The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity.

Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.

CAR T-cell therapy induces a high rate of prolonged remission in relapsed primary CNS lymphoma: Real-life results of the LOC network.

The prognosis of relapsed primary central nervous system lymphoma (PCNSL) remains dismal. CAR T-cells are a major contributor to systemic lymphomas, but their use in PCNSL is limited. From the LOC network database, we retrospectively selected PCNSL who had leukapheresis for CAR-T cells from the third line of treatment, and, as controls, PCNSL treated with any treatment, at least in the third line and considered not eligible for ASCT. Twenty-seven patients (median age: 68, median of three previous lines, including ASCT in 14/27) had leukapheresis, of whom 25 received CAR T-cells (tisa-cel: N = 16, axi-cel: N = 9) between 2020 and 2023. All but one received a bridging therapy. The median follow-up after leukapheresis was 20.8 months. The best response after CAR-T cells was complete response in 16 patients (64%). One-year progression-free survival from leukapheresis was 43% with a plateau afterward. One-year relapse-free survival was 79% for patients in complete or partial response at CAR T-cell infusion. The median overall survival was 21.2 months. Twenty-three patients experienced a cytokine release syndrome and 17/25 patients (68%) a neurotoxicity (five grade ≥3). The efficacy endpoints were significantly better in the CAR T-cell group than in the control group (N = 247) (median PFS: 3 months; median OS: 4.7 months; p < 0.001). This series represents the largest cohort of PCNSL treated with CAR T-cells reported worldwide. CAR T-cells are effective in relapsed PCNSL, with a high rate of long-term remission and a reassuring tolerance profile. The results seem clearly superior to those usually observed in this setting.

Comparative clinical and molecular landscape of primary and secondary myelofibrosis: Superior performance of MIPSS70+ v2.0 over MYSEC-PM.

Comparative clinical characteristics, molecular landscape and prognosis scoring for primary (PMF) and secondary myelofibrosis (SMF).

Quantitative in situ synchrotron X-ray analysis of the ALD/MLD growth of transition metal dichalcogenide TiS2 ultrathin films.

We present the results of a full quantitative analysis of X-ray absorption spectroscopy (XAS) performed in situ during the growth of ultrathin titanium disulfide (TiS2) films via an innovative two-step process, i.e. atomic layer deposition/molecular layer deposition (ALD/MLD) followed by annealing. This growth strategy aims at separating the growth process from the crystallization process by first creating an amorphous Ti-thiolate that is converted later to crystalline TiS2via thermal annealing. The simultaneous analysis of Ti and S K-edge XAS spectra, exploiting the insights from density functional theory calculations, allows us to shed light on the chemical and structural mechanisms underlying the main steps of growth. The nature of the bonding at the base of the interface creation with the SiO2 substrate is disclosed in this study. Evidence of a progressive incorporation of S in the amorphous Ti-thiolate is given. Finally, it is shown that the annealing step plays a critical role since the transformation of the Ti-thiolate into nanocrystalline TiS2 and the loss of S are simultaneously induced, validating the two-step synthesis approach, which entails distinct growth and crystallization steps. These observations contribute to a deeper understanding of the bonding mechanism at the interface and provide insights for future research in this field and the generation of ultra-thin layered materials.

Towards large scale integration of MoS2/graphene heterostructure with ALD-grown MoS2.

In the pursuit of ultrathin and highly sensitive photodetectors, a promising approach involves leveraging the combination of light-sensitive two-dimensional (2D) semiconducting transition-metal dichalcogenides, such as MoS2and the high electrical conductivity of graphene. Over the past decade, exfoliated 2D materials and electron-beam lithography have been used extensively to demonstrate feasibility on single devices. But for these devices to be used in the real-world systems, it is necessary to demonstrate good device performance similar to lab-based devices with repeatability of the results from device to device and a path to large scale manufacturing. To work in this way, a fabrication process of MoS2/graphene vertical heterostructures with a wafer-scale integration in a CMOS compatible foundry environment is evaluated here. Large-scale atomic layer deposition on 8 inch silicon wafers is used for the growth of MoS2layers which are then transferred on a 4 inch graphene-based wafer. The MoS2/graphene phototransistors are fabricated collectively, achieving a minimum channel length of 10µm. The results measured on dozen of devices demonstrate a photoresponsivity of 50 A W-1and a remarkable sensitivity as low as 10 nW at 660 nm. These results not only compete with lab-based photodetectors made of chemical vapor deposition grown MoS2layers transferred on graphene, but also pave the way for the large-scale integration of these emerging 2D heterostructures in optoelectronic devices and sensors.

