Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and seasonal variations of secondary organic aerosol from terpenoids over China

A majority of global secondary organic aerosol (SOA) comes from terpenoids. In this study, we carried out a 1 year nationwide observation of pinenes (α‐ and β‐pinene) and SOA tracers from monoterpenes (SOAM) and β‐caryophyllene (SOAC) over China for the first time. SOAM and SOAC tracers ranged from 9.80 to 49.0 ng m−3 and 1.72 to 7.72 ng m−3, respectively, with high levels in southern China. Pinenes ranged from 34 to 102 parts per trillion by volume, with α‐pinene dominant over β‐pinene. SOAM tracers were correlated between paired sites, suggesting a regional impact of SOAM, while pinenes were uncorrelated between sites due to their rapid oxidation. High levels of SOAM tracers were observed in spring and summer. However, at the Hailun site in Northeast China, SOAM tracers increased during winter. The positive correlation between SOAM tracers and the biomass burning (BB) tracer levoglucosan during winter at Hailun indicated that the unexpected increase of SOAM was associated with BB. The SOAC tracer, β‐caryophyllenic acid, increased during winter and was positively correlated with levoglucosan, suggesting substantial contributions from BB to SOAC production in wintertime. Together with SOA tracers from isoprene, these tracers were applied to estimate biogenic secondary organic carbon (BSOC) from isoprene, monoterpenes, and β‐caryophyllene. The annual average BSOC was 0.91 ± 0.41 μgC m−3,with the majority from monoterpenes and the highest level in Southwest China. BSOC was elevated from April to September and was lowest in January and February. BSOC composition dramatically changed from a monoterpene majority in fall‐spring to an isoprene majority in summer.
Enhanced carbon export to the abyssal depths driven by atmosphere dynamics

Long‐term biogeochemical observations are critical to understand the natural ability of the oceans to fix CO2 into organic carbon and export it to the deep as sinking particles. Here we present results from a 3 year (2010–2013) sediment trap deployment that allowed detecting interannual variations of carbon fluxes beyond 4000 m depth in the Eastern Mediterranean Sea. Anomalous atmospheric conditions triggering strong heat losses in winter–spring 2012 resulted in convective mixing, nutrient uplifting, and a diatom‐dominated bloom southeast of Crete. Phytoplankton growth, reinforced by the arrival of nutrients from airborne Etna volcano ash, was the highest in the last decade (satellite‐derived Chl a concentrations up to 1.9 mg m−3). This situation caused carbon export to increase by 2 orders of magnitude (12.2 mg m−2 d−1) with respect to typical values, which demonstrates how pulses of sinking fresh phytodetritus linked to rare atmospheric processes can episodically impact one of the most oligotrophic environments in the world ocean.
Clonal Parabacteroides from Gut Microfistulous Tracts as Transmissible Cytotoxic Succinate-Commensal Model of Crohn’s Disease Complications

Crohn’s disease (CD) has been traditionally viewed as a chronic inflammatory disease that cause gut wall thickening and complications, including fistulas, by mechanisms not understood. By focusing on Parabacteroides distasonis (presumed modern succinate-producing commensal probiotic), recovered from intestinal microfistulous tracts (cavernous fistulous micropathologies CavFT proposed as intermediate between ‘mucosal fissures’ and ‘fistulas’) in two patients that required surgery to remove CD-damaged ilea, we demonstrate that such isolates exert pathogenic/pathobiont roles in mouse models of CD. Our isolates are clonally-related; potentially emerging as transmissible in the community and mice; proinflammatory and adapted to the ileum of germ-free mice prone to CD-like ileitis (SAMP1/YitFc) but not healthy mice (C57BL/6J), and cytotoxic/ATP-depleting to HoxB8-immortalized bone marrow derived myeloid cells from SAMP1/YitFc mice when concurrently exposed to succinate and extracts from CavFT-derived E. coli, but not to cells from healthy mice. With unique genomic features supporting recent genetic exchange with Bacteroides fragilis-BGF539, evidence of international presence in primarily human metagenome databases, these CavFT Pdis isolates could represent to a new opportunistic Parabacteroides species, or subspecies (‘cavitamuralis’) adapted to microfistulous niches in CD.
Pregnancy affects flight behavior in big brown bats (Eptesicus fuscus)

