Research to classrooms: a co-designed curriculum brings All of Us data to secondary schools.

OBJECTIVES: We describe new curriculum materials for engaging secondary school students in exploring the "big data" in the NIH All of Us Research Program's Public Data Browser and the co-design processes used to collaboratively develop the materials. We also describe the methods used to develop and validate assessment items for studying the efficacy of the materials for student learning as well as preliminary findings from these studies. MATERIALS AND METHODS: Secondary-level biology teachers from across the United States participated in a 2.5-day Co-design Summer Institute. After learning about the All of Us Research Program and its Data Browser, they collaboratively developed learning objectives and initial ideas for learning experiences related to exploring the Data Browser and big data. The Genetic Science Learning Center team at the University of Utah further developed the educators' ideas. Additional teachers and their students participated in classroom pilot studies to validate a 22-item instrument that assesses students' knowledge. Educators completed surveys about the materials and their experiences. RESULTS: The "Exploring Big Data with the All of Us Data Browser" curriculum module includes 3 data exploration guides that engage students in using the Data Browser, 3 related multimedia pieces, and teacher support materials. Pilot testing showed substantial growth in students' understanding of key big data concepts and research applications. DISCUSSION AND CONCLUSION: Our co-design process provides a model for educator engagement. The new curriculum module serves as a model for introducing secondary students to big data and precision medicine research by exploring diverse real-world datasets.

Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes.

Zika virus (ZIKV) is an emerging pathogen that causes devastating congenital defects. The overlapping epidemiology and immunologic cross-reactivity between ZIKV and dengue virus (DENV) pose complex challenges to vaccine design, given the potential for antibody-dependent enhancement of disease. Therefore, classification of ZIKV-specific antibody targets is of notable value. From a ZIKV-infected rhesus macaque, we identify ZIKV-reactive B cells and isolate potent neutralizing monoclonal antibodies (mAbs) with no cross-reactivity to DENV. We group these mAbs into four distinct antigenic groups targeting ZIKV-specific cross-protomer epitopes on the envelope glycoprotein. Co-crystal structures of representative mAbs in complex with ZIKV envelope glycoprotein reveal envelope-dimer epitope and unique dimer-dimer epitope targeting. All four specificities are serologically identified in convalescent humans following ZIKV infection, and representative mAbs from all four groups protect against ZIKV replication in mice. These results provide key insights into ZIKV-specific antigenicity and have implications for ZIKV vaccine, diagnostic, and therapeutic development.

Exploiting the Nanostructural Anisotropy of ß-Ga2O3 to Demonstrate Giant Improvement in Titanium/Gold Ohmic Contacts.

Here we demonstrate a dramatic improvement in Ti/Au ohmic contact performance by utilizing the anisotropic nature of ß-Ga2O3. Under a similar doping concentration, Ti/Au metallization on (100) Ga2O3 shows a specific contact resistivity 5.11 × 10-5 Ω·cm2, while that on (010) Ga2O3 is as high as 3.29 × 10-3 Ω·cm2. Temperature-dependent contact performance and analyses suggest that field emission or thermionic field emission is the dominant charge transport mechanism across the Ti/Au-(100) Ga2O3 junction, depending on whether reactive ion etching was used prior to metallization. Cross-sectional high-resolution microscopy and elemental mapping analysis show that the in situ-formed Ti-TiOx layer on (100) Ga2O3 is relatively thin (2-2.5 nm) and homogeneous, whereas that on (010) substrates is much thicker (3-5 nm) and shows nanoscale facet-like features at the interface. The anisotropic nature of monoclinic Ga2O3, including anisotropic surface energy and mass diffusivity, is likely to be the main cause of the differences observed under microscopy and in electrical properties. The findings here provide direct evidence and insights into the dependence of device performance on the atomic-scale structural anisotropy of ß-Ga2O3. Moreover, the investigative strategy here─combining comprehensive electrical and materials characterization of interfaces on different semiconductor orientations─can be applied to assess a variety of other anisotropic oxide junctions.

Thiomicrorhabdus heinhorstiae sp. nov. and Thiomicrorhabdus cannonii sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA.

Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1T and HH3T represent novel species belonging to the genus Thiomicrorhabdus. The genome G+C fraction of HH1T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C16 : 1, C18 : 1 and C16 : 0, with the addition of C10:0 3-OH in HH1T and C12 : 0 in HH3T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15-35 °C with optima of 32.8 °C for HH1T and 32 °C for HH3T. HH1T grew in media with [NaCl] 80-689 mM, with an optimum of 400 mM, while HH3T grew at 80-517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1T (=DSM 111584T=ATCC TSD-240T). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3T (=DSM 111593T=ATCC TSD-241T).

