, especially in immunologically compromised individuals. Here, we describe an mRNA-based platform enabling delivery of pathogen-specific immunoglobulin A (IgA) monoclonal antibodies into mucosal secretions. The platform consists of synthetic mRNA encoding IgA heavy, light, and joining (J) chains, packaged in lipid nanoparticles (LNPs) that express glycosylated, dimeric IgA with functional activity in vitro and in vivo. Importantly, mRNA-derived IgA had a significantly greater serum half-life and a more native glycosylation profile in mice than did a recombinantly produced IgA. Expression of an mRNA encoded Salmonella-specific IgA in mice resulted in intestinal localization and limited Peyer's patch invasion. The same mRNA-LNP technology was used to express a Pseudomonas-specific IgA that protected from a lung challenge. Leveraging the mRNA antibody technology as a means to intercept bacterial pathogens at mucosal surfaces opens up avenues for prophylactic and therapeutic interventions., Competing Interests: Declaration of interests C.E.D., A.F.R., T.Y., M.J.M., Z.W., Y.-T.L., B.R.F., S.H., D.L., R.K., S.L., C.J.H., I.L.R., H.K., M.K., A.C., and O.J.P. are employees of and shareholders in Moderna, Inc. C.E.D. and O.J.P. are co-inventors on international patent WO 2022/212191 A1. E.N. was an employee of and shareholder in Moderna Inc. at the time of the study., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

This study investigated the influence of large-diameter multifocal contact lenses on the ocular surface, visual quality, and visual function for presbyopic adults with dry eye syndromes. The study enrolled 40-55-year-old adults with presbyopia and dry eye syndromes (DES). The subjects were randomly assigned to three groups wearing different designs of contact lenses (Proclear, SMR, and Optimum) for 6-8 h a day for two weeks. Ocular surface health, tear quality, visual quality, and visual function were measured before and after lens wear. No significant difference was observed across all three groups for the amount of conjunctival redness, blink frequency (lens on), and stereopsis vision before and after wearing. Although there seemed to be a significant declining trend for corneal staining and limbal redness, non-invasive tear break-up time (TBUT), and lipid layer thickness while lens wear, the measured values were all within the normal range. Vice-versa after lens removal, results also showed significant improvement on lipid layer thickness, blink frequency (lens off), and contact TBUT. A significant improvement was observed in the modulation transfer function (MTF) of the total area ratio after wearing contact lenses. In contrast, the MTF of the high-order aberration area ratio resulting from lens wear was lower than that of the baseline measurement. There are also significant improvements observed for SMR and Optimum regarding near visual acuity, near point of accommodation, and the subjective questionnaire (OSDI and VBP) scores. Although it is difficult to avoid a specific negative impact on the ocular surface and tear film, visual function and visual quality can still be positively improved, especially shown on larger diameter and distance-center designed multifocal contact lenses., (© 2023. The Author(s).)

Intranasal vaccination represents a promising approach for preventing disease caused by respiratory pathogens by eliciting a mucosal immune response in the respiratory tract that may act as an early barrier to infection and transmission. This study investigated immunogenicity and protective efficacy of intranasally administered messenger RNA (mRNA)-lipid nanoparticle (LNP) encapsulated vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Syrian golden hamsters. Intranasal mRNA-LNP vaccination systemically induced spike-specific binding [immunoglobulin G (IgG) and IgA] and neutralizing antibodies. Intranasally vaccinated hamsters also had decreased viral loads in the respiratory tract, reduced lung pathology, and prevented weight loss after SARS-CoV-2 challenge. Together, this study demonstrates successful immunogenicity and protection against respiratory viral infection by an intranasally administered mRNA-LNP vaccine.

Introduction: Neuronal hyperactivity has been associated with many brain diseases. In the auditory system, hyperactivity has been linked to hyperacusis and tinnitus. Previous research demonstrated the development of hyperactivity in inferior colliculus (IC) neurons after sound overexposure, but the underlying mechanism of this hyperactivity remains unclear. The main goal of this study was to determine the mechanism of this hyperactivity., Methods: Experiments were performed on CBA/CaJ mice in a restrained, unanesthetized condition using intracellular recordings with sharp microelectrodes. Recordings were obtained from control (unexposed) and unilaterally sound overexposed groups of mice., Results: Our data suggest that sound exposure-induced hyperactivity was due to a depolarizing shift of the resting membrane potential (RMP) in the hyperactive neurons. The half width of action potentials in these neurons was also decreased after sound exposure. Surprisingly, we also found an RMP gradient in which neurons have more hyperpolarized RMPs with increasing depth in the IC. This gradient was altered in the overexposed animals., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Hsiao and Galazyuk.)

Background and Objectives: The Developmental Origins of Health and Disease hypothesis posits that early life adversity is associated with poor adult health outcomes. Epidemiological evidence has supported this framework by linking low birthweight with adult health and mortality, but the mechanisms remain unclear. Accelerated epigenetic aging may be a pathway to connect early life experiences with adult health outcomes, based on associations of accelerated epigenetic aging with increased morbidity and mortality., Methodology: Sixty-seven mother-infant dyads were recruited in the eastern Democratic Republic of Congo. Birthweight data were collected at birth, and blood samples were collected at birth and follow-up visits up to age 3. DNA methylation data were generated with the Illumina MethylationEPIC array and used to estimate epigenetic age. A multilevel model was used to test for associations between birthweight and epigenetic age acceleration., Results: Chronological age was highly correlated with epigenetic age from birth to age 3 ( r = 0.95, p < 2.2 × 10 -16 ). Variation in epigenetic age acceleration increased over time. Birthweight, dichotomized around 2500 g, predicted epigenetic age acceleration over the first 3 years of life ( b = -0.39, p = 0.005)., Conclusions and Implications: Our longitudinal analysis provides the first evidence for accelerated epigenetic aging that emerges between birth and age 3 and associates with low birthweight. These results suggest that early life experiences, such as low birthweight, may shape the trajectory of epigenetic aging in early childhood. Furthermore, accelerated epigenetic aging may be a pathway that links low birthweight and poor adult health outcomes., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.)

