Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporary storage of soil organic matter and acid neutralizing capacity during the process of pedogenetic acidification of forest soils in Kinki District, Japan

Abstract Pedogenetic acidification processes in forest soils derived from sedimentary rocks under mesic and thermic soil temperature regimes (MSTR and TSTR; corresponding to mean annual soil temperatures of 8–15°C and 15–22°C, respectively) in the Kinki District were investigated based on titratable alkalinity and acidity characteristics and soil solution composition. According to statistical analyses of the soil properties, the titratable alkalinity required to acidify soils to pH 3.0 was considered to be derived from reactions occurring at the surface of amorphous Al oxides, while titratable acidity at a pH ranging from 5.5 to 8.3 results from dissociation of acidic functional groups of soil humus and/or deprotonation of oxide surfaces. These reactions were generally more prevalent in MSTR soils. Based on the soil solution composition and titratable alkalinity and acidity in the soil profiles, two processes were postulated for pedogenetic acidification, that is, eluvi-illuviation of inorganic Al followed by subsequent adsorption of dissolved organic carbon (DOC) onto the precipitates of Al hydroxides and comigration of Al and DOC in the form of organo-mineral complexes. Both processes were conspicuous in MSTR soils and significantly contributed to soil organic matter storage in the subsoil layers. Pedogenetic acidification in forest soils with MSTR was characterized by an accumulation of acidity in the form of amorphous compounds and/or organo-mineral complexes in the B horizon. It seems, to some extent, similar to podzol formation, at least in terms of Al translocation. Amorphous Al hydroxides protect against further acidification through protonation and/or partial monomerization and can, thus, be regarded as a temporary storage of acid neutralizing capacity of the soil, which would be otherwise leached out directly from the soil profile. In contrast, the acid-buffering reactions of TSTR soils seemed to occur, if at all, mostly at or near the soil surface and the contribution of the B-horizon soils was limited.
An improved ChEC-seq method accurately maps the genome-wide binding of transcription coactivators and sequence-specific transcription factors

Mittal and colleagues have raised questions about mapping transcription factor locations on DNA using the MNase-based ChEC-seq method (Mittal et al., 2021). Partly due to this concern, we modified the experimental conditions of the MNase cleavage step and subsequent computational analyses, resulting in more stringent conditions for mapping protein-DNA interactions (Donczew et al., 2020). The revised method (dx.doi.org/10.17504/protocols.io.bizgkf3w) answers questions raised by Mittal et al. and, without changing earlier conclusions, identified widespread promoter binding of the transcription coactivators TFIID and SAGA at active genes. The revised method is also suitable for accurately mapping the genome-wide locations of DNA sequence-specific transcription factors.
BINARY METAL SORPTION BY PINE BARK : STUDY OF EQUILIBRIA AND MECHANISMS

ABSTRACT Pine bark was able to sorb cadmium, copper, and nickel ions from aqueous solutions. Binary equilibrium data from the combination of these metals were collected in this work using this sorbent. These data were modeled using three types of binary component equilibrium isotherms, all of which resulted in good fitting of the experimental data, with the Langmuir—Freundlich model resulting in their best representa- tion. In general, the capacity of bark for each metal in the binary system was lower than in the single metal systems. The study also examined the mechanisms of metal biosorption by bark. Scanning electron microscopy (SEM) and energy-dispersive x-ray (EDX) microanalyses revealed that metal ions were sorbed mainly at the cell wall of the bark and only a small amount of ions diffused into the cytoplasm. Both the EDX analysis and the atomic absorption spectrophotometry (AAS) measurements showed that ion exchange was an important mechanism in this sorption process. Electron spin resonance (ESR) .
Enhancing piezoelectric d33 coefficient in Li∕Ta-codoped lead-free (Na,K)NbO3 ceramics by compensating Na and K at a fixed ratio

Lead-free alkali niobate piezoelectric ceramics with nominal compositions [(Na0.535K0.480)0.942+xLi0.058](Nb0.90Ta0.10)O3 compensated with Na and K at a fixed and optimized ratio of 0.535:0.480 were prepared by normal sintering. The electrical properties were investigated with a special emphasis on the influence of compensating amount x of Na0.535K0.480. A phase transition from tetragonal to orthorhombic was observed as x was increased from 0 to 0.024, resulting in enhanced piezoelectric coefficient and planar electromechanical coupling coefficient from 216 and 38.1% to 268pC∕N and 46.2%, respectively. Our results indicate the importance of elaborate compositional control for enhancing piezoelectric properties in niobate-based ceramics.
Type IV pili share a conserved mechanism of motor-independent retraction that is an inherent property of the pilus filament

