Miracle-dz/UniFAR-FTUs huggingface dataset:
Sulfate-Reducing ElectroAutotrophs and Their Applications in Bioelectrochemical Systems

Electroautotrophs are microbes able to perform different biocathodic reactions by using CO2 as sole carbon source and electrochemical reducing power as a sole energy source. Electroautotrophy has been discovered in several groups of microorganisms, including iron-oxidizing bacteria, iron-reducing bacteria, nitrate-reducing bacteria, acetogens, methanogens and sulfate-reducing bacteria. The high diversity of electroautrophs results in a wide range of Bioelectrochemical Systems (BES) applications, ranging from bioproduction to bioremediation. In the last decade, particular research attention has been devoted towards the discovery, characterization and application of acetogenic and methanogenic electroautotrophs. Less attention has been given to autotrophic sulfate-reducing microorganisms, which are extremely interesting biocatalysts for multiple BES technologies, with concomitant CO2 fixation. They can accomplish water sulfate removal, hydrogen production and, in some case, even biochemicals production. This mini-review gives a journey into electroautotrophic ability of sulfate-reducing bacteria and highlights their possible importance for biosustainable applications. More specifically, general metabolic features of autotrophic sulfate reducers are introduced. Recently discovered strains able to perform extracellular electron uptake and possible molecular mechanisms behind this electron transfer capacity are explored. Finally, BES technologies based on sulfate-reducing electroautotrophs are illustrated.
Stability and Robustness in Influence Maximization

In the well-studied Influence Maximization problem, the goal is to identify a set of k nodes in a social network whose joint influence on the network is maximized. A large body of recent work has justified research on Influence Maximization models and algorithms with their potential to create societal or economic value. However, in order to live up to this potential, the algorithms must be robust to large amounts of noise, for they require quantitative estimates of the influence, which individuals exert on each other; ground truth for such quantities is inaccessible, and even decent estimates are very difficult to obtain. We begin to address this concern formally. First, we exhibit simple inputs on which even very small estimation errors may mislead every algorithm into highly suboptimal solutions. Motivated by this observation, we propose the Perturbation Interval model as a framework to characterize the stability of Influence Maximization against noise in the inferred diffusion network. Analyzing the susceptibility of specific instances to estimation errors leads to a clean algorithmic question, which we term the Influence Difference Maximization problem. However, the objective function of Influence Difference Maximization is NP-hard to approximate within a factor of O(n1−ε) for any ε > 0. Given the infeasibility of diagnosing instability algorithmically, we focus on finding influential users robustly across multiple diffusion settings. We define a Robust Influence Maximization framework wherein an algorithm is presented with a set of influence functions. The algorithm’s goal is to identify a set of k nodes who are simultaneously influential for all influence functions, compared to the (function-specific) optimum solutions. We show strong approximation hardness results for this problem unless the algorithm gets to select at least a logarithmic factor more seeds than the optimum solution. However, when enough extra seeds may be selected, we show that techniques of Krause et al. can be used to approximate the optimum robust influence to within a factor of 1−1/e. We evaluate this bicriteria approximation algorithm against natural heuristics on several real-world datasets. Our experiments indicate that the worst-case hardness does not necessarily translate into bad performance on real-world datasets; all algorithms perform fairly well.
The prosody of rhetorical vs. information-seeking questions in Icelandic

This paper reports on a production experiment investigating the prosodic realization of rhetorical questions (RQs) as compared to information seeking questions (ISQs) in Icelandic. It looks at two question types: polar questions ( Borðar einhver límónur? 'Does anybody eat limes? ') and wh- questions ( Hver borðar límónur? 'Who eats limes? '). The main results are as follows. (i) In both question types, the boundary tone fails to contribute to the distinction between ISQs and RQs. It is L% almost across the board. (ii) The semantic difference between ISQs and RQs is reflected in the nuclear accents: In wh- questions, ISQs have more monotonal (H*/! H*/^H*) pitch accents, while RQs have more bitonal ones (mostly L+H*/L+! H*/L+^H*) In polar questions, nuclear accents are mostly L+H, but the timing of the rise differs (more L*+H in ISQs, more L+H* in RQs). (iii) The first word of the utterance and the nuclear syllable are longer in RQs than in ISQs in both question types. Within the nuclear syllable, both onset and rhyme are lengthened. Taken together, prosody helps to distinguish between ISQs and RQs, but the terminus of the intonational contour (boundary tone) is not essential.
Ferredoxin/thioredoxin system plays an important role in the chloroplastic NADP status of Arabidopsis