Zika virus (ZIKV), an arbovirus transmitted by mosquitoes, was identified as a cause of congenital disease during a major outbreak in the Americas in 2016. Vaccine design strategies relied on limited available isolate sequence information due to the rapid response necessary. The first-generation ZIKV mRNA vaccine, mRNA-1325, was initially generated and, as additional strain sequences became available, a second mRNA vaccine, mRNA-1893, was developed. Herein, we compared the immune responses following mRNA-1325 and mRNA-1893 vaccination and reported that mRNA-1893 generated comparable neutralizing antibody titers to mRNA-1325 at 1/20th of the dose and provided complete protection from ZIKV challenge in non-human primates. In-depth characterization of these vaccines indicated that the observed immunologic differences could be attributed to a single amino acid residue difference that compromised mRNA-1325 virus-like particle formation., (© 2023. The Author(s).)

Background: Perinatal health outcomes are influenced by a variety of socioeconomic, behavioral, and economic factors that reduce access to health services. Despite these observations, rural communities continue to face barriers, including a lack of resources and the fragmentation of health services., Objective: To evaluate patterns in health outcomes, health behaviors, socioeconomic vulnerability, and sociodemographic characteristics across rural and nonrural counties within a single health system catchment area., Methods: Socioeconomic vulnerability metrics, health care access as determined by licensed provider metrics, and behavioral data were obtained from FlHealthCHARTS.gov and the County Health Rankings. County-level birth and health data were obtained from the Florida Department of Health. The University of Florida Health Perinatal Catchment Area (UFHPCA) was defined as all Florida counties where ≥5% of all infants were delivered at Shands Hospital between June 2011 and April 2017., Results: The UFHPCA included 3 nonrural and 10 rural counties that represented more than 64,000 deliveries. Nearly 1 in 3 infants resided in a rural county, and 7 out of 13 counties did not have a licensed obstetrician gynecologist. Maternal smoking rates (range 6.8%-24.8%) were above the statewide rate (6.2%). Except for Alachua County, breastfeeding initiation rates (range 54.9%-81.4%) and access to household computing devices (range 72.8%-86.4%) were below the statewide rate (82.9% and 87.9%, respectively). Finally, we found that childhood poverty rates (range 16.3%-36.9%) were above the statewide rate (18.5%). Furthermore, risk ratios suggested negative health outcomes for residents of counties within the UFHPCA for each measure, except for infant mortality and maternal deaths, which lacked sample sizes to adequately test., Conclusions: The health burden of the UFHPCA is characterized by rural counties with increased maternal death, neonatal death, and preterm birth, as well as adverse health behaviors that included increased smoking during pregnancy and lower levels of breastfeeding relative to nonrural counties. Understanding perinatal health outcomes across a single health system has potential to not only estimate community needs but also facilitate planning of health care initiatives and interventions in rural and low-resource communities., Competing Interests: No competing financial interests exist., (© Dominick J. Lemas et al., 2022; Published by Mary Ann Liebert, Inc.)

For a vaccine to achieve durable immunity and optimal efficacy, many require a multi-dose primary vaccination schedule that acts to first "prime" naive immune systems and then "boost" initial immune responses by repeated immunizations (ie, prime-boost regimens). In the context of the global coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 2-dose primary vaccination regimens were often selected with short intervals between doses to provide rapid protection while still inducing robust immunity. However, emerging post-authorization evidence has suggested that longer intervals between doses 1 and 2 for SARS-CoV-2 vaccines may positively impact robustness and durability of immune responses. Here, the dosing interval for mRNA-1273, a messenger RNA based SARS-CoV-2 vaccine administered on a 2-dose primary schedule with 4 weeks between doses, was evaluated in mice by varying the dose interval between 1 and 8 weeks and examining immune responses through 24 weeks after dose 2. A dosing interval of 6 to 8 weeks generated the highest level of antigen-specific serum immunoglobulin G binding antibody titers. Differences in binding antibody titers between mRNA-1273 1 µg and 10 µg decreased over time for dosing intervals of ≥4 weeks, suggesting a potential dose-sparing effect. Longer intervals (≥4 weeks) also increased antibody-dependent cellular cytotoxicity activity and numbers of antibody-secreting cells (including long-lived plasma cells) after the second dose. An interval of 6 to 8 weeks elicited the strongest CD8+ T-cell responses, while an interval of 3 weeks elicited the strongest CD4+ T-cell response. Overall, these results suggest that in a non-pandemic setting, a longer interval (≥6 weeks) between the doses of the primary series for mRNA-1273 may induce more durable immune responses., Competing Interests: All authors are employees of Moderna, Inc., and hold stock/stock options from the company. The authors declare that this study received funding from Moderna, Inc. The funder was involved in the study design, collection, analysis, interpretation of data, and the writing of this article or the decision to submit it for publication., (Copyright © 2022 Garcia-Dominguez, Henry, Ma, Jani, Amato, Manning, Freyn, Davis, Hsiao, Li, Koch, Elbashir, DiPiazza, Carfi, Edwards and Bahl.)

Introduction: The COVID-19 pandemic created an unprecedented need for population-level clinical trials focused on the discovery of life-saving therapies and treatments. However, there is limited information on perception of research participation among perinatal populations, a population of particular interest during the pandemic., Methods: Eligible respondents were 18 years or older, were currently pregnant or had an infant (≤12 months old), and lived in Florida within 50 miles of sites participating in the OneFlorida Clinical Research Consortium. Respondents were recruited via Qualtrics panels between April and September 2020. Respondents completed survey items about barriers and facilitators to participation and answered sociodemographic questions., Results: Of 533 respondents, most were between 25 and 34 years of age ( n = 259, 49%) and identified as White ( n = 303, 47%) and non-Hispanic ( n = 344, 65%). Facebook was the most popular social media platform among our respondents. The most common barriers to research participation included poor explanation of study goals, discomforts to the infant, and time commitment. Recruitment through healthcare providers was perceived as the best way to learn about clinical research studies. When considering research participation, "myself" had the greatest influence, followed by familial ties. Noninvasive biological samples were highly acceptable. Hispanics had higher positive perspectives on willingness to participate in a randomized study ( p = 0.009). Education ( p = 0.007) had significant effects on willingness to release personal health information., Conclusion: When recruiting women during the pregnancy and postpartum periods for perinatal studies, investigators should consider protocols that account for common barriers and preferred study information sources. Social media-based recruitment is worthy of adoption., (© The Author(s) 2022.)

