julilili42/papers huggingface dataset:
The record and trends of natural disasters caused by gullies in Brazil
2023-10-12

Abstract Ravines and gullies are advanced stages of linear erosion that occur in many countries, causing economic, social, and environmental impacts. This research aims at analyzing the official record of disasters caused by ravines and gullies in Brazil, with a focus on analyzing the economic impacts. The Brazilian Civil Defense Integrated Information System (S2ID) database was applied in the analysis, combined with a bibliographic review made in the Scopus database. The results obtained from the civil defense database show a growing trend in the number of disasters related to ravines and gullies in the last decade (2011–2020), with 76 cases recorded between January 2013 and May 2019. From these 76 cases, 24 of them were further analyzed to provide information about the socioeconomic impacts. In total, an estimated loss of US$ 54 million was recorded in the considered period. The greatest economic impacts were related to damage to public infrastructure, such as sanitary and sewage water system, buildings and, especially, residential areas in urban perimeters. The spatial distribution of disasters related to linear erosion in Brazil suggests a connection between the development of ravines and gullies and the agricultural frontier of the country, especially in the North and Midwest regions, including the biomes of Cerrado (Brazilian Savanna) and Amazon Rainforest, where the greatest changes in land use occurred between the end of the twentieth and the beginning of the twenty-first century. Although the S2ID is an important data base for analyzing the impacts caused by ravines and gullies, the results suggest that the system's records do not account for medium- and long-term impacts.
Clustering Schizophrenia Genes by Their Temporal Expression Patterns Aids Functional Interpretation
2023-10-12

Abstract Background Schizophrenia is a highly heritable brain disorder with a typical symptom onset in early adulthood. The 2-hit hypothesis posits that schizophrenia results from differential early neurodevelopment, predisposing an individual, followed by a disruption of later brain maturational processes that trigger the onset of symptoms. Study design We applied hierarchical clustering to transcription levels of 345 genes previously linked to schizophrenia, derived from cortical tissue samples from 56 donors across the lifespan. We subsequently calculated clustered-specific polygenic risk scores for 743 individuals with schizophrenia and 743 sex- and age-matched healthy controls. Study results Clustering revealed a set of 183 genes that was significantly upregulated prenatally and downregulated postnatally and 162 genes that showed the opposite pattern. The prenatally upregulated set of genes was functionally annotated to fundamental cell cycle processes, while the postnatally upregulated set was associated with the immune system and neuronal communication. We found an interaction between the 2 scores; higher prenatal polygenic risk showed a stronger association with schizophrenia diagnosis at higher levels of postnatal polygenic risk. Importantly, this finding was replicated in an independent clinical cohort of 3233 individuals. Conclusions We provide genetics-based evidence that schizophrenia is shaped by disruptions of separable biological processes acting at distinct phases of neurodevelopment. The modeling of genetic risk factors that moderate each other’s effect, informed by the timing of their expression, will aid in a better understanding of the development of schizophrenia.
Unnatural Endotype B PPAPs as Novel Compounds with Activity against Mycobacterium tuberculosis
2023-10-12

Pre-SARS-CoV-2, tuberculosis was the leading cause of death by a single pathogen. Repetitive exposure of <i>Mycobacterium tuberculosis</i>(Mtb) supported the development of multidrug- and extensively drug-resistant strains, demanding novel drugs. Hyperforin, a natural type A polyprenylated polycyclic acylphloroglucinol from St. John's wort, exhibits antidepressant and antibacterial effects also against <i>Mtb</i>. Yet, Hyperforin's instability limits the utility in clinical practice. Here, we present photo- and bench-stable type B PPAPs with enhanced antimycobacterial efficacy. <b>PPAP22</b> emerged as a lead compound, further improved as the sodium salt <b>PPAP53</b>, drastically enhancing solubility. <b>PPAP53</b> inhibits the growth of virulent extracellular and intracellular <i>Mtb</i> without harming primary human macrophages. Importantly, <b>PPAP53</b> is active against drug-resistant strains of <i>Mtb</i>. Furthermore, we analyzed the in vitro properties of <b>PPAP53</b> in terms of CYP induction and the PXR interaction. Taken together, we introduce type PPAPs as a new class of antimycobacterial compounds, with remarkable antibacterial activity and favorable biophysical properties.
Autoantibodies to beta tubulin in autoimmune liver diseases—Relation to pANCA and clinical relevance
2023-10-12