Distinct clinico-molecular arterial and venous thrombosis scores for myeloproliferative neoplasms risk stratification.

Current recommended risk scores to predict thrombotic events associated with myeloproliferative neoplasms (MPN) do not discriminate between arterial and venous thrombosis despite their different physiopathology. To define novel stratification systems, we delineated a comprehensive landscape of MPN associated thrombosis across a large long-term follow-up MPN cohort. Prior arterial thrombosis, age >60 years, cardiovascular risk factors and presence of TET2 or DNMT3A mutations were independently associated with arterial thrombosis in multivariable analysis. ARTS, an ARterial Thrombosis Score, based on these four factors, defined low- (0.37% patients-year) and high-risk (1.19% patients-year) patients. ARTS performance was superior to the two-tiered conventional risk stratification in our training cohort, across all MPN subtypes, as well as in two external validation cohorts. Prior venous thrombosis and presence of a JAK2V617F mutation with a variant allelic frequency ≥50% were independently associated with venous thrombosis. The discrimination potential of VETS, a VEnous Thrombosis Score based on these two factors, was poor, similar to the two-tiered conventional risk stratification. Our study pinpoints arterial and venous thrombosis clinico-molecular differences and proposes an arterial risk score for more accurate patients' stratification. Further improvement of venous risk scores, accounting for additional factors and considering venous thrombosis as a heterogeneous entity is warranted.

Swelling induced debonding of thin hydrogel films grafted on silicon substrates.

We report on the delamination of thin (≈µm) hydrogel films grafted to silicon substrates under the action of swelling stresses. Poly(dimetylacrylamide) (PDMA) films are synthesized by simultaneously cross-linking and grafting preformed polymer chains onto the silicon substrate using a thiol-ene reaction. The grafting density at the film/substrate interface is tuned by varying the surface density of reactive thiol-silane groups on the silicon substrate. Delamination of the films from well controlled line defects with low adhesion is monitored under a humid water vapor flow ensuring full saturation of the polymer network. A propagating delamination of the film is observed under the action of differential swelling stresses at the debonding front. A threshold thickness for the onset of this delamination is evidenced which is increasing with grafting density while the debonding velocity is also observed to decrease with an increase in grafting density. These observations are discussed within the framework of a nonlinear fracture mechanics model which assumes that the driving force for crack propagation is the difference between the swelling state of the bonded and delaminated parts of the film. Using this model, the threshold energy for crack initiation was determined from the measured threshold thickness and discussed in relation to the surface density of reactive thiol groups on the substrate.

Integration of urban science and urban climate adaptation research: opportunities to advance climate action.

There is a growing recognition that responding to climate change necessitates urban adaptation. We sketch a transdisciplinary research effort, arguing that actionable research on urban adaptation needs to recognize the nature of cities as social networks embedded in physical space. Given the pace, scale and socioeconomic outcomes of urbanization in the Global South, the specificities and history of its cities must be central to the study of how well-known agglomeration effects can facilitate adaptation. The proposed effort calls for the co-creation of knowledge involving scientists and stakeholders, especially those historically excluded from the design and implementation of urban development policies.

Biochip array technology for new psychoactive substances detection in biological samples: Evaluation of the specificity of the Randox Evidence Investigator®.

BACKGROUND: The need to detect new psychoactive substances in biological samples is of crucial interest. In this paper, the specificity of a benchtop immunoanalyzer commercialized by Randox was evaluated on real patient samples. METHOD: The Evidence Investigator was assessed to screen for NPS on 80 serum and urine samples coming from patients admitted to the emergency department. Targeted NPS were included in various categories such as synthetic cannabinoids, opioids and benzodiazepines. Results were compared with a chromatographic technique coupled with mass spectrometry. RESULTS: No NPS was detected by the reference technique. Concerning immunoanalysis, some piperazines were positive, caused by the presence of medicine containing this chemical structure. Clonazepam and fentanyl derivatives were confirmed in some cases, but sometimes the positivity was explained by other opiates or benzodiazepines, which also explained two samples falsely positive for etizolam. CONCLUSIONS: The Randox Evidence Investigator was rapid and easy to use. It can be used as a first intention but always followed by a more specific technique in order to detect false positive result.

SARS-CoV-2 seroprevalence in health care workers from 10 hospitals in Quebec, Canada: a cross-sectional study.

