Genetic and environmental interactions contribute to immune variation in rewilded mice.

The relative and synergistic contributions of genetics and environment to interindividual immune response variation remain unclear, despite implications in evolutionary biology and medicine. Here we quantify interactive effects of genotype and environment on immune traits by investigating C57BL/6, 129S1 and PWK/PhJ inbred mice, rewilded in an outdoor enclosure and infected with the parasite Trichuris muris. Whereas cellular composition was shaped by interactions between genotype and environment, cytokine response heterogeneity including IFNγ concentrations was primarily driven by genotype with consequence on worm burden. In addition, we show that other traits, such as expression of CD44, were explained mostly by genetics on T cells, whereas expression of CD44 on B cells was explained more by environment across all strains. Notably, genetic differences under laboratory conditions were decreased following rewilding. These results indicate that nonheritable influences interact with genetic factors to shape immune variation and parasite burden.

The γδ IEL effector API5 masks genetic susceptibility to Paneth cell death.

Loss of Paneth cells and their antimicrobial granules compromises the intestinal epithelial barrier and is associated with Crohn's disease, a major type of inflammatory bowel disease1-7. Non-classical lymphoid cells, broadly referred to as intraepithelial lymphocytes (IELs), intercalate the intestinal epithelium8,9. This anatomical position has implicated them as first-line defenders in resistance to infections, but their role in inflammatory disease pathogenesis requires clarification. The identification of mediators that coordinate crosstalk between specific IEL and epithelial subsets could provide insight into intestinal barrier mechanisms in health and disease. Here we show that the subset of IELs that express γ and δ T cell receptor subunits (γδ IELs) promotes the viability of Paneth cells deficient in the Crohn's disease susceptibility gene ATG16L1. Using an ex vivo lymphocyte-epithelium co-culture system, we identified apoptosis inhibitor 5 (API5) as a Paneth cell-protective factor secreted by γδ IELs. In the Atg16l1-mutant mouse model, viral infection induced a loss of Paneth cells and enhanced susceptibility to intestinal injury by inhibiting the secretion of API5 from γδ IELs. Therapeutic administration of recombinant API5 protected Paneth cells in vivo in mice and ex vivo in human organoids with the ATG16L1 risk allele. Thus, we identify API5 as a protective γδ IEL effector that masks genetic susceptibility to Paneth cell death.

Recruitment and Maintenance of CX3CR1+CD4+ T Cells during Helminth Infection.

Distinct subsets of T lymphocytes express CX3CR1 under inflammatory conditions, but little is known about CX3CR1+CD4+ T cells during type 2 inflammation in helminth infections. In this study, we used a fate-mapping mouse model to characterize CX3CR1+CD4+ T cells during both acute Nippostrongylus brasiliensis and chronic Schistosoma mansoni murine models of helminth infections, revealing CX3CR1+CD4+ T cells to be an activated tissue-homing subset with varying capacity for cytokine production. Tracking these cells over time revealed that maintenance of CX3CR1 itself along with a TH2 phenotype conferred a survival advantage in the inflamed tissue. Single-cell RNA sequencing analysis of fate-mapped CX3CR1+CD4+ T cells from both the peripheral tissue and the spleen revealed a considerable level of diversity and identified a distinct population of BCL6+TCF-1+PD1+CD4+ T cells in the spleen during helminth infections. Conditional deletion of BCL6 in CX3CR1+ cells resulted in fewer CX3CR1+CD4+ T cells during infection, indicating a role in sustaining CD4+ T cell responses to helminth infections. Overall, our studies revealed the behavior and heterogeneity of CX3CR1+CD4+ T cells during type 2 inflammation in helminth infections and identified BCL6 to be important in their maintenance.

Bacterial contact induces polar plug disintegration to mediate whipworm egg hatching.

