Compositional Signatures Research Articles

Ultraviolet-photoluminescence and trace element analyses in Ga-rich sphalerite from the Djebel Gustar Zn-Pb deposit, Algeria

The Djebel Gustar Zn-Pb deposit in northeastern Algeria is one of many carbonate-hosted base metal deposits in the Atlas metallogenic province of North Africa. The sphalerite in this deposit occurs in five distinct types that differ in texture, mineral assemblage, chemical composition, and UV photoluminescence signature. Detailed investigation of trace elements by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) showed that the sphalerite is significantly enriched in the critical metal Ga. The trace element concentrations of the different sphalerite types correlated well with their photoluminescence color; with Mn2+ (orange-yellow), Cu+ (green), and Ga3+ (red) being the dominant activators. We suggest that the Ga enrichment in the Djebel Gustar deposit is the result of formation conditions that include the mixing of a Cl-rich fluid carrying mainly Zn and Pb with a more reduced and Cl-poor fluid containing considerable organic matter and/or calcite with adsorbed Ga(OH)3. This Ga was subsequently incorporated into sphalerite, rather than forming a stoichiometric Ga phase. Furthermore, our study demonstrates that UV photoluminescence of low Fe sphalerite has the potential to become a simple and affordable tool for preliminary characterization of sphalerite ores in mining and exploration with respect to critical elements such as Ga.

Multipole decomposition of tensor interactions of fermionic probes with composite particles and BSM signatures in nuclear reactions

A multipole decomposition of a cross section is a useful tool to simplify the analysis of reactions due to their symmetry properties. By using a new approach to decompose antisymmetric tensor-type interactions within the multipole analysis, we introduce a general mathematical formalism for working with tensor couplings. This allows us to present a general tensor nuclear response, which is particularly useful for ongoing $\ensuremath{\beta}$-decay experiments looking for physics beyond the Standard Model (BSM), as well as other exotic particle scatterings off nuclei, e.g., in dark matter direct detection experiments. Using this method, BSM operators identify with the known Standard Model operators, eliminating the need for calculations of additional matrix elements. We present in detail BSM expressions useful for $\ensuremath{\beta}$-decay experiments and give an exemplary application for $^{6}\mathrm{He}$ $\ensuremath{\beta}$-decay, although the formalism is easily generalizable for calculating other exotic scattering reactions.

Foraminifera associated with cold seeps in marine sediments

Cold seep foraminifera have attracted considerable attention as they provide valuable insights into the study of cold seeps. This study provides a comprehensive overview of the manifestations of foraminifera in cold seep environments and methane seepage activities. Certain taxa of benthic foraminifera, such as Uvigerina, Bolivina, Bulimina, Chilostomella, Globobulimina, Nonionella, Melonis, Epistominella, Cibicidoides, and Globocassidulina, are known to inhabit geochemical conditions induced by methane-rich environments and may feed on associated methanotrophic microbial communities. Secondary mineralization on foraminifera shells is a widespread manifestation in seep sediments, and alters the microstructure, elementary composition, and isotopic signatures of foraminifera. On one hand, the precipitation of secondary authigenic Mg-rich, Mn-rich, Sr-rich, and Ba-rich calcite coatings have been observed on microfossils. On the other hand, micron-sized crystal pyrite and gypsum aggregates can also grow on the foraminifera walls. The negative δ13C and positive δ18O anomalies in both planktonic and benthic foraminifera from seep-associated sediments can serve as proxies for tracing past seepage activities, either in their live form or being adulterated by methane-derived authigenic carbonate after deposition. Seeping activities are recognized with a significant impact on benthic foraminifera, and the presence of cold seep-related species and significant isotopic anomalies in shells can be used to reconstruct past methane seepage events. Intensive methane seepage tends to suppress benthic foraminifera populations, while moderate intensity seepage may lead to a thriving benthic foraminiferal community, with hypoxia-enduring taxa such as Uvigerina, Melonis, and Bulimina being predominant. In contrast, oxygen-loving epibenthic taxa such as Cibicidoides often occur in areas of low methane flux. Compared to planktonic foraminifera, the single species of benthic foraminifera can provide a more comprehensive record of seepage evolution. Live benthic specimens are preferred for in-situ seep studies, while the superimposition of secondary minerals on the original shells should not be ignored when observing dead individuals. The significance of the evolution of methane seepage, changes in environmental parameters of the living habitat, and species sensitivity in cold seeps are emphasized in explaining the variation in foraminiferal assemblages and fluctuations in stable isotopes.