Pregnancy involves increased body mass and decreased locomotor performance in many species and can be especially impactful on volant animals. To test the hypothesis that bats modify flight behavior to adjust for pregnancy-related increases in mass, we recorded thermal video from a maternity colony of big brown bats (Eptesicus fuscus) as they emerged from a roost, during periods associated with pregnancy and post-pregnancy. From video tracking, we calculated the vertical drop distance before upward motion (UM), time from emergence until UM, average speeds before and after UM, and average wingbeat rate per second (WBR). Bats recorded during the pregnancy period had a significantly larger drop distance, longer time until UM, faster flight speed before UM, and higher WBR compared to bats recorded during the non-pregnancy period. Our results suggest that pregnancy has a significant effect on flight in female bats, with a particularly strong impact on achieving UM after emergence. However, the higher WBR recorded from bats flying during the pregnancy period implies that bats acclimate to such changes in body mass by altering their flight behaviors to sustain UM while pregnant.
Prevotella are major contributors of sialidases in the human vaginal microbiome

Elevated bacterial sialidase activity in the female genital tract is strongly associated with poor health outcomes including preterm birth and bacterial vaginosis. These negative effects may arise from sialidase-mediated degradation of the protective mucus layer in the cervicovaginal environment. Prior biochemical studies of vaginal bacterial sialidases have focused solely on the bacterial vaginosis-associated organism Gardnerella vaginalis. Despite their implications for sexual and reproductive health, sialidases from other vaginal bacteria have not been characterized. Here, we show that vaginal Prevotella species produce active sialidases that possess variable activity toward mucin. These sialidases are highly conserved across clades of Prevotella from different geographies, hinting at their importance globally. Finally, we find that Prevotella sialidases, including mucin-degrading enzymes from Prevotella timonensis, are highly prevalent and abundant in human vaginal metagenomes and metatranscriptomes, Together, our results identify Prevotella as a critical source of sialidases in the vaginal microbiome, improving our understanding of this detrimental bacterial activity. Significance Statement Sialidase activity in the vaginal microbiome is increased in bacterial vaginosis and strongly associated with other adverse health outcomes. Sialidase enzymes release sialic acid from host-derived glycans in the vaginal environment, altering their structures and functions. However, biochemical studies of vaginal bacterial sialidases have been limited to one genus, Gardnerella. In this work, we identify and characterize multiple active sialidase enzymes in vaginal bacteria of the genus Prevotella. We find that Prevotella sialidases are more prevalent and abundant in vaginal microbial communities than Gardnerella sialidases. Our work highlights Prevotella bacteria as an underappreciated source of sialidase activity with important implications for both our understanding of vaginal health and therapeutic development.
Diagnosing Bone Fracture to Assess Early Hominin Behaviour, Meat-Eating, and Socioecology at FLK-Zinjanthropus, Olduvai Gorge, Tanzania

