Uberon: towards a comprehensive multi-species anatomy ontology

The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between the CARO upper-level ontology and species-specific anatomical ontologies

Exploring prenatal testing preferences among US pregnant individuals: A discrete choice experiment

Although there are numerous benefits to diagnostic prenatal testing, such as fetal exome sequencing, there are also consequences, including the possibility of receiving variants of uncertain significance or identifying secondary findings. In this study, we utilized a survey-based discrete choice experiment to elicit the preferences of pregnant people in Northern California for hypothetical prenatal genomic tests. Pregnant individuals were invited to complete the survey through advertisements on social media. Five test attributes were studied: likelihood of getting a result, time taken to receive results, who explains results, reporting of uncertain results, and reporting of secondary findings. The survey also gathered information about the participants' demographics, current and past pregnancies, and tolerance of uncertainty using the IUS-12 scale. Participants were eligible if they were female, currently 24 or more weeks pregnant, and able to read/write enough English or Spanish to complete an online survey. Overall, participants (n = 56) preferred the option of having a prenatal test over not having a prenatal test (p < 0.01) and had substantially higher preferences for tests with the highest likelihood of getting a result (p < 0.01). There were also positive preferences for tests that reported secondary findings (p = 0.01) and those where results were returned by a genetic specialist (vs. their prenatal provider) (p = 0.04). These findings can be used to guide conversations between pregnant individuals and genetics specialists, such as genetic counselors, as they weigh the pros and cons of diagnostic prenatal testing options

Use of Continuous Renal Replacement Therapy for Removal of Dabigatran in a Patient in Need of Emergent Surgery

Purpose. To report the ability to remove serum dabigatran using continuous renal replacement therapy (CRRT) in a patient with life-threatening bleeding. Summary. A 77-year-old female with history of atrial fibrillation who takes dabigatran for stroke prevention presented with abdominal pain. Patient was found to have bleeding and possible mesenteric ischemia and was taken to the operating room and had continued bleeding postoperatively. CRRT was initiated for the removal of any remaining dabigatran, with serum dabigatran levels collected to evaluate removal of dabigatran with CRRT. This patient had an increased dabigatran level prior to intervention, which decreased to an undetectable level after use of CRRT. Greater than 80% of the drug was removed due to 4 hours of CRRT and residual kidney function. Reversal of dabigatran is an area of current research with recent FDA approval of idarucizumab for use. Conclusion. Bleeding may occur as a result of the use of dabigatran and change in patient’s clinical condition. Use of CRRT may be an option in removing serum dabigatran in the case of a life-threatening bleed

Use of Continuous Renal Replacement Therapy for Removal of Dabigatran in a Patient in Need of Emergent Surgery

Purpose. To report the ability to remove serum dabigatran using continuous renal replacement therapy (CRRT) in a patient with life-threatening bleeding. Summary. A 77-year-old female with history of atrial fibrillation who takes dabigatran for stroke prevention presented with abdominal pain. Patient was found to have bleeding and possible mesenteric ischemia and was taken to the operating room and had continued bleeding postoperatively. CRRT was initiated for the removal of any remaining dabigatran, with serum dabigatran levels collected to evaluate removal of dabigatran with CRRT. This patient had an increased dabigatran level prior to intervention, which decreased to an undetectable level after use of CRRT. Greater than 80% of the drug was removed due to 4 hours of CRRT and residual kidney function. Reversal of dabigatran is an area of current research with recent FDA approval of idarucizumab for use. Conclusion. Bleeding may occur as a result of the use of dabigatran and change in patient’s clinical condition. Use of CRRT may be an option in removing serum dabigatran in the case of a life-threatening bleed

A Prospective Study of Predictors and Consequences of Hooking Up for Sexual Minority Women

