julilili42/papers huggingface dataset:
Phages Affect Soil Dissolved Organic Matter Mineralization by Shaping Bacterial Communities
2025-01-21

Viruses are considered to regulate bacterial communities and terrestrial nutrient cycling, yet their effects on bacterial metabolism and the mechanisms of carbon (C) dynamics during dissolved organic matter (DOM) mineralization remain unknown. Here, we added active and inactive bacteriophages (phages) to soil DOM with original bacterial communities and incubated them at 18 or 23 °C for 35 days. Phages initially (1-4 days) reduced CO<sub>2</sub> efflux rate by 13-21% at 18 °C and 3-30% at 23 °C but significantly (<i>p</i> < 0.05) increased by 4-29% at 18 °C and 9-41% at 23 °C after 6 days, raising cumulative CO<sub>2</sub> emissions by 14% at 18 °C and 21% at 23 °C. Phages decreased dominant bacterial taxa and increased bacterial community diversity (consistent with a "cull-the-winner" dynamic), thus altering the predicted microbiome functions. Specifically, phages enriched some taxa (such as <i>Pseudomonas</i>, <i>Anaerocolumna</i>, and <i>Caulobacter</i>) involved in degrading complex compounds and consequently promoted functions related to C cycling. Higher temperature facilitated phage-bacteria interactions, increased bacterial diversity, and enzyme activities, boosting DOM mineralization by 16%. Collectively, phages impact soil DOM mineralization by shifting microbial communities and functions, with moderate temperature changes modulating the magnitude of these processes but not qualitatively altering their behavior.
The Impact of Loneliness on Late-Life Depression and Anxiety During the COVID-19 Pandemic
2025-01-21

Our results suggest an association of significant loneliness during the COVID-19 pandemic and a clinically relevant worsening of depressive and anxiety symptoms in older adults. Loneliness assessments and interventions may be incorporated into treatments for LLD, particularly during pandemics or other crises.
Succinate receptor 1 signaling mutually depends on subcellular localization and cellular metabolism
2025-01-21

Succinate is a pivotal tricarboxylic acid cycle metabolite but also specifically activates the G i ‐ and G q ‐coupled succinate receptor 1 (SUCNR1). Contradictory roles of succinate and succinate‐SUCNR1 signaling include reports about its anti‐ or pro‐inflammatory effects. The link between cellular metabolism and localization‐dependent SUCNR1 signaling qualifies as a potential cause for the reported conflicts. To systematically address this connection, we used a diverse set of methods, including several bioluminescence resonance energy transfer‐based biosensors, dynamic mass redistribution measurements, second messenger and kinase phosphorylation assays, calcium imaging, and metabolic analyses. Different cellular metabolic states were mimicked using glucose (Glc) or glutamine (Gln) as available energy substrates to provoke differential endogenous succinate (SUC) production. We show that SUCNR1 signaling, localization, and metabolism are mutually dependent, with SUCNR1 showing distinct spatial and energy substrate‐dependent G i and G q protein activation. We found that Gln‐consumption associated with a higher rate of oxidative phosphorylation causes increased extracellular SUC concentrations, accompanied by a higher rate of SUCNR1 internalization, reduced miniG q protein recruitment to the plasma membrane, and lower Ca 2+ signals. In Glc, under basal conditions, SUCNR1 causes stronger G q than G i protein activation, while the opposite is true upon stimulation with an agonist. In addition, SUCNR1 specifically interacts with miniG proteins in endosomal compartments. In THP‐1 cells, polarized to M2‐like macrophages, endogenous SUCNR1‐mediated G i signaling stimulates glycolysis, while G q signaling inhibits the glycolytic rate. Our results suggest that the metabolic context determines spatially dependent SUCNR1 signaling, which in turn modulates cellular energy homeostasis and mediates adaptations to changes in SUC concentrations.
Clinical Outcome of Endothelium-Outward Preloaded Descemet Membrane Endothelial Keratoplasty in Long-Term Dextran-Containing Transport Medium Preservation
2025-01-21