This study develops a fractographic method to diagnose hammerstone- and carnivore induced fracture. This is important because interpretations of hominin entry into the carnivore guild and evolution of meat-eating are based on rare tool and tooth marks in Oldowan (2.5-1.8mya) fossil assemblages. Consequently, estimating hominin and carnivore involvement is difficult, and questions remain about Oldowan hominin’s position in the carnivore guild and socioecology. One aspect of bone damage, fracture surfaces, is ubiquitous, but largely unstudied. The fractographic (study of fracture surfaces) method is based on fracture principals, particularly how differences in static- and impact-loading affect material response and fracture features resulting from loading extremes. The method is applied to analysis of fracture features in a) the Amboseli Hyaena Den assemblage, b) an experimental hammerstone-broken assemblage, c) a Plio-Pleistocene assemblage previously interpreted as a carnivore accumulation, FLK-NN2 (Olduvai Gorge), and d) the zooarchaeological assemblage from FLK-Zinj, (Olduvai Gorge). This is the first zooarchaeological/taphonomic study to demonstrate that a) static and impact fracture differ fundamentally in applied load size and material responses to loading extremes, b) impact-forces are significantly greater than the maximum carnivore bite-force, c) cones, incipient flakes, radiating cracks, and lateral stress features are characteristic of impact fracture, and e) Oldowan hominins at FLK-Zinj were responsible for breakage of 54% of the limb assemblage (a 37% – 40% increase over estimates based on percussion marks). The socioecological implications of the habitual transport of food from death and/or kill sites to secondary locations are explored by examining reasons why social carnivores transport food. Aspects of modern carnivore behaviour suggest general mammalian constraints that may have predicated food transport by early Homo. Early Homo food transport behaviour was structured by anti-predator defense strategies associated with a) foraging in an open habitat rich with competing predators, b) the lack of masticatory and digestive apparatus to quickly consume animal tissue, and c) the presence of altricial young in the hominin group.
A Module-Level Configuration Methodology for Programmable Camouflaged Logic

Logic camouflage is a widely adopted technique that mitigates the threat of intellectual property (IP) piracy and overproduction in the integrated circuit (IC) supply chain. Camouflaged logic achieves functional obfuscation through physical-level ambiguity and post-manufacturing programmability. However, discussions on programmability are confined to the level of logic cells/gates, limiting the broader-scale application of logic camouflage. In this work, we propose a novel module-level configuration methodology for programmable camouflaged logic that can be implemented without additional hardware ports and with negligible resources. We prove theoretically that the configuration of the programmable camouflaged logic cells can be achieved through the inputs and netlist of the original module. Further, we propose a novel lightweight ferroelectric FET (FeFET)-based reconfigurable logic gate (rGate) family and apply it to the proposed methodology. With the flexible replacement and the proposed configuration-aware conversion algorithm, this work is characterized by the input-only programming scheme as well as the combination of high output error rate and point-function-like defense. Evaluations show an average of >95% of the alternative rGate location for camouflage, which is sufficient for the security-aware design. We illustrate the exponential complexity in function state traversal and the enhanced defense capability of locked blackbox against SAT attacks compared to key-based methods. We also preserve an evident output Hamming distance and introduce negligible hardware overheads in both gate-level and module-level evaluations under typical benchmarks.
Quaternary marine terrace chronology, North Canterbury, New Zealand, using amino acid racemization and infrared-stimulated luminescence

Abstract Extensive marine terraces along the North Canterbury coast of the South Island of New Zealand record uplift in this tectonically active area. Although the terraces have been studied previously, applications of Quaternary geochronological techniques to the region have been limited. We use infrared-stimulated luminescence (IRSL), amino acid racemization (AAR), and radiocarbon to determine ages of terraces at three locations—Glenafric, Motunau Beach, and Haumuri Bluff. We develop an AAR calibration curve for the mollusk species Tawera spissa from sites of known age, including the sedimentary sequence of the Whanganui Basin. Bayesian model averaging of the results is used to estimate ages of marine shells from the North Canterbury terraces. By using both IRSL and AAR, we are able to confirm ages using two independent dating methods and to identify one IRSL result that is likely in error. We develop new age estimates for the marine terraces of North Canterbury and propose correlations between sites. This terrace chronology differs significantly from most previous studies, highlighting the importance of numerical dating. The most extensive terraces are from marine isotope stages (MISs) 5a and 5c, with partial reoccupation of one terrace during MIS 3, whereas MIS 5e terraces are notably lacking among those dated.
Statistical Properties of Cloud Propagation over Sumatra during CPEA-I