Dissolved Inorganic Carbon-Accumulating Complexes from Autotrophic Bacteria from Extreme Environments.

In nature, concentrations of dissolved inorganic carbon (DIC; CO2 + HCO3- + CO32-) can be low, and autotrophic organisms adapt with a variety of mechanisms to elevate intracellular DIC concentrations to enhance CO2 fixation. Such mechanisms have been well studied in Cyanobacteria, but much remains to be learned about their activity in other phyla. Novel multisubunit membrane-spanning complexes capable of elevating intracellular DIC were recently described in three species of bacteria. Homologs of these complexes are distributed among 17 phyla in Bacteria and Archaea and are predicted to consist of one, two, or three subunits. To determine whether DIC accumulation is a shared feature of these diverse complexes, seven of them, representative of organisms from four phyla, from a variety of habitats, and with three different subunit configurations, were chosen for study. A high-CO2-requiring, carbonic anhydrase-deficient (ΔyadF ΔcynT) strain of Escherichia coli Lemo21(DE3), which could be rescued via elevated intracellular DIC concentrations, was created for heterologous expression and characterization of the complexes. Expression of all seven complexes rescued the ability of E. coli Lemo21(DE3) ΔyadF ΔcynT to grow under low-CO2 conditions, and six of the seven generated measurably elevated intracellular DIC concentrations when their expression was induced. For complexes consisting of two or three subunits, all subunits were necessary for DIC accumulation. Isotopic disequilibrium experiments clarified that CO2 was the substrate for these complexes. In addition, the presence of an ionophore prevented the accumulation of intracellular DIC, suggesting that these complexes may couple proton potential to DIC accumulation. IMPORTANCE To facilitate the synthesis of biomass from CO2, autotrophic organisms use a variety of mechanisms to increase intracellular DIC concentrations. A novel type of multisubunit complex has recently been described, which has been shown to generate measurably elevated intracellular DIC concentrations in three species of bacteria, raising the question of whether these complexes share this capability across the 17 phyla of Bacteria and Archaea where they are found. This study shows that DIC accumulation is a trait shared by complexes with various subunit structures, from organisms with diverse physiologies and taxonomies, suggesting that this trait is universal among them. Successful expression in E. coli suggests the possibility of their expression in engineered organisms synthesizing compounds of industrial importance from CO2.

Role of the Thoracic Radiologist in the Evaluation and Management of Solid and Subsolid Lung Nodules.

In this review, the authors describe the imaging characteristics of solid and subsolid nodules as well as their management recommendations including the use of image-guided percutaneous biopsy and preoperative coil localization. Using case presentations, they offer practical management tips for the most commonly encountered nodule nodules in a thoracic surgical practice.

Area-Selective Atomic Layer Deposition Patterned by Electrohydrodynamic Jet Printing for Additive Manufacturing of Functional Materials and Devices.

There is an increasing interest in additive nanomanufacturing processes, which enable customizable patterning of functional materials and devices on a wide range of substrates. However, there are relatively few techniques with the ability to directly 3D print patterns of functional materials with sub-micron resolution. In this study, we demonstrate the use of additive electrohydrodynamic jet (e-jet) printing with an average line width of 312 nm, which acts as an inhibitor for area-selective atomic layer deposition (AS-ALD) of a range of metal oxides. We also demonstrate subtractive e-jet printing with solvent inks that dissolve polymer inhibitor layers in specific regions, which enables localized AS-ALD within those regions. The chemical selectivity and morphology of e-jet patterned polymers towards binary and ternary oxides of ZnO, Al2O3, and SnO2 were quantified using X-ray photoelectron spectroscopy, atomic force microscopy, and Auger electron spectroscopy. This approach enables patterning of functional oxide semiconductors, insulators, and transparent conducting oxides with tunable composition, Å-scale control of thickness, and sub-µm resolution in the x-y plane. Using a combination of additive and subtractive e-jet printing with AS-ALD, a thin-film transistor was fabricated using zinc-tin-oxide for the semiconductor channel and aluminum-doped zinc oxide as the source and drain electrical contacts. In the future, this technique can be used to print integrated electronics with sub-micron resolution on a variety of substrates.