An extrahepatic manifestation of nephropathies can be a feature of the chronic hepatitis C virus (HCV) infection. Albuminuria is a major risk factor for nephropathies and chronic kidney disease (CKD). The correlation between HCV genotypes and albuminuria is still unclear. In this study, investigations have been done for the biomedical tools and methodologies used in the National Health and Nutrition Examination Survey (NHANES) public database. We searched the 2007−2016 NHANES public database to retrieve data regarding the different HCV genotypes and clinical scenarios. This study attempted to investigate the impacts of HCV genetic diversity, associated comorbidities, and racial differences on albuminuria. The urine albumin/creatinine ratio (ACR) was the primary endpoint. Among 40,856 participants, 336 participants with positive and 237 with negative HCV RNA tests were analyzed, excluding 14,454 participants with negative HCV antibodies and 25,828 which were missed. After controlling for sex, race, education level, smoking, diabetes mellitus, hepatitis B, alcohol use, and body mass index (BMI) with a generalized linear equation, HCV genotype 2 was more likely than any other genotype to cause albuminuria based on the urine ACR (p < 0.001). The generalized linear equation also demonstrated a significantly higher urine ACR, including hepatitis B (p < 0.001), diabetes mellitus (p < 0.001), and smoking (p = 0.026). In summary, the patients with HCV genotype 2 presented with increased albuminuria in comparison with other HCV genotypes in this 10-year retrospective analysis. HCV infection could be a risk factor of CKD; early diagnosis and appropriate treatment may improve clinical outcomes.

Interleukin-2 (IL-2) is critical for regulatory T cell (Treg) function and homeostasis. At low doses, IL-2 can suppress immune pathologies by expanding Tregs that constitutively express the high affinity IL-2Rα subunit. However, even low dose IL-2, signaling through the IL2-Rβ/γ complex, may lead to the activation of proinflammatory, non-Treg T cells, so improving specificity toward Tregs may be desirable. Here we use messenger RNAs (mRNA) to encode a half-life-extended human IL-2 mutein (HSA-IL2m) with mutations promoting reliance on IL-2Rα. Our data show that IL-2 mutein subcutaneous delivery as lipid-encapsulated mRNA nanoparticles selectively activates and expands Tregs in mice and non-human primates, and also reduces disease severity in mouse models of acute graft versus host disease and experimental autoimmune encephalomyelitis. Single cell RNA-sequencing of mouse splenic CD4 + T cells identifies multiple Treg states with distinct response dynamics following IL-2 mutein treatment. Our results thus demonstrate the potential of mRNA-encoded HSA-IL2m immunotherapy to treat autoimmune diseases., (© 2022. The Author(s).)

Background: Care plans are central to effective care delivery for people with multiple chronic conditions. But existing care plans-which typically are difficult to share across care settings and care team members-poorly serve people with multiple chronic conditions, who often receive care from numerous clinicians in multiple care settings. Comprehensive, shared electronic care (e-care) plans are dynamic electronic tools that facilitate care coordination and address the totality of health and social needs across care contexts. They have emerged as a potential way to improve care for individuals with multiple chronic conditions., Objective: To review the landscape of e-care plans and care plan-related initiatives that could allow the creation of a comprehensive, shared e-care plan and inform a joint initiative by the National Institutes of Health and the Agency for Healthcare Research and Quality to develop e-care planning tools for people with multiple chronic conditions., Methods: We conducted a scoping review, searching literature from 2015 to June 2020 using Scopus, Clinical Key, and PubMed; we also searched the gray literature. To identify initiatives potentially missing from this search, we interviewed expert informants. Relevant data were then identified and extracted in a structured format for data synthesis and analysis using an expanded typology of care plans adapted to our study context. The extracted data included (1) the perspective of the initiatives; (2) their scope, (3) network, and (4) context; (5) their use of open syntax standards; and (6) their use of open semantic standards., Results: We identified 7 projects for e-care plans and 3 projects for health care data standards. Each project provided critical infrastructure that could be leveraged to promote the vision of a comprehensive, shared e-care plan. All the e-care plan projects supported both broad goals and specific behaviors; 1 project supported a network of professionals across clinical, community, and home-based networks; 4 projects included social determinants of health. Most projects specified an open syntax standard, but only 3 specified open semantic standards., Conclusions: A comprehensive, shared, interoperable e-care plan has the potential to greatly improve the coordination of care for individuals with multiple chronic conditions across multiple care settings. The need for such a plan is heightened in the wake of the ongoing COVID-19 pandemic. While none of the existing care plan projects meet all the criteria for an optimal e-care plan, they all provide critical infrastructure that can be leveraged as we advance toward the vision of a comprehensive, shared e-care plan. However, critical gaps must be addressed in order to achieve this vision., (©Jenna M Norton, Alex Ip, Nicole Ruggiano, Tolulope Abidogun, Djibril Souleymane Camara, Helen Fu, Bat-Zion Hose, Saadia Miran, Chun-Ju Hsiao, Jing Wang, Arlene S Bierman. Originally published in the Journal of Medical Internet Research (https://www.jmir.org), 10.06.2022.)

Phenylalanine ammonia-lyase (PAL) catalyzes the nonoxidative deamination of phenylalanine to yield trans -cinnamic acid and ammonia. Recombinant Bambusa oldhamii BoPAL1/2 proteins were immobilized onto electrospun nanofibers by dextran polyaldehyde as a cross-linking agent. A central composite design (CCD)-response surface methodology (RSM) was utilized to optimize the electrospinning parameters. Escherichia coli expressed eBoPAL2 exhibited the highest catalytic efficiency among four enzymes. The optimum conditions for fabricating nanofibers were determined as follows: flow rate of 0.10 mL/h, voltage of 13.8 kV, and distance of 13 cm. The response surface models were used to obtain the smaller the fiber diameters as well as the highest PAL activity in the enzyme immobilization. Compared with free BoPALs, immobilized BoPALs can be reused for at least 6 consecutive cycles. The remained activity of the immobilized BoPAL proteins after storage at 4 °C for 30 days were between 75 and 83%. In addition, the tolerance against denaturants of the immobilized BoPAL proteins were significantly enhanced. As a result, the dextran polyaldehyde natural cross-linking agent can effectively replace traditional chemical cross-linking agents for the immobilization of the BoPAL enzymes. The PAL/nylon 6/polyvinyl alcohol (PVA)/chitosan (CS) nanofibers made are extremely stable and are practical for industrial applications in the future.