Hooking up, which refers to a sexual encounter (ranging from kissing to penetrative sex) between individuals who are not in a committed relationship, is an increasingly normative form of sexual exploration among emerging adults. Past research has focused on hookups within a heteronormative context, and some of this work has examined hookups as a way to cope with distress. Building on this work, we examined the role of hookups as a means for lesbian and bisexual women to cope with minority stress through increasing connection and engagement with the LGBTQ (lesbian/gay/bisexual/transgender/queer or questioning) community. A nationally recruited sample of 520 lesbian and bisexual women ages 18 to 25 completed questionnaires regarding their hookup behaviors as part of a longitudinal study. Childhood sexual abuse, posttraumatic stress symptoms, alcohol use, minority stress, and involvement and connectedness with the LGBTQ community were also assessed. First, regression analyses were used to examine baseline predictors of hookup behaviors reported at a 12-month follow-up. Findings revealed that alcohol use was associated with a greater likelihood of any subsequent hookups, and individuals reporting more minority stress subsequently hooked up with more partners. Second, hookup behaviors at 12 months were examined as predictors of outcomes at a 24-month follow-up, after controlling for baseline variables. Findings revealed that hookup behaviors were associated with reduced minority stress as well as increased involvement with and connectedness to the LGBTQ community, suggesting hookups may serve a protective function. Overall, findings support the notion that for sexual minority women, hookups may operate as a means of coping and connection

Uberon, an integrative multi-species anatomy ontology

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.or

Integrating phenotype ontologies across multiple species

Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology

Methotrexate Encephalopathy: Two Cases in Adult Cancer Patients, Who Recovered with Pathophysiologically Based Therapy

Background/Objectives: Neurotoxicity is a serious and sometimes fatal adverse effect that can occur following methotrexate treatment. We describe two adult patients with hematological malignancies with methotrexate encephalopathy who recovered with dextromethorphan therapy. Results: Case 1 : A 24-year-old male with acute lymphoblastic leukemia developed the acute onset of bilateral facial weakness and slurred speech after his first treatment with high-dose intravenous methotrexate. The clinical scenario and a head magnetic resonance imaging supported a diagnosis of methotrexate encephalopathy. Treatment with dextromethorphan was coincident with recovery. Case 2 : A 65-year-old female with recurrent diffuse large B-cell lymphoma was treated with high- dose intravenous methotrexate. Two weeks after a cycle, she developed hypoactive delirium, marked lethargy, ocular ataxia, and a right-sided facial weakness. Within 2 days of starting dextromethorphan, there was improvement with clinical recovery. Conclusions: These two cases suggest that N -methyl d -aspartate receptor activation by homocysteine may play an important role in the pathogenesis of methotrexate neurotoxicity

Mapping the tilt of the Milky Way bulge velocity ellipsoids with ARGOS and Gaia DR2

Until the recent advent of $Gaia$ Data Release 2 (DR2) and deep multi-object spectroscopy, it has been difficult to obtain 6-D phase space information for large numbers of stars beyond 4 kpc, in particular towards the Galactic centre, where dust and crowding effects are significant. In this study we combine line-of-sight velocities from the Abundances and Radial velocity Galactic Origins Survey (ARGOS) spectroscopic survey with proper motions from $Gaia$ DR2, to obtain a sample of $\sim$ 7,000 red clump stars with 3-D velocities. We perform a large scale stellar kinematics study of the Milky Way (MW) bulge to characterize the bulge velocity ellipsoids. We measure the tilt $l_{v}$ of the major-axis of the velocity ellipsoid in the radial-longitudinal velocity plane in 20 fields across the bulge. The tilt or vertex deviation, is characteristic of non-axisymmetric systems and a significant tilt is a robust indicator of non-axisymmetry or bar presence. We compare the observations to the predicted kinematics of an N-body boxy-bulge model formed from dynamical instabilities. In the model, the $l_{v}$ values are strongly correlated with the angle ($\alpha$) between the bulge major-axis and the Sun-Galactic centre line-of-sight. We use a maximum likelihood method to obtain an independent measurement of $\alpha$, from bulge stellar kinematics alone. The most likely value of $\alpha$ given our model is $\alpha = (29 \pm 3)^{\circ}$. In the Baade's window, the metal-rich stars display a larger vertex deviation ($l_{v} = -40^{\circ}$) than the metal-poor stars ($l_{v} = 10^{\circ}$) but we do not detect significant $l_{v}-$metallicity trends in the other fields.Comment: 13 pages, 11 figure