SchNet - a deep learning architecture for molecules and materials

Deep learning has led to a paradigm shift in artificial intelligence, including web, text and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning in general and deep learning in particular is ideally suited for representing quantum-mechanical interactions, enabling to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for \emph{molecules and materials} where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study of the quantum-mechanical properties of C$_{20}$-fullerene that would have been infeasible with regular ab initio molecular dynamics

Perceptions of Next-of-Kin/Loved Ones about Last Gift Rapid Research Autopsy Study Enrolling People with HIV/AIDS at the End of Life: A Qualitative Interview Study

A growing number of people living with HIV/AIDS are participating in HIV cure-related research at the end of life (EOL). Due to the novelty of EOL HIV cure-related research, there is a need to understand how their next-of-kin (NOK) perceive such research. We conducted in-depth interviews with NOK of the Last Gift study participants at the University of California, San Diego. The Last Gift study occurs in the context of the EOL and involves a full body donation. NOK completed two interviews: (1) shortly after the participants' enrollment in the study and (2) following death. We applied thematic analysis to analyze qualitative data. NOK included seven individuals (five males and two females), including two spouses, one ex-partner, one sister, a grandmother/grandfather, and a close friend. Thematic analysis revealed five key themes: (1) NOK viewed the Last Gift program in a positive light and had an accurate overall understanding of the study; (2) NOK identified factors that motivated participants to donate their body to science; (3) NOK identified benefits of the Last Gift program for both the donors and themselves; (4) NOK did not perceive any physical risks or decisional regrets of study but wanted to minimize psychosocial impacts and ensure the dignity of participants at all times; and (5) NOK noted elements that remained essential to the successful implementation of EOL HIV cure-related research, such as early involvement and clear communication. Our study uniquely contributes to increased understanding and knowledge of what is important from the point of view of supportive NOK to ensure successful implementation of EOL HIV cure-related research. More research will be needed to understand perspectives of less supportive NOK

Altruism: Scoping Review of the Literature and Future Directions for HIV Cure-Related Research

Introduction The question of what motivates people to participate in research is particularly salient in the HIV field. While participation in HIV research was driven by survival in the 1980’s and early 1990’s, access to novel therapies became the primary motivator with the advent of combination antiretroviral therapy (cART) in the late 1990s. In the HIV cure-related research context, the concept of altruism has remained insufficiently studied. Methods We conducted a scoping review to better contextualize and understand how altruism is or could be operationalized in HIV cure-related research. We drew from the fields of altruism in general, clinical research, cancer, and HIV clinical research–including the HIV prevention, treatment, and cure-related research fields. Discussion Altruism as a key motivating factor for participation in clinical research has often been intertwined with the desire for personal benefit. The cancer field informs us that reasons for participation usually are multi-faceted and complex. The HIV prevention field offers ways to organize altruism–either by the types of benefits achieved (e.g., societal versus personal), or the origin of the values that motivate research participation. The HIV treatment literature reveals the critical role of clinical interactions in fostering altruism. There remains a dearth of in-depth knowledge regarding reasons surrounding research participation and the types of altruism displayed in HIV cure-related clinical research. Conclusion Lessons learned from various research fields can guide questions which will inform the assessment of altruism in future HIV cure-related research

“My Death Will Not [Be] in Vain”: Testimonials from Last Gift Rapid Research Autopsy Study Participants Living with HIV at the End of Life

End-of-life (EOL) HIV cure-related research provides a novel approach to studying HIV reservoirs. The Last Gift is a rapid autopsy research study at the University of California San Diego that enrolls terminally ill people living with HIV (PLWHIV) with a desire to contribute to HIV cure-related research. We conducted in-depth baseline and follow-up interviews with Last Gift study participants. We analyzed interview data applying conventional content analysis. Since summer 2017, 13 participants have been enrolled (n = 11 males and 2 females; aged 45-89 years) and 8 participants interviewed. Terminal illnesses included cancers, heart diseases, and neurodegenerative illnesses. Our analysis revealed five key themes: (1) The Last Gift study has tremendous meaning for participants at the end of their life. (2) HIV-specific altruism was a primary motivator to join the Last Gift study, nested within the context of community, scientific advancement, and moral obligation. (3) Participants did not expect physical benefits yet they perceived emotional/psychological, financial, and societal/scientific benefits. (4) There were minimal participant-perceived risks and concerns. (5) Last Gift participants expressed immense gratitude toward study staff. The Last Gift study provides a framework for ethical HIV cure-related research at EOL and highlighted participants' perspectives, motivations, and experiences. Knowing how PLWHIV understand and experience such studies will remain critical to designing ethical, fully informed HIV cure research protocols that are acceptable to PLWHIV

Cognitive-affective depressive symptoms and substance use among Latino and non-Latino White patients in HIV care: an analysis of the CFAR network of integrated clinical systems cohort.

The disparity in viral suppression rates between Latino and non-Latino White patients in HIV care appears to be narrowing, but it is unclear if depression and substance use perpetuate this disparity. We analyzed electronic medical records from the CFAR network of integrated clinical systems cohort. First observations/enrollment data collected between 2007 and 2013 were analyzed, which included survey (race/ethnicity, depression, substance use, adherence) and clinical data (viral suppression). We estimated indirect effects with a regression-based bootstrapping method. In 3129 observations, Latinos and non-Latino Whites did not differ in depression or alcohol use (ORs 1.11, 0.99, ns), but did in drug use (OR 1.13, p < .001). For all patients, depression and substance use were indirectly associated with small increases (ORs 1.02-1.66) in the odds for a detectable viral load, via worse adherence. We conclude that variables not captured in EMR systems (e.g., health literacy, structural factors) may better explain viral suppression disparities that persist

The Brief Human Immunodeficiency Virus (HIV) Index: A Rapid 3-Item Scale to Measure Engagement in HIV Care

We created a brief version of The Index, a validated patient-reported measure that has potential to quickly identify patients at risk for poor retention. We analyzed Index scores from 2406 patients from 2016 to 2017 in a national cohort of patients in human immunodeficiency virus (HIV) care. Index scores predicted poor retention 12 months after administered