FACT – a framework for the functional interpretation of high-throughput experiments

BACKGROUND: Interpreting the results of high-throughput experiments, such as those obtained from DNA-microarrays, is an often time-consuming task due to the high number of data-points that need to be analyzed in parallel. It is usually a matter of extensive testing and unknown beforehand, which of the possible approaches for the functional analysis will be the most informative RESULTS: To address this problem, we have developed the Flexible Annotation and Correlation Tool (FACT). FACT allows for detection of important patterns in large data sets by simplifying the integration of heterogeneous data sources and the subsequent application of different algorithms for statistical evaluation or visualization of the annotated data. The system is constantly extended to include additional annotation data and comparison methods. CONCLUSION: FACT serves as a highly flexible framework for the explorative analysis of large genomic and proteomic result sets. The program can be used online; open source code and supplementary information are available at

Investigating the lived experience of LGBT+ people with dementia and their care partners: a scoping review

Dementia, a global health priority, poses a disproportionately high risk to lesbian, gay, bisexual and trans plus (LGBT+)/gender and sexuality diverse people. Despite this, little research has explored the lived experience of LGBT+ people with dementia or their care partners. This scoping review aims to understand what the literature reveals about their experiences, the ways in which their lives have been investigated, to inform future research, policy and practice. Using an established scoping review methodology, we identified seven papers that reported empirical research on the lived experience of LGBT+ people with dementia and their care partners. Only a single study reported on in two of the papers included people who were trans. This in itself reveals how rarely LGBT+ people are asked to speak about how dementia has shaped their lives in academic research. Our reflexive thematic analysis indicates that LGBT+ people with dementia and their care partners endure overlapping forms of disadvantage. This results in heightened experiences of fear and discrimination, lack of services and compounded social isolation. Importantly, while dementia was embodied as interference and loss by LGBT+ people, it was their gender and sexuality differences that provided solace, even in the face of disadvantage. Importantly, people's relationships with LGBT+ identities were framed as fundamental for safety, resilience and wellbeing, rather than a complicating or confounding factor in living with dementia

Manganese doping for enhanced magnetic brightening and circular polarization control of dark excitons in paramagnetic layered hybrid metal-halide perovskites.

Materials combining semiconductor functionalities with spin control are desired for the advancement of quantum technologies. Here, we study the magneto-optical properties of novel paramagnetic Ruddlesden-Popper hybrid perovskites Mn:(PEA)2PbI4 (PEA = phenethylammonium) and report magnetically brightened excitonic luminescence with strong circular polarization from the interaction with isolated Mn2+ ions. Using a combination of superconducting quantum interference device (SQUID) magnetometry, magneto-absorption and transient optical spectroscopy, we find that a dark exciton population is brightened by state mixing with the bright excitons in the presence of a magnetic field. Unexpectedly, the circular polarization of the dark exciton luminescence follows the Brillouin-shaped magnetization with a saturation polarization of 13% at 4 K and 6 T. From high-field transient magneto-luminescence we attribute our observations to spin-dependent exciton dynamics at early times after excitation, with first indications for a Mn-mediated spin-flip process. Our findings demonstrate manganese doping as a powerful approach to control excitonic spin physics in Ruddlesden-Popper perovskites, which will stimulate research on this highly tuneable material platform with promise for tailored interactions between magnetic moments and excitonic states

LGBTQI cancer patients' quality of life and distress : a comparison by gender, sexuality, age, cancer type and geographical remoteness

Background: There is growing acknowledgement of the psycho-social vulnerability of lesbian, gay, bisexual, transgender, queer and/or intersex (LGBTQI) people with cancer. The majority of research to date has focused on cisgender adults with breast or prostate cancer. Study Aim: This study examined psycho-social factors associated with distress and quality of life for LGBTQI cancer patients and survivors, across a range of sexualities and gender identities, intersex status, tumor types, ages and urban/ rural/remote location using an intersectional theoretical framework. Method: 430 LGBTQI people with cancer completed an online survey, measuring distress, quality of life (QOL), and a range of psycho-social variables. Participants included 216 (50.2%) cisgender women, 145 (33.7%) cisgender men, and 63 (14.7%) transgender and gender diverse (TGD) people. Thirty-one (7.2%) participants reported intersex variation and 90 (20%) were adolescents or young adults (AYA), aged 15-39. The majority lived in urban areas (54.4%) and identified as lesbian, gay or bisexual (73.7%), with 10.9% identifying as bisexual, and 10.5% as queer, including reproductive (32.4%) and non-reproductive (67.6%) cancers. Results: Forty-one percent of participants reported high or very high distress levels, 3-6 times higher than previous non-LGBTQI cancer studies. Higher rates of distress and lower QOL were identified in TGD compared to cisgender people, AYAs compared to older people, those who identify as bisexual or queer, compared to those who identify as lesbian, gay or homosexual, and those who live in rural or regional areas, compared to urban areas. Elevated distress and lower QOL was associated with greater minority stress (discrimination in life and in cancer care, discomfort being LGBTQI, lower outness) and lower social support, in these subgroups. There were no differences between reproductive and non-reproductive cancers. For the whole sample, distress and poor QOL were associated with physical and sexual concerns, the impact of cancer on gender and LGBTQI identities, minority stress, and lack of social support. Conclusion: LGBTQI people with cancer are at high risk of distress and impaired QOL. Research and oncology healthcare practice needs to recognize the diversity of LGBTQI communities, and the ways in which minority stress and lack of social support may affect wellbeing