Abstract There was evidence that perinuclear antineutrophil cytoplasmic antibodies (pANCA) in autoimmune liver diseases react with human beta-tubulin-5 (TBB5). Here, we reevaluate the specificity and clinical relevance of anti-TBB5 antibodies. Patients with untreated autoimmune hepatitis (AIH; n = 53), AIH under immunosuppressive therapy (AIH-IS; n = 125), primary sclerosing cholangitis (PSC; n = 40), primary biliary cholangitis (PBC; n = 250), nonautoimmune liver diseases (n = 158), inflammatory bowel diseases (IBD; n = 30), and healthy individuals (n = 62) were tested by enzyme-linked immunosorbent assay for IgG- and IgA-antibodies against recombinant human TBB5. pANCA were detected by immunofluorescence test. Sera were absorbed with TBB5 coupled to cyanogen bromide-activated sepharose. Prevalence and reactivity of IgG anti-TBB5 were significantly higher in patients with untreated AIH (68%; arbitrary units [AU] median: 369) than in PSC (28%; AU median: 84, P &amp;lt; 0.001), other liver diseases (14%; AU median: 185, P &amp;lt; 0.0001), IBD (3%; AU median: 111, P &amp;lt; 0.0001), and healthy controls (3%; AU median: 135; P &amp;lt; 0.0001). Anti-TBB5 did not correlate with pANCA, and immunoprecipitation with TBB5 did not abolish pANCA reactivity. In untreated AIH, anti-TBB5-reactivity was significantly higher than in AIH-IS. Transaminases decreased under IS preferentially in anti-TBB5-negative patients. There was no correlation between anti-TBB5-reactivity and histological stages. IgA-anti-TBB5 was mainly found in alcohol-associated liver disease (ALD; 39%). Our data do not support TBB5 as an autoantigenic target of pANCA. However, IgG-anti-TBB5 showed high specificity for (untreated) AIH. While they did not correlate with histological and laboratory parameters, their presence may indicate a poor response to IS.
Role of iron-carbon interactions in the release of greenhouse gases from permafrost soils
2023-10-12

As permafrost thaws, vast stocks of organic carbon which accumulated over long time periods within these soils are vulnerable to microbial decomposition and carbon may be released as the greenhouse gases CO 2 and CH 4 . The release of these greenhouse gases from permafrost systems is expected to lead to runaway positive feedbacks. The timescale and magnitude of the permafrost-climate feedback is highly uncertain as knowledge gaps remain regarding the rate of decomposition of permafrost organic carbon. These knowledge gaps stem, in part, from lacking understanding of the association between organic carbon (in the form of natural organic matter) and minerals, especially high surface area iron (oxyhydr)oxide minerals. This iron-carbon association has the potential to stabilize the organic matter, lower its bioavailability and therefore protect it from biodegradation – representing a “rusty carbon sink”. In this work, we investigated the coupling of iron and carbon cycles in permafrost peatlands and its effect on greenhouse gas release. Our initial work showed that up to 20% of the organic carbon in intact permafrost sites may be associated with iron(III) (oxyhydr)oxides and thereby protected from microbial decomposition. We then found that at the onset of thaw, this association is broken down, likely due to the microbial reduction and dissolution of iron(III) minerals. As a consequence, the previously protected organic carbon is thus released and becomes bioavailable. Using microbiological and molecular biological tools as well as greenhouse gas measurements, we linked this breakdown to an increase in the abundance of methanogenic microorganisms and concentrations of methane. Additional work also suggests that part of the released organic carbon may re-associate with dissolved iron in thaw ponds to form flocs. Currently, we are investigating the molecular composition of organic matter with high-resolution mass spectrometry techniques (FT-ICR-MS) as it undergoes these redox processes with the goal of linking bioavailability to composition. We complement our studies with laboratory microbial enrichment and isolation approaches and microbial community analyses to determine the microbial key players controlling iron(III) reduction and the potential for subsequent microbial Fe(II) oxidation. Collectively, the results of this project suggest that upon thawing, organic matter previously associated with minerals is mobilized and is likely susceptible to microbially mediated release as CO 2 and CH 4 .
Microbial pyrite formation: mineral morphology and precipitation kinetics
2023-10-12