Purpose: To analyze the clinical outcome of organ-cultured endothelium-outward preloaded DMEK (pDMEK) using the RAPID cartridge. Methods: This prospective study included 80 eyes of 80 patients who received a pDMEK. Best-corrected visual acuity (BCVA), endothelial cell count (ECC), and central corneal thickness were measured preoperatively and 4 to 6 weeks, 3 months, 6 months, and 1 year postoperatively. The difficulty of graft preparation and implantation, rebubbling, and re-DMEK frequency were evaluated. Results: The graft preparation time was 5.3 ± 1.2 minutes on average. After preparation, the ECC before preloading was 2652 ± 180 cells/mm 2 ( P = 0.9, endothelial cell loss [ECL] = 0.8%). After pDMEK, the cornea started to clear up after 1.6 ± 1 day. Compared with the preoperative values, BCVA and central corneal thickness significantly improved during the postoperative course ( P &lt; 0.0001). At the first follow-up examination, the ECL was 43% ( P &lt; 0.0001) and remained stable throughout the follow-up period (all P &gt; 0.5). Rebubbling was necessary in 39/80 patients (48.75%). One patient (1/80, 1.25%) required a re-DMEK after 1 year owing to secondary graft failure with insufficient ECC. Conclusions: The clinical results after endothelium-outward pDMEK showed a significant improvement in BCVA and corneal thickness over the 1-year follow-up period, but the relatively high rebubbling rate and ECL should be taken into account. Therefore, we recommend that further comparative clinical studies should be conducted.
The InP(100) Surface Phase Diagram: From the Gas Phase to the Electrochemical Environment
2025-01-21

The versatile optoelectronic properties of the material class of III-V semiconductors enable the highest performance in photovoltaic and photoelectrochemical solar cells. While a high level of control and understanding with respect to different surface reconstructions of these compounds in gas-phase ambient has been reached, the situation in an electrochemical environment still poses challenges. Here, we therefore have undertaken a computational study of the InP(100) surface in the presence of hydrogen and chlorine, mimicking the contact with a hydrochloric acid-containing electrolyte, aiming at an understanding of ion adsorption and dominant surface reconstructions with respect to applied potential and electrolyte concentration. For this purpose, the most stable surface terminations for hydrogen and chlorine (co)adsorption from the gas phase as well as the corresponding phase diagrams have been determined with respect to the hydrogen and chlorine chemical potential. In this context, we also introduce a quantitative type of phase diagram to highlight the stability of surface phases with respect to competing structures. Finally, by making use of the computational hydrogen electrode approach, these results were then transferred to the potential domain. We find that hydrogen (chlorine) adsorption is dominating at more (less) cathodic potentials, while coadsorption is limited to small fractions of the phase space. This allows us to determine experimentally accessible phases for which no detrimental effects, such as the creation of in-gap surface states, are to be expected.
Safety of Human USH1C Transgene Expression Following Subretinal Injection in Wild-Type Pigs
2025-01-21

Early-phase clinical imaging, electrophysiology, and histopathological assessments indicated that subretinal administration of OT_USH_101 was well tolerated in the low-dose treatment arm. OT_USH_101 treatment resulted in high expression of human USH1C_a1. Although histopathological changes were not severe, more frequent changes were observed in the high-dose group.
Probing dark star parameters through f-mode gravitational wave signals
2025-01-21

Theoretical models of self-interacting dark matter offer a promising solution to several unresolved issues within the collisionless cold dark matter framework. For asymmetric dark matter, these self-interactions may encourage gravitational collapse, potentially leading to the creation of compact objects primarily composed of dark matter. By considering both fermionic and bosonic equations of state, we analyze the equilibrium structure of non-rotating dark stars, examining their bulk properties and comparing them with baryonic neutron stars. We show that the frequency and damping rate of -mode oscillations of dark compact stars can be expressed in terms of universal functions of stellar mass, radius and moment of inertia. Finally, by employing the universality in the -mode, we propose a scheme to infer accurate values of the physical parameters of dark compact stars from their -mode gravitational wave signal.
Self-other generalisation shapes social interaction and is disrupted in borderline personality disorder
2025-01-21

