Analysis of BMAA enantiomers in cycads, cyanobacteria, and mammals: in vivo formation and toxicity of D-BMAA

We acknowledge support from the John and Josephine Louis Foundation and the Deerbrook Charitable Trust. PBW acknowledges the use of the EPSRC UK National Mass Spectrometry Facility at Swansea University

Mapping coherence in measurement via full quantum tomography of a hybrid optical detector

Quantum states and measurements exhibit wave-like --- continuous, or particle-like --- discrete, character. Hybrid discrete-continuous photonic systems are key to investigating fundamental quantum phenomena, generating superpositions of macroscopic states, and form essential resources for quantum-enhanced applications, e.g. entanglement distillation and quantum computation, as well as highly efficient optical telecommunications. Realizing the full potential of these hybrid systems requires quantum-optical measurements sensitive to complementary observables such as field quadrature amplitude and photon number. However, a thorough understanding of the practical performance of an optical detector interpolating between these two regions is absent. Here, we report the implementation of full quantum detector tomography, enabling the characterization of the simultaneous wave and photon-number sensitivities of quantum-optical detectors. This yields the largest parametrization to-date in quantum tomography experiments, requiring the development of novel theoretical tools. Our results reveal the role of coherence in quantum measurements and demonstrate the tunability of hybrid quantum-optical detectors.Comment: 7 pages, 3 figure

Lost in reviews:Looking for the involvement of stakeholders, patients, public and other non-researcher contributors in realist reviews

The involvement of non‐researcher contributors (eg, stakeholders, patients and the public, decision and policy makers, experts, lay contributors) has taken a variety of forms within evidence syntheses. Realist reviews are a form of evidence synthesis that involves non‐researcher contributors yet this practice has received little attention. In particular, the role of patient and public involvement (PPI) has not been clearly documented. This review of reviews describes the ways in which contributor involvement, including PPI, is documented within healthcare realist reviews published over the last five years. A total of 448 papers published between 2014 and 2019 were screened, yielding 71 full‐text papers included in this review. Statements about contributor involvement were synthesized across each review using framework analysis. Three themes are described in this article including nomenclature, nature of involvement, and reporting impact.Papers indicate that contributor involvement in realist reviews refers to stakeholders, experts, or advisory groups (ie, professionals, clinicians, or academics). Patients and the public are occasionally subsumed into these groups and in doing so, the nature and impact of their involvement become challenging to identify and at times, is lost completely. Our review findings indicate a need for the realist review community to develop guidance to support researchers in their future collaboration with contributors, including patients and the public

Early Outcomes of MDR-TB Treatment in a High HIV-Prevalence Setting in Southern Africa

BACKGROUND: Little is known about treatment of multidrug-resistant tuberculosis (MDR-TB) in high HIV-prevalence settings such as sub-Saharan Africa. METHODOLOGY/PRINCIPAL FINDINGS: We did a retrospective analysis of early outcomes of the first cohort of patients registered in the Lesotho national MDR-TB program between July 21, 2007 and April 21, 2008. Seventy-six patients were included for analysis. Patient follow-up ended when an outcome was recorded, or on October 21, 2008 for those still on treatment. Fifty-six patients (74%) were infected with HIV; the median CD4 cell count was 184 cells/microl (range 5-824 cells/microl). By the end of the follow-up period, study patients had been followed for a median of 252 days (range 12-451 days). Twenty-two patients (29%) had died, and 52 patients (68%) were alive and in treatment. In patients who did not die, culture conversion was documented in 52/54 patients (96%). One patient had defaulted, and one patient had transferred out. Death occurred after a median of 66 days in treatment (range 12-374 days). CONCLUSIONS/SIGNIFICANCE: In a region where clinicians and program managers are increasingly confronted by drug-resistant tuberculosis, this report provides sobering evidence of the difficulty of MDR-TB treatment in high HIV-prevalence settings. In Lesotho, an innovative community-based treatment model that involved social and nutritional support, twice-daily directly observed treatment and early empiric use of second-line TB drugs was successful in reducing mortality of MDR-TB patients. Further research is urgently needed to improve MDR-TB treatment outcomes in high HIV-prevalence settings

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

Background: The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ωxy for the paths between any two pairs of leaves (x, y), what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however. Results: We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity (n^4 log n) w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP. Conclusions: The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations.Human Evolutionary Biolog