BACKGROUND: The COVID-19 pandemic has disproportionately affected health care workers. We sought to estimate SARS-CoV-2 seroprevalence among hospital health care workers in Quebec, Canada, after the first wave of the pandemic and to explore factors associated with SARS-CoV-2 seropositivity. METHODS: Between July 6 and Sept. 24, 2020, we enrolled health care workers from 10 hospitals, including 8 from a region with a high incidence of COVID-19 (the Montréal area) and 2 from low-incidence regions of Quebec. Eligible health care workers were physicians, nurses, orderlies and cleaning staff working in 4 types of care units (emergency department, intensive care unit, COVID-19 inpatient unit and non-COVID-19 inpatient unit). Participants completed a questionnaire and underwent SARS-CoV-2 serology testing. We identified factors independently associated with higher seroprevalence. RESULTS: Among 2056 enrolled health care workers, 241 (11.7%) had positive SARS-CoV-2 serology. Of these, 171 (71.0%) had been previously diagnosed with COVID-19. Seroprevalence varied among hospitals, from 2.4% to 3.7% in low-incidence regions to 17.9% to 32.0% in hospitals with outbreaks involving 5 or more health care workers. Higher seroprevalence was associated with working in a hospital where outbreaks occurred (adjusted prevalence ratio 4.16, 95% confidence interval [CI] 2.63-6.57), being a nurse or nursing assistant (adjusted prevalence ratio 1.34, 95% CI 1.03-1.74) or an orderly (adjusted prevalence ratio 1.49, 95% CI 1.12-1.97), and Black or Hispanic ethnicity (adjusted prevalence ratio 1.41, 95% CI 1.13-1.76). Lower seroprevalence was associated with working in the intensive care unit (adjusted prevalence ratio 0.47, 95% CI 0.30-0.71) or the emergency department (adjusted prevalence ratio 0.61, 95% CI 0.39-0.98). INTERPRETATION: Health care workers in Quebec hospitals were at high risk of SARS-CoV-2 infection, particularly in outbreak settings. More work is needed to better understand SARS-CoV-2 transmission dynamics in health care settings.

The Biobanque québécoise de la COVID-19 (BQC19)-A cohort to prospectively study the clinical and biological determinants of COVID-19 clinical trajectories.

SARS-CoV-2 infection causing the novel coronavirus disease 2019 (COVID-19) has been responsible for more than 2.8 million deaths and nearly 125 million infections worldwide as of March 2021. In March 2020, the World Health Organization determined that the COVID-19 outbreak is a global pandemic. The urgency and magnitude of this pandemic demanded immediate action and coordination between local, regional, national, and international actors. In that mission, researchers require access to high-quality biological materials and data from SARS-CoV-2 infected and uninfected patients, covering the spectrum of disease manifestations. The "Biobanque québécoise de la COVID-19" (BQC19) is a pan-provincial initiative undertaken in Québec, Canada to enable the collection, storage and sharing of samples and data related to the COVID-19 crisis. As a disease-oriented biobank based on high-quality biosamples and clinical data of hospitalized and non-hospitalized SARS-CoV-2 PCR positive and negative individuals. The BQC19 follows a legal and ethical management framework approved by local health authorities. The biosamples include plasma, serum, peripheral blood mononuclear cells and DNA and RNA isolated from whole blood. In addition to the clinical variables, BQC19 will provide in-depth analytical data derived from the biosamples including whole genome and transcriptome sequencing, proteome and metabolome analyses, multiplex measurements of key circulating markers as well as anti-SARS-CoV-2 antibody responses. BQC19 will provide the scientific and medical communities access to data and samples to better understand, manage and ultimately limit, the impact of COVID-19. In this paper we present BQC19, describe the process according to which it is governed and organized, and address opportunities for future research collaborations. BQC19 aims to be a part of a global communal effort addressing the challenges of COVID-19.

The persistence of ancient settlements and urban sustainability.

We propose a dedicated research effort on the determinants of settlement persistence in the ancient world, with the potential to significantly advance the scientific understanding of urban sustainability today. Settlements (cities, towns, villages) are locations with two key attributes: They frame human interactions and activities in space, and they are where people dwell or live. Sustainability, in this case, focuses on the capacity of structures and functions of a settlement system (geography, demography, institutions) to provide for continuity of safe habitation. The 7,000-y-old experience of urbanism, as revealed by archaeology and history, includes many instances of settlements and settlement systems enduring, adapting to, or generating environmental, institutional, and technological changes. The field of urban sustainability lacks a firm scientific foundation for understanding the long durée, relying instead on narratives of collapse informed by limited case studies. We argue for the development of a new interdisciplinary research effort to establish scientific understanding of settlement and settlement system persistence. Such an effort would build upon the many fields that study human settlements to develop new theories and databases from the extensive documentation of ancient and premodern urban systems. A scientific foundation will generate novel insights to advance the field of urban sustainability.