Abstract Generalising information from ourselves to others, and others to ourselves allows for both a dependable source of navigation and adaptability in interpersonal exchange. Disturbances to social development in sensitive periods can cause enduring and distressing damage to lasting healthy relationships. However, identifying the mechanisms of healthy exchange has been difficult. We introduce a theory of self-other generalisation tested with data from a three-phase social value orientation task - the Intentions Game. We involved individuals with (n=50) and without (n=53) a diagnosis of borderline personality disorder and assessed whether self-other information generalisation may explain interpersonal (in)stability. Healthy controls initially used their preferences to predict others and were influenced by their partners, leading to self-other convergence. In contrast, individuals with borderline personality disorder maintained distinct self-other representations, generating a new neutral prior to begin learning. Both groups steadily reduced their updating over time, with healthy participants showing increased sensitivity to update beliefs. Furthermore, we explored theory-driven individual differences underpinning learning. Overall, the findings provide a clear explanation of how self-other generalisation constrains and assists learning, how childhood adversity disrupts this through separation of internalised beliefs and makes clear predictions about the mechanisms of social information integration under uncertainty.
Self-other generalisation shapes social interaction and is disrupted in borderline personality disorder
2025-01-21

Generalising information from ourselves to others, and others to ourselves allows for both a dependable source of navigation and adaptability in interpersonal exchange. Disturbances to social development in sensitive periods can cause enduring and distressing damage to lasting healthy relationships. However, identifying the mechanisms of healthy exchange has been difficult. We introduce a theory of self-other generalisation tested with data from a three-phase social value orientation task – the Intentions Game. We involved humans with ( n =50) and without ( n =53) a diagnosis of borderline personality disorder and assessed whether infractions to self-other generalisation may explain prior findings of disrupted social learning and instability. Healthy controls initially used their preferences to predict others and were influenced by their partners, leading to self-other convergence. In contrast, individuals with borderline personality disorder maintained distinct self-other representations when learning about others. This allowed for equal predictive performance compared to controls despite reduced updating sensitivity. Furthermore, we explored theory-driven individual differences underpinning contagion. Overall, the findings provide a clear explanation of how self-other generalisation constrains and assists learning, and how childhood adversity is associated with separation of internalised beliefs. Our model makes clear predictions about the mechanisms of social information generalisation concerning both joint and individual reward.
Andexanet alfa in patients with factor Xa inhibitor-associated intracranial hemorrhage: The prospective observational multicenter ASTRO-DE study
2025-01-21

Background: Hematoma expansion after intracranial hemorrhage (ICH) in anticoagulated patients significantly influences clinical outcomes and mortality, emphasizing the need for effective reversal agents. Andexanet alfa is a specific reversal agent for factor Xa-associated major bleeding. Aims: The Andexanet alfa: non-interventional study at STROke centers in Germany (Deutschland, DE) (ASTRO-DE) study collected real-world evidence on the effect of andexanet alfa on mitigating hematoma expansion and altering prognosis in rivaroxaban- or apixaban-treated patients with ICH. Methods: ASTRO-DE was a prospective non-interventional cohort study conducted at 25 certified stroke centers in Germany. The primary outcome was the hematoma volume change and the proportion of patients with hematoma growth ⩽33% within 12–72 h or until first control imaging. Secondary endpoints included in-hospital thromboembolic events and mortality up to 90 days. Results: A total of 137 patients (47.4% male, mean age = 80.0 years) with ICH (92.6% spontaneous, 87.4% intracerebral), mean National Institutes of Health Stroke Scale (NIHSS) on admission of 11.2 points, and mean initial hematoma volume of 26.5 mL (median = 14.1 mL) were analyzed. Ninety patients (65.7%) suffered ICH while treated with apixaban and 47 (34.3%) with rivaroxaban. The median time between symptom onset and application of andexanet alfa was 3.3 h, door-to-needle time was 1.1 h. The mean change in hematoma volume until the first control imaging, conducted after a median of 15.6 h, was 2.3 mL (95% confidence interval (CI) = 0.4–4.2), while the change within 12–72 h was 1.8 mL (95% CI = 0.4–3.2). Hematoma growth ⩽33% was achieved in 90.3% of the 93 evaluable patients based on first control imaging and in 90.5% of the 63 evaluable patients, considering only imaging performed within the 12–72 h window. During hospitalization, death occurred in 30/137 patients (21.9%) and 17 thromboembolic events in 11/137 (8.0%) patients. The 90-day mortality was 47/128 (36.7%). Conclusion: ASTRO-DE is the first prospective observational study systematically collecting standardized clinical routine data with andexanet alfa treatment. The study demonstrated favorable hemostasis and minimal mean hematoma volume growth in patients with ICH associated with apixaban or rivaroxaban treatment. Data access statement: Data are available upon reasonable request by contacting the corresponding author.
How parental factors shape the plant embryo
2025-01-21