Objective: Despite a proliferation of applications (apps) to conveniently collect patient-reported outcomes (PROs) from patients, PRO data are yet to be seamlessly integrated with electronic health records (EHRs) in a way that improves interoperability and scalability. We applied the newly created PRO standards from the Office of the National Coordinator for Health Information Technology to facilitate the collection and integration of standardized PRO data. A novel multitiered architecture was created to enable seamless integration of PRO data via Substitutable Medical Apps and Reusable Technologies on Fast Healthcare Interoperability Resources apps and scaled to different EHR platforms in multiple ambulatory settings., Materials and Methods: We used a standards-based approach to deploy 2 apps that source and surface PRO data in real-time for provider use within the EHR and which rely on PRO assessments from an external center to streamline app and EHR integration., Results: The apps were developed to enable patients to answer validated assessments (eg, a Patient-Reported Outcomes Measurement Information System including using a Computer Adaptive Test format). Both apps were developed to populate the EHR in real time using the Health Level Seven FHIR standard allowing providers to view patients' data during the clinical encounter. The process of implementing this architecture with 2 different apps across 18 ambulatory care sites and 3 different EHR platforms is described., Conclusion: Our approach and solution proved feasible, secure, and time- and resource-efficient. We offer actionable guidance for this technology to be scaled and adapted to promote adoption in diverse ambulatory care settings and across different EHRs., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Neural hyperactivity induced by sound exposure often correlates with the development of hyperacusis and/or tinnitus. In laboratory animals, hyperactivity is typically induced by unilateral sound exposure to preserve one ear for further testing of hearing performance. Most ascending fibers in the auditory system cross into the superior olivary complex and then ascend contralaterally. Therefore, unilateral exposure should be expected to mostly affect the contralateral side above the auditory brain stem. On the other hand, it is well known that a significant number of neurons have crossing fibers at every level of the auditory pathway, which may spread the effect of unilateral exposure onto the ipsilateral side. Here we demonstrate that unilateral sound exposure causes development of hyperactivity in both the contra and ipsilateral inferior colliculus in mice. We found that both the spontaneous firing rate and bursting activity were increased significantly compared to unexposed mice. The neurons with characteristic frequencies at or above the center frequency of exposure showed the greatest increase. Surprisingly, this increase was more pronounced in the ipsilateral inferior colliculus. This study highlights the importance of considering both ipsi- and contralateral effects in future studies utilizing unilateral sound exposure., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Hsiao and Galazyuk.)

Intracerebral hemorrhage (ICH) is a devastating neurological disorder characterized by an exacerbation of neuroinflammation and neuronal injury, for which few effective therapies are available at present. Inhibition of excessive neuroglial activation has been reported to alleviate ICH-related brain injuries. In the present study, the anti-ICH activity and microglial mechanism of ergosta-7,9(11),22-trien-3β-ol (EK100), a bioactive ingredient from Asian medicinal herb Antrodia camphorate , were evaluated. Post-treatment of EK100 significantly attenuated neurobehavioral deficit and MRI-related brain lesion in the mice model of collagenase-induced ICH. Additionally, EK100 alleviated the inducible expression of cyclooxygenase (COX)-2 and the activity of matrix metalloproteinase (MMP)-9 in the ipsilateral brain regions. Consistently, it was shown that EK100 concentration-dependently inhibited the expression of COX-2 protein in Toll-like receptor (TLR)-4 activator lipopolysaccharide (LPS)-activated microglial BV-2 and primary microglial cells. Furthermore, the production of microglial prostaglandin E 2 and reactive oxygen species were attenuated by EK100. EK100 also attenuated the induction of astrocytic MMP-9 activation. Among several signaling pathways, EK100 significantly and concentration-dependently inhibited activation of c-Jun N-terminal kinase (JNK) MAPK in LPS-activated microglial BV-2 cells. Consistently, ipsilateral JNK activation was markedly inhibited by post-ICH-treated EK100 in vivo. In conclusion, EK100 exerted the inhibitory actions on microglial JNK activation, and attenuated brain COX-2 expression, MMP-9 activation, and brain injuries in the mice ICH model. Thus, EK100 may be proposed and employed as a potential therapeutic agent for ICH.

Clinicians face competing pressures of being clinically productive while using imperfect electronic health record (EHR) systems and maximizing face-to-face time with patients. EHR use is increasingly associated with clinician burnout and underscores the need for interventions to improve clinicians' experiences. With an aim of addressing this need, we share evidence-based informatics approaches, pragmatic next steps, and future research directions to improve 3 of the highest contributors to EHR burden: (1) documentation, (2) chart review, and (3) inbox tasks. These approaches leverage speech recognition technologies, natural language processing, artificial intelligence, and redesign of EHR workflow and user interfaces. We also offer a perspective on how EHR vendors, healthcare system leaders, and policymakers all play an integral role while sharing responsibility in helping make evidence-based sociotechnical solutions available and easy to use., (Published by Oxford University Press on behalf of the American Medical Informatics Association 2020. This work is written by US Government employees and is in the public domain in the US.)

Importance: The association of the nasal microbiome with outcomes in surgical patients is poorly understood., Objective: To characterize the composition of nasal microbiota in patients undergoing clean elective surgical procedures and to examine the association between characteristics of preoperative nasal microbiota and occurrence of postoperative infection., Design, Setting, and Participants: Using a nested matched case-control design, 53 individuals who developed postoperative infection were matched (approximately 3:1 by age, sex, and surgical procedure) with 144 individuals who were not infected (ie, the control group). The 2 groups were selected from a prospective cohort of patients undergoing surgical procedures at 2 tertiary care university hospitals in Baltimore, Maryland, who were at high risk for postoperative infectious complications. Included individuals were aged 40 years or older; had no history of autoimmune disease, immunocompromised state, immune-modulating medication, or active infection; and were scheduled to undergo elective cardiac, vascular, spinal, or intracranial surgical procedure. Data were analyzed from October 2015 through September 2020., Exposures: Nasal microbiome cluster class served as the main exposure. An unsupervised clustering method (ie, grades of membership modeling) was used to classify nasal microbial samples into 2 groups based on features derived from 16S ribosomal RNA gene sequencing. The microbiome cluster groups were derived independently and agnostic of baseline clinical characteristics and infection status., Main Outcomes and Measures: Composite of surgical site infection, bacteremia, and pneumonia occurring within 6 months after surgical procedure., Results: Among 197 participants (mean [SD] age, 64.1 [10.6] years; 63 [37.7%] women), 553 bacterial taxa were identified from preoperative nasal swab samples. A 2-cluster model (with 167 patients in cluster 1 and 30 patients in cluster 2) accounted for the largest proportion of variance in microbial profiles using grades of membership modeling and was most parsimonious. After adjusting for potential confounders, the probability of assignment to cluster 2 was associated with 6-fold higher odds of infection after surgical procedure (odds ratio [OR], 6.18; 95% CI, 3.33-11.7; P < .001) independent of baseline clinical characteristics, including nasal carriage of Staphylococcus aureus. Intrasample (ie, α) diversity was inversely associated with infectious outcome in both clusters (OR, 0.57; 95% CI, 0.42-0.75; P < .001); however, probability of assignment to cluster 2 was associated with higher odds of infection independent of α diversity (OR, 4.61; 95% CI, 2.78-7.86; P < .001)., Conclusions and Relevance: These findings suggest that the nasal microbiome was an independent risk factor associated with infectious outcomes among individuals who underwent elective surgical procedures and may serve as a biomarker associated with infection susceptibility in this population.

