The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data

Tribal Relationships in the Gesneriaceae: Evidence from DNA Sequences of the Chloroplast Gene \u3cem\u3endh\u3c/em\u3eF

The tribal relationships of the Gesneriaceae are investigated using ndhF sequences. A full analysis of 70 taxa including 16 species from the Scrophulariaceae, Bigoniaceae, and Acanthaceae as outgroups, resulted in two most-parsimonious trees of 5610 steps each. In all trees the Gesneriaceae were a monophyletic group and Paulownia was the closest single-species outgroup for the analysis. Further analyses eliminated all but the members of the Gesneriaceae and Paulownia in order to better asses relationships within the family. The smaller analysis resulted in a single most-parsimonious tree of 4613 steps. The Klugieae are identified as the sister to the remainder of the family and could potentially be separated as a distinct subfamily. The subfamilies Cyrtandroideae (excluding Klugieae) and Gesnerioideae are monophyletic. The placement of Coronallthereae in Cyrtandroideae does not have support from this analysis, whereas its placement in Gesnerioideae is supported. Alternatively Coronanthereae could be segregated as a seperate subfamily but in order to avoid a paraphyletic Gesnerioideae would either include the Napeantheae and Beslerieae or elevate these two tribes to an additional subfamily. Within Gesnerioideae the genus Sinningia is removed from the tribe Gloxinieae into the Sinningieae, which also contains the recently combined species Sinningia brasiliensis (Lietzia), as well as Paliavana and Vanhouttea. The Episcieae, Gesnerieae, Napeantheae, and Beslerieae are identified as monophyletic groups, as are the remainder of the Gloxineae with Sinningia sensu lato removed. Within Cyrtandroideae, several well-supported, monophyletic lineages within the large, heterogeneous tribe Didymocarpeae are identified, and with the current data the tribe Trichosporeae appears to be polyphyletic. The distribution of chromosome numbers, nodal anatomy, placental structure, and stem modification are examined based on these molecular trees

Implications of Electronics Constraints for Solid-State Quantum Error Correction and Quantum Circuit Failure Probability

In this paper we present the impact of classical electronics constraints on a solid-state quantum dot logical qubit architecture. Constraints due to routing density, bandwidth allocation, signal timing, and thermally aware placement of classical supporting electronics significantly affect the quantum error correction circuit's error rate. We analyze one level of a quantum error correction circuit using nine data qubits in a Bacon-Shor code configured as a quantum memory. A hypothetical silicon double quantum dot quantum bit (qubit) is used as the fundamental element. A pessimistic estimate of the error probability of the quantum circuit is calculated using the total number of gates and idle time using a provably optimal schedule for the circuit operations obtained with an integer program methodology. The micro-architecture analysis provides insight about the different ways the electronics impact the circuit performance (e.g., extra idle time in the schedule), which can significantly limit the ultimate performance of any quantum circuit and therefore is a critical foundation for any future larger scale architecture analysis.Comment: 10 pages, 7 figures, 3 table

Racial and Ethnic Differences in Total Knee Arthroplasty in the Veterans Affairs Health Care System, 2001-2013

OBJECTIVE: To examine black-white and Hispanic-white differences in total knee arthroplasty from 2001 to 2013 in a large cohort of patients diagnosed with osteoarthritis (OA) in the Veterans Affairs (VA) health care system. METHODS: Data were from the VA Musculoskeletal Disorders cohort, which includes data from electronic health records of more than 5.4 million veterans with musculoskeletal disorders diagnoses. We included white (non-Hispanic), black (non-Hispanic), and Hispanic (any race) veterans, age ≥50 years, with an OA diagnosis from 2001-2011 (n = 539,841). Veterans were followed from their first OA diagnosis until September 30, 2013. As a proxy for increased clinical severity, analyses were also conducted for a subsample restricted to those who saw an orthopedic or rheumatology specialist (n = 148,844). We used Cox proportional hazards regression to examine racial and ethnic differences in total knee arthroplasty by year of OA diagnosis, adjusting for age, sex, body mass index, physical and mental diagnoses, and pain intensity scores. RESULTS: We identified 12,087 total knee arthroplasty procedures in a sample of 473,170 white, 50,172 black, and 16,499 Hispanic veterans. In adjusted models examining black-white and Hispanic-white differences by year of OA diagnosis, total knee arthroplasty rates were lower for black than for white veterans diagnosed in all but 2 years. There were no Hispanic-white differences regardless of when diagnosis occurred. These patterns held in the specialty clinic subsample. CONCLUSION: Black-white differences in total knee arthroplasty appear to be persistent in the VA, even after controlling for potential clinical confounders

Gender Differences in Demographic and Clinical Correlates among Veterans with Musculoskeletal Disorders

Background Studies suggest that women may be at greater risk for developing chronic pain and pain-related disability. Methods Because musculoskeletal disorders (MSD) are the most frequently endorsed painful conditions among veterans, we sought to characterize gender differences in sociodemographic and clinical correlates among veterans upon entry into Veterans Health Administration's Musculoskeletal Disorders Cohort (n = 4,128,008). Results Women were more likely to be younger, Black, unmarried, and veterans of recent conflicts. In analyses adjusted for gender differences in sociodemographics, women were more likely to have diagnoses of fibromyalgia, temporomandibular disorders, and neck pain. Almost one in five women (19.4%) had more than one MSD diagnosis, compared with 15.7% of men; this higher risk of MSD multimorbidity remained in adjusted analyses. Adjusting for sociodemographics, women with MSD were more likely to have migraine headache and depressive, anxiety, and bipolar disorders. Women had lower odds of cardiovascular diseases, substance use disorders, and several MSDs, including back pain conditions. Men were more likely to report “no pain” on the pain intensity Numeric Rating Scale, whereas more women (41%) than men (34%) reported moderate to severe pain (Numeric Rating Scale 4+). Conclusions Because women veterans are more likely to have conditions such as fibromyalgia and mental health conditions, along with greater pain intensity in the setting of MSD, women-specific pain services may be needed