Pyrite (FeS 2 ) is a mineral of wide interest due to its importance in the biogeochemical cycling of Fe and S, which is tied to those of carbon and other trace metals and nutrients. The mineral itself has potential applications as biosignatures, for environmental remediation and as semiconductors. Despite being a common authigenic mineral in sedimentary environments, most laboratory-based experiments have failed to form pyrite in microbial cultures at ambient temperatures. To fill this knowledge gap, we have employed cultivation-based approaches, using different combinations of microorganisms (Fe(III)- and S 0 -reducers; S 0 -disproportionaters) and initial Fe and S sources to identify the conditions that are optimal for pyrite formation. Scanning electron microscopy (SEM), Raman spectroscopy and X-ray diffraction (XRD) demonstrate that pyrite is not formed within ~3 years at circumneutral pH when oxidants (e.g., Fe(III) minerals, elemental sulfur, S 0 ) are exhausted. In contrast, pyrite is formed within months when S 0 and Fe(III) minerals are both present. The precipitation timescale is consistent with those expected in sedimentary environments Mansor and Fantle 2019), albeit some natural pyrite framboids are expected to form even faster Rickard 2019). The pyrite crystals formed in our experiments are in the low micrometer range, with either a spherical or euhedral morphology depending on the initial crystallinity of the supplied Fe(III) minerals. Framboids are not formed in our system, perhaps due to the relatively slow precipitation kinetics. Time-based sampling indicates mackinawite (FeS) as the first product, with rare (and minor) detection of greigite (Fe 3 S 4 ) and vivianite [Fe 3 (PO 4 ) 2 .8H 2 O]. We hypothesize that pyrite formation and growth proceed mainly from transformation of precursor minerals, with potential contributions via dissolution-precipitation and/or particle attachment pathways. Our preliminary study is the first step in optimizing a system for microbial pyrite formation, with the intention of investigating the properties and the reactivity of the mineral with implications for biosignatures, environmental remediation and industrial applications.
Nonhuman primates exploit the prior assumption that the visual world is vertical
2023-10-12

Here we show that the principles that characterize the human perception of the vertical are shared by another old world primate species, the rhesus monkey, suggesting phylogenetic continuity. In both species the integration of visual and vestibular information on the orientation of the head relative to the world is similarly constrained by the prior assumption that the visual world is vertical in the sense of having an orientation that is congruent with the gravity vector.
Single-value fMRI scores reflect both stage and risk across the Alzheimer’s disease continuum
2023-10-12

Abstract Single-value scores reflecting the deviation from (FADE score) or similarity with (SAME score) prototypical novelty-related and memory-related functional magnetic resonance imaging (fMRI) activation patterns in young adults have been proposed as imaging biomarkers of healthy neurocognitive aging. Here, we tested the utility of these scores as potential diagnostic and prognostic markers in Alzheimer’s disease (AD) and risk states like mild cognitive impairment (MCI) or subjective cognitive decline (SCD). To this end, we analyzed subsequent memory fMRI data from individuals with SCD, MCI, and AD dementia as well as healthy controls (HC) and first-degree relatives of AD dementia patients (AD-rel) who participated in the multi-center DELCODE study (N = 468). Based on the individual participants’ whole-brain fMRI novelty and subsequent memory responses, we calculated the FADE and SAME scores and assessed their association with AD risk stage, neuropsychological test scores, CSF amyloid positivity, and ApoE genotype. Memory-based FADE and SAME scores showed a considerably larger deviation from a reference sample of young adults in the MCI and AD dementia groups compared to HC, SCD and AD-rel. In addition, novelty-based scores significantly differed between the MCI and AD dementia groups. Across the entire sample, single-value scores correlated with neuropsychological test performance. The novelty-based SAME score further differed between Aβ-positive and Aβ-negative individuals in SCD and AD-rel, and between ApoE ε4 carriers and non-carriers in AD-rel. Hence, FADE and SAME scores are associated with both cognitive performance and individual risk factors for AD. Their potential utility as diagnostic and prognostic biomarkers warrants further exploration, particularly in individuals with SCD and healthy relatives of AD dementia patients.
Traces of life in Río Tinto (Spain): Decoupling of morphological and geochemical biosignatures
2023-10-12

