Decoding semantic relatedness and prediction from EEG: A classification method comparison.

Machine-learning (ML) decoding methods have become a valuable tool for analyzing information represented in electroencephalogram (EEG) data. However, a systematic quantitative comparison of the performance of major ML classifiers for the decoding of EEG data in neuroscience studies of cognition is lacking. Using EEG data from two visual word-priming experiments examining well-established N400 effects of prediction and semantic relatedness, we compared the performance of three major ML classifiers that each use different algorithms: support vector machine (SVM), linear discriminant analysis (LDA), and random forest (RF). We separately assessed the performance of each classifier in each experiment using EEG data averaged over cross-validation blocks and using single-trial EEG data by comparing them with analyses of raw decoding accuracy, effect size, and feature importance weights. The results of these analyses demonstrated that SVM outperformed the other ML methods on all measures and in both experiments.

Prescribed fire selects for a pyrophilous soil sub-community in a northern California mixed conifer forest.

Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above-ground response to fire has been well-documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold-change, while differentially abundant bacterial taxa generally had a negative fold-change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub-community composed of burn-associated indicator taxa that were positively differentially abundant was enriched for non-neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process-driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.

Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development.

Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire-responsive fungal colonizers of post-fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes. Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum, Pyronema omphalodes, Tricharina praecox, Geopyxis carbonaria, Morchella snyderi, and Peziza echinospora. A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. A comparative transcriptome analysis of P. domesticum under two conditions - growing on charcoal, and during sexual development - identified modules of genes that are co-expressed in the charcoal and light-induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition. Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum.

Role for dithiolopyrrolones in disrupting bacterial metal homeostasis.

Natural products harbor unique and complex structures that provide valuable antibiotic scaffolds. With an increase in antibiotic resistance, natural products once again hold promise for new antimicrobial therapies, especially those with unique scaffolds that have been overlooked due to a lack of understanding of how they function. Dithiolopyrrolones (DTPs) are an underexplored class of disulfide-containing natural products, which exhibit potent antimicrobial activities against multidrug-resistant pathogens. DTPs were thought to target RNA polymerase, but conflicting observations leave the mechanisms elusive. Using a chemical genomics screen in Escherichia coli, we uncover a mode of action for DTPs-the disruption of metal homeostasis. We show that holomycin, a prototypical DTP, is reductively activated, and reduced holomycin chelates zinc with high affinity. Examination of reduced holomycin against zinc-dependent metalloenzymes revealed that it inhibits E. coli class II fructose bisphosphate aldolase, but not RNA polymerase. Reduced holomycin also strongly inhibits metallo-ß-lactamases in vitro, major contributors to clinical carbapenem resistance, by removing active site zinc. These results indicate that holomycin is an intracellular metal-chelating antibiotic that inhibits a subset of metalloenzymes and that RNA polymerase is unlikely to be the primary target. Our work establishes a link between the chemical structures of DTPs and their antimicrobial action; the ene-dithiol group of DTPs enables high-affinity metal binding as a central mechanism to inhibit metabolic processes. Our study also validates the use of chemical genomics in characterizing modes of actions of antibiotics and emphasizes the potential of metal-chelating natural products in antimicrobial therapy.

High Spatial Resolution Imaging Mass Spectrometry Reveals Chemical Heterogeneity Across Bacterial Microcolonies.

Microbes interact with the world around them at the chemical level. However, directly examining the chemical exchange between microbes and microbes and their environment, at ecological scales, i.e., the scale of a single bacterial cell or small groups of cells, remains a key challenge. Here we address this obstacle by presenting a methodology that enables matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) of bacterial microcolonies. By combining optimized sample preparation with subatmospheric pressure MALDI, we demonstrate that chemical output from groups of as few as ∼50 cells can be visualized with MALDI-IMS. Application of this methodology to Bacillus subtilis and Streptomyces coelicolor revealed heterogeneity in chemical output across microcolonies and asymmetrical metabolite production when cells grew within physiological gradients produced by Medicago sativa roots. Taken together, these results indicate that MALDI-IMS can readily visualize metabolites made by very small assemblages of bacterial cells and that even these small groups of cells can differentially produce metabolites in response to local chemical gradients.

Language Membership Identification Precedes Semantic Access: Suppression during Bilingual Word Recognition.

