Longitudinal molecular trajectories of diffuse glioma in adults.

The evolutionary processes that drive universal therapeutic resistance in adult patients with diffuse glioma remain unclear1,2. Here we analysed temporally separated DNA-sequencing data and matched clinical annotation from 222 adult patients with glioma. By analysing mutations and copy numbers across the three major subtypes of diffuse glioma, we found that driver genes detected at the initial stage of disease were retained at recurrence, whereas there was little evidence of recurrence-specific gene alterations. Treatment with alkylating agents resulted in a hypermutator phenotype at different rates across the glioma subtypes, and hypermutation was not associated with differences in overall survival. Acquired aneuploidy was frequently detected in recurrent gliomas and was characterized by IDH mutation but without co-deletion of chromosome arms 1p/19q, and further converged with acquired alterations in the cell cycle and poor outcomes. The clonal architecture of each tumour remained similar over time, but the presence of subclonal selection was associated with decreased survival. Finally, there were no differences in the levels of immunoediting between initial and recurrent gliomas. Collectively, our results suggest that the strongest selective pressures occur during early glioma development and that current therapies shape this evolution in a largely stochastic manner.

Indigenous knowledge and the shackles of wilderness.

The environmental crises currently gripping the Earth have been codified in a new proposed geological epoch: the Anthropocene. This epoch, according to the Anthropocene Working Group, began in the mid-20th century and reflects the "great acceleration" that began with industrialization in Europe [J. Zalasiewicz et al., Anthropocene 19, 55-60 (2017)]. Ironically, European ideals of protecting a pristine "wilderness," free from the damaging role of humans, is still often heralded as the antidote to this human-induced crisis [J. E. M. Watson et al., Nature, 563, 27-30 (2018)]. Despite decades of critical engagement by Indigenous and non-Indigenous observers, large international nongovernmental organizations, philanthropists, global institutions, and nation-states continue to uphold the notion of pristine landscapes as wilderness in conservation ideals and practices. In doing so, dominant global conservation policy and public perceptions still fail to recognize that Indigenous and local peoples have long valued, used, and shaped "high-value" biodiverse landscapes. Moreover, the exclusion of people from many of these places under the guise of wilderness protection has degraded their ecological condition and is hastening the demise of a number of highly valued systems. Rather than denying Indigenous and local peoples' agency, access rights, and knowledge in conserving their territories, we draw upon a series of case studies to argue that wilderness is an inappropriate and dehumanizing construct, and that Indigenous and community conservation areas must be legally recognized and supported to enable socially just, empowering, and sustainable conservation across scale.

Low-Latency Wireless Network Extension for Industrial Internet of Things.

The timely delivery of critical messages in real-time environments is an increasing requirement for industrial Internet of Things (IIoT) networks. Similar to wired time-sensitive networking (TSN) techniques, which bifurcate traffic flows based on priority, the proposed wireless method aims to ensure that critical traffic arrives rapidly across multiple hops to enable numerous IIoT use cases. IIoT architectures are migrating toward wirelessly connected edges, creating a desire to extend TSN-like functionality to a wireless format. Existing protocols possess inherent challenges to achieving this prioritized low-latency communication, ranging from rigidly scheduled time division transmissions, scalability/jitter of carrier-sense multiple access (CSMA) protocols, and encryption-induced latency. This paper presents a hardware-validated low-latency technique built upon receiver-assigned code division multiple access (RA-CDMA) techniques to implement a secure wireless TSN-like extension suitable for the IIoT. Results from our hardware prototype, constructed on the IntelFPGA Arria 10 platform, show that (sub-)millisecond single-hop latencies can be achieved for each of the available message types, ranging from 12 bits up to 224 bits of payload. By achieving one-way transmission of under 1 ms, a reliable wireless TSN extension with comparable timelines to 802.1Q and/or 5G is achievable and proven in concept through our hardware prototype.

Genetic mapping of species differences via in vitro crosses in mouse embryonic stem cells.