The Río Tinto system located in southern Spain is a 100-km long acidic (pH ≈ 2.3) river rich in dissolved iron, sulfate and heavy metals. The red-tinted river, formed as a product of natural acid rock drainage that has been exacerbated over the years by anthropogenic mining activities, hosts a variety of extremophilic microorganisms that are potential analogues to those found on early Earth and ancient Mars. Here we detailed the investigation of potential biosignatures in the forms of microbialites and sediments deposited along the river. The 20-50 cm thick microbialites (estimated age at most 100 years) are composed of layered structures of Fe(III) minerals with alternating porosities. High resolution imaging and elemental mapping coupled to mineralogical analysis suggest the transformation of K-jarosite (KFe 3 (SO 4 ) 2 (OH) 6 ; V m = 153 cm 3 /mol) to goethite ( α -FeOOH; V m = 21 cm 3 /mol), generating porosities in the process due to a reduction in the molar volume V m . Meanwhile, riverbed sediments are composed of mixtures of schwertmannite (Fe 8 O 8 (OH) 6 (SO 4 ) · nH 2 O), jarosite, goethite and other minor minerals (ferrihydrite, lepidocrocite, hematite). Culture experiments indicate that crystalline jarosite is formed via transformation from poorly-crystalline schwertmannite (Fe 8 O 8 (OH) 6 (SO 4 ) · nH 2 O), but that the presence of Acidithiobacillus thiooxidans actually inhibits this transformation, possibly due to organic matter stabilization of schwertmannite. Fe isotopic analyses show no clear variations between layers in the microbialites (δ 56 Fe = -0.85 ± 0.10 ‰), while the riverbed sediments indicate progressively more negative values downstream over a 5-km distance (δ 56 Fe = +0.4 to -0.8‰). The spatial isotopic pattern of the riverbed sediments is consistent with rapid microbial oxidation of Fe 2+ and inconsistent with the much slower abiotic Fe 2+ oxidation rate. Taken together, our results show that while the microbialites’ structure is suggestive of microbially-induced precipitation, its geochemical features are not. Meanwhile, the inconspicuous-looking riverbed sediments provide clear evidence of biogenicity from their isotopic compositions. This highlights the challenge in detecting life especially when decoupling of morphological and geochemical biosignatures is to be expected.
Stability of coorbital planets around binaries
2023-10-12

In previous hydrodynamical simulations, we found a mechanism for nearly circular binary stars, like Kepler-413, to trap two planets in a stable 1:1 resonance. Therefore, the stability of coorbital configurations becomes a relevant question for planet formation around binary stars. Here, we investigate the coorbital planet stability using a Kepler-413 analogue as example and then expanding the parameters to study general n-body stability of planet pairs in eccentric horseshoe orbits around binaries. The stability is tested by evolving the planet orbits for binary periods with varying initial semi-major axes and planet eccentricities. The unstable region of a single circumbinary planet is used as a comparison to the investigated coorbital configurations in this work. We confirm previous findings on the stability of single planets and find a first order linear relation between orbit eccentricity and pericentre to identify stable orbits for various binary configurations. Such a linear relation is also found for the stability of 1:1 resonant planets around binaries. Stable orbits for eccentric horseshoe configurations exist with a pericentre closer than seven binary separations and, in the case of Kepler-413, the pericentre of the first stable orbit can be approximated by .
Testosterone and the Amygdala’s Functional Connectivity in Women and Men
2023-10-13

The amygdala contains androgen receptors and is involved in various affective and social functions. An interaction between testosterone and the amygdala’s functioning is likely. We investigated the amygdala’s resting-state functional connectivity (rsFC) network in association with testosterone in 94 healthy young adult women and men (final data available for analysis from 42 women and 39 men). Across the whole sample, testosterone was positively associated with the rsFC between the right amygdala and the right middle occipital gyrus, and it further predicted lower agreeableness scores. Significant sex differences appeared for testosterone and the functional connectivity between the right amygdala and the right superior frontal gyrus (SFG), showing higher testosterone levels with lower connectivity in women. Sex further predicted the openness and agreeableness scores. Our results show that testosterone modulates the rsFC between brain areas involved in affective processing and executive functions. The data indicate that the cognitive control of the amygdala via the frontal cortex is dependent on the testosterone levels in a sex-specific manner. Testosterone seems to express sex-specific patterns (1) in networks processing affect and cognition, and (2) in the frontal down-regulation of the amygdala. The sex-specific coupling between the amygdala and the frontal cortex in interaction with the hormone levels may drive sex-specific differences in a variety of behavioral phenomena that are further associated with psychiatric illnesses that show sex-specific prevalence rates.
Platform (In)Justice: Exploring Research Priorities and Practical Solutions
2023-10-13