The red leg dilemma: a scoping review of the challenges of diagnosing lower limb cellulitis

Background: Suspected lower limb cellulitis presentations are commonly misdiagnoses, resulting in avoidable antibiotic prescribing or hospital admissions. Understanding the challenges posed in diagnosing cellulitis may help enhance future care.Objectives: To examine and map out the challenges and facilitators identified by patients and health professionals in diagnosing lower limb cellulitis.Methods: A scoping systematic review was performed in MEDLINE and Embase in October 2017. Thematic analysis was used to identify key themes. Quantitative data was summarised by narrative synthesis.Results: Three themes were explored: (i) clinical case reports of misdiagnosis, (ii) service development and (iii) diagnostic aids. Forty‐seven different pathologies were misdiagnosed, including seven malignancies. Two different services have been piloted to reduce the misdiagnosis rates of lower limb cellulitis and save costs. Four studies have looked at biochemical markers, imaging and a scoring tool to aid diagnosis.Conclusions: This review highlights the range of alternative pathologies that can be misdiagnosed as cellulitis, and emerging services and diagnostic aids developed to minimise misdiagnosis. Future work should focus on gaining a greater qualitative understanding of the diagnostic challenges from the perspective of patients and clinicians.This article is protected by copyright. All rights reserved

Standardised data on initiatives—STARDIT: Beta version

Background and objective: There is currently no standardised way to share information across disciplines about initiatives, including fields such as health, environment, basic science, manufacturing, media and international development. All problems, including complex global problems such as air pollution and pandemics require reliable data sharing between disciplines in order to respond effectively. Current reporting methods also lack information about the ways in which different people and organisations are involved in initiatives, making it difficult to collate and appraise data about the most effective ways to involve different people. The objective of STARDIT (Standardised Data on Initiatives) is to address current limitations and inconsistencies in sharing data about initiatives. The STARDIT system features standardised data reporting about initiatives, including who has been involved, what tasks they did, and any impacts observed. STARDIT was created to help everyone in the world find and understand information about collective human actions, which are referred to as ‘initiatives’. STARDIT enables multiple categories of data to be reported in a standardised way across disciplines, facilitating appraisal of initiatives and aiding synthesis of evidence for the most effective ways for people to be involved in initiatives. This article outlines progress to date on STARDIT; current usage; information about submitting reports; planned next steps and how anyone can become involved. Method: STARDIT development is guided by participatory action research paradigms, and has been co-created with people from multiple disciplines and countries. Co-authors include cancer patients, people affected by rare diseases, health researchers, environmental researchers, economists, librarians and academic publishers. The co-authors also worked with Indigenous peoples from multiple countries and in partnership with an organisation working with Indigenous Australians. Results and discussion: Over 100 people from multiple disciplines and countries have been involved in co-designing STARDIT since 2019. STARDIT is the first open access web-based data-sharing system which standardises the way that information about initiatives is reported across diverse fields and disciplines, including information about which tasks were done by which stakeholders. STARDIT is designed to work with existing data standards. STARDIT data will be released into the public domain (CC0) and integrated into Wikidata; it works across multiple languages and is both human and machine readable. Reports can be updated throughout the lifetime of an initiative, from planning to evaluation, allowing anyone to be involved in reporting impacts and outcomes. STARDIT is the first system that enables sharing of standardised data about initiatives across disciplines. A working Beta version was publicly released in February 2021 (ScienceforAll.World/STARDIT). Subsequently, STARDIT reports have been created for peer-reviewed research in multiple journals and multiple research projects, demonstrating the usability. In addition, organisations including Cochrane and Australian Genomics have created prospective reports outlining planned initiatives. Conclusions: STARDIT can help create high-quality standardised information on initiatives trying to solve complex multidisciplinary global problems

Phosphate Starvation Triggers Production and Secretion of an Extracellular Lipoprotein in Caulobacter crescentus