Petrology of Bengal Fan turbidites (IODP Expeditions 353 and 354): provenance versus diagenetic control

ABSTRACT High-resolution petrographic and heavy-mineral analyses of Bengal Fan turbidites from six cores drilled during IODP Expeditions 353 and 354 elucidate factors controlling their intersample compositional variability as a key to understanding sedimentary processes and erosional evolution of the Himalayan belt since the Miocene. Bengal Fan turbidites are feldspatho-quartzose to litho-feldspatho-quartzose with plagioclase > K-feldspar; slow-settling micas increase in abundance in very fine sand and coarse silt. The feldspar/quartz ratio and higher-rank metamorphic rock fragments notably increase from uppermost Miocene to Pleistocene deposits, which is ascribed to the onset of rapid exhumation of the Eastern Himalayan syntaxis since ∼ 5 Ma. The same trends are documented in Nicobar Fan turbidites, confirming that they belong to the same sedimentary system. Both Bengal and Nicobar fans record a pulse in mass accumulation rate at Tortonian times, when supply of sedimentary and very-low-grade metasedimentary detritus reflected accelerated exhumation of the Lesser Himalaya. In contrast to foreland-basin sediments, where ferromagnesian minerals have been completely dissolved in strata as young as Pliocene–Pleistocene, in both Bengal–Nicobar and Indus fans amphibole invariably represents about half of the moderately rich to rich transparent-heavy-mineral suite, demonstrating that amphibolite-facies Greater Himalaya metamorphic rocks were widely exposed in the Himalayan range well before the late Miocene and possibly since the late Oligocene, as indicated by a few sillimanite and kyanite grains in Bengal Fan sediments as old as 23 Ma and 28 Ma, respectively. Diagenetic dissolution strongly affected olivine and pyroxene in strata older than the middle and early Pleistocene, respectively, whereas amphibole decreases markedly through progressively older Miocene strata. Ferromagnesian minerals and sillimanite are almost completely dissolved in lower Miocene strata, where durable zircon, tourmaline, rutile, and apatite make up half of the strongly depleted heavy-mineral assemblage. Quaternary turbidites from the six studied cores have virtually the same compositional signatures, testifying to efficient homogenization by turbidite transport and reworking across the fan. Turbidites in western cores closer to peninsular India (U1444A and U1454B) are not different from those in eastern cores, indicating very minor supply from the subcontinent. Forward-mixing calculations based on integrated petrographic and heavy-mineral data indicate that sand supply from the Brahmaputra River to Quaternary turbidites was four times larger than supply from the Ganga River, indicating up to six times higher sediment yields and erosion rates in the Brahmaputra than in the Ganga catchment, largely reflecting superfast erosion of the Eastern Himalayan syntaxis.

WITHDRAWN: Disturbances of purine and lipid metabolism in the microbiota-gut-brain axis in male adolescent nonhuman primates with depressive-like behaviors

IntroductionMajor depressive disorder (MDD) in adolescents is a widespread and growing global public health concern with unique characteristics and pathophysiological mechanisms that are distinct from MDD in adults. ObjectiveThe purpose of our work was to address this knowledge gap about the unique characteristics and pathophysiological mechanisms of adolescent depression from a microbiota-gut-brain (MGB) axis perspective. MethodTen healthy male cynomolgus macaques (Macaca fascicularis) were paired into five pairs based on age and body weight, and two cynomolgus macaques from each pair were randomly allocated to chronic unpredictable mild stress group, or unstressed control group. At endpoint, microbe composition from cecum, ascending colon, transverse colon, and descending colon were analyzed by metagenome sequencing, and the metabolite profiles of MGB axis including central (prefrontal cortex, hippocampus and amygdala) and peripheral (plasma, gut and feces of cecum, ascending colon, transverse colon and descending colon) samples were analyzed by metabolomic profiling. Then, we compare the gut microbiome and metabolic signatures in MGB axis between adolescent and adult depressed macaques. ResultsThe microbial composition and gut-brain metabolic signatures were widely divergent between adolescent and adult depressed macaques, though the phylum Firmicutes and lipid metabolism pathways were persistently altered in both populations. Purine and arginine biosynthesis metabolism were a specific hallmark of adolescent depressed macaques, while fatty acyl metabolism was specially altered in adult. These differential metabolic pathways in adolescent and adult depressed macaques were mainly mapped into the prefrontal cortex and hippocampus, respectively. Notably, the genus Clostridium and Haemophilus, characteristically disturbed in adolescent depressed macaques but not in adult, were also significantly associated with the majority of purine metabolites in MGB axis. ConclusionThese findings provide a new framework describing divergent pathophysiological mechanisms between adolescent and adult depression, and may open new windows for more effective treatment strategies of adolescent depression.

Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies

BackgroundSince the onset of the SARS-CoV-2 pandemic, bioinformatic analyses have been performed to understand the nucleotide and synonymous codon usage features and mutational patterns of the virus. However, comparatively few have attempted to perform such analyses on a considerably large cohort of viral genomes while organizing the plethora of available sequence data for a month-by-month analysis to observe changes over time. Here, we aimed to perform sequence composition and mutation analysis of SARS-CoV-2, separating sequences by gene, clade, and timepoints, and contrast the mutational profile of SARS-CoV-2 to other comparable RNA viruses.MethodsUsing a cleaned, filtered, and pre-aligned dataset of over 3.5 million sequences downloaded from the GISAID database, we computed nucleotide and codon usage statistics, including calculation of relative synonymous codon usage values. We then calculated codon adaptation index (CAI) changes and a nonsynonymous/synonymous mutation ratio (dN/dS) over time for our dataset. Finally, we compiled information on the types of mutations occurring for SARS-CoV-2 and other comparable RNA viruses, and generated heatmaps showing codon and nucleotide composition at high entropy positions along the Spike sequence.ResultsWe show that nucleotide and codon usage metrics remain relatively consistent over the 32-month span, though there are significant differences between clades within each gene at various timepoints. CAI and dN/dS values vary substantially between different timepoints and different genes, with Spike gene on average showing both the highest CAI and dN/dS values. Mutational analysis showed that SARS-CoV-2 Spike has a higher proportion of nonsynonymous mutations than analogous genes in other RNA viruses, with nonsynonymous mutations outnumbering synonymous ones by up to 20:1. However, at several specific positions, synonymous mutations were overwhelmingly predominant.ConclusionsOur multifaceted analysis covering both the composition and mutation signature of SARS-CoV-2 gives valuable insight into the nucleotide frequency and codon usage heterogeneity of SARS-CoV-2 over time, and its unique mutational profile compared to other RNA viruses.

A Novel Radiogenomics Biomarker for Predicting Treatment Response and Pneumotoxicity From Programmed Cell Death Protein or Ligand-1 Inhibition Immunotherapy in NSCLC

IntroductionPatient selection for checkpoint inhibitor immunotherapy is currently guided by programmed death-ligand 1 (PD-L1) expression obtained from immunohistochemical staining of tumor tissue samples. This approach is susceptible to limitations resulting from the dynamic and heterogeneous nature of cancer cells and the invasiveness of the tissue sampling procedure. To address these challenges, we developed a novel computed tomography (CT) radiomic-based signature for predicting disease response in patients with NSCLC undergoing programmed cell death protein 1 (PD-1) or PD-L1 checkpoint inhibitor immunotherapy. MethodsThis retrospective study comprises a total of 194 patients with suitable CT scans out of 340. Using the radiomic features computed from segmented tumors on a discovery set of 85 contrast-enhanced chest CTs of patients diagnosed with having NSCLC and their CD274 count, RNA expression of the protein-encoding gene for PD-L1, as the response vector, we developed a composite radiomic signature, lung cancer immunotherapy—radiomics prediction vector (LCI-RPV). This was validated in two independent testing cohorts of 66 and 43 patients with NSCLC treated with PD-1 or PD-L1 inhibition immunotherapy, respectively. ResultsLCI-RPV predicted PD-L1 positivity in both NSCLC testing cohorts (area under the curve [AUC] = 0.70, 95% confidence interval [CI]: 0.57–0.84 and AUC = 0.70, 95% CI: 0.46–0.94). In one cohort, it also demonstrated good prediction of cases with high PD-L1 expression exceeding key treatment thresholds (>50%: AUC = 0.72, 95% CI: 0.59–0.85 and >90%: AUC = 0.66, 95% CI: 0.45–0.88), the tumor’s objective response to treatment at 3 months (AUC = 0.68, 95% CI: 0.52–0.85), and pneumonitis occurrence (AUC = 0.64, 95% CI: 0.48–0.80). LCI-RPV achieved statistically significant stratification of the patients into a high- and low-risk survival group (hazard ratio = 2.26, 95% CI: 1.21–4.24, p = 0.011 and hazard ratio = 2.45, 95% CI: 1.07–5.65, p = 0.035). ConclusionsA CT radiomics-based signature developed from response vector CD274 can aid in evaluating patients’ suitability for PD-1 or PD-L1 checkpoint inhibitor immunotherapy in NSCLC.

