Mathematical Modeling and Association Analysis Decipher the Impact of the Gut Microbiome on Cancer Immunotherapy.

Unlabelled: The gut microbiome has emerged as a key regulator of response to cancer immunotherapy. However, a better understanding of the underlying mechanisms by which the microbiome influences immunotherapy is needed to identify strategies to optimize outcomes. To this end, we developed a mathematical model to obtain insights into the effect of the microbiome on the immune system and immunotherapy response.

Variational inference for microbiome survey data with application to global ocean data.

Linking sequence-derived microbial taxa abundances to host (patho-)physiology or habitat characteristics in a reproducible and interpretable manner has remained a formidable challenge for the analysis of microbiome survey data. Here, we introduce a flexible probabilistic modeling framework, VI-MIDAS (variational inference for microbiome survey data analysis), that enables joint estimation of context-dependent drivers and broad patterns of associations of microbial taxon abundances from microbiome survey data. VI-MIDAS comprises mechanisms for direct coupling of taxon abundances with covariates and taxa-specific latent coupling, which can incorporate spatio-temporal information and taxon-taxon interactions.

Seasonal Variation in Antioxidant Defence Biomarkers and ROMO1 Gene Expression in Relation to Semen Quality of Goat Bucks.

The oxidative status of seminal fluid is a critical factor in producing high-quality sperm doses for artificial insemination. This study aimed to investigate the impact of seasonal variations on oxidative stress biomarkers and ROMO1 (Reactive Oxygen Modulator 1) gene expression in Barbari and Sirohi bucks. Four ejaculates of adult breeding Barbari and Sirohi bucks, six from each breed, were collected fortnightly using an artificial vagina during the summer and winter seasons for the study.

Dynamic Nuclear Polarization with P1 Centers in Diamond.

Substitutional nitrogen impurities within the diamond lattice, known as P1 centers, have unpaired electrons that can mediate microwave driven dynamic nuclear polarization (DNP). In this paper we explore DNP of the bulk C spins in micrometer-sized P1 diamond particles and demonstrate a 550-fold DNP enhancement of the bulk C spins at room temperature in a 9 T magnetic field or 250 GHz for ≈ 2 electrons. We study the DNP mechanisms, exploring their dependence on sample spinning frequency and microwave irradiation frequency using both continuous wave and frequency swept microwave irradiation, and discuss the results alongside recent DNP studies in the literature.

Light-Induced Metallic and Paramagnetic Defects in Halide Perovskites from Magnetic Resonance.

Halide perovskites are promising next-generation solar cell materials, but their commercialization is hampered by their propensity to degrade under operating conditions, particularly under heat, humidity, and light. Identifying degradation products and linking them to the degradation mechanism at the atomic scale is necessary to design more stable perovskite materials. Here we use magnetic resonance methods to identify and characterize the formation of both metallic lead clusters and Pb defects upon light-induced degradation of methylammonium lead halide perovskite using nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) measurements.

CRISPR-based electrochemical biosensors for animal health: Recent advances.

Animal diseases are a major concern to animal welfare, human health and the global economy. Early detection, prevention and control of these animal diseases are crucial to ensure sustainability of livestock sector, to reduce farm losses and protecting public health. Points of care (POC) devices are small, portable instruments that provide rapid results thus reduce the risk of disease transmission and enable early intervention.

Stabilization of highly efficient perovskite solar cells with a tailored supramolecular interface.

The presence of defects at the interface between the perovskite film and the carrier transport layer poses significant challenges to the performance and stability of perovskite solar cells (PSCs). Addressing this issue, we introduce a dual host-guest (DHG) complexation strategy to modulate both the bulk and interfacial properties of FAPbI-rich PSCs. Through NMR spectroscopy, a synergistic effect of the dual treatment is observed.

Hydrogen Diffusion in Hybrid Perovskites from Exchange NMR.

Ion migration is an important phenomenon affecting the performance of hybrid perovskite solar cells. It is particularly challenging, however, to disentangle the contribution of H diffusion from that of other ions, and the atomic-scale mechanism remains unclear. Here, we use H exchange NMR to prove that H ions exchange between MA cations on the time scale of seconds for both MAPbI and FAMAPbI perovskites.

TARO: tree-aggregated factor regression for microbiome data integration.

Motivation: Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data.

Soil moisture precipitation feedbacks in the Eastern European Alpine region in convection-permitting climate simulations.

A novel convection permitting modelling framework that combines a pseudo-global warming approach with continuously forced deep soil moisture from prescribed perturbation storylines is applied in the Eastern European Alpine region and parts of the Pannonian Basin to investigate soil moisture precipitation (SMP) feedbacks on summertime precipitation and the feedbacks' role under changed climate conditions. A set of 1-year convection-permitting (3 km horizontal grid spacing) soil moisture sensitivity simulations with the regional climate model of the Consortium for Small-Scale Modelling in Climate Mode are conducted. In order to account for global warming, end-of-the-century climate change effects from four global climate models, projecting the greenhouse gas concentration scenario RCP 8.

Dietary Plant Metabolites Induced Epigenetic Modification as a Novel Strategy for the Management of Prostate Cancer.

Prostate cancer is a widespread malignancy among men, with a substantial global impact on morbidity and mortality. Despite advances in conventional therapies, the need for innovative and less toxic treatments remains a priority. Emerging evidence suggests that dietary plant metabolites possess epigenetic-modifying properties, making them attractive candidates for prostate cancer treatment.

Axial-Equatorial Halide Ordering in Layered Hybrid Perovskites from Isotropic-Anisotropic Pb NMR.