NADP is a key electron carrier for a broad spectrum of redox reactions, including photosynthesis. Hence, chloroplastic NADP status, as represented by redox status (ratio of NADPH to NADP+ ) and pool size (sum of NADPH and NADP+ ), is critical for homeostasis in photosynthetic cells. However, the mechanisms and molecules that regulate NADP status in chloroplasts remain largely unknown. We have now characterized an Arabidopsis mutant with imbalanced NADP status (inap1), which exhibits a high NADPH/NADP+ ratio and large NADP pool size. inap1 is a point mutation in At2g04700, which encodes the catalytic subunit of ferredoxin/thioredoxin reductase. Upon illumination, inap1 demonstrated earlier increases in NADP pool size than the wild type did. The mutated enzyme was also found in vitro to inefficiently reduce m-type thioredoxin, which activates Calvin cycle enzymes, and NADP-dependent malate dehydrogenase to export reducing power to the cytosol. Accordingly, Calvin cycle metabolites and amino acids diminished in inap1 plants. In addition, inap1 plants barely activate NADP-malate dehydrogenase, and have an altered redox balance between the chloroplast and cytosol, resulting in inefficient nitrate reduction. Finally, mutants deficient in m-type thioredoxin exhibited similar light-dependent NADP dynamics as inap1. Collectively, the data suggest that defects in ferredoxin/thioredoxin reductase and m-type thioredoxin decrease the consumption of NADPH, leading to a high NADPH/NADP+ ratio and large NADP pool size. The data also suggest that the fate of NADPH is an important influence on NADP pool size.
Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli

Although functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements of microbial communities has remained poorly explored. Here, we experimentally mined novel constitutive promoter sequences in metagenomic libraries by combining a bi-directional reporter vector, high-throughput fluorescence assays and predictive computational methods. Through the expression profiling of fluorescent clones from two independent soil sample libraries, we have analyzed the regulatory dynamics of 260 clones with candidate promoters as a set of active metagenomic promoters in the host Escherichia coli. Through an in-depth analysis of selected clones, we were able to further explore the architecture of metagenomic fragments and to report the presence of multiple promoters per fragment with a dominant promoter driving the expression profile. These approaches resulted in the identification of 33 novel active promoters from metagenomic DNA originated from very diverse phylogenetic groups. The in silico and in vivo analysis of these individual promoters allowed the generation of a constitutive promoter consensus for exogenous sequences recognizable by E. coli in metagenomic studies. The results presented here demonstrates the potential of functional metagenomics for exploring environmental bacterial communities as a source of novel regulatory genetic parts to expand the toolbox for microbial engineering.
Refined Asymptotics for the Number of Leaves of Random Point Quadtrees

In the early 2000s, several phase change results from distributional convergence to distributional non-convergence have been obtained for shape parameters of random discrete structures. Recently, for those random structures which admit a natural martingale process, these results have been considerably improved by obtaining refined asymptotics for the limit behavior. In this work, we propose a new approach which is also applicable to random discrete structures which do not admit a natural martingale process. As an example, we obtain refined asymptotics for the number of leaves in random point quadtrees. More applications, for example to shape parameters in generalized m-ary search trees and random gridtrees, will be discussed in the journal version of this extended abstract.
Evaluating European Food Safety Authority Protection Goals for Honeybees (Apis mellifera): What Do They Mean for Pollination?

In recent years there has been growing concern regarding the sudden and unexplained failure of honeybee (Apis mellifera) colonies. Several factors have been suggested, including pesticides. In an effort to regulate their impact, guidance published by the European Food Safety Authority (EFSA) has recommended that the magnitude of effects on exposed colonies should not exceed 7% reduction in colony size after 2 brood cycles. However, fears have been raised regarding the practicality of measuring such a loss in the field. It is also unclear how this protection goal relates to maintaining the ecosystem services provided by bees, which we argue should be a primary objective for regulators. Here, we evaluate what these protection goals mean in relation to ecosystems performance using a computational colony model that incorporates mechanisms to simulate both lethal and sublethal pesticide effects. To these simulations, we apply a testing regime similar to that commonly used in field trials to produce standard assessment metrics. By relating these measures to losses in forager activity, we aim to identify which could be used as effective indicators of reduced ecoservice and to quantify acceptable limits below which performance can be maintained. Our findings show that loss of colony size is the best indicator of reduced ecoservice. Metrics that focus on specific colony functions such as increased brood or forager mortality are ineffective indicators for all types of simulated pesticide effects. At the levels of colony loss recommended by EFSA, using our default parameterization, we predict a loss of ecosystems performance of 3% to 4%. However, based on an extensive sensitivity analysis, it is clear that this estimate is subject to substantial uncertainty with losses under alternative parameterizations of up to 14%. Nevertheless, our model provides a valuable framework for assessing protection goals, allowing regulators to test relevant impacts and quantify their magnitude. Integr Environ Assess Manag 2018;14:750–758. © 2018 Crown Copyright and SETAC
The impact of asexual and sexual reproduction in spatial genetic structure within and between populations of the dioecious plant Marchantia inflexa (Marchantiaceae)