Analysis of HLA gene expression in patients with dMMR/MSI-H colorectal carcinoma resistant to immune checkpoint inhibitors.

202 Background: Large studies have identified immune checkpoint inhibitors (ICI) as an effective therapy for deficient mismatch repair/microsatellite instability high (dMMR/MSI-H) colorectal cancer (CRC). However, a subset of dMMR/MSI-H CRC patients exist that do not benefit from ICI and show rapid cancer progression within the first 6 months of therapy. Genetic alterations of the host immune system, including loss of β2M and single copy loss of HLA molecules, can contribute to innate resistance to ICI. In this study, we sought to analyze the role of expression of HLA genes and β2M as determinants of innate resistance to ICI by analyzing an extensive clinico-genomic database. Methods: Next-generation sequencing (NGS) of DNA (592-gene or whole exome) and RNA (whole transcriptome) was performed on CRC patient samples (n = 24,394) submitted to a CLIA-certified laboratory (Caris Life Sciences, Phoenix, AZ). dMMR/MSI-H was assessed by IHC/NGS. PD-L1 expression was tested by IHC (SP142; positive (+): ≥2+, ≥%5). Real world overall survival and treatment data were obtained from insurance claims data. Time-To-Next-treatment (TTNT) was calculated from start of ICI monotherapy to the start of next therapy, or death. Kaplan-Meier estimates were used for comparison. A composite signature of MHC II gene expression was tested for molecular associations. Immune cell infiltration was estimated by RNA deconvolution using quanTIseq. Statistical significance was determined using Fisher’s Exact/Mann Whitney/X2 tests. Results: We identified 1549 patients with dMMR/MSI-H CRC; 242 patients of these had received pembrolizumab or nivolumab. Using TTNT as a proxy for progression on treatment, we divided the patients into two cohorts: >180 days TTNT and <180 days TTNT. Following manual curation of the cases by two oncologists and limiting the patients to those who had received ≥ 2 doses of either ICI and at least 180 days of recorded follow up, we generated cohorts of 77 patients (>180 days TTNT; good responders) and 34 patients (<180 days TTNT; poor responders). High expression of HLA genes (HLA-DRB1, HLA-B, HLA-DQB1, HLA-DPB1, HLA-DPA1- p<0.02; fold change 2.1-3) was found in the good responder group. No β2M alterations were detected in either subgroup. After dividing the entire cohort into quartiles, patients in the highest quartile of expression for either CD74, HLA-DQA1, HLA-DQB1, HLA-DPB1 or HLA-DRB1 had improved survival when compared to lower expressors (p< 0.05). High MHC II signature expression was associated with an increased rate of PD-L1+ (34 vs 8%, p<0.0001) and infiltration of M1 macrophages (9.1 vs 4.9%, p<0.0001). Conclusions: We identify elevated expression of HLA genes involved in formation of the MHC-II complex as a potential biomarker of improved response to immunotherapy that could, if further validated, optimize patient selection for ICI in CRC.

Spatio-temporal remodelling of the composition and architecture of the human ovarian cortical extracellular matrix during in vitro culture.