Improving the development, monitoring and reporting of stroke rehabilitation research: consensus-based core recommendations from the Stroke Recovery and Rehabilitation Roundtable (SRRR)

Recent reviews have demonstrated that the quality of stroke rehabilitation research has continued to improve over the last four decades but despite this progress there are still many barriers in moving the field forward. Rigorous development, monitoring and complete reporting of interventions in stroke trials are essential in providing rehabilitation evidence that is robust, meaningful and implementable. An international partnership of stroke rehabilitation experts committed to develop consensus-based core recommendations with a remit of addressing the issues identified as limiting stroke rehabilitation research in the areas of developing, monitoring and reporting stroke rehabilitation interventions. Work exploring each of the three areas took place via multiple teleconferences and a two-day meeting in Philadelphia in May 2016. A total of 15 recommendations were made. To validate the need for the recommendations the group reviewed all stroke rehabilitation trials published in 2015 (n=182 papers). Our review highlighted that the majority of publications did not clearly describe how interventions were developed or monitored during the trial. In particular, under-reporting of the theoretical rationale for the intervention and the components of the intervention calls into question many interventions that have been evaluated for efficacy. More trials were found to have addressed the reporting of interventions recommendations than those related to development or monitoring. Nonetheless the majority of reporting recommendations were still not adequately described. To progress the field of stroke rehabilitation research and to ensure stroke patients receive optimal evidence based clinical care we urge the research community to endorse and adopt our recommendations

Assessing the Effectiveness of a Community Intervention for Monkeypox Prevention in the Congo Basin

Human monkeypox is a potentially severe illness that begins with a high fever soon followed by the development of a smallpox-like rash. Both monkeypox and smallpox are caused by infection with viruses in the genus Orthopoxvirus. But smallpox, which only affected humans, has been eradicated, whereas monkeypox continues to occur when humans come into contact with infected animals. There are currently no drugs specifically available for the treatment of monkeypox, and the use of vaccines for prevention is limited due to safety concerns. Therefore, monkeypox prevention depends on diminishing human contact with infected animals and preventing person-to-person spread of the virus. The authors describe a film-based method for community outreach intended to increase monkeypox knowledge among residents of communities in the Republic of the Congo. Outreach was performed to ∼23,600 rural Congolese. The effectiveness of the outreach was evaluated using a sample of individuals who attended small-group sessions. The authors found that among the participants, the ability to recognize monkeypox symptoms and the willingness to take ill family members to the hospital was significantly increased after seeing the films. In contrast, the willingness to deter some high-risk behaviors, such as eating animal carcasses found in the forest, remained fundamentally unchanged

Expanding Clinical Presentations Due to Variations in THOC2 mRNA Nuclear Export Factor

Multiple TREX mRNA export complex subunits (e.g., THOC1, THOC2, THOC5, THOC6, THOC7) have now been implicated in neurodevelopmental disorders (NDDs), neurodegeneration and cancer. We previously implicated missense and splicing-defective THOC2 variants in NDDs and a broad range of other clinical features. Here we report 10 individuals from nine families with rare missense THOC2 variants including the first case of a recurrent variant (p.Arg77Cys), and an additional individual with an intragenic THOC2 microdeletion (Del-Ex37-38). Ex vivo missense variant testing and patient-derived cell line data from current and published studies show 9 of the 14 missense THOC2 variants result in

Reliability, validity and psychometric properties of the Greek translation of the zung depression rating scale

INTRODUCTION: The current study aimed to assess the reliability, validity and psychometric properties of the Greek translation of the Zung Depression Rating Scale (ZDRS). METHODS: The study sample included 40 depressed patients 29.65 ± 9.38 years old and 120 normal comparison subjects 27.23 ± 10.62 years old. In 20 of them (12 patients and 8 comparison subjects) the instrument was re-applied 1–2 days later. Translation and Back Translation was made. Clinical Diagnosis was reached by consensus of two examiners with the use of the SCAN v.2.0 and the IPDE. Statistical Analysis included ANOVA, the Pearson Product Moment Correlation Coefficient, Principal Components Analysis and Discriminant Function Analysis and the calculation of Cronbach's alpha (α) RESULTS: Both Sensitivity and specificity exceed 90.00 at 44/45, Chronbach's alpha for the total scale was equal to 0.09, suggesting that the scale covers a broad spectrum of symptoms. Factor analysis revealed five factors (anxiety-depression, thought content, gastrenterological symptoms, irritability and social-interpersonal functioning). The test-retest reliability was satisfactory (Pearson's R between 0.92). CONCLUSION: The ZDRS-Greek translation is both reliable and valid and is suitable for clinical and research use with satisfactory properties. Its properties are similar to those reported in the international literature, although the literature is limited. However one should always have in mind the limitations inherent in the use of self-report scales