People have shaped most of terrestrial nature for at least 12,000 years.

Archaeological and paleoecological evidence shows that by 10,000 BCE, all human societies employed varying degrees of ecologically transformative land use practices, including burning, hunting, species propagation, domestication, cultivation, and others that have left long-term legacies across the terrestrial biosphere. Yet, a lingering paradigm among natural scientists, conservationists, and policymakers is that human transformation of terrestrial nature is mostly recent and inherently destructive. Here, we use the most up-to-date, spatially explicit global reconstruction of historical human populations and land use to show that this paradigm is likely wrong. Even 12,000 y ago, nearly three quarters of Earth's land was inhabited and therefore shaped by human societies, including more than 95% of temperate and 90% of tropical woodlands. Lands now characterized as "natural," "intact," and "wild" generally exhibit long histories of use, as do protected areas and Indigenous lands, and current global patterns of vertebrate species richness and key biodiversity areas are more strongly associated with past patterns of land use than with present ones in regional landscapes now characterized as natural. The current biodiversity crisis can seldom be explained by the loss of uninhabited wildlands, resulting instead from the appropriation, colonization, and intensifying use of the biodiverse cultural landscapes long shaped and sustained by prior societies. Recognizing this deep cultural connection with biodiversity will therefore be essential to resolve the crisis.

Distinct immunopathological mechanisms of EBV-positive and EBV-negative posttransplant lymphoproliferative disorders.

EBV-positive and EBV-negative posttransplant lymphoproliferative disorders (PTLDs) arise in different immunovirological contexts and might have distinct pathophysiologies. To examine this hypothesis, we conducted a multicentric prospective study with 56 EBV-positive and 39 EBV-negative PTLD patients of the K-VIROGREF cohort, recruited at PTLD diagnosis and before treatment (2013-2019), and compared them to PTLD-free Transplant Controls (TC, n = 21). We measured absolute lymphocyte counts (n = 108), analyzed NK- and T cell phenotypes (n = 49 and 94), and performed EBV-specific functional assays (n = 16 and 42) by multiparameter flow cytometry and ELISpot-IFNγ assays (n = 50). EBV-negative PTLD patients, NK cells overexpressed Tim-3; the 2-year progression-free survival (PFS) was poorer in patients with a CD4 lymphopenia (CD4+ <300 cells/mm3 , p <  .001). EBV-positive PTLD patients presented a profound NK-cell lymphopenia (median = 60 cells/mm3 ) and a high proportion of NK cells expressing PD-1 (vs. TC, p = .029) and apoptosis markers (vs. TC, p < .001). EBV-specific T cells of EBV-positive PTLD patients circulated in low proportions, showed immune exhaustion (p = .013 vs. TC) and poorly recognized the N-terminal portion of EBNA-3A viral protein. Altogether, this broad comparison of EBV-positive and EBV-negative PTLDs highlight distinct patterns of immunopathological mechanisms between these two diseases and provide new clues for immunotherapeutic strategies and PTLD prognosis.

Expanding the momentum field of view in angle-resolved photoemission systems with hemispherical analyzers.

In photoelectron spectroscopy, the measured electron momentum range is intrinsically related to the excitation photon energy. Low photon energies <10 eV are commonly encountered in laser-based photoemission and lead to a momentum range that is smaller than the Brillouin zones of most materials. This can become a limiting factor when studying condensed matter with laser-based photoemission. An additional restriction is introduced by widely used hemispherical analyzers that record only electrons photoemitted in a solid angle set by the aperture size at the analyzer entrance. Here, we present an upgrade to increase the effective solid angle that is measured with a hemispherical analyzer. We achieve this by accelerating the photoelectrons toward the analyzer with an electric field that is generated by a bias voltage on the sample. Our experimental geometry is comparable to a parallel plate capacitor, and therefore, we approximate the electric field to be uniform along the photoelectron trajectory. With this assumption, we developed an analytic, parameter-free model that relates the measured angles to the electron momenta in the solid and verify its validity by comparing with experimental results on the charge density wave material TbTe3. By providing a larger field of view in momentum space, our approach using a bias potential considerably expands the flexibility of laser-based photoemission setups.