Discovering the genetic changes underlying species differences is a central goal in evolutionary genetics. However, hybrid crosses between species in mammals often suffer from hybrid sterility, greatly complicating genetic mapping of trait variation across species. Here, we describe a simple, robust, and transgene-free technique to generate "in vitro crosses" in hybrid mouse embryonic stem (ES) cells by inducing random mitotic cross-overs with the drug ML216, which inhibits the DNA helicase Bloom syndrome (BLM). Starting with an interspecific F1 hybrid ES cell line between the Mus musculus laboratory mouse and Mus spretus (∼1.5 million years of divergence), we mapped the genetic basis of drug resistance to the antimetabolite tioguanine to a single region containing hypoxanthine-guanine phosphoribosyltransferase (Hprt) in as few as 21 d through "flow mapping" by coupling in vitro crosses with fluorescence-activated cell sorting (FACS). We also show how our platform can enable direct study of developmental variation by rederiving embryos with contribution from the recombinant ES cell lines. We demonstrate how in vitro crosses can overcome major bottlenecks in mouse complex trait genetics and address fundamental questions in evolutionary biology that are otherwise intractable through traditional breeding due to high cost, small litter sizes, and/or hybrid sterility. In doing so, we describe an experimental platform toward studying evolutionary systems biology in mouse and potentially in human and other mammals, including cross-species hybrids.

Climate change reduces resilience to fire in subalpine rainforests.

Climate change is affecting the distribution of species and the functioning of ecosystems. For species that are slow growing and poorly dispersed, climate change can force a lag between the distributions of species and the geographic distributions of their climatic envelopes, exposing species to the risk of extinction. Climate also governs the resilience of species and ecosystems to disturbance, such as wildfire. Here we use species distribution modelling and palaeoecology to assess and test the impact of vegetation-climate disequilibrium on the resilience of an endangered fire-sensitive rainforest community to fires. First, we modelled the probability of occurrence of Athrotaxis spp. and Nothofagus gunnii rainforest in Tasmania (hereon "montane rainforest") as a function of climate. We then analysed three pollen and charcoal records spanning the last 7,500 cal year BP from within both high (n = 1) and low (n = 2) probability of occurrence areas. Our study indicates that climatic change between 3,000 and 4,000 cal year bp induced a disequilibrium between montane rainforests and climate that drove a loss of resilience of these communities. Current and future climate change are likely to shift the geographic distribution of the climatic envelopes of this plant community further, suggesting that current high-resilience locations will face a reduction in resilience. Coupled with the forecast of increasing fire activity in southern temperate regions, this heralds a significant threat to this and other slow growing, poorly dispersed and fire sensitive forest systems that are common in the southern mid to high latitudes.

FGFR2 risk SNPs confer breast cancer risk by augmenting oestrogen responsiveness.

The fibroblast growth factor receptor 2 (FGFR2) locus is consistently the top hit in genome-wide association studies for oestrogen receptor-positive (ER(+)) breast cancer. Yet, its mode of action continues to be controversial. Here, we employ a systems biology approach to demonstrate that signalling via FGFR2 counteracts cell activation by oestrogen. In the presence of oestrogen, the oestrogen receptor (ESR1) regulon (set of ESR1 target genes) is in an active state. However, signalling by FGFR2 is able to reverse the activity of the ESR1 regulon. This effect is seen in multiple distinct FGFR2 signalling model systems, across multiple cells lines and is dependent on the presence of FGFR2. Increased oestrogen exposure has long been associated with an increased risk of breast cancer. We therefore hypothesized that risk variants should reduce FGFR2 expression and subsequent signalling. Indeed, transient transfection experiments assaying the three independent variants of the FGFR2 risk locus (rs2981578, rs35054928 and rs45631563) in their normal chromosomal context show that these single-nucleotide polymorphisms (SNPs) map to transcriptional silencer elements and that, compared with wild type, the risk alleles augment silencer activity. The presence of risk variants results in lower FGFR2 expression and increased oestrogen responsiveness. We thus propose a molecular mechanism by which FGFR2 can confer increased breast cancer risk that is consistent with oestrogen exposure as a major driver of breast cancer risk. Our findings may have implications for the clinical use of FGFR2 inhibitors.

Effects of ambient temperature on nitrogen uptake and elimination in humans.

Tissue nitrogen (N2) exchange is primarily dependent on circulation, which may be modified by body thermal status. Thermal effects on uptake and washout of N2 have not been systematically investigated earlier. In the present study of eight subjects, N2 was washed out in thermally neutral ambient conditions (TN; skin temperature (Ts) = 33.69 ± 0.84 degrees C), then washed in during either TN, cool (Ts 30.25 ± 4.15 degrees C) or warm (Ts = 35.81 ± 0.82 degrees C) conditions. It was then washed out during various combinations of those conditions. N2 exchange was monitored during 125 minutes of breathing a normoxic oxygen/argon mixture (Phase I) followed by room air for 125 minutes of N2 reloading (Phase II; no N2 recording) and then 125 minutes N2 washout (Phase III) in order to determine the amount of N2 taken up during Phase II. Cool conditions reduced cardiac output, while warm conditions increased it compared to TN. Among the five Phase I TN recordings in the eight subjects (i.e., 40 control experiments) the N2 yield averaged 857.2 ± 15.3 mL. The reloaded N2 volume in Phase II was significantly smaller during the cool condition (8%, p ≤ 0.05) and significantly larger (22%, p ≤ 0.05) during the warm. The N2 washed out in 125 minutes was significantly less during cold (6%, p ≤ 0.05) and greater during warm conditions (18%, p ≤ 0.05). These observations are consistent with previously reported circulatory changes in cool and warm conditions and effects of thermal status on venous gas bubble dynamics and incidents of decompression sickness.