Previous research suggests that bilingual comprehenders access lexical representations of words in both languages nonselectively. However, it is unclear whether global language suppression plays a role in guiding attention to target language representations during ongoing lexico-semantic processing. To help clarify this issue, this study examined the relative timing of language membership and meaning activation during visual word recognition. Spanish-English bilinguals performed simultaneous semantic and language membership classification tasks on single words during EEG recording. Go/no-go ERP latencies provided evidence that language membership information was accessed before semantic information. Furthermore, N400 frequency effects indicated that the depth of processing of words in the nontarget language was reduced compared to the target language. These results suggest that the bilingual brain can rapidly identify the language to which a word belongs and subsequently use this information to selectively modulate the degree of processing in each language accordingly.

Sensitivity to Referential Ambiguity in Discourse: The Role of Attention, Working Memory, and Verbal Ability.

The establishment of reference is essential to language comprehension. The goal of this study was to examine listeners' sensitivity to referential ambiguity as a function of individual variation in attention, working memory capacity, and verbal ability. Participants listened to stories in which two entities were introduced that were either very similar (e.g., two oaks) or less similar (e.g., one oak and one elm). The manipulation rendered an anaphor in a subsequent sentence (e.g., oak) ambiguous or unambiguous. EEG was recorded as listeners comprehended the story, after which participants completed tasks to assess working memory, verbal ability, and the ability to use context in task performance. Power in the alpha and theta frequency bands when listeners received critical information about the discourse entities (e.g., oaks) was used to index attention and the involvement of the working memory system in processing the entities. These measures were then used to predict an ERP component that is sensitive to referential ambiguity, the Nref, which was recorded when listeners received the anaphor. Nref amplitude at the anaphor was predicted by alpha power during the earlier critical sentence: Individuals with increased alpha power in ambiguous compared with unambiguous stories were less sensitive to the anaphor's ambiguity. Verbal ability was also predictive of greater sensitivity to referential ambiguity. Finally, increased theta power in the ambiguous compared with unambiguous condition was associated with higher working-memory span. These results highlight the role of attention and working memory in referential processing during listening comprehension.

Natural products in soil microbe interactions and evolution.

In recent years, bacterial interspecies interactions mediated by small molecule natural products have been found to give rise to a surprising array of phenotypes in soil-dwelling bacteria, especially among Streptomyces and Bacillus species. This review examines these interspecies interactions, and the natural products involved, as they have been presented in literature stemming from four disciplines: soil science, interspecies microbiology, ecology, and evolutionary biology. We also consider how these interactions fit into accepted paradigms of signaling, cueing, and coercion.

Deaf readers' response to syntactic complexity: evidence from self-paced reading.

This study was designed to determine the feasibility of using self-paced reading methods to study deaf readers and to assess how deaf readers respond to two syntactic manipulations. Three groups of participants read the test sentences: deaf readers, hearing monolingual English readers, and hearing bilingual readers whose second language was English. In Experiment 1, the participants read sentences containing subject-relative or object-relative clauses. The test sentences contained semantic information that would influence online processing outcomes (Traxler, Morris, & Seely Journal of Memory and Language 47: 69-90, 2002; Traxler, Williams, Blozis, & Morris Journal of Memory and Language 53: 204-224, 2005). All of the participant groups had greater difficulty processing sentences containing object-relative clauses. This difficulty was reduced when helpful semantic cues were present. In Experiment 2, participants read active-voice and passive-voice sentences. The sentences were processed similarly by all three groups. Comprehension accuracy was higher in hearing readers than in deaf readers. Within deaf readers, native signers read the sentences faster and comprehended them to a higher degree than did nonnative signers. These results indicate that self-paced reading is a useful method for studying sentence interpretation among deaf readers.

Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms.

Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.

Family Medicine Clinician Screening and Barriers to Communication on Food Insecurity: A CERA General Membership Survey.

PURPOSE: Food insecurity (FI) is a hidden epidemic associated with worsening health outcomes affecting 33.8 million people in the US in 2021. Although studies demonstrate the importance of health care clinician assessment of a patient's food insecurity, little is known about whether Family Medicine clinicians (FMC) discuss FI with patients and what barriers influence their ability to communicate about FI. This study evaluated FM clinicians' food insecurity screening practices to evaluate screening disparities and identify barriers that influence the decision to communicate about FI. METHODS: Data were gathered and analyzed as part of the 2022 Council of Academic Family Medicine's Educational Research Alliance survey of Family Medicine general membership. RESULTS: The majority of respondents reported (66.9%) that their practice has a screening system for food insecurity, and most practices used a verbal screen with staff other than the clinician (41%) at specific visits (63.8%). Clinicians reported "rarely or never asking about FI" 40% of the time and only asking "always or frequently" 6.7% of the time. Inadequate time during appointments (44.5%) and other medical issues taking priority (29.4%) were identified as the most common barriers. The lack of resources available in the community was a significant barrier for clinicians who worked in rural areas. CONCLUSIONS: This survey provides insight into food insecurity screening disparities and identifies obstacles to FMC screening, such as time constraints, lack of resources, and knowledge of available resources. Understanding current communication practices could create opportunities for interventions to identify food insecurity and impact "Food as Medicine."