Cloud propagation over Sumatra and the surrounding area (10 ° S-10 ° N, 70 ° -120 ° E) during the Coupling Processes in the Equatorial Atmosphere-I (CPEA-I) campaign (10 April to 9 May 2004) was tracked using brightness temperature (T b ) data from the GOES-9 satellite. The cloud tracking was based on three-dimensional data with a t hreshold of T b < 210 K. During the campaign, westward-moving clouds were more dominant than eastward-moving systems, with a ratio of approximately 4:1. This characteristic coincided with the dominant easterly wind aloft . Most cloud s propagated with a speed varying between 4 and 35 m/s, with a mean value of 13 . 7 m/s. If the westward and eastward propagations were separated, the average duration, speed, and span of the westward (eastward) moving clouds are 7 . 7 (5.8 h) , -14 . 5 (9.8 m/s ) , and 435 . 5 (187.1 km ) , respectively. The c h aracteristic s of cloud propagation during the CPEA-I were influenced by environmental factors such as relative hum i dity, temperature, the vertical movement of air, and wind shear . Such factors interact ed with the inactive and active phases of the Madden - Julian Oscillation .
Diverse domain architectures of CheA histidine kinase, a central component of bacterial and archaeal chemosensory systems

ABSTRACT Chemosensory systems in bacteria and archaea are complex, multi-protein pathways that enable rapid cellular responses to environmental changes. The CheA histidine kinase is a central component of chemosensory systems. In contrast to other histidine kinases, it lacks a sensor (input) domain and utilizes dedicated chemoreceptors for sensing. CheA is a multi-domain protein; in model organisms as diverse as Escherichia coli and Bacillus subtilis, it contains five single-copy domains. Deviations from this canonical domain architecture have been reported, however, a broad genome-wide analysis of CheA diversity is lacking. Here, we present the results of a genomic survey of CheA domain composition carried out using an unbiased set of thousands of CheA sequences from bacteria and archaea. We found that four out of five canonical CheA domains comprise a minimal functional unit (core domains), as they are present in all surveyed CheA homologs. The most common deviations from a classical five-domain CheA architecture are the lack of a P2/CheY-binding domain, which is missing from more than half of CheA homologs, and the acquisition of a response regulator receiver (CheY-like) domain, which is present in ~35% of CheA homologs. We also document other deviations from classical CheA architecture, including bipartite CheA proteins, domain duplications, and fusions, and reveal that phylogenetically defined CheA classes have pre-dominant domain architectures. This study lays a foundation for a better classification of CheA homologs and identifies targets for experimental investigations. IMPORTANCE We found that in contrast to the best-studied model organisms, such as Escherichia coli and Bacillus subtilis, most bacterial and archaeal species have a CheA protein with a different domain composition. We report variations in CheA architecture, such as domain duplication and acquisition as well as class-specific domain composition. Our results will be of interest to those working on signal transduction in bacteria and archaea and lay the foundation for experimental studies. We found that in contrast to the best-studied model organisms, such as Escherichia coli and Bacillus subtilis, most bacterial and archaeal species have a CheA protein with a different domain composition. We report variations in CheA architecture, such as domain duplication and acquisition as well as class-specific domain composition. Our results will be of interest to those working on signal transduction in bacteria and archaea and lay the foundation for experimental studies.
Hyporheic flow and dissolved oxygen distribution in fish nests: The effects of open channel velocity, permeability patterns, and groundwater upwelling

Many fish lay their eggs in nests, or redds, which they construct in sediment. The viability of eggs depends on many factors, particularly their oxygenation. Because dissolved oxygen is typically saturated within the stream channel, the dissolved oxygen distribution within the redd depends on whether or not hyporheic flow and transport occur within the sediment. We conducted a series of flume and numerical flow and age transport modeling experiments with the aim of understanding the effects of salmonid redds on the hyporheic transport of young oxygenated water. Hyporheic flow was visualized directly through dye injections. Dissolved oxygen throughout the fish nest was measured using a planar optode. Experiments were conducted at various open channel flow velocities in order to understand their effect on dissolved oxygen, and computational simulations considered various sediment textures and ambient groundwater upwelling rates to add process‐level insight. We found that, as also shown by previous studies, the redd topography induces multiscale hyporheic flow that effectively flushes the egg pocket location with younger presumably oxygenated water; older water upwells and forms anoxic zones. This pattern persists even at the lowest channel flow rates and at small upwelling velocities of older ambient groundwater which splits the multiscale hyporheic flow cells into isolated pockets. Large groundwater upwelling rates can shut down all the hyporheic flushing. The relatively coarse texture of the redd further promotes hyporheic flushing of the redd sediment with oxygenated water. Thus, redd morphology and sediment texture optimally combine to induce hyporheic exchange flow that delivers young oxygenated water to the egg pocket.
Modelling Rust’s Reference Ownership Analysis Declaratively in Datalog