As an intracellular pathogen, the reproduction of the hepatitis B virus (HBV) depends on the occupancy of host metabolism machinery. Here we test a hypothesis if HBV may govern intracellular biosynthesis to achieve a productive reproduction. To test this hypothesis, we set up an affinity purification screen for host factors that interact with large viral surface antigens (LHBS). This identified pyruvate kinase isoform M2 (PKM2), a key regulator of glucose metabolism, as a binding partner of viral surface antigens. We showed that the expression of viral LHBS affected oligomerization of PKM2 in hepatocytes, thereby increasing glucose consumption and lactate production, a phenomenon known as aerobic glycolysis. Reduction of PKM2 activity was also validated in several different models, including HBV-infected HepG2-NTCP-C4 cells, adenovirus mediated HBV gene transduction and transfection with a plasmid containing complete HBV genome on HuH-7 cells. We found the recovery of PKM2 activity in hepatocytes by chemical activators, TEPP-46 or DASA-58, reduced expressions of viral surface and core antigens. In addition, reduction of glycolysis by culturing in low-glucose condition or treatment with 2-deoxyglucose also decreased expressions of viral surface antigen, without affecting general host proteins. Finally, TEPP-46 largely suppressed proliferation of LHBS-positive cells on 3-dimensional agarose plates, but showed no effect on the traditional 2-dimensional cell culture. Taken together, these results indicate that HBV-induced metabolic switch may support its own translation in hepatocytes. In addition, aerobic glycolysis is likely essential for LHBS-mediated oncogenesis. Accordingly, restriction of glucose metabolism may be considered as a novel strategy to restrain viral protein synthesis and subsequent oncogenesis during chronic HBV infection., Competing Interests: The authors have declared that no competing interests exist.

Background: Electronic health records (EHRs) hold great potential for longitudinal mother-baby studies, ranging from assessing study feasibility to facilitating patient recruitment to streamlining study visits and data collection. Existing studies on the perspectives of pregnant and breastfeeding women on EHR use have been limited to the use of EHRs to engage in health care rather than to participate in research., Objective: The aim of this study is to explore the perspectives of pregnant and breastfeeding women on releasing their own and their infants' EHR data for longitudinal research to identify factors affecting their willingness to participate in research., Methods: We conducted semistructured interviews with pregnant or breastfeeding women from Alachua County, Florida. Participants were asked about their familiarity with EHRs and EHR patient portals, their comfort with releasing maternal and infant EHR data to researchers, the length of time of the data release, and whether individual research test results should be included in the EHR. The interviews were transcribed verbatim. Transcripts were organized and coded using the NVivo 12 software (QSR International), and coded data were thematically analyzed using constant comparison., Results: Participants included 29 pregnant or breastfeeding women aged between 22 and 39 years. More than half of the sample had at least an associate degree or higher. Nearly all participants (27/29, 93%) were familiar with EHRs and had experience accessing an EHR patient portal. Less than half of the participants (12/29, 41%) were willing to make EHR data available to researchers for the duration of a study or longer. Participants' concerns about sharing EHRs for research purposes emerged in 3 thematic domains: privacy and confidentiality, transparency by the research team, and surrogate decision-making on behalf of infants. The potential release of sensitive or stigmatizing information, such as mental or sexual health history, was considered in the decisions to release EHRs. Some participants viewed the simultaneous use of their EHRs for both health care and research as potentially beneficial, whereas others expressed concerns about mixing their health care with research., Conclusions: This exploratory study indicates that pregnant and breastfeeding women may be willing to release EHR data to researchers if researchers adequately address their concerns regarding the study design, communication, and data management. Pregnant and breastfeeding women should be included in EHR-based research as long as researchers are prepared to address their concerns., (©Austen Hentschel, Chu J Hsiao, Lynn Y Chen, Lauren Wright, Jennifer Shaw, Xinsong Du, Elizabeth Flood-Grady, Christopher A Harle, Callie F Reeder, Magda Francois, Adetola Louis-Jacques, Elizabeth Shenkman, Janice L Krieger, Dominick J Lemas. Originally published in JMIR Pediatrics and Parenting (http://pediatrics.jmir.org), 05.03.2021.)

Background Current estimates of sexual harassment across the academic hierarchy are subject to recall bias and have limited comparability between studies due to inconsistent time frames queried for each stage of training. No studies have surveyed medical students, residents/fellows, and faculty collectively and many studies exclude a wide range of sexual harassment behaviors. We assessed the incidence of sexual harassment across the different stages of academic medicine over the same time frame and within the same institutional culture. Methodology Medical students, residents/fellows, and faculty at the same academic medical campus completed a prospective online study of sexual harassment experiences in 2018. We used a tool that comprehensively assessed sexual harassment behaviors and asked about the perpetrators. Pearson's chi-square and Fisher's exact tests (for cell counts <5) were used to compare responses by academic status and gender. Participants were also asked to suggest ways to improve knowledge about university/hospital policies, support services, and reporting process on sexual harassment. Results One-third of 515 respondents (18% of invitations) reported experiencing sexual harassment in 2018. Overall, 52% of medical students, 31% of residents/fellows, and 25% of faculty respondents experienced sexual harassment. Of these, 46% of women and 19% of men reported sexual harassment experiences. The most common experiences across all levels of academic hierarchy were offensive and sexually suggestive comments or jokes and offensive and intrusive questions about one's private life or physical appearance. The most common perpetrators were "student, intern, resident, or fellow," followed by "patient or patient's family member." To improve knowledge about the policies and services regarding sexual harassment, participants suggested facilitating easy access to resources, increasing awareness, assuring confidentiality, protecting against retaliation, and continued education and reminders about the topic. Conclusions Sexual harassment may be more prevalent than the literature suggests and incidence tends to decrease with increasing academic hierarchy. Harassment can often be subtle and can pass under the radar., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2021, Hsiao et al.)