The bacterial microbiota promotes the life cycle of the intestine-dwelling whipworm Trichuris by mediating hatching of parasite eggs ingested by the mammalian host. Despite the enormous disease burden associated with Trichuris colonization, the mechanisms underlying this transkingdom interaction have been obscure. Here, we used a multiscale microscopy approach to define the structural events associated with bacteria-mediated hatching of eggs for the murine model parasite Trichuris muris. Through the combination of scanning electron microscopy (SEM) and serial block face SEM (SBFSEM), we visualized the outer surface morphology of the shell and generated 3D structures of the egg and larva during the hatching process. These images revealed that exposure to hatching-inducing bacteria catalyzed asymmetric degradation of the polar plugs prior to exit by the larva. Unrelated bacteria induced similar loss of electron density and dissolution of the structural integrity of the plugs. Egg hatching was most efficient when high densities of bacteria were bound to the poles. Consistent with the ability of taxonomically distant bacteria to induce hatching, additional results suggest chitinase released from larva within the eggs degrade the plugs from the inside instead of enzymes produced by bacteria in the external environment. These findings define at ultrastructure resolution the evolutionary adaptation of a parasite for the microbe-rich environment of the mammalian gut.

Single-Cell Analysis of CX3CR1+ Cells Reveals a Pathogenic Role for BIRC5+ Myeloid Proliferating Cells Driven by Staphylococcus aureus Leukotoxins.

Our previous studies identified a population of stem cell-like proliferating myeloid cells within inflamed tissues that could serve as a reservoir for tissue macrophages to adopt different activation states depending on the microenvironment. By lineage-tracing cells derived from CX3CR1+ precursors in mice during infection and profiling by single-cell RNA sequencing, in this study, we identify a cluster of BIRC5+ myeloid cells that expanded in the liver during chronic infection with either the parasite Schistosoma mansoni or the bacterial pathogen Staphylococcus aureus. In the absence of tissue-damaging toxins, S. aureus infection does not elicit these BIRC5+ cells. Moreover, deletion of BIRC5 from CX3CR1-expressing cells results in improved survival during S. aureus infection. Hence the combination of single-cell RNA sequencing and genetic fate-mapping CX3CR1+ cells revealed a toxin-dependent pathogenic role for BIRC5 in myeloid cells during S. aureus infection.

Staphylococcus aureus induces a muted host response in human blood that blunts the recruitment of neutrophils.

Staphylococcus aureus is an opportunistic pathogen and chief among bloodstream-infecting bacteria. S. aureus produces an array of human-specific virulence factors that may contribute to immune suppression. Here, we defined the response of primary human phagocytes following infection with S. aureus using RNA-sequencing (RNA-Seq). We found that the overall transcriptional response to S. aureus was weak both in the number of genes and in the magnitude of response. Using an ex vivo bacteremia model with fresh human blood, we uncovered that infection with S. aureus resulted in the down-regulation of genes related to innate immune response and cytokine and chemokine signaling. This muted transcriptional response was conserved across diverse S. aureus clones but absent in blood exposed to heat-killed S. aureus or blood infected with the less virulent staphylococcal species Staphylococcus epidermidis. Notably, this signature was also present in patients with S. aureus bacteremia. We identified the master regulator S. aureus exoprotein expression (SaeRS) and the SaeRS-regulated pore-forming toxins as key mediators of the transcriptional suppression. The S. aureus-mediated suppression of chemokine and cytokine transcription was reflected by circulating protein levels in the plasma. Wild-type S. aureus elicited a soluble milieu that was restrictive in the recruitment of human neutrophils compared with strains lacking saeRS. Thus, S. aureus blunts the inflammatory response resulting in impaired neutrophil recruitment, which could promote the survival of the pathogen during invasive infection.

Single-Cell Transcriptional Survey of Ileal-Anal Pouch Immune Cells From Ulcerative Colitis Patients.