Accelerated Aging Stability of ß-Ga2O3-Titanium/Gold Ohmic Interfaces.

Stable ohmic contacts are critical to enable efficient operation of high-voltage electronic devices using ultrawide bandgap semiconductors. Here we perform, for the first time, thermally accelerated aging of Ti/Au ohmic interfaces to (010) ß-Ga2O3. We find that a heavily doped semiconductor, doped n-type by Si-ion implantation, treated with reactive ion etch (RIE), results in a low specific contact resistance of ∼10-5 Ω cm2 that is stable upon accelerated thermal aging at 300 °C for 108 h. The low resistance interface is due to thermionic field emission of electrons over an inhomogeneous barrier. Scanning/transmission electron microscopy indicates that the multi-layered structure and elemental distribution across the contact interface, formed during a 1 min 470 °C post-metallization anneal, do not change noticeably over the aging period. A ∼1 nm interfacial layer is observed by high-resolution microscopy at the Ti-TiOx/Ga2O3 interface on all samples exposed to RIE, which may contribute to their excellent stability. In addition, longer-range facet-like interfacial features are observed, which may contribute to the inhomogeneous barrier. In contrast, Ti/Au junctions to moderately doped (010) Ga2O3 made with no RIE treatment exhibit a high contact resistance that increases upon accelerated aging, along with a partially lattice-matched interface. The methods used here to understand the process, structure, and electrical property relationships for Ti/Au contact interfaces to ß-Ga2O3 can be applied to assess and tune the stability of a variety of other oxide-semiconductor interfaces.

Adenovirus Vector-Based Vaccines Confer Maternal-Fetal Protection against Zika Virus Challenge in Pregnant IFN-αßR-/- Mice.

Maternal infection with Zika virus (ZIKV) can lead to microcephaly and other congenital abnormalities of the fetus. Although ZIKV vaccines that prevent or reduce viremia in non-pregnant mice have been described, a maternal vaccine that provides complete fetal protection would be desirable. Here, we show that adenovirus (Ad) vector-based ZIKV vaccines induce potent neutralizing antibodies that confer robust maternal and fetal protection against ZIKV challenge in pregnant, highly susceptible IFN-αßR-/- mice. Moreover, passive transfer of maternal antibodies from vaccinated dams protected pups against post-natal ZIKV challenge. These data suggest that Ad-based ZIKV vaccines may be able to provide protection in pregnant females against fetal ZIKV transmission in utero as well as in infants against ZIKV infection after birth.

Lack of therapeutic efficacy of an antibody to α4ß7 in SIVmac251-infected rhesus macaques.

Sustained virologic control of human immunodeficiency virus type 1 (HIV-1) infection after discontinuation of antiretroviral therapy (ART) is a major goal of the HIV-1 cure field. A recent study reported that administration of an antibody against α4ß7 induced durable virologic control after ART discontinuation in 100% of rhesus macaques infected with an attenuated strain of simian immunodeficiency virus (SIV) containing a stop codon in nef We performed similar studies in 50 rhesus macaques infected with wild-type, pathogenic SIVmac251. In animals that initiated ART during either acute or chronic infection, anti-α4ß7 antibody infusion had no detectable effect on the viral reservoir or viral rebound after ART discontinuation. These data demonstrate that anti-α4ß7 antibody administration did not provide therapeutic efficacy in the model of pathogenic SIVmac251 infection of rhesus macaques.

Adenoviral vector type 26 encoding Zika virus (ZIKV) M-Env antigen induces humoral and cellular immune responses and protects mice and nonhuman primates against ZIKV challenge.

In 2015, there was a large outbreak of Zika virus (ZIKV) in Brazil. Despite its relatively mild impact on healthy adults, ZIKV infection during pregnancy has been associated with severe birth defects. Currently, there is no ZIKV vaccine available, but several vaccine candidates based on the ZIKV membrane (M) and envelope (Env) structural proteins showed promising results in preclinical and clinical studies. Here, the immunogenicity and protective efficacy of a non-replicating adenoviral vector type 26 (Ad26) that encodes the ZIKV M-Env antigens (Ad26.ZIKV.M-Env) was evaluated in mice and non-human primates (NHP). Ad26.ZIKV.M-Env induced strong and durable cellular and humoral immune responses in preclinical models. Humoral responses were characterized by Env-binding and ZIKV neutralizing antibody responses while cellular responses were characterized by ZIKV reactive CD4+ and CD8+ T cells. Importantly, a single immunization with a very low dose of 4x107 vp of Ad26.ZIKV.M-Env protected mice from ZIKV challenge. In NHP, a single immunization with a typical human dose of 1x1011 vp of Ad26.ZIKV.M-Env also induced Env-binding and ZIKV neutralizing antibodies and Env and M specific cellular immune responses that associated with complete protection against viremia from ZIKV challenge as measured in plasma and other body fluids. Together these data provide the rationale to progress the Ad26.ZIKV.M-Env candidate vaccine to clinical testing.