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.

Interspecies modulation of bacterial development through iron competition and siderophore piracy.

While soil-dwelling actinomycetes are renowned for secreting natural products, little is known about the roles of these molecules in mediating actinomycete interactions. In a previous co-culture screen, we found that one actinomycete, Amycolatopsis sp. AA4, inhibited aerial hyphae formation in adjacent colonies of Streptomyces coelicolor. A siderophore, amychelin, mediated this developmental arrest. Here we present genetic evidence that confirms the role of the amc locus in the production of amychelin and in the inhibition of S. coelicolor development. We further characterize the Amycolatopsis sp. AA4 - S. coelicolor interaction by examining expression of developmental and iron acquisition genes over time in co-culture. Manipulation of iron availability and/or growth near Amycolatopsis sp. AA4 led to alterations in expression of the critical developmental gene bldN, and other key downstream genes in the S. coelicolor transcriptional cascade. In Amycolatopsis sp. AA4, siderophore genes were downregulated when grown near S. coelicolor, leading us to find that deferrioxamine E, produced by S. coelicolor, could be readily utilized by Amycolatopsis sp. AA4. Collectively these results suggest that competition for iron via siderophore piracy and species-specific siderophores can alter patterns of gene expression and morphological differentiation during actinomycete interactions.

Surface-active antibiotic production is a multifunctional adaptation for postfire microbes.

Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microbes. While it is thought that fire-adapted microbes lie at the forefront of postfire ecosystem recovery, the specific strategies that these microbes use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp . RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia caledonica str. F3, led to the discovery of rhlM , whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ in order to navigate, grow, and outcompete other soil community members in postfire environments. Significance Statement: Wildfires are increasing in frequency and intensity at a global scale. Microbes are the first colonizers of soil after fire events, but the adaptations that help these organisms survive in postfire environments are poorly understood. In this work, we show that a bacterium isolated from burned soil produces an unusual rhamnolipid biosurfactant that exhibits antimicrobial activity, enhances motility, and solubilizes potential nutrients derived from pyrolyzed organic matter. Collectively, our findings demonstrate that bacteria leverage specialized metabolites with multiple functions to meet the demands of life in postfire environments. Furthermore, this work reveals the potential of probing perturbed environments for the discovery of unique compounds and enzymes.

Improving Chronic Pain Management in a Family Medicine Residency.

BACKGROUND AND OBJECTIVE: Although the opioid epidemic continues to affect millions of Americans, many family physicians feel underprepared to perform chronic pain management (CPM) and treat opioid use disorder (OUD). To address this gap, we created organizational policy changes and implemented a didactic curriculum to help improve patient care, including medication-assisted treatment (MAT) into our residency. We investigated whether the educational program improved the comfort and ability of family physicians to prescribe opioids and utilize MAT. METHOD: Clinic policies and protocols were updated to align with the 2016 Centers for Disease Control and Prevention Guidelines for Prescribing Opioids. A didactic curriculum was created to improve resident and faculty comfort with CPM and introduce MAT. An online survey was completed pre- and postintervention between December 2019 and February 2020, utilizing paired sample t test and percentage effective (z test) to assess for change in provider comfort with opioid prescribing. Assessments were made using clinical metrics to monitor compliance with the new policy. RESULTS: Following the interventions, providers reported improved comfort with CPM (P=.001) and perception of MAT (P<.0001). Within the clinical setting there was significant improvement in the number of CPM patients who had a pain management agreement on file (P<.001) and completed a urine drug screen within the past year (P<.001). CONCLUSION: Provider comfort with CPM and OUD increased over the course of the intervention. We were also able to introduce MAT, adding a tool to the toolbox to help our residents and graduates treat OUD.

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.

Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli.

Bacteria comprehensively reorganize their global gene expression when faced with starvation. The alarmone ppGpp facilitates this massive response by co-ordinating the downregulation of genes of the translation apparatus, and the induction of biosynthetic genes and the general stress response. Such a large reorientation requires the activities of multiple regulators, yet the regulatory network downstream of ppGpp remains poorly defined. Transcription profiling during isoleucine depletion, which leads to gradual starvation (over > 100 min), allowed us to identify genes that required ppGpp, Lrp and RpoS for their induction and to deduce the regulon response times. Although the Lrp and RpoS regulons required ppGpp for their activation, they were not induced simultaneously. The data suggest that metabolic genes, i.e. those of the Lrp regulon, require only a low level of ppGpp for their induction. In contrast, the RpoS regulon was induced only when high levels of ppGpp accumulated. We tested several predictions of a model that explains how bacteria allocate transcriptional resources between metabolism and stress response by discretely tuning two regulatory circuits to different levels of ppGpp. The emergent regulatory structure insures that stress survival circuits are only triggered if homeostatic metabolic networks fail to compensate for environmental deficiencies.