Bandgap-tuneable mixed-halide 3D perovskites are of interest for multi-junction solar cells, but suffer from photoinduced spatial halide segregation. Mixed-halide 2D perovskites are more resistant to halide segregation and are promising coatings for 3D perovskite solar cells. The properties of mixed-halide compositions depend on the local halide distribution, which is challenging to study at the level of single octahedra.

Dissecting the Impact of the Gut Microbiome on Cancer Immunotherapy.

The gut microbiome has emerged as a key regulator of response to cancer immunotherapy. However, there is a gap in our understanding of the underlying mechanisms by which the microbiome influences immunotherapy. To this end, we developed a mathematical model based on i) gut microbiome data derived from preclinical studies on melanomas after fecal microbiota transplant, ii) mechanistic modeling of antitumor immune response, and iii) robust association analysis of murine and human microbiome profiles with model-predicted immune profiles.

Dual inhibitors of HDAC and other epigenetic regulators: A novel strategy for cancer treatment.

A significant advancement in the field of epigenetic drug discovery has been evidenced in recent years. Epigenetic alterations are hereditary, nevertheless reversible variations to DNA or histone adaptations that regulate gene function individualistically of the fundamental sequence. The design and synthesis of various drugs targeting epigenetic regulators open a new door for epigenetic-targeted therapies to parade worthwhile therapeutic potential for haematological and solid malignancies.

TARO: tree-aggregated factor regression for microbiome data integration.

Motivation: Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data.

Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment.

Despite the continuous progress in food science and technology, the global burden of foodborne illnesses remains substantial, with pathogens in food causing millions of infections each year. Traditional microbiological culture methods are inadequate in detecting the full spectrum of these microorganisms, highlighting the need for more comprehensive detection strategies. This review paper aims to elucidate the relationship between foodborne pathogen colonization and the composition of the poultry microbiome, and how this knowledge can be used for improved food safety.

Gut Microbiome in Patients With Early-Stage and Late-Stage Melanoma.

Importance: The gut microbiome modulates the immune system and responses to immunotherapy in patients with late-stage melanoma. It is unknown whether fecal microbiota profiles differ between healthy individuals and patients with melanoma or if microbiota profiles differ among patients with different stages of melanoma. Defining gut microbiota profiles in individuals without melanoma and those with early-stage and late-stage melanoma may reveal features associated with disease progression.

Climate change amplified the 2009 extreme landslide event in Austria.

Landslides are an important natural hazard in mountainous regions. Given the triggering and preconditioning by meteorological conditions, it is known that landslide risk may change in a warming climate, but whether climate change has already affected individual landslide events is still an open question, partly owing to landslide data limitations and methodological challenges in climate impact attribution. Here, we demonstrate the substantial influence of anthropogenic climate change on a severe event in the southeastern Alpine forelands with some estimated 952 individual landslides in June 2009.

Optically Enhanced Solid-State H NMR Spectroscopy.

Low sensitivity is the primary limitation to extending nuclear magnetic resonance (NMR) techniques to more advanced chemical and structural studies. Photochemically induced dynamic nuclear polarization (photo-CIDNP) is an NMR hyperpolarization technique where light is used to excite a suitable donor-acceptor system, creating a spin-correlated radical pair whose evolution drives nuclear hyperpolarization. Systems that exhibit photo-CIDNP in solids are not common, and this effect has, up to now, only been observed for C and N nuclei.

Dynamic Nuclear Polarization of Inorganic Halide Perovskites.

The intrinsic low sensitivity of nuclear magnetic resonance (NMR) experiments limits their utility for structure determination of materials. Dynamic nuclear polarization (DNP) under magic angle spinning (MAS) has shown tremendous potential to overcome this key limitation, enabling the acquisition of highly selective and sensitive NMR spectra. However, so far, DNP methods have not been explored in the context of inorganic lead halide perovskites, which are a leading class of semiconductor materials for optoelectronic applications.

Light-Induced Halide Segregation in 2D and Quasi-2D Mixed-Halide Perovskites.

Photoinduced halide segregation hinders widespread application of three-dimensional (3D) mixed-halide perovskites. Much less is known about this phenomenon in lower-dimensional systems. Here, we study photoinduced halide segregation in lower-dimensional mixed iodide-bromide perovskites (PEAMA Pb (Br I ), with PEA: phenethylammonium and MA: methylammonium) through time-dependent photoluminescence (PL) spectroscopy.

Neoadjuvant chemotherapy plus nivolumab with or without ipilimumab in operable non-small cell lung cancer: the phase 2 platform NEOSTAR trial.

Neoadjuvant ipilimumab + nivolumab (Ipi+Nivo) and nivolumab + chemotherapy (Nivo+CT) induce greater pathologic response rates than CT alone in patients with operable non-small cell lung cancer (NSCLC). The impact of adding ipilimumab to neoadjuvant Nivo+CT is unknown. Here we report the results and correlates of two arms of the phase 2 platform NEOSTAR trial testing neoadjuvant Nivo+CT and Ipi+Nivo+CT with major pathologic response (MPR) as the primary endpoint.

Photoacoustic imaging to monitor outcomes during hyperbaric oxygen therapy: validation in a small cohort and case study in a bilateral chronic ischemic wound.

Hyperbaric oxygen therapy (HBO2) is a common therapeutic modality that drives oxygen into hypoxic tissue to promote healing. Here, ten patients undergoing HBO2 underwent PA oximetry of the left radial artery and forearm pre- and post-HBO2; this cohort validated the use of PA imaging in HBO2. There was a significant increase in radial artery oxygenation after HBO2 (p = 0.