Therapeutic and protective efficacy of a dengue antibody against Zika infection in rhesus monkeys.

Strategies to treat Zika virus (ZIKV) infection in dengue virus (DENV)-endemic areas are urgently needed. Here we show that a DENV-specific antibody against the E-dimer epitope (EDE) potently cross-neutralizes ZIKV and provides robust therapeutic efficacy as well as prophylactic efficacy against ZIKV in rhesus monkeys. Viral escape was not detected, suggesting a relatively high bar to escape. These data demonstrate the potential for antibody-based therapy and prevention of ZIKV.

Fetal Neuropathology in Zika Virus-Infected Pregnant Female Rhesus Monkeys.

The development of interventions to prevent congenital Zika syndrome (CZS) has been limited by the lack of an established nonhuman primate model. Here we show that infection of female rhesus monkeys early in pregnancy with Zika virus (ZIKV) recapitulates many features of CZS in humans. We infected 9 pregnant monkeys with ZIKV, 6 early in pregnancy (weeks 6-7 of gestation) and 3 later in pregnancy (weeks 12-14 of gestation), and compared findings with uninfected controls. 100% (6 of 6) of monkeys infected early in pregnancy exhibited prolonged maternal viremia and fetal neuropathology, including fetal loss, smaller brain size, and histopathologic brain lesions, including microcalcifications, hemorrhage, necrosis, vasculitis, gliosis, and apoptosis of neuroprogenitor cells. High-resolution MRI demonstrated concordant lesions indicative of deep gray matter injury. We also observed spinal, ocular, and neuromuscular pathology. Our data show that vascular compromise and neuroprogenitor cell dysfunction are hallmarks of CZS pathogenesis, suggesting novel strategies to prevent and to treat this disease.

Rapid Cloning of Novel Rhesus Adenoviral Vaccine Vectors.

Human and chimpanzee adenovirus vectors are being developed to circumvent preexisting antibodies against common adenovirus vectors such as Ad5. However, baseline immunity to these vectors still exists in human populations. Traditional cloning of new adenovirus vaccine vectors is a long and cumbersome process that takes 2 months or more and that requires rare unique restriction enzyme sites. Here we describe a novel, restriction enzyme-independent method for rapid cloning of new adenovirus vaccine vectors that reduces the total cloning procedure to 1 week. We developed 14 novel adenovirus vectors from rhesus monkeys that can be grown to high titers and that are immunogenic in mice. All vectors grouped with the unusual adenovirus species G and show extremely low seroprevalence in humans. Rapid cloning of novel adenovirus vectors is a promising approach for the development of new vector platforms. Rhesus adenovirus vectors may prove useful for clinical development.IMPORTANCE To overcome baseline immunity to human and chimpanzee adenovirus vectors, we developed 14 novel adenovirus vectors from rhesus monkeys. These vectors are immunogenic in mice and show extremely low seroprevalence in humans. Rhesus adenovirus vectors may prove useful for clinical development.

Modified Barium Swallow for Evaluation of Dysphagia.

Deglutition, or the act of swallowing, allows food and fluids to move through the upper gastrointestinal tract. Difficulty swallowing, known as dysphagia, causes a host of complications for patients. Fluoroscopic evaluation of dysphagia enables appropriate diagnosis and treatment. This evaluation commonly is accomplished with a swallowing dysfunction study, also known as a modified barium swallow procedure.

Homologous recombination deficiency (HRD) status predicts response to standard neoadjuvant chemotherapy in patients with triple-negative or BRCA1/2 mutation-associated breast cancer.