Primary axis formation is the first step of embryonic patterning in flowering plants and recent findings highlight the importance of parent-of-origin effects in this process. Apical-basal patterning has a strong influence on suspensor development, an extra-embryonic organ involved in nutrient transport to the embryo at an early stage of seed development. The endosperm, a second fertilization product, nourishes the embryo at later stages of seed development. Parent-of-origin effects are phenotypic effects that depend on whether a causal gene is inherited from the mother or the father. They are discussed in the context of the parental conflict theory in relation to nutrient allocation to the offspring. Imprinting is an important mechanism leading to uniparental gene expression in the endosperm and maternal control of its development. The parental conflict theory would predict that, with limited resources available, there is a competition between paternal alleles to increase nutrient supply, allowing rapid development and seed filling. A parental conflict might therefore shape the evolution of genes that can influence the allocation of nutrients to the seeds. However, we will also discuss other possible causes that might select genes for uniparental contribution. New data show that parent-of-origin effects also occur during the early stages of embryo development. These appear to be caused primarily by the carry-over of gamete-derived factors. In this review, we will highlight the molecular pathways that control apical-basal patterning in the early embryo and discuss recent findings in the context of the parental conflict theory and alternative explanations.
Genomics yields biological and phenotypic insights into bipolar disorder
2025-01-22

Bipolar disorder is a leading contributor to the global burden of disease<sup>1</sup>. Despite high heritability (60-80%), the majority of the underlying genetic determinants remain unknown<sup>2</sup>. We analysed data from participants of European, East Asian, African American and Latino ancestries (n = 158,036 cases with bipolar disorder, 2.8 million controls), combining clinical, community and self-reported samples. We identified 298 genome-wide significant loci in the multi-ancestry meta-analysis, a fourfold increase over previous findings<sup>3</sup>, and identified an ancestry-specific association in the East Asian cohort. Integrating results from fine-mapping and other variant-to-gene mapping approaches identified 36 credible genes in the aetiology of bipolar disorder. Genes prioritized through fine-mapping were enriched for ultra-rare damaging missense and protein-truncating variations in cases with bipolar disorder<sup>4</sup>, highlighting convergence of common and rare variant signals. We report differences in the genetic architecture of bipolar disorder depending on the source of patient ascertainment and on bipolar disorder subtype (type I or type II). Several analyses implicate specific cell types in the pathophysiology of bipolar disorder, including GABAergic interneurons and medium spiny neurons. Together, these analyses provide additional insights into the genetic architecture and biological underpinnings of bipolar disorder.
Depressive Symptoms and Amyloid Pathology
2025-01-22