BACKGROUND & AIMS: Restorative proctocolectomy with ileal pouch-anal anastomosis is a surgical procedure in patients with ulcerative colitis refractory to medical therapies. Pouchitis, the most common complication, is inflammation of the pouch of unknown etiology. To define how the intestinal immune system is distinctly organized during pouchitis, we analyzed tissues from patients with and without pouchitis and from patients with ulcerative colitis using single-cell RNA sequencing (scRNA-seq). METHODS: We examined pouch lamina propria CD45+ hematopoietic cells from intestinal tissues of ulcerative colitis patients with (n = 15) and without an ileal pouch-anal anastomosis (n = 11). Further in silico meta-analysis was performed to generate transcriptional interaction networks and identify biomarkers for patients with inflamed pouches. RESULTS: In addition to tissue-specific signatures, we identified a population of IL1B/LYZ+ myeloid cells and FOXP3/BATF+ T cells that distinguish inflamed tissues, which we further validated in other scRNA-seq datasets from patients with inflammatory bowel disease (IBD). Cell-type-specific transcriptional markers obtained from scRNA-seq was used to infer representation from bulk RNA sequencing datasets, which further implicated myeloid cells expressing IL1B and S100A8/A9 calprotectin as interacting with stromal cells, and Bacteroidales and Clostridiales bacterial taxa. We found that nonresponsiveness to anti-integrin biologic therapies in patients with ulcerative colitis was associated with the signature of IL1B+/LYZ+ myeloid cells in a subset of patients. CONCLUSIONS: Features of intestinal inflammation during pouchitis and ulcerative colitis are similar, which may have clinical implications for the management of pouchitis. scRNA-seq enables meta-analysis of multiple studies, which may facilitate the identification of biomarkers to personalize therapy for patients with IBD. The processed single cell count tables are provided in Gene Expression Omnibus; GSE162335. Raw sequence data are not public and are protected by controlled-access for patient privacy.

A comparative analysis of SARS-CoV-2 antivirals characterizes 3CLpro inhibitor PF-00835231 as a potential new treatment for COVID-19.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of Coronavirus Disease 2019 (COVID-19). There is a dire need for novel effective antivirals to treat COVID-19, as the only approved direct-acting antiviral to date is remdesivir, targeting the viral polymerase complex. A potential alternate target in the viral life cycle is the main SARS-CoV-2 protease 3CLpro (Mpro). The drug candidate PF-00835231 is the active compound of the first anti-3CLpro regimen in clinical trials. Here, we perform a comparative analysis of PF-00835231, the pre-clinical 3CLpro inhibitor GC-376, and the polymerase inhibitor remdesivir, in alveolar basal epithelial cells modified to express ACE2 (A549+ACE2 cells). We find PF-00835231 with at least similar or higher potency than remdesivir or GC-376. A time-of-drug-addition approach delineates the timing of early SARS-CoV-2 life cycle steps in A549+ACE2 cells and validates PF-00835231's early time of action. In a model of the human polarized airway epithelium, both PF-00835231 and remdesivir potently inhibit SARS-CoV-2 at low micromolar concentrations. Finally, we show that the efflux transporter P-glycoprotein, which was previously suggested to diminish PF-00835231's efficacy based on experiments in monkey kidney Vero E6 cells, does not negatively impact PF-00835231 efficacy in either A549+ACE2 cells or human polarized airway epithelial cultures. Thus, our study provides in vitro evidence for the potential of PF-00835231 as an effective SARS-CoV-2 antiviral and addresses concerns that emerged based on prior studies in non-human in vitro models.Importance:The arsenal of SARS-CoV-2 specific antiviral drugs is extremely limited. Only one direct-acting antiviral drug is currently approved, the viral polymerase inhibitor remdesivir, and it has limited efficacy. Thus, there is a substantial need to develop additional antiviral compounds with minimal side effects and alternate viral targets. One such alternate target is its main protease, 3CLpro (Mpro), an essential component of the SARS-CoV-2 life cycle processing the viral polyprotein into the components of the viral polymerase complex. In this study, we characterize a novel antiviral drug, PF-00835231, which is the active component of the first-in-class 3CLpro-targeting regimen in clinical trials. Using 3D in vitro models of the human airway epithelium, we demonstrate the antiviral potential of PF-00835231 for inhibition of SARS-CoV-2.

Comparison of contemporary and historical outcomes of elective and ruptured open abdominal aortic aneurysm repair.