How does in vitro culture alter the human ovarian cortical extracellular matrix (ECM) network structure? The ECM composition and architecture vary in the different layers of the ovarian cortex and are remodelled during in vitro culture. The ovarian ECM is the scaffold within which follicles and stromal cells are organized. Its composition and structural properties constantly evolve to accommodate follicle development and expansion. Tissue preparation for culture of primordial follicles within the native ECM involves mechanical loosening; this induces undefined modifications in the ECM network and alters cell-cell contact, leading to spontaneous follicle activation. Fresh ovarian cortical biopsies were obtained from six women aged 28-38 years (mean ± SD: 32.7 ± 4.1 years) at elective caesarean section. Biopsies were cut into fragments of ∼4 × 1 × 1 mm and cultured for 0, 2, 4, or 6 days (D). Primordial follicle activation, stromal cell density, and ECM-related protein (collagen, elastin, fibronectin, laminin) positive area in the entire cortex were quantified at each time point using histological and immunohistological analysis. Collagen and elastin content, collagen fibre characteristics, and follicle distribution within the tissue were further quantified within each layer of the human ovarian cortex, namely the outer cortex, the mid-cortex, and the cortex-medulla junction regions. Primordial follicle activation occurred concomitantly with a loosening of the ovarian cortex during culture, characterized by an early decrease in stromal cell density from 3.6 ± 0.2 × 106 at day 0 (D0) to 2.8 ± 0.1 × 106 cells/mm3 at D2 (P = 0.033) and a dynamic remodelling of the ECM. Notably, collagen content gradually fell from 55.5 ± 1.7% positive area at D0 to 42.3 ± 1.1% at D6 (P = 0.001), while elastin increased from 1.1 ± 0.2% at D0 to 1.9 ± 0.1% at D6 (P = 0.001). Fibronectin and laminin content remained stable. Moreover, collagen and elastin distribution were uneven throughout the cortex and during culture. Analysis at the sub-region level showed that collagen deposition was maximal in the outer cortex and the lowest in the mid-cortex (69.4 ± 1.2% versus 53.8 ± 0.8% positive area, respectively, P < 0.0001), and cortical collagen staining overall decreased from D0 to D2 (65.2 ± 2.4% versus 60.6 ± 1.8%, P = 0.033) then stabilized. Elastin showed the converse distribution, being most concentrated at the cortex-medulla junction (3.7 ± 0.6% versus 0.9 ± 0.2% in the outer cortex, P < 0.0001), and cortical elastin peaked at D6 compared to D0 (3.1 ± 0.5% versus 1.3 ± 0.2%, P < 0.0001). This was corroborated by a specific signature of the collagen fibre type across the cortex, indicating a distinct phenotype of the ovarian cortical ECM depending on region and culture period that might be responsible for the spatio-temporal and developmental pattern of follicular distribution observed within the cortex. N/A. Ovarian cortical biopsies were obtained from women undergoing caesarean sections. As such, the data obtained may not accurately reflect the ECM distribution and structure of non-pregnant women. Clarifying the composition and architecture signature of the human ovarian cortical ECM provides a foundation for further exploration of ovarian microenvironments. It is also critical for understanding the ECM-follicle interactions regulating follicle quiescence and awakening, leading to improvements in both in vitro activation and in vitro growth techniques. Medical Research Council grant MR/R003246/1 and Wellcome Trust Collaborative Award in Science: 215625/Z/19/Z. The authors have no conflicts to declare. N/A.

DOP31 Gut metabolomic and compositional signatures predict response to treatment with exclusive enteral nutrition in children with active Crohn’s disease

Abstract Background Predicting response to treatment with exclusive enteral nutrition (EEN) in paediatric Crohn’s disease (CD) can lead to more personalised, cost-effective, and efficacious therapy. We explored the ability of pre-treatment clinical and multi-omics parameters to predict faecal calprotectin (FCal) levels at EEN completion. Methods In 37 children [median (IQR), 12.4y (10.1, 15.0)] with active CD, disease parameters, dietary intake, 19 inflammatory cytokines, and 92 plasma inflammation-related proteomic markers in plasma, diet-related bacterial metabolites and 1H NMR metabolomics in faeces, as well as the faecal, duodenal, ileal, ascending and descending colon microbiome (16S rRNA sequencing), and dietary intake were measured prior to EEN initiation. Fifteen children responded to EEN (RS) and 12 not (non-RS) using a FCal cut-off &amp;lt;300. Results Disease and host immunological parameters did not predict FCal levels at EEN completion. Responders had lower fibre intake, half the concentration of butyrate, acetate, phenylacetate and higher bacterial richness, in faeces, than non-RS. A model trained with the discriminant duodenal operational taxonomic units (OTUs) demonstrated a sensitivity of 67%, specificity of 90% and positive predictive value of 80% to differentiate RS from non-RS. The predictive ability of the faecal and the microbiomes of other mucosal sites was inferior to that of the duodenum. In multicomponent prediction including all datasets and faecal microbiome, higher levels of phenylacetate and relative abundance of OTU of Bacteroides, were predictive of non-RS with a sensitivity of 73%, specificity of 81% and positive predictive value of 73%. Replacing the faecal with the duodenal microbiome in a subset of participants (n=14), produced a model with 100% accuracy to predict RS from non-RS. The single most important variable in this model was a Lachnospira OTU which was absent in all RS but highly abundant in non-RS. Conclusion We identified pre-treatment microbial signals and diet-related metabolites which may comprise targets for pre-treatment optimisation and personalised nutritional therapy in CD.

Immunologic prediction of long COVID.

In addition to the acute phase of SARS-CoV-2 infection, a significant percentage of patients experience a prolonged illness with varying symptomatology. Longitudinal SARS-CoV-2 patient-centric immunologic, inflammatory and metabolic data collection has allowed the generation of a composite signature to predict recovery.