Feeling the past: the absence of experimental evidence for anomalous retroactive influences on text processing.

In two self-paced reading experiments, we investigated the hypothesis that information moves backward in time to influence prior behaviors (Bem Journal of Personality and Social Psychology 100:407-425, 2011a). In two of Bem's experiments, words were presented after target pictures in a pleasantness judgment task. In a condition in which the words were consistent with the emotional valence of the picture, reaction times to the pictures were significantly shorter , as compared with a condition in which the words were inconsistent with the emotional valence of the picture. Bem Journal of Personality and Social Psychology 100:407-425, (2011a) interpreted these results as showing a "retroactive priming" effect resulting from precognition. To test the precognition hypothesis, we adapted a standard repetition priming paradigm from psycholinguistics. In the experiments, participants read a set of texts. In one condition, the participants read the same text twice. In other conditions, participants read two different texts. The precognition hypothesis predicts that readers who encounter the same text twice will experience reductions in processing load during their first encounter with the text. Hence, these readers' average reading times should be shorter than those of readers who encounter the target text only once. Our results indicated that readers processed the target text faster the second time they read it. Also, their reading times decreased as their experience with the self-paced reading procedure increased. However, participants read the target text equally quickly during their initial encounter with the text, whether or not the text was subsequently repeated. Thus, the experiments demonstrated normal repetition priming and practice effects but offered no evidence for retroactive influences on text processing.

Ecological drivers of division of labour in Streptomyces.

Division of labour occurs when different individuals, cells or tissues become specialised to perform complementary tasks that benefit the whole organism or social group. Although long studied in multicellular organisms and colonies of social insects, several recent studies have established that division of labour is common in microorganisms. We review recent work on the division of labour in unicellular and multicellular bacteria, with a particular focus on reproductive and metabolic divisions of labour in actinomycetes. Actinomycetes show enormous variation in sporophore morphology and spore production patterns that likely affect the potential for cooperative interactions within colonies. They also display both irreversible genetic and spatiotemporally regulated phenotypic divisions of labour that structure antibiotic production. We highlight outstanding questions in this group of multicellular bacteria and outline factors that can modify the expression of division of labour across microbes.

Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor.

Bacterial natural products have historically been a deep source of new medicines, but their slowed discovery in recent decades has put a premium on developing strategies that enhance the likelihood of capturing novel compounds. Here, we used a straightforward approach that capitalizes on the interactive ecology of "rare" actinomycetes. Specifically, we screened for interactions that triggered the production of antimicrobials that inhibited the growth of a bacterial strain with exceptionally diverse natural antimicrobial resistance. This strategy led to the discovery of a family of antimicrobials we term the dynaplanins. Heterologous expression enabled identification of the dynaplanin biosynthetic gene cluster, which was missed by typical algorithms for natural product gene cluster detection. Genome sequencing of partially resistant mutants revealed a 2-oxo acid dehydrogenase E2 subunit as the likely molecular target of the dynaplanins, and this finding was supported by computational modeling of the dynaplanin scaffold within the active site of this enzyme. Thus, this simple strategy, which leverages microbial interactions and natural antibiotic resistance, can enable discovery of molecules with unique antimicrobial activity. In addition, these results indicate that primary metabolism may be a direct target for inhibition via chemical interference in competitive microbial interactions. IMPORTANCE Many antibiotics were originally discovered from microbes. However, in recent decades, resistance to current treatments has risen, while novel antibiotic discovery has become increasingly challenging. Thus, there is a need to develop new strategies to find novel antimicrobials. Here, we incorporated three levels of innovation into a single, simple discovery pipeline: focusing on understudied bacteria with a high potential for producing antibiotics, growing these bacteria in binary microbial interactions, and screening for activity against a multidrug-resistant bacterium. This led us to discover a family of antimicrobials that we call the dynaplanins, which are synthesized by genes that were not detected by typical prediction algorithms. We found that dynaplanins likely block the function of one of three related enzymes called 2-oxo acid dehydrogenases, which are vital to cellular metabolism. Overall, our strategy based on bacterial competition led to discovery of a novel antibiotic that inhibits the ability to metabolize nutrients.