Objectives: The primary aim is to provide a summary of evidence for the diagnostic accuracies of multiplex PCR gastrointestinal (GI) panels-BioFire FilmArray and Luminex xTAG on the detection of gastroenteritis pathogens. The secondary aim is to compare the performance of these GI panels head to head., Methods: A comprehensive search up to 1 December 2019 was conducted on PubMed, Embase, Ovid Medline and Web of Science for studies that used FilmArray or Luminex xTAG Gastrointestinal Pathogen Panel (GPP) for diagnosis of acute gastroenteritis. A summary of diagnostic accuracies for the 16 pathogens were calculated by comparing the GI panels to the current gold standards (conventional standard microbiology techniques such as culture or PCR for bacteria, PCR or enzyme immunoassay (EIA) for viruses, microscopy or EIA for parasite). Hierarchical summary receiver operating characteristic (HSROC) curve analysis, pretest and post-test probabilities were used for estimating the pathogen detection performance., Results: A total of 11 studies with 7085 stool samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with specificity ≧0.98 and area under the ROC curve (AUROC) ≧0.97 for all the pathogens except for Yersinia enterocolitica (AUROC 0.91). The FilmArray panel demonstrated a higher sensitivity than xTAG GPP for most of the pathogens with the exception of Rotavirus A (xTAG GPP and FilmArray were both 0.93)., Conclusions: This is the first meta-analysis that is a head-to-head comparison examining the performance of the novel multiplex PCR-based tests Luminex xTAG GPP and FilmArray GI panel in detecting each pathogen. Point estimates calculated from eligible studies showed that both GI panels are highly accurate and may provide important diagnostic information for early identification of gastroenteritis. In addition, although FilmArray has higher sensitivity and post-test probability than xTAG GPP for most of the pathogens, how this will translate to a clinical setting remains unclear., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Investigation of the microbiome during early life has stimulated an increasing number of cohort studies in pregnant and breastfeeding women that require non-invasive biospecimen collection. The objective of this study was to explore pregnant and breastfeeding women's perspectives on longitudinal clinical studies that require non-invasive biospecimen collection and how they relate to study logistics and research participation., Methods: We completed in-depth semi-structured interviews with 40 women who were either pregnant (n = 20) or breastfeeding (n = 20) to identify their understanding of longitudinal clinical research, the motivations and barriers to their participation in such research, and their preferences for providing non-invasive biospecimen samples., Results: Perspectives on research participation were focused on breastfeeding and perinatal education. Participants cited direct benefits of research participation that included flexible childcare, lactation support, and incentives and compensation. Healthcare providers, physician offices, and social media were cited as credible sources and channels for recruitment. Participants viewed lengthy study visits and child protection as the primary barriers to research participation. The barriers to biospecimen collection were centered on stool sampling, inadequate instructions, and drop-off convenience., Conclusion: Women in this study were interested in participating in clinical studies that require non-invasive biospecimen collection, and motivations to participate center on breastfeeding and the potential to make a scientific contribution that helps others. Effectively recruiting pregnant or breastfeeding participants for longitudinal microbiome studies requires protocols that account for participant interests and consideration for their time.

BACKGROUNDObesity has been associated with attenuated vaccine responses and an increased risk of contracting pneumococcal pneumonia, but no study to our knowledge has assessed the impact of obesity and genetics on 23-valent pneumococcal vaccine (PPSV23) efficacy. We assessed the relationship of obesity (primary analysis) and stimulator of interferon genes (STING1) genotype (secondary analysis) on PPSV23 efficacy.METHODSNonobese (BMI 22-25 kg/m2) and obese participants (BMI ≥30 kg/m2) were given a single dose of PPSV23. Blood was drawn immediately prior to and 4-6 weeks after vaccination. Serum samples were used to assess PPSV23-specific antibodies. STING1 genotypes were identified using PCR on DNA extracted from peripheral blood samples.RESULTSForty-six participants were categorized as nonobese (n = 23; 56.5% women; mean BMI 23.3 kg/m2) or obese (n = 23; 65.2% women; mean BMI 36.3 kg/m2). Obese participants had an elevated fold change in vaccine-specific responses compared with nonobese participants (P < 0.0001). The WT STING1 group (R232/R232) had a significantly higher PPSV23 response than individuals with a single copy of HAQ-STING1 regardless of BMI (P = 0.0025). When WT was assessed alone, obese participants had a higher fold serotype-specific response compared with nonobese participants (P < 0.0001), but no difference was observed between obese and nonobese individuals with 1 HAQ allele (P = 0.693).CONCLUSIONSThese observations demonstrate a positive association between obesity and PPSV23 efficacy specifically in participants with the WT STING1 genotype.TRIAL REGISTRATIONClinicalTrials.gov NCT02471014.FUNDINGThis research was supported by the NIH and the University of Florida MD-PhD Training Program.

Cellular heterogeneity in gene expression is driven by cellular processes, such as cell cycle and cell-type identity, and cellular environment such as spatial location. The cell cycle, in particular, is thought to be a key driver of cell-to-cell heterogeneity in gene expression, even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq to measure cell cycle phase and gene expression levels in human induced pluripotent stem cells (iPSCs). By using these data, we developed a novel approach to characterize cell cycle progression. Although standard methods assign cells to discrete cell cycle stages, our method goes beyond this and quantifies cell cycle progression on a continuum. We found that, on average, scRNA-seq data from only five genes predicted a cell's position on the cell cycle continuum to within 14% of the entire cycle and that using more genes did not improve this accuracy. Our data and predictor of cell cycle phase can directly help future studies to account for cell cycle-related heterogeneity in iPSCs. Our results and methods also provide a foundation for future work to characterize the effects of the cell cycle on expression heterogeneity in other cell types., (© 2020 Hsiao et al.; Published by Cold Spring Harbor Laboratory Press.)

Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and analysis approaches. In addition, when samples from multiple tissues were studied in a comparative framework, individuals and tissues were confounded. We designed a multitissue comparative study of gene expression and DNA methylation in primates that minimizes confounding effects by using a balanced design with respect to species, tissues, and individuals. We also developed a comparative analysis pipeline that minimizes biases attributable to sequence divergence. Thus, we present the most comprehensive catalog of similarities and differences in gene expression and DNA methylation levels between livers, kidneys, hearts, and lungs, in humans, chimpanzees, and rhesus macaques. We estimate that overall, interspecies and inter-tissue differences in gene expression levels can only modestly be accounted for by corresponding differences in promoter DNA methylation. However, the expression pattern of genes with conserved inter-tissue expression differences can be explained by corresponding interspecies methylation changes more often. Finally, we show that genes whose tissue-specific regulatory patterns are consistent with the action of natural selection are highly connected in both gene regulatory and protein-protein interaction networks., (© 2020 Blake et al.; Published by Cold Spring Harbor Laboratory Press.)

A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in both speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. Chromatin conformation capture technologies have enabled genome-wide quantifications of such distal 3D interactions. However, relatively little comparative research in primates has been done using such technologies. To address this gap, we used Hi-C to characterize 3D chromatin interactions in induced pluripotent stem cells (iPSCs) from humans and chimpanzees. We also used RNA-seq to collect gene expression data from the same lines. We generally observed that lower-order, pairwise 3D genomic interactions are conserved in humans and chimpanzees, but higher order genomic structures, such as topologically associating domains (TADs), are not as conserved. Inter-species differences in 3D genomic interactions are often associated with gene expression differences between the species. To provide additional functional context to our observations, we considered previously published chromatin data from human stem cells. We found that inter-species differences in 3D genomic interactions, which are also associated with gene expression differences between the species, are enriched for both active and repressive marks. Overall, our data demonstrate that, as expected, an understanding of 3D genome reorganization is key to explaining regulatory evolution., Competing Interests: The authors have declared that no competing interests exist.

Background: Patient-Reported Outcomes (PROs) can be used to inform the clinical management of individuals, including patient self-management, care planning, and goal setting. Despite a rapid proliferation of technology to collect and integrate PROs in clinical care, uptake by patients and healthcare providers remains sub optimal. A consideration of systems factors to understand these challenges is needed., Objectives: To apply the socio-technical systems (STS) model as a framework for understanding the usability and functional requirements of patients collecting PRO data using applications (apps), and of healthcare providers using these data at the point of care in ambulatory settings., Methods: With questions guided by the STS model, semi-structured interviews were conducted with eighteen patients and nine healthcare providers to elicit feedback about facilitators and barriers to successful use of PRO apps and PRO data in ambulatory settings. Patient participants were selected to fit into two categories: older, low utilizers of technology with less than a bachelor's degree, and younger higher utilizers of technology with at least a bachelor's degree. Participants were from primary and specialty care practices. Data were analyzed inductively to identify emergent themes., Results: Younger patients were only interested in using a PRO app if they had an active health issue to track. The nine older patients preferred passive means of data collection if they were to track a health issue, and preferred direct contact with their healthcare provider and using office visits to share information. All patients desired optimal usability and emphasized bidirectional communication in an app that is transparent about privacy. All nine healthcare providers agreed that PRO data would be most useful and relevant if key patient populations were targeted based on the specific measure. In this case the healthcare providers noted potentially optimal utility of collecting physical function PRO data for patients 65 and older. Access to the data was highlighted by each healthcare provider stating that these data would be most useful if they were seamlessly integrated into the electronic health record., Discussion: Several emergent themes were identified under the five selected dimensions of the STS model (clinical content, human computer interface, hardware and software computing infrastructure, people, and workflow and communication). Findings highlighted the continued need for innovative methods to obtain more rapid cycle, continuous feedback to identify system factors impacting use of these technologies., Conclusion: The STS model provides a comprehensive framework that can be applied to collect patient and healthcare provider feedback to better guide the design and implementation of new health information technology., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.)

The primary cilium is a tiny cell protrusion known to transduce key extracellular signals, including those of the sonic hedgehog pathway, which activates Gli transcription factors for various cellular functions. To understand the significance of the Gli2 transcription factor in fibroblasts, we establish a Gli2-knockout NIH3T3 cell line by CRISPR/Cas9 technology. Surprisingly, NIH3T3 fibroblasts lacking Gli2 expression through gene knockout or RNA interference possess longer primary cilia after stimulation of ciliogenesis by serum starvation. This lengthening of primary cilia is associated with enhanced autophagy-mediated Ofd1 degradation, and can be reversed by pharmacological and genetic inhibition of autophagy. Meanwhile, flow cytometry reveals that Gli2 -/- NIH3T3 fibroblasts exhibit a delay in cell cycle re-entry after serum re-stimulation. Ablation of their primary cilia through Kif3a knockdown rescues the delay in cell cycle re-entry. These results suggest that Gli2 plays an unexpected role in cell cycle re-entry through an autophagy-mediated regulation on ciliary length in fibroblasts., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2018. Published by The Company of Biologists Ltd.)

Background: There is substantial interest in the evolutionary forces that shaped the regulatory framework in early human development. Progress in this area has been slow because it is difficult to obtain relevant biological samples. Induced pluripotent stem cells (iPSCs) may provide the ability to establish in vitro models of early human and non-human primate developmental stages., Results: Using matched iPSC panels from humans and chimpanzees, we comparatively characterize gene regulatory changes through a four-day time course differentiation of iPSCs into primary streak, endoderm progenitors, and definitive endoderm. As might be expected, we find that differentiation stage is the major driver of variation in gene expression levels, followed by species. We identify thousands of differentially expressed genes between humans and chimpanzees in each differentiation stage. Yet, when we consider gene-specific dynamic regulatory trajectories throughout the time course, we find that at least 75% of genes, including nearly all known endoderm developmental markers, have similar trajectories in the two species. Interestingly, we observe a marked reduction of both intra- and inter-species variation in gene expression levels in primitive streak samples compared to the iPSCs, with a recovery of regulatory variation in endoderm progenitors., Conclusions: The reduction of variation in gene expression levels at a specific developmental stage, paired with overall high degree of conservation of temporal gene regulation, is consistent with the dynamics of a conserved developmental process.