Life in oligotrophic environments necessitates quick adaptive responses to a sudden lack of nutrients. Secretion of specific degradative enzymes into the extracellular medium is a means to mobilize the required nutrient from nearby sources. The aquatic bacterium Caulobacter crescentus must often face changes in its environment such as phosphate limitation. Evidence reported in this paper indicates that under phosphate starvation, C. crescentus produces a membrane surface-anchored lipoprotein named ElpS subsequently released into the extracellular medium. A complete set of 12 genes encoding a type II secretion system (T2SS) is located adjacent to the elpS locus in the C. crescentus genome. Deletion of this T2SS impairs release of ElpS in the environment, which surprisingly remains present at the cell surface, indicating that the T2SS is not involved in the translocation of ElpS to the outer membrane but rather in its release. Accordingly, treatment with protease inhibitors prevents release of ElpS in the extracellular medium suggesting that ElpS secretion relies on a T2SS-secreted protease. Finally, secretion of ElpS is associated with an increase in alkaline phosphatase activity in culture supernatants, suggesting a role of the secreted protein in inorganic phosphate mobilization. In conlusion, we have shown that upon phosphate starvation, C. crescentus produces an outer membrane bound lipoprotein, ElpS, which is further cleaved and released in the extracellular medium in a T2SS-dependent manner. Our data suggest that ElpS is associated with an alkaline phosphatase activity, thereby allowing the bacterium to gather inorganic phosphates from a poor environment

Keeping the Faith: African American Faith Leaders’ Perspectives and Recommendations for Reducing Racial Disparities in HIV/AIDS Infection

In Philadelphia, 66% of new HIV infections are among African Americans and 2% of African Americans are living with HIV. The city of Philadelphia has among the largest numbers of faith institutions of any city in the country. Although faith-based institutions play an important role in the African American community, their response to the AIDS epidemic has historically been lacking. We convened 38 of Philadelphia’s most influential African American faith leaders for in-depth interviews and focus groups examining the role of faith-based institutions in HIV prevention. Participants were asked to comment on barriers to engaging faith-based leaders in HIV prevention and were asked to provide normative recommendations for how African American faith institutions can enhance HIV/AIDS prevention and reduce racial disparities in HIV infection. Many faith leaders cited lack of knowledge about Philadelphia’s racial disparities in HIV infection as a common reason for not previously engaging in HIV programs; others noted their congregations’ existing HIV prevention and outreach programs and shared lessons learned. Barriers to engaging the faith community in HIV prevention included: concerns about tacitly endorsing extramarital sex by promoting condom use, lack of educational information appropriate for a faith-based audience, and fear of losing congregants and revenue as a result of discussing human sexuality and HIV/AIDS from the pulpit. However, many leaders expressed a moral imperative to respond to the AIDS epidemic, and believed clergy should play a greater role in HIV prevention. Many participants noted that controversy surrounding homosexuality has historically divided the faith community and prohibited an appropriate response to the epidemic; many expressed interest in balancing traditional theology with practical public health approaches to HIV prevention. Leaders suggested the faith community should: promote HIV testing, including during or after worship services and in clinical settings; integrate HIV/AIDS topics into health messaging and sermons; couch HIV/AIDS in social justice, human rights and public health language rather than in sexual risk behavior terms; embrace diverse approaches to HIV prevention in their houses of worship; conduct community outreach and host educational sessions for youth; and collaborate on a citywide, interfaith HIV testing and prevention campaign to combat stigma and raise awareness about the African American epidemic. Many African American faith-based leaders are poised to address racial disparities in HIV infection. HIV prevention campaigns should integrate leaders’ recommendations for tailoring HIV prevention for a faith-based audience

Highly Accurate Diagnosis of Pleural Tuberculosis by Immunological Analysis of the Pleural Effusion

Pleural TB is notoriously difficult to diagnose due to its paucibacillary nature yet it is the most common cause of pleural effusions in TB endemic countries such as The Gambia. We identified both cellular and soluble biomarkers in the pleural fluid that allowed highly accurate diagnosis of pleural TB compared to peripheral blood markers. Multi-plex cytokine analysis on unstimulated pleural fluid showed that IP-10 resulted in a positive likelihood ratio (LR) of 9.6 versus 2.8 for IFN-γ; a combination of IP-10, IL-6 and IL-10 resulted in an AUC of 0.96 and positive LR of 10. A striking finding was the significantly higher proportion of PPD-specific IFN-γ+TNF-α+ cell population (PPD-IGTA) in the pleural fluid compared to peripheral blood of TB subjects. Presence of this pleural PPD-IGTA population resulted in 95% correct classification of pleural TB disease with a sensitivity of 95% and specificity of 100%. These data suggest that analysis of the site of infection provides superior diagnostic accuracy compared to peripheral blood for pleural TB, likely due to the sequestration of effector cells at this acute stage of disease