Background and Aims In dioecious plants, sexual reproduction requires close proximity to potential mates, but clonal growth can increase this distance and, therefore, reduce the probability of mating. Reduction in sexual propagules can lead to decreased dispersal and gene flow between populations. Gene flow and clonal growth may be further influenced by the size of the habitat patch. The effects of habitat size and reproductive mode (sexual or asexual reproduction) on spatial genetic structure and segregation of the sexes were tested by quantifying the distributions of genotypes and the sexes using the dioecious liverwort Marchantia inflexa. Methods Plants were sampled from five pairs of small-large habitat patches to identify within- and among-population spatial genetic structure using 12 microsatellite markers. Spatial distributions were calculated as the likelihood that pairs of individuals were the same sex or genotype, and it was determined how that likelihood was affected by habitat patch size (small/large). Key Results Asexual reproduction dominates within populations, and asexual dispersal also occurred across populations. Spatial segregation of the sexes was observed within populations; males were more likely to be near individuals of the same sex than were females. Although the likelihood of both sexes being near members of the same sex was similarly greater on small habitat patches, on large habitat patches male genotypes were almost 15 % more likely to be near clonemates than were female genotypes. Conclusions The results show a sex difference in clonal clumping that was dependent upon habitat size, suggesting differential colonization and/or survival between males and females. The sexes and genotypes being structured differently within and among populations have implications for the persistence of populations and the interactions between them. This study demonstrates that studying only the sexes and not their genotypes (or vice versa) can limit our understanding of the extent to which reproductive modes (sexual or asexual) influence genetic structure both within and between populations.
CHIRON: Deployment-quality Detection of Java Cryptographic Vulnerabilities

Cryptographic API misuses threaten software security. Examples include exposed secrets, predictable random numbers, and vulnerable certificate verification. Our goal in this work is to produce deployment-quality program analysis tools for automatically inspecting various cryptographic API uses in complex Java programs. The main challenge is how to reduce false positives (FP) without compromising analysis quality. Unfortunately, state-of-the-art solutions in this space were not designed to be deployment-grade and did not address this issue. Our main technical innovation is a set of algorithms for systematically removing irrelevant elements (from program slices) to reduce false alerts. We evaluated our tool, CHIRON, on 46 high-impact large-scale Apache projects and 240 Android apps, which generates many security insights. We observed violations for most of our 16 rules. 86% of the Android vulnerabilities come from the libraries. There is a widespread insecure practice of storing plaintext passwords. We manually went through the 2,009 Apache alerts and confirmed 1,961 true positives (2.39% FP rate). We contacted Apache with our security findings. This helped multiple popular Apache projects to harden their code, including Spark, Ranger, and Ofbiz. We also discuss the pragmatic constraints that hinder secure coding.
Shape Engineering of Biomass-Derived Nanoparticles from Hollow Spheres to Bowls through Solvent-Induced Buckling.

The realization of asymmetric hollow carbonaceous nanostructures remains a great challenge, especially when biomass is chosen as the carbon resource through hydrothermal carbonization (HTC). Herein, a simple and straightforward solvent-induced buckling strategy is demonstrated for the synthesis of asymmetric spherical and bowl-like carbonaceous nanomaterials. The formation of the bowl-like morphology was attributed to the buckling of the spherical shells induced by the dissolution of the oligomers. The bowl-like particles prepared through this solvent-driven approach demonstrated a well-controlled morphology and a uniform particle size of approximately 360 nm. The obtained nanospheres and nanobowls were loaded with CoS2 nanoparticles to act as heterogeneous catalysts for the selective hydrogenation of aromatic nitro compounds. As expected, the CoS2 /nanobowls catalyst showed good tolerance to a wide scope of reducible groups and afforded both high activity and selectivity in almost all the tested substrates.
Complex Climate Response to Astronomical Forcing: The Middle-Pleistocene Transition in Glacial Cycles and Changes in Frequency Locking

Through the past few million years large ice sheets have repeatedly grown and disappeared on the Northern hemisphere. These are the Pleistocene glaciations. They are related to the changing solar heating of the Earth due to changes in Earth's orbit and axis of rotation. The climate response to these changes is highly non-trivial and non-linear, expressing the complex nature of the climate system. Many aspects of glacial cycles still need a convincing explanation, one particular mystery being the change from approximately 40 kyr (kilo year) glacial cycles to approximately 100 kyr cycles around 1 million years ago. This transition is called the middle Pleistocene transition (MPT). Here we review some conceptual models to explain the dynamics of glacial cycles and possible dynamical causes of the MPT. We especially focus on the well studied van del Pol oscillator as a conceptual model for the glacial cycles and propose that the MPT is a result of changes in frequency locking of the climate system to the astronomical forcing. This is compared to a recently presented model that relates the MPT to a transcritical bifurcation in the structure of a generic critical/slow manifold for a fast-slow dynamical system.
ATF2, but not ATF3, participates in the maintenance of nerve injury-induced tactile allodynia and thermal hyperalgesia