BACKGROUND: Recently, open abdominal aortic aneurysm (AAA) repair (OSR) has become less common and will often be reserved for patients with more complex aortic anatomy. Despite improvements in patient management, the reduced surgical volume has raised concerns for potentially worsened outcomes in the contemporary era (2014-2019) compared with an earlier era in which OSR was more widely practiced (2005-2010). In the present study, we compared the 30-day outcomes of open AAA repair between these two eras. METHODS: The American College of Surgeons National Quality Improvement Program general database was queried for open AAA repair using the Current Procedural Terminology and International Classification of Diseases, 9th and 10th, codes. The cases were stratified into two groups by operation year: 2005 to 2010 (early) and 2014 to 2019 (contemporary). In each era, the cases were further divided into elective and ruptured groups. The 30-day outcomes, including mortality, major morbidity, postoperative sepsis, and unplanned reoperation, were compared between the contemporary and early eras in the elective and ruptured groups. Preoperative variables with a P value <.25 were adjusted for in the multivariate analysis. RESULTS: In the contemporary and early eras, 3749 and 3798 patients had undergone elective OSR and 1148 and 907 had undergone ruptured OSR, respectively. These samples were of similar sizes owing to the National Quality Improvement Program sampling process and our relatively strict inclusion criteria. In the contemporary era, fewer patients were elderly and fewer were smokers or had hypertension or dyspnea in the elective and rupture cohorts. More patients had had American Society of Anesthesiologists class >3 in the elective contemporary era (39% vs 24%; P < .0001). The contemporary elective repair group demonstrated increased 30-day mortality (3.7% vs 3.2%; adjusted odds ratio [aOR], 1.36; P = .006), major adverse cardiac events (5.7% vs 3.4%; aOR, 1.87; P < .0001), and bleeding requiring transfusion (58.5% vs 13.7%; aOR, 8.96; P < .0001). The incidence of pulmonary complications (12.1% vs 15.2%; aOR, 0.80; P = .02) and sepsis (3.7% vs 8.4%; aOR, 0.47; P < .0001) had decreased in the contemporary era, with a similar rate of unplanned reoperations (8.4% vs 7.7%; aOR, 1.16; P = .09). The incidence of renal complications in the contemporary era had increased, with a statistically significant difference. However, the absolute increase of <0.5% was likely not clinically relevant (5.5% vs 5.1%; aOR, 1.23; P = .049). In the ruptured cohort, contemporary repair was associated with increased 30-day mortality (41.4% vs 40%; aOR, 1.53; P < .0001), major adverse cardiac events (25.8% vs 12.8%; aOR, 2.49; P < .0001), and bleeding requiring transfusion (88.2% vs 27%; aOR, 23.03; P < .0001). The incidence of pulmonary complications (36.9% vs 48.1%; aOR, 0.67; P < .0001), sepsis (14.6% vs 23%; aOR, 0.75; P = .03), and unplanned reoperations (18.1% vs 22.7%; aOR, 0.74; P = .008) had decreased in the contemporary OSR group. No differences were detected in the incidence of renal complications. CONCLUSIONS: The 30-day mortality has worsened after open AAA repair in the elective and rupture settings despite the improvements in perioperative management over the years. These complications likely stem from increased bleeding events and major cardiac events, which were increased in the contemporary era.

Distinct Features of Human Myeloid Cell Cytokine Response Profiles Identify Neutrophil Activation by Cytokines as a Prognostic Feature during Tuberculosis and Cancer.

Myeloid cells are a vital component of innate immunity and comprise monocytes, macrophages, dendritic cells, and granulocytes. How myeloid cell lineage affects activation states in response to cytokines remains poorly understood. The cytokine environment and cellular infiltrate during an inflammatory response may contain prognostic features that predict disease outcome. In this study, we analyzed the transcriptional responses of human monocytes, macrophages, dendritic cells, and neutrophils in response to stimulation by IFN-γ, IFN-ß, IFN-λ, IL-4, IL-13, and IL-10 cytokines to better understand the heterogeneity of activation states in inflammatory conditions. This generated a myeloid cell-cytokine-specific response matrix that can infer representation of myeloid cells and the cytokine environment they encounter during infection, in tumors and in whole blood. Neutrophils were highly responsive to type 1 and type 2 cytokine stimulation but did not respond to IL-10. We identified transcripts specific to IFN-ß stimulation, whereas other IFN signature genes were upregulated by both IFN-γ and IFN-ß. When we used our matrix to deconvolute blood profiles from tuberculosis patients, the IFN-ß-specific neutrophil signature was reduced in tuberculosis patients with active disease, whereas the shared response to IFN-γ and IFN-ß in neutrophils was increased. When applied to glioma patients, transcripts of neutrophils exposed to IL-4/IL-13 and monocyte responses to IFN-γ or IFN-ß emerged as opposing predictors of patient survival. Hence, by dissecting how different myeloid cells respond to cytokine activation, we can delineate biological roles for myeloid cells in different cytokine environments during disease processes, especially during infection and tumor progression.

Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures.

Helminth infection and dietary intake can affect the intestinal microbiota, as well as the immune system. Here we analyzed the relationship between fecal microbiota and blood profiles of indigenous Malaysians, referred to locally as Orang Asli, in comparison to urban participants from the capital city of Malaysia, Kuala Lumpur. We found that helminth infections had a larger effect on gut microbial composition than did dietary intake or blood profiles. Trichuris trichiura infection intensity also had the strongest association with blood transcriptional profiles. By characterizing paired longitudinal samples collected before and after deworming treatment, we determined that changes in serum zinc and iron levels among the Orang Asli were driven by changes in helminth infection status, independent of dietary metal intake. Serum zinc and iron levels were associated with changes in the abundance of several microbial taxa. Hence, there is considerable interplay between helminths, micronutrients and the microbiota on the regulation of immune responses in humans.

The Causal Role of Left and Right Superior Temporal Gyri in Speech Perception in Noise: A Transcranial Magnetic Stimulation Study.

Successful perception of speech in everyday listening conditions requires effective listening strategies to overcome common acoustic distortions, such as background noise. Convergent evidence from neuroimaging and clinical studies identify activation within the temporal lobes as key to successful speech perception. However, current neurobiological models disagree on whether the left temporal lobe is sufficient for successful speech perception or whether bilateral processing is required. We addressed this issue using TMS to selectively disrupt processing in either the left or right superior temporal gyrus (STG) of healthy participants to test whether the left temporal lobe is sufficient or whether both left and right STG are essential. Participants repeated keywords from sentences presented in background noise in a speech reception threshold task while receiving online repetitive TMS separately to the left STG, right STG, or vertex or while receiving no TMS. Results show an equal drop in performance following application of TMS to either left or right STG during the task. A separate group of participants performed a visual discrimination threshold task to control for the confounding side effects of TMS. Results show no effect of TMS on the control task, supporting the notion that the results of Experiment 1 can be attributed to modulation of cortical functioning in STG rather than to side effects associated with online TMS. These results indicate that successful speech perception in everyday listening conditions requires both left and right STG and thus have ramifications for our understanding of the neural organization of spoken language processing.

Cognitive mechanisms underpinning successful perception of different speech distortions.

Few studies thus far have investigated whether perception of distorted speech is consistent across different types of distortion. This study investigated whether participants show a consistent perceptual profile across three speech distortions: time-compressed, noise-vocoded, and speech in noise. Additionally, this study investigated whether/how individual differences in performance on a battery of audiological and cognitive tasks links to perception. Eighty-eight participants completed a speeded sentence-verification task with increases in accuracy and reductions in response times used to indicate performance. Audiological and cognitive task measures include pure tone audiometry, speech recognition threshold, working memory, vocabulary knowledge, attention switching, and pattern analysis. Despite previous studies suggesting that temporal and spectral/environmental perception require different lexical or phonological mechanisms, this study shows significant positive correlations in accuracy and response time performance across all distortions. Results of a principal component analysis and multiple linear regressions suggest that a component based on vocabulary knowledge and working memory predicted performance in the speech in quiet, time-compressed and speech in noise conditions. These results suggest that listeners employ a similar cognitive strategy to perceive different temporal and spectral/environmental speech distortions and that this mechanism is supported by vocabulary knowledge and working memory.

Recording Out-of-Hospital Cardiac Arrest Treatment via a Mobile Smartphone Application: A Feasibility Simulation Study.