Phosphorylation of proteins on serine, threonine, and tyrosine residues is a ubiquitous post-translational modification that plays a key part of essentially every cell signaling process. It is reasonable to assume that inter-individual variation in protein phosphorylation may underlie phenotypic differences, as has been observed for practically any other molecular regulatory phenotype. However, we do not know much about the extent of inter-individual variation in phosphorylation because it is quite challenging to perform a quantitative high throughput study to assess inter-individual variation in any post-translational modification. To test our ability to address this challenge with SILAC-based mass spectrometry, we quantified phosphorylation levels for three genotyped human cell lines within a nested experimental framework, and found that genetic background is the primary determinant of phosphoproteome variation. We uncovered multiple functional, biophysical, and genetic associations with germline driven phosphopeptide variation. Variants affecting protein levels or structure were among these associations, with the latter presenting, on average, a stronger effect. Interestingly, we found evidence that is consistent with a phosphopeptide variability buffering effect endowed from properties enriched within longer proteins. Because the small sample size in this 'pilot' study may limit the applicability of our genetic observations, we also undertook a thorough technical assessment of our experimental workflow to aid further efforts. Taken together, these results provide the foundation for future work to characterize inter-individual variation in post-translational modification levels and reveal novel insights into the nature of inter-individual variation in phosphorylation.

Background: Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription., Results: To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee, and rhesus macaque. We further integrated messenger RNA and protein level measurements collected from matching cell lines. We find that, in addition to transcriptional regulation, the major factor determining protein level divergence between human and closely related species is post-translational buffering. Inter-species divergence in transcription is generally propagated to the level of protein translation. In contrast, gene expression divergence is often attenuated post-translationally, potentially mediated through post-translational modifications., Conclusions: Results from our analysis indicate that post-translational buffering is a conserved mechanism that led to relaxation of selective constraint on transcript levels in humans.

Much evidence has indicated that matrix metalloproteinases (MMPs) participate in the progression of neuroinflammatory disorders. The present study was undertaken to investigate the inhibitory effect and mechanism of the antipsychotic haloperidol on MMP activation in the stimulated THP-1 monocytic cells. Haloperidol exerted a strong inhibition on tumor necrosis factor- (TNF-) α -induced MMP-9 gelatinolysis of THP-1 cells. A concentration-dependent inhibitory effect of haloperidol was observed in TNF- α -induced protein and mRNA expression of MMP-9. On the other hand, haloperidol slightly affected cell viability and tissue inhibition of metalloproteinase-1 levels. It significantly inhibited the degradation of inhibitor- κ B- α (I κ B α ) in activated cells. Moreover, it suppressed activated nuclear factor- κ B (NF- κ B) detected by a mobility shift assay, NF- κ B reporter gene, and chromatin immunoprecipitation analyses. Consistent with NF- κ B inhibition, haloperidol exerted a strong inhibition of lipopolysaccharide- (LPS-) induced MMP-9 gelatinolysis but not of transforming growth factor- β 1-induced MMP-2. In in vivo studies, administration of haloperidol significantly attenuated LPS-induced intracerebral MMP-9 activation of the brain homogenate and the in situ in C57BL/6 mice. In conclusion, the selective anti-MMP-9 activation of haloperidol could possibly involve the inhibition of the NF- κ B signal pathway. Hence, it was found that haloperidol treatment may represent a bystander of anti-MMP actions for its conventional psychotherapy.

Grade of membership models, also known as "admixture models", "topic models" or "Latent Dirichlet Allocation", are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple "populations", and in natural language processing to model documents having words from multiple "topics". Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells. We also provide methods to help interpret the clusters, by identifying genes that are distinctively expressed in each cluster. By applying these methods to several example RNA-seq applications we demonstrate their utility in identifying and summarizing structure and heterogeneity. Applied to data from the GTEx project on 53 human tissues, the approach highlights similarities among biologically-related tissues and identifies distinctively-expressed genes that recapitulate known biology. Applied to single-cell expression data from mouse preimplantation embryos, the approach highlights both discrete and continuous variation through early embryonic development stages, and highlights genes involved in a variety of relevant processes-from germ cell development, through compaction and morula formation, to the formation of inner cell mass and trophoblast at the blastocyst stage. The methods are implemented in the Bioconductor package CountClust.

Single-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single-cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias. We found that the major source of variation in the gene expression data was driven by genotype, but we also observed substantial variation between the technical replicates. We observed that the conversion of reads to molecules using the UMIs was impacted by both biological and technical variation, indicating that UMI counts are not an unbiased estimator of gene expression levels. Based on our results, we suggest a framework for effective scRNA-seq studies.

Previous genome-wide association studies using P-values to select single nucleotide polymorphisms (SNPs) have suffered from high false-positive and false-negative results. This case-control study recruited 713 late-onset Alzheimer's disease (LOAD) cases and controls aged ≥65 from three teaching hospitals in northern Taiwan from 2007 to 2010. Performance metrics were used to select SNPs in stage 1, which were then genotyped to another dataset (stage 2). Four SNPs (CPXM2 rs2362967, APOC1 rs4420638, ZNF521 rs7230380, and rs12965520) were identified for LOAD by both traditional P-values (without correcting for multiple tests) and performance metrics. After correction for multiple tests, no SNPs were identified by traditional P-values. Simultaneous testing of APOE e4 and APOC1 rs4420638 (the SNP with the best performance in the performance metrics) significantly improved the low sensitivity of APOE e4 from 0.50 to 0.78. A point-based genetic model including these 2 SNPs and important covariates was constructed. Compared with elders with low-risks score (0-6), elders belonging to moderate-risk (score = 7-11) and high-risk (score = 12-18) groups showed a significantly increased risk of LOAD (adjusted odds ratio = 7.80 and 46.93, respectively; P trend  < 0.0001). Performance metrics allow for identification of markers with moderate effect and are useful for creating genetic tests with clinical and public health implications.

Type IV paraesophageal hernia (PEH) is very rare, and is characterized by the intrathoracic herniation of the abdominal viscera other than the stomach into the chest. We describe a 78-year-old woman who presented at our emergency department because of epigastric pain that she had experienced over the past 24 h. On the day after admission, her pain became severe and was accompanied by right chest pain and dyspnea. Chest radiography revealed an intrathoracic intestinal gas bubble occupying the right lower lung field. Emergency explorative laparotomy identified a type IV PEH with herniation of only the terminal ileum through a hiatal defect into the right thoracic cavity. In this report, we also present a review of similar cases in the literature published between 1980 and 2015 in PubMed. There were four published cases of small bowel herniation into the thoracic cavity during this period. Our patient represents a rare case of an individual diagnosed with type IV PEH with incarceration of only the terminal ileum.