Transcription factors are proteins that modulate the transcriptional rate of target genes in the nucleus in response to extracellular or cytoplasmic signals. Activating transcription factors 2 (ATF2) and 3 (ATF3) respond to environmental signals and maintain cellular homeostasis. There is evidence that inflammation and nerve injury modulate ATF2 and ATF3 expression. However, the function of these transcription factors in pain is unknown. The purpose of this study was to investigate the contribution of ATF2 and ATF3 to nerve injury-induced neuropathic pain. L5/6 spinal nerve ligation induced tactile allodynia and thermal hyperalgesia. Moreover, nerve damage enhanced ATF2 and ATF3 protein expression in injured L5/6 dorsal root ganglia and spinal cord but not in uninjured L4 dorsal root ganglia. Nerve damage also enhanced ATF2 immunoreactivity in dorsal root ganglia and spinal cord 7 to 21 days post-injury. Repeated intrathecal post-treatment with a small-interfering RNA targeted against ATF2 (ATF2 siRNA) or anti-ATF2 antibody partially reversed tactile allodynia and thermal hyperalgesia. In contrast, ATF3 siRNA or anti-ATF3 antibody did not modify nociceptive behaviors. ATF2 immunoreactivity was found in dorsal root ganglia and spinal cord co-labeling with NeuN mainly in non-peptidergic (IB4+) but also in peptidergic (CGRP+) neurons. ATF2 was found mainly in small- and medium-sized neurons. These results suggest that ATF2, but not ATF3, found in strategic sites related to spinal nociceptive processing and participates in the maintenance of neuropathic pain in rats.
Barriers and enablers to aligning rehabilitation goals to patient life roles following acquired brain injury

BACKGROUND/AIM Life roles are integral to occupational therapy practice. Goal setting is a method of establishing priorities to measure outcomes. While acquired brain injury can impact a person's ability to fulfil meaningful life roles, the alignment of goals set in rehabilitation to life roles, is unclear. This study aimed to (i) explore the alignment of goals with life roles for people with an acquired brain injury participating in inpatient rehabilitation; and (ii) identify barriers and enablers to life role discussions within a patient-directed goal setting framework. METHOD A mixed-methods study was conducted on an inpatient rehabilitation unit in Victoria, Australia. Quantitative data were obtained from a retrospective file audit of randomly selected medical records. Qualitative data were collected through: a) interviews with patients and their families; and b) A focus group with occupational therapists. Thematic analysis of both audit data and narrative data was undertaken. RESULTS Thirty files were examined and demonstrated 33% alignment between goals and life roles. Four interviews were completed with patients, with a family member participating in two of these. Themes identified were: readiness, role concept, recovery concept and goal review. Five therapists attended the focus group. Themes identified were: Patient factors, goal review, expectations, role change and environment. Interview and focus group data identified that barriers to life role discussions included: lack of patient and family readiness, patients' difficulty understanding role concept, focus on impairments and lack of family/ significant others support. Enablers included: having early conversations involving family, regular goal review and use of standardised tools. CONCLUSION Goal setting in alignment with life roles is important in acquired brain injury rehabilitation, but may be limited. This process can be enhanced by including patients and their significant others in early goal setting conversations, along with regular goal review across the rehabilitation process.
Detection of race-specific resistance against Puccinia coronata f. sp. avenae in Brachypodium species

Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in non-host species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling, but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine if effector-triggered immunity contributes to non-host resistance to P. coronata f. sp. avenae in Brachypodium species.
The microbiome in autoimmune diseases

The microbiome is represented by microorganisms which live in a symbiotic way with the mammalian. Microorganisms have the ability to influence different physiological aspects such as the immune system, metabolism and behaviour. In recent years, several studies have highlighted the role of the microbiome in the pathogenesis of autoimmune diseases. Notably, in systemic lupus erythematosus an alteration of the intestinal flora (lower Firmicutes/Bacteroidetes ratio) has been described. Conversely, changes to the gut commensal and periodontal disease have been proposed as important factors in the pathogenesis of rheumatoid arthritis. At the same time, other autoimmune diseases (i.e. systemic sclerosis, Sjögren’s syndrome and anti‐phospholipid syndrome) also share modifications of the microbiome in the intestinal tract and oral flora. Herein, we describe the role of the microbiome in the maintenance homeostasis of the immune system and then the alterations of the microorganisms that occur in systemic autoimmune diseases. Finally, we will consider the use of probiotics and faecal transplantation as novel therapeutic targets.