A patient-centric modeling framework captures recovery from SARS-CoV-2 infection

The biology driving individual patient responses to severe acute respiratory syndrome coronavirus 2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data and covering a year after disease onset, from 215 infected individuals with differing disease severities. Our analyses revealed distinct ‘systemic recovery’ profiles, with specific progression and resolution of the inflammatory, immune cell, metabolic and clinical responses. In particular, we found a strong inter-patient and intra-patient temporal covariation of innate immune cell numbers, kynurenine metabolites and lipid metabolites, which highlighted candidate immunologic and metabolic pathways influencing the restoration of homeostasis, the risk of death and that of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-19-systemic-recovery-prediction-app, designed to test our findings prospectively.

Preferential preservation of pre-aged terrestrial organic carbon by reactive iron in estuarine particles and coastal sediments of a large river-dominated estuary

Reactive iron (FeR) plays an important role in the preservation of organic carbon (OC) in coastal sediments, yet changes in the OC bound to FeR (OC-FeR), during transport and deposition, remain poorly understood. The main goal of this work is to investigate the variation of the age and composition of OC-FeR from estuarine suspended particulate matter (SPM) to coastal sediments, to further understand the role of FeR in the preservation of terrestrial OC exported from large rivers into marginal seas. We examined OC and its carbon isotopic composition (Δ14Cbulk, δ13Cbulk), specific surface area (SSA), grain size composition, lignin phenols, FeR, Mössbauer spectroscopy, and isotopic signatures of OC-FeR (Δ14COC-FeR, δ13COC-FeR) in SPM and surface sediments of the Changjiang Estuary. Particulate OC (POC) and FeR concentrations in SPM are significantly higher than in surface sediments, with no significant differences between surface- and bottom-water SPM. This indicates that loss of OC and FeR largely occurs at the sediment–water interface due in part, to rapid Fe cycling. The percentage of OC-FeR (fOC-FeR) in SPM (6.6 ± 1.9%) is similar to that in mobile-mud sediment (8.8 ± 1.8%). There are no significant differences in OC-FeR content (p > 0.05) from SPM to mobile-mud sediments, but non-OC-FeR largely decreases, suggesting that terrestrial OC-FeR has greater stability compared to terrestrial non-OC-FeR. Both δ13COC-FeR and Δ14COC-FeR are lower than bulk OC, indicating that FeR is mainly associated with pre-aged soil OC of terrestrial plant origin, especially in estuarine SPM and mobile-mud sediments. Taken together, binding with FeR is a potential long-term protection mechanism for terrestrial OC. Both Δ14Cbulk and Δ14COC-FeR decrease with an increase in the ratio of hematite to (super)paramagnetic Fe3+, indicating that high-crystallinity iron oxide is largely associated with pre-aged terrestrial OC, and there is a potential joint maturation mechanism between FeR and its associated OC. Based on literature comparisons of soils, estuarine SPM, and marine sediments, OC-FeR associations are controlled mainly by sedimentary regimes, FeR compositions, and OC sources. This work supports the notion that FeR plays an important role in the stabilization and transport of river-derived terrestrial OC.

Contrasts in dissolved, particulate, and sedimentary organic carbon from the Kolyma River to the East Siberian Shelf

Abstract. Arctic rivers will be increasingly affected by the hydrological and biogeochemical consequences of thawing permafrost. During transport, permafrost-derived organic carbon (OC) can either accumulate in floodplain and shelf sediments or be degraded into greenhouse gases prior to final burial. Thus, the net impact of permafrost OC on climate will ultimately depend on the interplay of complex processes that occur along the source-to-sink system. Here, we focus on the Kolyma River, the largest watershed completely underlain by continuous permafrost, and marine sediments of the East Siberian Sea, as a transect to investigate the fate of permafrost OC along the land–ocean continuum. Three pools of riverine OC were investigated for the Kolyma main stem and five of its tributaries: dissolved OC (DOC), suspended particulate OC (POC), and riverbed sediment OC (SOC). They were compared with earlier findings in marine sediments. Carbon isotopes (δ13C, Δ14C), lignin phenol, and lipid biomarker proxies show a contrasting composition and degradation state of these different carbon pools. Dual C isotope source apportionment calculations imply that old permafrost-OC is mostly associated with sediments (SOC; contribution of 68±10 %), and less dominant in POC (38±8 %), whereas autochthonous primary production contributes around 44±10 % to POC in the main stem and up to 79±11 % in tributaries. Biomarker degradation indices suggest that Kolyma DOC might be relatively degraded, regardless of its generally young age shown by previous studies. In contrast, SOC shows the lowest Δ14C value (oldest OC), yet relatively fresh compositional signatures. Furthermore, decreasing mineral surface area-normalised OC- and biomarker loadings suggest that SOC might be reactive along the land–ocean continuum and almost all parameters were subjected to rapid change when moving from freshwater to the marine environment. This suggests that sedimentary dynamics play a crucial role when targeting permafrost-derived OC in aquatic systems and support earlier studies highlighting the fact that the land–ocean transition zone is an efficient reactor and a dynamic environment. The prevailing inconsistencies between freshwater and marine research (i.e. targeting predominantly DOC and SOC respectively) need to be better aligned in order to determine to what degree thawed permafrost OC may be destined for long-term burial, thereby attenuating further global warming.

MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations.

Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.

The Composite Immune Risk Score predicts overall survival after allogeneic hematopoietic stem cell transplantation: A retrospective analysis of 1838 cases.

There has been little consensus on how to quantitatively assess immune reconstitution after hematopoietic stem cell transplantation (HSCT) as part of the standard of care. We retrospectively analyzed 11 150 post-transplant immune profiles of 1945 patients who underwent HSCT between 2012 and 2020. 1838 (94.5%) of the cases were allogeneic HSCT. Using the training set of patients (n=729), we identified a composite immune signature (integrating neutrophil, total lymphocyte, natural killer, total T, CD4+ T, and B cell counts in the peripheral blood) during days 91-180 after allogeneic HSCT that was predictive of early mortality and moreover simplified it into a formula for a Composite Immune Risk Score. When we verified the Composite Immune Risk Score in the validation (n=284) and test (n=391) sets of patients, a high score value was found to be associated with hazard ratios (HR) of 3.64 (95% C.I. 1.55-8.51; p=.0014) and 2.44 (95% C.I., 1.22-4.87; p=.0087), respectively, for early mortality. In multivariate analysis, a high Composite Immune Risk Score during days 91-180 remained an independent risk factor for early mortality after allogeneic HSCT (HR, 1.80; 95% C.I., 1.28-2.55; p=.00085). In conclusion, the Composite Immune Risk Score is easy to compute and could identify the high-risk patients of allogeneic HSCT who require targeted effort for prevention and control of infection.

Flood Depth Estimation in Agricultural Lands From L and C-Band Synthetic Aperture Radar Images and Digital Elevation Model

Flood depth is one of the important attributes in damage assessment especially in areas where agro-based activities takes place. Assessing impacted region turns out to be exceptionally difficult in the case of low-lying catchments with arable lands, which inundates due to extreme precipitation and flood modelling becomes impossible. Under these circumstances, SAR derived flood maps are valuable in removing different constraints related to flood modelling with high degree of profundity. Depth estimation from non-contact based methods requires, flood boundary as a primary input. However, detecting flood depth in emerging vegetation poses a complex challenge in terms of boundary estimation due to composite signatures that are manifested on SAR data. In this paper, a new approach is proposed to extract flood boundaries by fusing SAR data of two different frequencies, which are sensitive to water level changes. In the first step, wavelet fusion is applied to combine L- and C- band SAR data followed by Otsu’s segmentation method to extract varying levels of flood boundaries. In the second step, SRTM Digital Elevation Model (DEM) with 30m horizontal resolution is used on each boundary for statistical analysis based on which water surface levels are extracted. In the final step, depth levels are calculated from the water surface elevation and DEM. Floodwater Depth Estimation tool (FwDET) derived depth measurements are used to calibrate the statistical thresholds for derived flood depths. The study carried out on 2016 Assam flood event shows maximum flood depth of 1.56 meters in the selected study area and the results are verified with evidence-based ground truth collections which showed RMSE error of 0.25 meters from the measured values.

Reproducible microbiome composition signatures of anxiety and depressive symptoms

The gut microbiome is a significant contributor to mental health, with growing evidence linking its composition to anxiety and depressive disorders. Gut microbiome composition is associated with signs of anxiety and depression both in clinically diagnosed mood disorders and subclinically in the general population and may be influenced by dietary fibre intake and the presence of chronic pain. We provide an update of current evidence on the role of gut microbiome composition in depressive and anxiety disorders or symptoms by reviewing available studies. Analysing data from three independent cohorts (osteoarthritis 1 (OA1); n = 46, osteoarthritis 2 (OA2); n = 58, and healthy controls (CON); n = 67), we identified microbial composition signatures of anxiety and depressive symptoms at genus level and cross-validated our findings performing meta-analyses of our results with results from previously published studies. The genera Bifidobacterium (fixed-effect beta (95% CI) = −0.22 (−0.34, −0.10), p = 3.90e-04) and Lachnospiraceae NK4A136 group (fixed-effect beta (95% CI) = −0.09 (−0.13, −0.05), p = 2.53e-06) were found to be the best predictors of anxiety and depressive symptoms, respectively, across our three cohorts and published literature taking into account demographic and lifestyle covariates, such as fibre intake. The association with anxiety was robust in accounting for heterogeneity between cohorts and supports previous observations of the potential prophylactic effect of Bifidobacterium against anxiety symptoms.