Importance Depressive symptoms are associated with cognitive decline in older individuals. Uncertainty about underlying mechanisms hampers diagnostic and therapeutic efforts. This large-scale study aimed to elucidate the association between depressive symptoms and amyloid pathology. Objective To examine the association between depressive symptoms and amyloid pathology and its dependency on age, sex, education, and APOE genotype in older individuals without dementia. Design, Setting, and Participants Cross-sectional analyses were performed using data from the Amyloid Biomarker Study data pooling initiative. Data from 49 research, population-based, and memory clinic studies were pooled and harmonized. The Amyloid Biomarker Study has been collecting data since 2012 and data collection is ongoing. At the time of analysis, 95 centers were included in the Amyloid Biomarker Study. The study included 9746 individuals with normal cognition (NC) and 3023 participants with mild cognitive impairment (MCI) aged between 34 and 100 years for whom data on amyloid biomarkers, presence of depressive symptoms, and age were available. Data were analyzed from December 2022 to February 2024. Main Outcomes and Measures Amyloid-β1-42 levels in cerebrospinal fluid or amyloid positron emission tomography scans were used to determine presence or absence of amyloid pathology. Presence of depressive symptoms was determined on the basis of validated depression rating scale scores, evidence of a current clinical diagnosis of depression, or self-reported depressive symptoms. Results In individuals with NC (mean [SD] age, 68.6 [8.9] years; 5664 [58.2%] female; 3002 [34.0%] APOE ε4 carriers; 937 [9.6%] had depressive symptoms; 2648 [27.2%] had amyloid pathology), the presence of depressive symptoms was not associated with amyloid pathology (odds ratio [OR], 1.13; 95% CI, 0.90-1.40; P = .29). In individuals with MCI (mean [SD] age, 70.2 [8.7] years; 1481 [49.0%] female; 1046 [44.8%] APOE ε4 carriers; 824 [27.3%] had depressive symptoms; 1668 [55.8%] had amyloid pathology), the presence of depressive symptoms was associated with a lower likelihood of amyloid pathology (OR, 0.73; 95% CI 0.61-0.89; P = .001). When considering subgroup effects, in individuals with NC, the presence of depressive symptoms was associated with a higher frequency of amyloid pathology in APOE ε4 noncarriers (mean difference, 5.0%; 95% CI 1.0-9.0; P = .02) but not in APOE ε4 carriers. This was not the case in individuals with MCI. Conclusions and Relevance Depressive symptoms were not consistently associated with a higher frequency of amyloid pathology in participants with NC and were associated with a lower likelihood of amyloid pathology in participants with MCI. These findings were not influenced by age, sex, or education level. Mechanisms other than amyloid accumulation may commonly underlie depressive symptoms in late life.
The clinical and molecular landscape of diffuse hemispheric glioma, H3 G34-mutant
2025-01-22

Abstract Background Diffuse hemispheric glioma, histone 3 (H3) G34-mutant, has been newly defined in the 2021 World Health Organization (WHO) classification of central nervous system tumors. Here we sought to define the prognostic roles of clinical, neuroimaging, pathological, and molecular features of these tumors. Methods We retrospectively assembled a cohort of 114 patients (median age 22 years) with diffuse hemispheric glioma, H3 G34-mutant, central nervous system WHO grade 4, and profiled the imaging, histological, and molecular landscape of their tumors. Results Compared with glioblastoma, H3 G34-mutant diffuse hemispheric gliomas exhibited less avid contrast enhancement, necrosis, and edema on MRI. Comprehensive analyses of mutational and DNA copy number profiles revealed recurrent mutations in TP53 and ATRX, homozygous deletions of CDKN2A/B, and amplifications of PDGFRA, EGFR, CCND2, and MYCN. MGMT promoter methylation was detected in 79 tumors (75%); 11 tumors (13%) showed DNA copy number profiles suggestive of circumscribed deletions on 10q26.3 involving the MGMT locus. Median survival was 21.5 months. Female sex, gross total resection, and MGMT promoter methylation were positive prognostic factors on univariate analysis. Among radiological, pathological, and molecular features, the absence of pial invasion and the presence of microvascular proliferation and CDK6 amplification were positive prognostic factors on univariate analyses. Conclusions This study refines the clinical and molecular landscape of H3 G34-mutant diffuse hemispheric gliomas. Dedicated trials for this novel tumor type are urgently needed.
Soil Health Under Global Change and Human Impact
2025-01-22

ABSTRACT Soil health is pivotal to sustain biological productivity, maintain environmental quality, and ensure the health of plants, animals, and ultimately humans. Global changes—such as climate warming, elevated CO2 atmospheric concentration, droughts, and floods—as well as human impacts like land‐use change, chemical contamination, and application of fertilizer and pesticides, threaten soil health. Protecting soil health and raising global awareness on this topic are now critical to ensure sustainable management of natural and agricultural ecosystems under global change. This Special Issue includes 19 studies in three thematic groups. The first group includes methodological advances in the assessment of soil health, exploring new tools, techniques, and approaches for accurate evaluation. The second group encompasses studies examining how soil health responds to land‐use change, agricultural and forestry practices. The third group addresses human‐induced pollution and its effects on soil health. Overall, these studies provide contemporary insight into soil health in managed and natural ecosystems and methods for soil health evaluation. These contributions will shape strategies to sustain soil functions and preserve healthy soils for future generations, including efforts to meet Sustainable Development Goals for the 21st century.