This SIG calls for a global conversation around platform (in)justice. By focusing on the experiences of people residing in the Majority World (also known as Global South), we aim at creating a space for international and interdisciplinary exchange on socio-economically, politically, and culturally sensitive platform design and operation. The following topics motivate the SIG: concerns about equal access, structural discrimination, global inequities, and the desire to find solutions to those challenges. We invite the CSCW community to explore how attention to power relations, colonial residual, geopolitical tensions, and historical specificities can lead us to more sustainable and just platform designs. Through our SIG, we aspire to shape a research agenda for platform (in)justice that centers best practices and solutions to mediate some of the harms previously identified in the CSCW community. Going beyond this individual event, we will identify strategies of action that center the needs and assets of people residing in the Majority World when it comes to designing, upholding or challenging the frameworks enabling contemporary platforms.
Exclusive D-lactate-isomer production during a reactor-microbiome conversion of lactose-rich waste by controlling pH and temperature
2023-10-13

Abstract Lactate is among the top-ten-biobased products. It occurs naturally as D– or L-isomer and as a racemic mixture (DL-lactate). Generally, lactate with a high optical purity is more valuable. In searching for suitable renewable feedstocks for lactate production, unutilized organic waste streams are increasingly coming into focus. Here, we investigated acid whey, which is a lactose-rich byproduct of yogurt production, that represents a considerable environmental footprint for the dairy industry. We investigated the steering of the lactate-isomer composition in a continuous and open culture system (HRT = 0.6 d) at different pH values (pH 5.0 vs. pH 6.5) and process temperatures (38°C to 50°C). The process startup was achieved by autoinoculation. At a pH of 5.0 and a temperature of 47°C-50°C, exclusive D-lactate production occurred because of the dominance of Lactobacillus spp. (&gt; 95% of relative abundance). The highest volumetric D-lactate production rate of 722 ± 94.6 mmol C L -1 d -1 (0.90 ± 0.12 g L -1 h -1 ), yielding 0.93 ± 0.15 mmol C mmol C -1 , was achieved at a pH of 5.0 and a temperature of 44°C ( n = 18). At a pH of 6.5 and a temperature of 44°C, we found a mixture of DL-lactate (average D-to-L-lactate production rate ratio of 1.69 ± 0.90), which correlated with a high abundance of Streptococcus spp. and Enterococcus spp. However, exclusive L-lactate production could not be achieved. Our results show that for the continuous conversion of lactose-rich dairy waste streams, the pH was a critical process parameter to control the yield of lactate isomers by influencing the composition of the microbiota. In contrast, temperature adjustments allowed the improvement of bioprocess kinetics.
Cognitive Reserve Against Alzheimer’s Pathology Is Linked to Brain Activity During Memory Formation
2023-10-13

Abstract The cognitive reserve (CR) hypothesis posits that individuals can differ in how their brain function is disrupted by pathology associated with aging and neurodegeneration. Here, we tested this hypothesis in the Alzheimer’s disease continuum using longitudinal data from 490 participants of the DELCODE multicentric observational study. Brain function was measured using task fMRI of visual memory encoding. Using a multivariate moderation analysis we identified a CR-related activity pattern underlying successful memory encoding that moderated the detrimental effect of AD pathological load on cognitive performance. CR was mainly represented by a more pronounced expression of the task-active network encompassing the default mode network (DMN), anterior cingulate cortex (ACC) and inferior temporal regions including the fusiform gyrus. We devised personalized fMRI-based CR scores that moderated the impact of AD pathology on cognitive performance and were positively associated with years of education. Furthermore, higher CR scores were associated with slower cognitive decline over time. Our findings suggest maintenance of core cognitive circuits including the DMN and ACC as the primary mechanism of CR. Individual brain activity levels of these areas during memory encoding have prognostic value for future cognitive decline.