Paleovolcanology, geochemistry, and zircon U-Pb-Hf isotopes of the volcano-sedimentary sequences from the Ediacaran Campo Alegre-Corupá Basin, southern Brazil: Linking volcanism and tectonics during Western Gondwana consolidation

The Campo Alegre-Corupá Basin (CACB) records a well-documented sequence of volcano-sedimentary episodes associated with specific periods of crustal extension during the late-convergent to post-collisional tectonic stages of the consolidation of Western Gondwana. Two main volcano-sedimentary stages were detailed through stratigraphic and lithofaciological studies, combined with whole-rock geochemistry and zircon U-Pb-Hf analysis, resulting in a more complete understanding of the tectono-magmatic cycles and volcanological evolution of the CACB. During the Basin Stage (605–590 Ma), regional collisional tectonics was responsible for initiating the basin as a syn-orogenic rift, during which the sedimentary cycle progressed from alluvial fans at the northern limit of the basin to braided rivers and into a lake to the south. U-Pb geochronology and Lu-Hf isotope signatures of detrital zircon revealed that the sediments were mainly derived from the Paleoproterozoic basement of the Luis Alves Terrane, which constitutes the direct basement of the CACB, with contributions from the nearby Piên Magmatic Arc and possibly from the Curitiba Terrane to the North. The sedimentary strata were progressively covered by transitional to mildly alkaline OIB-like basalts, occurring mostly as lava flows with structural aspects suggestive of subaqueous to subaerial environments, interbedded with trachydacites and surge-like pyroclastic deposits. Large volumes of widespread and densely-welded to rheomorphic ignimbrite sheets within the CACB attest to a second infilling period corresponding to the Caldera Stage (583–577 Ma). This stage was inaugurated by the outpouring of trachytic and very subordinated IAB-like basaltic lava flows at ∼583 Ma. The caldera eruption seems to have been initiated by the production of pumiceous fallouts during an early Plinian-like period of decompression of shallow magma chambers at ∼580 Ma, during which the rift-related structural framework of the Basin Stage probably controlled the collapse of a graben-like caldera. Compositional and isotopic signatures suggest lithospheric mantle sources for the magmas from both volcanic stages and support a connection between basic-intermediate and silicic rocks from both bimodal associations. They also suggest a cogenetic nature between the silicic rocks from the Caldera Stage and the A-type granitoids from the nearby plutonic Graciosa Province.

Mantellic degassing of helium in an extensional active tectonic setting at the front of a magmatic arc (central Mexico)

Abstract The physicochemical and isotopic characteristics of groundwater and dissolved gas of central Mexico provide valuable information about the geologic and tectonic context of the area. Low–high-enthalpy manifestations (up to 98 °C in springs and more than 100 °C in geothermal wells) are distributed within the San Juan del Río, Querétaro, and Celaya hydrologic basins, located at the boundary between the current Mexican magmatic arc and an extensional continental area with intraplate volcanism called Mesa Central Province. Groundwaters in the study area represent a mixture between the cold water end-member with a Ca2+-Mg2+-HCO3-composition and a hydrothermal end-member enriched in Na+, K+, SO42−, and Cl-. Cold and hot groundwaters δ2H and δ18O plot along the same evaporation lines and do not exhibit a magmatic input. Dissolved and free gas do not show a typical volcanic composition signature. He and Ne isotope composition provide evidence of an important contribution of non-atmospheric noble gases. Although helium composition mainly has a crustal origin (21–83%), the mantellic contribution (1–39%) is higher than expected for an area lacking recent volcanism. A volatilerich magma aging at depth was discarded as the source of this mantellic helium signature but points out a recent mantellic contribution. Thus, we propose that mantellic helium comes from the sublithospheric mantle into the shallow crust through the highly permeable tectonic boundaries between the geologic provinces, namely the N−S Taxco−San Miguel de Allende and Chapala-Tula fault systems. Mantellic helium flow rates through these fault systems were estimated to have values ranging from 0.1 m/yr to 2.9 m/yr. This He flux range implies that aside from subduction, mantle volatile degassing enhanced by crustal fault systems is the main degassing process in the region studied.