Type IV pili (T4P) are dynamic surface appendages that promote virulence, biofilm formation, horizontal gene transfer, and motility in diverse bacterial species. Pilus dynamic activity is best characterized in T4P that use distinct ATPase motors for pilus extension and retraction. Many T4P systems, however, lack a dedicated retraction motor and the mechanism underlying this motor-independent retraction remains a mystery. Using the Vibrio cholerae competence pilus as a model system, we identify mutations in the major pilin gene that enhance motor-independent retraction. These mutants produced less stable pili, likely due to diminished pilin-pilin interactions within the filament. One mutation adds a bulky residue to α1C, a universally conserved feature of type IV pilins. We found that inserting a bulky residue into α1C of the retraction motor-dependent Acinetobacter baylyi com-petence T4P is sufficient to induce motor-independent retraction. Conversely, removing bulky residues from α1C of the retraction motor-independent V. cholerae toxin-co-regulated T4P stabilizes the filament and prevents retraction. Furthermore, alignment of pilins from the broader type IV filament (T4F) family indicated that retraction motor-independent T4P, Com pili, and type II secretion systems generally encode larger residues within α1C oriented toward the pilus core compared to retraction motor-dependent T4P. Together, our data demonstrate that motor-independent retraction relies on the inherent instability of the pilus filament that may be conserved in diverse T4Fs. This provides the first evidence for a long-standing, yet untested, model in which pili retract in the absence of a motor by spontaneous de-polymerization. SIGNIFICANCE Extracellular pilus filaments are critical for the virulence and persistence of many bacterial pathogens. A crucial property of these filaments is their ability to dynamically extend and retract from the bacterial surface. A detailed mechanistic understanding of pilus retraction, however, remains lacking in many systems. Here, we reveal that pilus retraction is an inherent property of the pilus filament. These observations are broadly relevant to diverse pilus systems, including those in many bacterial pathogens, and may help inform novel therapeutic strategies that aim to target pilus dynamic activity.
Stochastic effects on the establishment of mutants resistant to β-lactam antibiotics

For antibiotic resistance to arise, new resistant mutants must establish in a bacterial population before they can spread via natural selection. Understanding the stochastic factors influencing mutant establishment is crucial for a quantitative understanding of antibiotic resistance emergence. Here, we quantify the single-cell establishment probability of four Escherichia coli strains expressing β-lactamase alleles with different activity against the antibiotic cefotaxime, as a function of concentration. Using a simple branching model, we show that concentrations well below the minimal inhibitory concentration (MIC) can substantially hamper establishment, particularly for highly resistant mutants, suggesting cooperative effects due to antibiotic breakdown at high cell densities. We further show that variation among cell lineages may explain the more gradual influence of increased antibiotic concentrations on agar. Finally, we use the single-cell establishment probability to predict a strain’s MIC in the absence of social interactions, as a general reference to detect cooperative resistance effects.
Machine learning reveals cryptic dialects that guide mate choice in a songbird

Culturally transmitted communication signals – such as human language or bird song – can change over time through a process of cultural drift, and may consequently enhance the separation of populations, potentially leading to reproductive isolation1–4. Local song dialects have been identified in bird species with relatively simple songs where individuals show high cultural conformity5–10. In contrast, the emergence of cultural dialects has been regarded as unlikely11–13 for species with more variable song, such as the zebra finch (Taeniopygia guttata). Instead, it has been proposed that selection for individual recognition and distinctiveness may lead to a complete spread across the space of acoustic and syntactical possibilities11–15. However, another possibility is that analytical limitations have meant that subtle but possibly salient group differences have not yet been discovered in such species. Here we show that machine learning can distinguish the songs from multiple captive zebra finch populations with remarkable precision, and that these ‘cryptic song dialects’ drive strong assortative mating in this species. We studied mating patterns across three consecutive generations using captive populations that have evolved in isolation for about 100 generations. Cross-fostering eggs within and between these populations and quantifying social interactions of the resulting offspring later in life revealed that mate choice primarily targets cultural traits that are transmitted during a short developmental time window. Detailed social networks showed that females preferentially approached males whose song resembled that of their adolescent peers. Our study shows that birds can be surprisingly sensitive to cultural traits for mating that have hitherto remained cryptic, even in this well-studied species that is used as a model for song-learning13,14,16–28.
Unified Model for Structure Transition and Electrical Properties of InAs (001) Surfaces Studied by Scanning Tunneling Microscopy