Polonius is a Datalog reformulation of Rust’s signature static may-point-to analysis, the borrow check, used for alias control of references and to ensure aﬀine types. Polonius extends the previous borrow check to a full flow-sensitive analysis on Rust’s Mid-level Intermediate Representation, with the goal to eventually allow a number of desirable sound but currently disallowed patterns of coding to be accepted by the compiler. This thesis describes the current, partial implementation of Polonius, including the addition of (partial) initialisation and (full) liveness tracking contributed as part of the work for the thesis, ties it to the Oxide formal type system, and describes an exploratory study of input data for the borrow check generated by analysing circa circa 20 000 popular publicly available Git repositories found on GitHub and the Crates.io Rust package index. Some central findings from the study are that deallocations are uncommon relative to other variable uses, and that the full flow-sensitive analysis is typically seldom needed. Indeed, surprisingly many functions (circa 60%) actually do not create any references at all, and therefore does not need (most of) the Polonius analysis. Another conclusion from the study is that control-flow graph size and number of variables in the function under analysis seems to have the highest correlation to longer solve-times, and would therefore be useful proxies for the diﬀiculty of an input.
Géométrie différentielle Quasi-morphisme de Calabi sur les surfaces de genre supérieur

Calabi quasi-morphism on higher genus surfaces. We construct a homogeneous quasi-morphism Cal S on the group of Hamiltonian diffeomorphisms of a (closed, connected, oriented) surface S of genus greater or equal to 2, with the following property. For each connected open set U in S diffeomorphic to a disk or to an annulus, the restriction of Cal S to the subgroup of diffeomorphisms which are the time 1 map of a Hamiltonian isotopy in U , equals Calabi’s homomorphism. To cite this article: P. Py, C. R. Acad. Sci. Paris, Ser. I 341 (2005).  2005 Académie des sciences
Driver genes exome sequencing reveals distinct variants in African Americans with colorectal neoplasia

Background Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the United States. African Americans are disproportionately affected by CRC. Our hypothesis is that driver genes with known and novel mutations have an impact on CRC outcome in this population. Therefore, we investigated the variants’ profiles in a panel of 15 CRC genes. Patients & Methods Colorectal specimens (n=140) were analyzed by targeted exome sequencing using an Ion Torrent platform. Detected variants were validated in 36 samples by Illumina sequencing. The novel status of the validated variants was determined by comparison to publicly available databases. Annotated using ANNOVAR and in-silico functional analysis of these variants were performed to determine likely pathogenic variants. Results Overall, 121 known and novel variants were validated: APC (27%), AMER1 (3%), ARID1 (7%), MSH3 (12%), MSH6 (10%), BRAF (4%), KRAS (6%), FBXW7 (4%), PIK3CA (6%), SMAD4 (5%), SOX9 (2%), TCF7L2 (2%), TGFBR2 (5%), TP53 (7%). From these validated variants, 12% were novel in 8 genes (AMER1, APC, ARID1A, BRAF, MSH6, PIK3CA, SMAD4, and TCF7L2). Of the validated variants, 23% were non-synonymous, 14% were stopgains, 24% were synonymous and 39% were intronic variants. Conclusion We here report the specifics of variants’ profiles of African Americans with colorectal lesions. Validated variants showed that Tumor Suppressor Genes (TSGs) APC and ARID1 and DNA Mismatch repair (MMR) genes MSH3 and MSH6 are the genes with the highest numbers of validated variants. Oncogenes KRAS and PIK3CA are also altered and likely participate in the increased proliferative potential of the mutated colonic epithelial cells in this population.