BACKGROUND: Given the demanding nature of out-of-hospital cardiac arrest (OHCA) resuscitations, recordings of the times of interventions in EMS patient care reports (PCRs) are often inaccurate. The American Heart Association developed Full Code Pro (FCP), a smartphone application designed to assist EMS personnel in recording the timing of interventions performed. Through OHCA simulations, this study assessed the group size necessary to use the FCP recording functions accurately and safely without compromising patient care. Program evaluation was based on participant feedback surveys, data accuracy, delays between recording and performing interventions, and delays in care attributed to using the application, stratified by group size. METHODS: Simulations of a standard OHCA scenario using the Gaumard TraumaHal mannequin and a dedicated iPhone 5 preloaded with FCP version 3.4 were run with group sizes of 2-6 participants, with group sizes determined by participant availability. Participants included Connecticut certified paramedics and paramedic students who had completed the appropriate coursework. A 7-item feedback survey using a Likert scale established participant feedback on the application. Videos of the simulations were analyzed to assess for delays. One-way analysis of variance with trend analysis was used to test whether outcomes differed by group size and whether differences tended in one direction in parallel with group size. RESULTS: There were 37 simulations, including 142 participants. The feedback survey questions achieved a Cronbach's alpha of 0.91, signifying high reliability, and demonstrated a linear trend supporting greater satisfaction with FCP as group size increases (p < 0.001). Similarly, increasing group size displayed linear trends with greater numbers of interventions recorded (p = 0.009) and fewer missed and false recordings (p = 0.002). Delays revealed significant linear trends (p = 0.018 for delays in recording and p < 0.001 for delays in care), as increasing group size corresponded with lesser delays. Greatest improvement was noted to be between groups of 3 and 4 participants. CONCLUSIONS: OHCA simulations using FCP demonstrate increased provider comfort, increased recording accuracy, and decreased delays as the group size increased. While the application may improve recordings for PCRs and future research, the data suggest a sufficient number of EMS personnel (>3) should be present to achieve reliable data without compromising patient care.

Stimulating Multiple-Demand Cortex Enhances Vocabulary Learning.

It is well established that networks within multiple-demand cortex (MDC) become active when diverse skills and behaviors are being learnt. However, their causal role in learning remains to be established. In the present study, we first performed functional magnetic resonance imaging on healthy female and male human participants to confirm that MDC was most active in the initial stages of learning a novel vocabulary, consisting of pronounceable nonwords (pseudowords), each associated with a picture of a real object. We then examined, in healthy female and male human participants, whether repetitive transcranial magnetic stimulation of a frontal midline node of the cingulo-opercular MDC affected learning rates specifically during the initial stages of learning. We report that stimulation of this node, but not a control brain region, substantially improved both accuracy and response times during the earliest stage of learning pseudoword-object associations. This stimulation had no effect on the processing of established vocabulary, tested by the accuracy and response times when participants decided whether a real word was accurately paired with a picture of an object. These results provide evidence that noninvasive stimulation to MDC nodes can enhance learning rates, thereby demonstrating their causal role in the learning process. We propose that this causal role makes MDC candidate target for experimental therapeutics; for example, in stroke patients with aphasia attempting to reacquire a vocabulary.SIGNIFICANCE STATEMENT Learning a task involves the brain system within which that specific task becomes established. Therefore, successfully learning a new vocabulary establishes the novel words in the language system. However, there is evidence that in the early stages of learning, networks within multiple-demand cortex (MDC), which control higher cognitive functions, such as working memory, attention, and monitoring of performance, become active. This activity declines once the task is learnt. The present study demonstrated that a node within MDC, located in midline frontal cortex, becomes active during the early stage of learning a novel vocabulary. Importantly, noninvasive brain stimulation of this node improved performance during this stage of learning. This observation demonstrated that MDC activity is important for learning.

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.

BACKGROUND: Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research. RESULTS: We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics. CONCLUSIONS: WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.

Using transcranial magnetic stimulation of the undamaged brain to identify lesion sites that predict language outcome after stroke.