Thermal stability of the ( 2×4) structures on InAs and GaAs (001) surfaces is studied by using scanning tunneling microscopy with atomic resolution. Even just before the transition to a ( 4×2) structure, the annealed InAs surface has much lower density of kinks in the dimer vacancy rows than the annealed GaAs. This difference leads to a unified model that can explain both the 1st order phase transition and the peculiar electric properties of an InAs (001) surface.
Cued Naming and the left inferior frontal cortex

Clinical studies have shown that naming can be behaviorally facilitated by priming, e.g., phonemic cues reduce anomia. Rehabilitation of language is argued to rely upon the same processes of priming in healthy speakers. Here we show, in healthy older adults, the immediate facilitatory behavioral and neural priming elicited by phonemic cues presented during an fMRI experiment of overt naming; thus, bridging the gap between lesion and neuroimaging studies. Four types of auditory cues were presented concurrently with an object picture (e.g., cat): (i) word (i.e., the target name (/kat/), (ii) initial phoneme segment (e.g., /ka/), (iii) final phoneme segment (/at/), or (iv) acoustic (noise) control cue. Naming was significantly faster with word, initial and final phonemic cues compared to noise; and word and initial cues compared to final cues, with no difference between word and initial cues. A neural priming effect – a significant decrease in neural activity – was observed in the left inferior frontal cortex (LIFC, pars triangularis, BA45) and the anterior insula bilaterally consistent with theories of primed articulatory encoding and post-lexical selection. The reverse contrast revealed increased activation in left posterior dorsal supramarginal gyrus for word cues that, we argue, may reflect integration of semantic and phonology processing during word rather than phonemic conditions. Taken together, these data from unimpaired speakers identified nodes within the naming network affected by phonemic cues. Activity within these regions may act as a possible biomarker to index anomic individuals’ responsiveness to phonemically cued anomia treatment.
Evolution of lower levels of inter-locus sexual conflict in D. melanogaster populations under strong selection for rapid development

D. melanogaster laboratory populations subjected to selection for rapid development and early reproduction have been found to have evolved reduced adult body size and lower levels of inter-locus sexual conflict compared to their ancestral controls. We tested the contribution of a smaller body to the evolution of reduced sexual conflict in these populations, since body size differences are known to affect sexual conflict levels in this species. We cultured larvae from the control populations at high density to obtain flies as small as those from the selected populations. The effect of body size reduction on sexual conflict was asymmetric, with smaller body size resulting in reduced male manipulative ability but not female resistance to mating-induced harm. These results were not due to differences in behavioural patterns of smaller flies, such as differences in overall mating exposure of females to different types of males. We hypothesize that evolution for rapid development and the correlated reduction in body size has resulted in lower male manipulative ability, and sexually antagonistic co-evolution has lowered female resistance to such manipulations. These populations have also evolved incipient reproductive isolation from their controls, likely through sexual conflict (reported earlier), and our results support the view that this is an outcome of strong, directional selection for rapid development.
Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

Plant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the composition of bacterial taxa on the phylum and genus levels. Alpha diversity was significantly altered by BOA or quercetin, but not by gramine. BOA treatment caused an increase in the relative abundances of only four genera, three of them belonging to the Actinobacteriota. Gramine or quercetin treatment resulted in the increase in relative abundance of 13 or 14 genera, respectively, most of them belonging to the Proteobacteria. The relative abundance of 22 genera was decreased after BOA treatment, 16 of which were also decreased by gramine or quercetin. Isolation and characterization of cultivable bacterial indicated an enrichment in specific Arthrobacter or Pseudomonas strains. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a broad-spectrum inhibitory effect, with only few genera able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, benzoxazolinone or gramine biosynthesis which have evolved in different barley species, is accompanied with the association with distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.
Absorption spectrum and decay kinetics of triplet pentacene in solution, studied by flash photolysis

The absorption spectrum of triplet pentacene in benzene and cyclohexane was determined at 50°C and assignments of the peaks were made. A kinetic study of the triplet absorption showed that the triplet decays by three competing processes: (1) a temperature-independent (between –96 and +50°C) radiationless transition to the ground state, (2) a triplet-triplet quenching process of low efficiency, and (3) a reversible reaction with ground-state pentacene producing a transient compound assumed to be a pentacene dimer.
Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia

Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here we searched for IRES trans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb and PSPC1 as well as nucleolin and Rps2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response. Highlights Paraspeckle formation correlates with activation of translation via internal ribosome entry sites (IRES) in mouse hypoxic cardiomyocytes as well as in tumoral cells. The long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator of (lymph)angiogenic and cardioprotective factor expression in this process. IRES-containing mRNA is recruited into paraspeckles during hypoxia. Paraspeckle proteins p54nrb and PSPC1 as well as two p54nrb-interacting proteins, nucleolin and RPS2, contribute to this process. Paraspeckle appears as a platform for IRESome formation in the nucleus. The Neat1 isoforms widely regulate the translation of mRNAs containing IRESs and of genes involved in the stress response. GRAPHICAL ABSTRACT
Immune deposit and vasculopathy in metabolic-active lung tissues of patients with pulmonary tuberculosis

Metabolic activity in pulmonary lesion is associated with disease severity and relapse risk in tuberculosis. However, the nature of the metabolic activity associated with tuberculosis in humans remains unclear. Previous works indicate that tuberculosis bears resemblance transcriptionally with systemic lupus erythematosus in peripheral blood, except that the plasma cell component was absent in tuberculosis. Here we reported that the missing transcriptional component was present within the metabolic active tissues in the lung of patients with sputum culture-negative tuberculosis, within which increased levels of circulating immune complexes and anti-dsDNA antibodies were found relative to nearby non-metabolic active tissues. Histological examination revealed specific vascular deposition of immune complexes, neutrophil extracellular traps, and vascular necrosis in the metabolic-active tissue. Thus, tuberculosis-initiated metabolic activity was associated with hyperactive antibody responses and vascular pathology, and shared features with systemic lupus erythematosus and other autoimmune diseases. We discussed these observations in the context of earlier literatures demonstrating that similar effects could be induced in humans and animal models by complete freund’s adjuvant, the most potent antibody response inducer ever reported. Our small case series, if verified in a larger size study, might help inform host-directed therapies to alleviate disease progression and augment treatment efficacy. IMPORTANCE In patients with pulmonary tuberculosis, lung tissues were destroyed by a hyperactive inflammatory response towards M. tuberculosis. The mechanisms underlying the inflammatory response are still poorly understood. Using 18F-FDG avidity as a surrogate marker of inflammation, we have identified that hyper-inflamed tissues possessed features associated with systemic lupus erythematosus: gene expression signatures of plasma cell and immunoglobulins and increased levels of anti-dsDNA antibodies, immune deposits, and vasculopathy. This observation might suggest an explanation to why patients with tuberculosis share more gene expression signatures with autoimmune diseases than infectious diseases and why they are more likely to develop autoimmune diseases. Defining the inflammatory responses at the lesion could help inform host-directed therapies to intervene disease progression or even accelerate cure.
Homeostatic Response to Three Years of Experimental Warming Suggests High Intrinsic Natural Resistance in the Páramos to Warming in the Short Term

Páramos, tropical alpine ecosystems, host one of the world’s most diverse alpine floras, account for the largest water reservoirs in the Andes, and some of the largest soil carbon pools worldwide. It is of global importance to understand the future of this extremely carbon-rich ecosystem in a warmer world and its role on global climate feedbacks. This study presents the result of the first in situ warming experiment in two Colombian páramos using Open-Top Chambers. We evaluated the response to warming of several ecosystem carbon balance-related processes, including decomposition, soil respiration, photosynthesis, plant productivity, and vegetation structure after 3 years of warming. We found that OTCs are an efficient warming method in the páramo, increasing mean air temperature by 1.7°C and mean daytime temperature by 3.4°C. The maximum air temperature differences between OTC and control was 23.1°C. Soil temperature increased only by 0.1°C. After 3 years of warming using 20 OTC (10 per páramo) in a randomized block design, we found no evidence that warming increased CO2 emissions from soil respiration, nor did it increase decomposition rate, photosynthesis or productivity in the two páramos studied. However, total C and N in the soil and vegetation structure are slowly changing as result of warming and changes are site dependent. In Sumapaz, shrubs, and graminoids cover increased in response to warming while in Matarredonda we observed an increase in lichen cover. Whether this change in vegetation might influence the carbon sequestration potential of the páramo needs to be further evaluated. Our results suggest that páramos ecosystems can resist an increase in temperature with no significant alteration of ecosystem carbon balance related processes in the short term. However, the long-term effect of warming could depend on the vegetation changes and how these changes alter the microbial soil composition and soil processes. The differential response among páramos suggest that the response to warming could be highly dependent on the initial conditions and therefore we urgently need more warming experiments in páramos to understand how specific site characteristics will affect their response to warming and their role in global climate feedbacks.