Delivering PACT-principled care: are specialty care patients being left behind?

BACKGROUND: With the reorganization of primary care into Patient Aligned Care Teams (PACT) teams, the Veteran Affairs Health System (VA) aims to ensure all patients receive care based on patient-centered medical home (PCMH) principles. However, some patients receive the preponderance of care from specialty rather than primary care clinics because of the special nature of their clinical conditions. We examined seven VA (HIV) clinics as a model to test the extent to which such patients receive PCMH-principled care. OBJECTIVE: To examine the extent to which HIV specialty care in VA conforms to PCMH principles. DESIGN: Qualitative study. PARTICIPANTS: Forty-one HIV providers from seven HIV clinics and 20 patients from four of these clinics. APPROACH: We conducted semi-structured interviews with HIV clinic providers and patients about care practices and adherence to PCMH principles. Using an iterative approach, data was analyzed using both a content analysis and an a priori, PCMH-principled coding strategy. KEY RESULTS: Patients with HIV receive varying levels of PCMH-principled care across a range of VA HIV clinic structures. The more PCMH-principled HIV clinics largely functioned as PCMHs; patients received integrated, coordinated, comprehensive primary care within a dedicated HIV clinic. In contrast, some clinics were unable to meet the criteria of being a patient's medical home, and instead functioned primarily as a place to receive HIV-related services with limited care coordination. Patients from the less PCMH-principled clinics reported less satisfaction with their care. CONCLUSIONS: Even in a large, integrated healthcare system, there is wide variation in patients' receipt of PCMH-principled care in specialty care settings. In order to meet the goal of having all patients receiving PCMH-principled care, there needs to be careful consideration of where primary and specialty care services are delivered and coordinated. The best mechanisms for ensuring that patients with complex medical conditions receive PCMH-principled care may need to be tailored to different specialty care contexts.

Determining the Public Health Impact of Climate Change: A National Study Using a Health Impact Assessment Approach in Wales.

Objective: Climate change is recognised as the biggest threat to global health of the 21st century and impacts on health and wellbeing through a range of factors. Due to this, the need to take action in order to protect population health and wellbeing is becoming ever more urgent. Methods: In 2019, Public Health Wales carried out a comprehensive mixed-method Health Impact Assessment (HIA) of climate change. Unlike other risk assessments, it appraised the potential impact of climate change on health and inequalities in Wales through participatory workshops, stakeholder consultations, systematic literature reviews and case studies. Results: The HIA findings indicate potential impacts across the wider determinants of health and wellbeing. For example, air quality, excess heat/cold, flooding, economic productivity, infrastructure, and community resilience. A range of impacts were identified across population groups, settings, and geographical areas. Conclusion: These findings can inform decision-makers to prepare for climate change plans and policies using an evidence-informed approach. The work has demonstrated the value of a HIA approach by mobilising a range of evidence through a transparent process, resulting in transferrable learning for others.

Central implementation strategies outperform local ones in improving HIV testing in Veterans Healthcare Administration facilities.

BACKGROUND: Pilot data suggest that a multifaceted approach may increase HIV testing rates, but the scalability of this approach and the level of support needed for successful implementation remain unknown. OBJECTIVE: To evaluate the effectiveness of a scaled-up multi-component intervention in increasing the rate of risk-based and routine HIV diagnostic testing in primary care clinics and the impact of differing levels of program support. DESIGN: Three arm, quasi-experimental implementation research study. SETTING: Veterans Health Administration (VHA) facilities. PATIENTS: Persons receiving primary care between June 2009 and September 2011 INTERVENTION: A multimodal program, including a real-time electronic clinical reminder to facilitate HIV testing, provider feedback reports and provider education, was implemented in Central and Local Arm Sites; sites in the Central Arm also received ongoing programmatic support. Control Arm sites had no intervention MAIN MEASURES: Frequency of performing HIV testing during the 6 months before and after implementation of a risk-based clinical reminder (phase I) or routine clinical reminder (phase II). KEY RESULTS: The adjusted rate of risk-based testing increased by 0.4 %, 5.6 % and 10.1 % in the Control, Local and Central Arms, respectively (all comparisons, p < 0.01). During phase II, the adjusted rate of routine testing increased by 1.1 %, 6.3 % and 9.2 % in the Control, Local and Central Arms, respectively (all comparisons, p < 0.01). At study end, 70-80 % of patients had been offered an HIV test. CONCLUSIONS: Use of clinical reminders, provider feedback, education and social marketing significantly increased the frequency at which HIV testing is offered and performed in VHA facilities. These findings support a multimodal approach toward achieving the goal of having every American know their HIV status as a matter of routine clinical practice.