"Surviving discrimination by pulling together" : LGBTQI cancer patient and carer experiences of minority stress and social support

Background: Lesbian, gay, bisexual, transgender, queer and/or intersex (LGBTQI) people with cancer and their carers report poorer psychological outcomes than the general non-LGBTQI cancer population. There is growing acknowledgement that these health inequities can be explained by minority stress, which can be buffered by social support. Study Aim: To examine subjective experiences of minority stress and social support for LGBTQI people with cancer and their carers, drawing on qualitative findings from the Out with Cancer study. Method: An online survey including open ended items was completed by 430 LGBTQI cancer patients and 132 partners and other carers, representing a range of tumor types, sexual and gender identities, age and intersex status. A sub-sample of 104 patients and 31 carers completed an interview, with a follow-up photovoice activity and second interview completed by 45 patients and 10 carers. Data was thematically analysed using an intersectional theoretical framework. Results: Historical and present-day experiences of discrimination, violence, family rejection and exclusion created a legacy of distress and fear. This impacted on trust of healthcare professionals and contributed to distress and unmet needs in cancer survivorship and care. Social support, often provided by partners and other chosen family, including intimate partners and other LGBTQI people, buffered the negative impacts of minority stress, helping LGBTQI patients deal with cancer. However, some participants lacked support due to not having a partner, rejection from family of origin and lack of support within LGBTQI communities, increasing vulnerability to poor psychological wellbeing. Despite the chronic, cumulative impacts of minority stress, LGBTQI patients and carers were not passive recipients of discriminatory and exclusion in cancer care, demonstrating agency and resistance through collective action and advocacy. Conclusion: LGBTQI people have unique socio-political histories and present-day psycho-social experiences that contribute to distress during cancer. Social support serves to buffer and ameliorate this distress. There is a need for cancer healthcare professionals and support services to be aware of and responsive to these potential vulnerabilities, including the intersectional differences in experiences of minority stress and social support. There is also a need for recognition and facilitation of social support among LGBTQI people with cancer and their carers

LGBTQI inclusive cancer care : a discourse analytic study of health care professional, patient and carer perspectives

Background: Awareness of the specific needs of LGBTQI cancer patients has led to calls for inclusivity, cultural competence, cultural safety and cultural humility in cancer care. Examination of oncology healthcare professionals’ (HCP) perspectives is central to identifying barriers and facilitators to inclusive LGBTQI cancer care. Study Aim: This study examined oncology HCPs perspectives in relation to LGBTQI cancer care, and the implications of HCP perspectives and practices for LGBTQI patients and their caregivers. Method: 357 oncology HCPs in nursing (40%), medical (24%), allied health (19%) and leadership (11%) positions took part in a survey; 48 HCPs completed an interview. 430 LGBTQI patients, representing a range of tumor types, sexual and gender identities, age and intersex status, and 132 carers completed a survey, and 104 LGBTQI patients and 31 carers undertook an interview. Data were analysed using thematic discourse analysis. Results: Three HCP subject positions – ways of thinking and behaving in relation to the self and LGBTQI patients – were identified:’Inclusive and reflective’ practitioners characterized LGBTQI patients as potentially vulnerable and offered inclusive care, drawing on an affirmative construction of LGBTQI health. This resulted in LGBTQI patients and their carers feeling safe and respected, willing to disclose sexual orientation and gender identity (SOGI) status, and satisfied with cancer care. ‘Egalitarian practitioners’ drew on discourses of ethical responsibility, positioning themselves as treating all patients the same, not seeing the relevance of SOGI information. This was associated with absence of LGBTQI-specific information, patient and carer anxiety about disclosure of SOGI, feelings of invisibility, and dissatisfaction with healthcare. ‘Anti-inclusive’ practitioners’ expressed open hostility and prejudice towards LGBTQI patients, reflecting a cultural discourse of homophobia and transphobia. This was associated with patient and carer distress, feelings of negative judgement, and exclusion of same-gender partners. Conclusion: Derogatory views and descriptions of LGBTQI patients, and cis-normative practices need to be challenged, to ensure that HCPs offer inclusive and affirmative care. Building HCP’s communicative competence to work with LGBTQI patients needs to become an essential part of basic training and ongoing professional development. Visible indicators of LGBTQI inclusivity are essential, alongside targeted resources and information for LGBTQI people

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Manganese doping for enhanced magnetic brightening and circular polarization control of dark excitons in paramagnetic layered hybrid metal-halide perovskites

Combining magnetic and semiconducting properties in a single material offers great technological potential, all the more so if these are coupled with good optical properties. Here, Neumann et al. present a Manganese doped Ruddlesden-Popper perovskite with this trifecta of attributes