PURPOSE: Defects in the homologous recombination (HR) DNA repair pathway sensitize tumors to therapeutics that target this pathway. A significant proportion of triple-negative breast cancers (TNBC) carry HR defects. The HRD assay is highly associated with sensitivity to neoadjuvant platinum-based chemotherapy in TNBC. Standard chemotherapy consists of some combination of an anthracycline, cyclophosphamide, and taxane. This study assesses the association of HR deficiency status with response to standard neoadjuvant chemotherapy in TNBC or BRCA1/2 mutation-associated breast cancer. METHODS: Tumor samples were retrospectively obtained from 45 TNBC patients and 2 BRCA1/2 mutant, hormone receptor-positive/HER2-negative breast cancer patients who received anthracycline- and/or taxane-based neoadjuvant chemotherapy at Stanford University or Cedars-Sinai Medical Centers. The HRD score and tumor BRCA1/2 mutation status were determined from baseline tumor biopsies. HR deficient tumors were those with a HRD score of ≥ 42 or a tumor BRCA1/2 mutation. Response was categorized by the residual cancer burden (RCB) index. RESULTS: HR deficient patients were more likely to achieve a pathologic complete response (pCR) compared with non-deficient patients (OR 13.06, CI 1.52-11.241, p = 0.0028). Among BRCA1/2 mutation wild-type patients, HR deficient patients were more likely to achieve a pCR (OR 16, 95% CI 1.65-160.41, p = 0.0041) compared with HR non-deficient patients. Further, HRD scores were highly concordant pre- and post-therapy (Spearman correlation > 99%). CONCLUSIONS: HR deficiency status is significantly associated with response to standard neoadjuvant chemotherapy in TNBC. This observation is consistent with the mechanisms of action of doxorubicin and cyclophosphamide as DNA damaging agents.

A Biopsychosocial Approach to Pain Management.

INTRODUCTION: The goal of this project was to implement a biopsychosocial approach to pain management and measure the effects on patient perception of pain. It was hypothesized that the intervention would positively impact patients' perception of pain. METHODS: A validated survey, the Revised American Pain Society Patient Outcome Questionnaire, was administered to patients on the day of discharge from Avera McKennan Hospital Orthopedics Unit 2-East and 2-West following total joint replacement. Prior to data collection, 2-East was renovated to create more welcoming and comfortable patient rooms. Pre-intervention data was gathered April through June of 2017. In July, a four-hour staff training session on alternative comfort measures and pain medication administration took place. Post-intervention data was gathered July through September of 2017. Data was analyzed via Microsoft Office Excel using t-test and chi-square analyses. RESULTS: Statistically significant improvement was seen on 2-East in pain severity and relief, least amount of pain reported, use of non-medicine methods, and impact of pain on sleep, activities, and negative emotions. Analysis of 2-East and 2-West combined revealed a decrease in overall pain, medication side effects, and impact of pain on sleep, activity, and negative emotions, although not statistically significant. In addition, there was an increase in helpfulness of information, ability to participate in decisions about pain management, and use of nonpharmacologic strategies, although not statistically significant. CONCLUSIONS: The study found outcomes consistent with the hypothesis, although not all results were statistically significant. The complementary use of nonpharmacologic interventions shows promise for improving patient experiences post-surgery. However, more research would be necessary to recommend the widespread implementation of these techniques.

Durability and correlates of vaccine protection against Zika virus in rhesus monkeys.

An effective Zika virus (ZIKV) vaccine will require long-term durable protection. Several ZIKV vaccine candidates have demonstrated protective efficacy in nonhuman primates, but these studies have typically involved ZIKV challenge shortly after vaccination at peak immunity. We show that a single immunization with an adenovirus vector-based vaccine, as well as two immunizations with a purified inactivated virus vaccine, afforded robust protection against ZIKV challenge in rhesus monkeys at 1 year after vaccination. In contrast, two immunizations with an optimized DNA vaccine, which provided complete protection at peak immunity, resulted in reduced protective efficacy at 1 year that was associated with declining neutralizing antibody titers to subprotective levels. These data define a microneutralization log titer of 2.0 to 2.1 as the threshold required for durable protection against ZIKV challenge in this model. Moreover, our findings demonstrate that protection against ZIKV challenge in rhesus monkeys is possible for at least 1 year with a single-shot vaccine.

Medical Imaging and Infertility.

Infertility affects many couples, and medical imaging plays a vital role in its diagnosis and treatment. Radiologic technologists benefit from having a broad understanding of infertility risk factors and causes. This article describes the typical structure and function of the male and female reproductive systems, as well as congenital and acquired conditions that could lead to a couple's inability to conceive. Medical imaging procedures performed for infertility diagnosis are discussed, as well as common interventional options available to patients.