Chronostratigraphy of sediment cores from Lake Selina, southeastern Australia: Radiocarbon, optically stimulated luminescence, paleomagnetism, authigenic beryllium isotopes and elemental data.

This Data in Brief paper comprises dataset obtained for sediment cores collected from Lake Selina, located in the West Coast Range of Tasmania, Australia. Datasets include radiocarbon and optically stimulated luminescence age estimates, elemental composition, beryllium isotopes, magnetic properties and the paleomagnetic record measured on the cores assigned as TAS1402 (Location: Tasmania, Year: 2014, Site number: 02). The multi-proxy dataset was used to develop a chronostratigraphy for the 5.5 m and 270,000 year old record. See Lisé-Pronovost et al. (2021) (10.1016/j.quageo.2021.101152) for interpretation and discussion. The data presented in this study serve as an archive for future studies focusing on Earth system dynamics and the timeline and linkages of environmental changes across Tasmania, the Southern Hemisphere and at a global scale.

Laws, Policies, and Collective Agreements Protecting Low-wage and Digital Platform Workers During the COVID-19 Pandemic.

In the context of the COVID-19 pandemic, this commentary describes and compares shifting employment and occupational health social protections of low-wage workers, including self-employed digital platform workers. Through a focus on eight advanced economy countries, this paper identifies how employment misclassification and definitions of employees were handled in law and policy. Debates about minimum wage and occupational health and safety standards as they relate to worker well-being are considered. Finally, we discuss promising changes introduced during the COVID-19 pandemic that protect the health of low-wage and self-employed workers. Overall, we describe an ongoing "haves" and a "have not" divide, with on the one extreme, traditional job arrangements with good work-and-health social protections and, on the other extreme, low-wage and self-employed digital platform workers who are mostly left out of schemes. However, during the pandemic small and often temporary gains occurred and are discussed.

PFKFB4 interacts with FBXO28 to promote HIF-1α signaling in glioblastoma.

Glioblastoma is a highly aggressive brain tumor for which there is no cure. The metabolic enzyme 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 4 (PFKFB4) is essential for glioblastoma stem-like cell (GSC) survival but its mode of action is unclear. Understanding the role of PFKFB4 in tumor cell survival could allow it to be leveraged in a cancer therapy. Here, we show the importance of PFKFB4 for glioblastoma growth in vivo in an orthotopic patient derived mouse model. In an evaluation of patient tumor samples of different cancer entities, PFKFB4 protein was found to be overexpressed in prostate, lung, colon, mammary and squamous cell carcinoma, with expression level correlating with tumor grade. Gene expression profiling in PFKFB4-silenced GSCs revealed a downregulation of hypoxia related genes and Western blot analysis confirmed a dramatic reduction of HIF (hypoxia inducible factor) protein levels. Through mass spectrometric analysis of immunoprecipitated PFKFB4, we identified the ubiquitin E3 ligase, F-box only protein 28 (FBXO28), as a new interaction partner of PFKFB4. We show that PFKFB4 regulates the ubiquitylation and subsequent proteasomal degradation of HIF-1α, which is mediated by the ubiquitin ligase activity of FBXO28. This newly discovered function of PFKFB4, coupled with its cancer specificity, provides a new strategy for inhibiting HIF-1α in cancer cells.

A novel patient stratification strategy to enhance the therapeutic efficacy of dasatinib in glioblastoma.