Transcranial magnetic stimulation focused on either the left anterior supramarginal gyrus or opercular part of the left inferior frontal gyrus has been reported to transiently impair the ability to perform phonological more than semantic tasks. Here we tested whether phonological processing abilities were also impaired following lesions to these regions in right-handed, English speaking adults, who were investigated at least 1 year after a left-hemisphere stroke. When our regions of interest were limited to 0.5 cm3 of grey matter centred around sites that had been identified with transcranial magnetic stimulation-based functional localization, phonological impairments were observed in 74% (40/54) of patients with damage to the regions and 21% (21/100) of patients sparing these regions. This classification accuracy was better than that observed when using regions of interest centred on activation sites in previous functional magnetic resonance imaging studies of phonological processing, or transcranial magnetic stimulation sites that did not use functional localization. New regions of interest were generated by redefining the borders of each of the transcranial magnetic stimulation sites to include areas that were consistently damaged in the patients with phonological impairments. This increased the incidence of phonological impairments in the presence of damage to 85% (46/54) and also reduced the incidence of phonological impairments in the absence of damage to 15% (15/100). The difference in phonological processing abilities between those with and without damage to these 'transcranial magnetic stimulation-guided' regions remained highly significant even after controlling for the effect of lesion size. The classification accuracy of the transcranial magnetic stimulation-guided regions was validated in a second sample of 108 patients and found to be better than that for (i) functional magnetic resonance imaging-guided regions; (ii) a region identified from an unguided lesion overlap map; and (iii) a region identified from voxel-based lesion-symptom mapping. Finally, consistent with prior findings from functional imaging and transcranial magnetic stimulation in healthy participants, we show how damage to our transcranial magnetic stimulation-guided regions affected performance on phonologically more than semantically demanding tasks. The observation that phonological processing abilities were impaired years after the stroke, suggests that other brain regions were not able to fully compensate for the contribution that the transcranial magnetic stimulation-guided regions make to language tasks. More generally, our novel transcranial magnetic stimulation-guided lesion-deficit mapping approach shows how non-invasive stimulation of the healthy brain can be used to guide the identification of regions where brain damage is likely to cause persistent behavioural effects.

The effect of speech distortion on the excitability of articulatory motor cortex.

It has become increasingly evident that human motor circuits are active during speech perception. However, the conditions under which the motor system modulates speech perception are not clear. Two prominent accounts make distinct predictions for how listening to speech engages speech motor representations. The first account suggests that the motor system is most strongly activated when observing familiar actions (Pickering and Garrod, 2013). Conversely, Wilson and Knoblich's account asserts that motor excitability is greatest when observing less familiar, ambiguous actions (Wilson and Knoblich, 2005). We investigated these predictions using transcranial magnetic stimulation (TMS). Stimulation of the lip and hand representations in the left primary motor cortex elicited motor evoked potentials (MEPs) indexing the excitability of the underlying motor representation. MEPs for lip, but not for hand, were larger during perception of distorted speech produced using a tongue depressor, relative to naturally produced speech. Additional somatotopic facilitation yielded significantly larger MEPs during perception of lip-articulated distorted speech sounds relative to distorted tongue-articulated sounds. Critically, there was a positive correlation between MEP size and the perception of distorted speech sounds. These findings were consistent with predictions made by Wilson & Knoblich (Wilson and Knoblich, 2005), and provide direct evidence of increased motor excitability when speech perception is difficult.

Inferior parietal lobule contributions to visual word recognition.

This study investigated how the left inferior parietal lobule (IPL) contributes to visual word recognition. We used repetitive TMS to temporarily disrupt neural information processing in two anatomical fields of the IPL, namely, the angular (ANG) and supramarginal (SMG) gyri, and observed the effects on reading tasks that focused attention on either the meaning or sounds of written words. Relative to no TMS, stimulation of the left ANG selectively slowed responses in the meaning, but not sound, task, whereas stimulation of the left SMG affected responses in the sound, but not meaning, task. These results demonstrate that ANG and SMG doubly dissociate in their contributions to visual word recognition. We suggest that this functional division of labor may be understood in terms of the distinct patterns of cortico-cortical connectivity resulting in separable functional circuits.

How Early Does the Brain Distinguish between Regular Words, Irregular Words, and Pseudowords during the Reading Process? Evidence from Neurochronometric TMS.

Cognitive theories on reading propose that the characteristics of written stimuli determine how they are processed in the brain. However, whether the brain distinguishes between regular words, irregular words, and pseudowords already at an early stage of the reading process is still subject to debate. Here we used chronometric TMS to address this issue. During the first 140 msec of regular word, irregular word, and pseudoword reading, TMS was used to disrupt the function of the ventral occipitotemporal, posterior middle temporal, and supramarginal gyri, which are key areas involved in orthographic, semantic, and phonological processing, respectively. Early TMS stimulation delivered on posterior middle temporal and supramarginal gyri affected regular and irregular word, but not pseudoword, reading. In contrast, ventral occipitotemporal disruption affected both word and pseudoword reading. We thus found evidence for an early distinction between word and pseudoword processing in the semantic and phonological systems, but not in the orthographic system.