BACKGROUND: Glioblastoma is the most common primary malignancy of the central nervous system with a dismal prognosis. Genomic signatures classify isocitrate dehydrogenase 1 (IDH)-wildtype glioblastoma into three subtypes: proneural, mesenchymal, and classical. Dasatinib, an inhibitor of proto-oncogene kinase Src (SRC), is one of many therapeutics which, despite promising preclinical results, have failed to improve overall survival in glioblastoma patients in clinical trials. We examined whether glioblastoma subtypes differ in their response to dasatinib and could hence be evaluated for patient enrichment strategies in clinical trials. METHODS: We carried out in silico analyses on glioblastoma gene expression (TCGA) and single-cell RNA-Seq data. In addition, in vitro experiments using glioblastoma stem-like cells (GSCs) derived from primary patient tumors were performed, with complementary gene expression profiling and immunohistochemistry analysis of tumor samples. RESULTS: Patients with the mesenchymal subtype of glioblastoma showed higher SRC pathway activation based on gene expression profiling. Accordingly, mesenchymal GSCs were more sensitive to SRC inhibition by dasatinib compared to proneural and classical GSCs. Notably, SRC phosphorylation status did not predict response to dasatinib treatment. Furthermore, serpin peptidase inhibitor clade H member 1 (SERPINH1), a collagen-related heat-shock protein associated with cancer progression, was shown to correlate with dasatinib response and with the mesenchymal subtype. CONCLUSION: This work highlights further molecular-based patient selection strategies in clinical trials and suggests the mesenchymal subtype as well as SERPINH1 to be associated with response to dasatinib. Our findings indicate that stratification based on gene expression subtyping should be considered in future dasatinib trials.

The loss of an indigenous constructed landscape following British invasion of Australia: An insight into the deep human imprint on the Australian landscape.

Indigenous people play an integral role in shaping natural environments, and the disruption to Indigenous land management practices has profound effects on the biosphere. Here, we use pollen, charcoal and dendrochronological analyses to demonstrate that the Australian landscape at the time of British invasion in the 18th century was a heavily constructed one-the product of millennia of active maintenance by Aboriginal Australians. Focusing on the Surrey Hills, Tasmania, our results reveal how the removal of Indigenous burning regimes following British invasion instigated a process of ecological succession and the encroachment of cool temperate rainforest (i.e. later-stage vegetation communities) into grasslands of conservation significance. This research provides empirical evidence to challenge the long-standing portrayal of Indigenous Australians as low-impact 'hunter-gatherers' and highlights the relevance and critical value of Indigenous fire management in this era of heightened bushfire risk and biodiversity loss.

A Set of Cell Lines Derived from a Genetic Murine Glioblastoma Model Recapitulates Molecular and Morphological Characteristics of Human Tumors.

Glioblastomas (GBM) are the most aggressive tumors affecting the central nervous system in adults, causing death within, on average, 15 months after diagnosis. Immunocompetent in-vivo models that closely mirror human GBM are urgently needed for deciphering glioma biology and for the development of effective treatment options. The murine GBM cell lines currently available for engraftment in immunocompetent mice are not only exiguous but also inadequate in representing prominent characteristics of human GBM such as infiltrative behavior, necrotic areas, and pronounced tumor heterogeneity. Therefore, we generated a set of glioblastoma cell lines by repeated in vivo passaging of cells isolated from a neural stem cell-specific Pten/p53 double-knockout genetic mouse brain tumor model. Transcriptome and genome analyses of the cell lines revealed molecular heterogeneity comparable to that observed in human glioblastoma. Upon orthotopic transplantation into syngeneic hosts, they formed high-grade gliomas that faithfully recapitulated the histopathological features, invasiveness and immune cell infiltration characteristic of human glioblastoma. These features make our cell lines unique and useful tools to study multiple aspects of glioblastoma pathomechanism and to test novel treatments in an intact immune microenvironment.

Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype.

Glioblastoma frequently exhibits therapy-associated subtype transitions to mesenchymal phenotypes with adverse prognosis. Here, we perform multi-omic profiling of 60 glioblastoma primary tumours and use orthogonal analysis of chromatin and RNA-derived gene regulatory networks to identify 38 subtype master regulators, whose cell population-specific activities we further map in published single-cell RNA sequencing data. These analyses identify the oligodendrocyte precursor marker and chromatin modifier SOX10 as a master regulator in RTK I-subtype tumours. In vitro functional studies demonstrate that SOX10 loss causes a subtype switch analogous to the proneural-mesenchymal transition observed in patients at the transcriptomic, epigenetic and phenotypic levels. SOX10 repression in an in vivo syngeneic graft glioblastoma mouse model results in increased tumour invasion, immune cell infiltration and significantly reduced survival, reminiscent of progressive human glioblastoma. These results identify SOX10 as a bona fide master regulator of the RTK I subtype, with both tumour cell-intrinsic and microenvironmental effects.