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Weber, K. A.

Publications and source records attributed to Weber, K. A..

8 recordsLinked to original sources

Methanobacterium nebraskense sp. nov., a hydrogenotrophic methanogen isolated from saline wetland soil

A hydrogenotrophic methanogen, designated strain ACI-7T, was isolated from an alkaline, saline wetland located in eastern Nebraska, USA. Cells were identified as non-motile rods (0.9-4.2 m in length and 0.2-0.4 {micro}m in diameter) that occurred singly, in chains, and as long filaments and twisted aggregates. Strain ACI-7T utilized H2 + CO2 or formate as methanogenic substrates and required growth factors present in yeast extract for continuous cultivation. The strain grew at 20-45{degrees}C (optimum, 40{degrees}C), at pH 6.5-8.5 (optimum, pH 7.3) and with 0-2.5% NaCl (optimum, 0-1%). The genomic G+C content of ACI-7T was 31.79 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated strain ACI-7T was affiliated with the genus Methanobacterium, most closely related to Methanobacterium oryzae FPiT (97.1% sequence similarity) and Methanobacterium veterum MK4T (96.9% sequence similarity). Overall genome relatedness indices for strain ACI-7T compared to other Methanobacterium species ranged from 68.45-78.17% for average nucleotide identity and 18.9-25.7% for digital DNA-DNA hybridization. Morphological, physiological, and genomic characteristics indicate that strain ACI-7T represents a novel species, for which the name Methanobacterium nebraskense sp. nov. is proposed. The type strain is ACI-7T (=DSM 118696T=ATCC TSD-487T).

microbiology↗

Differential encoding of noxious heat and self-reported pain along corticospinal networks: a simultaneous spinal cord-brain fMRI study

Chronic pain poses a substantial public health burden. Elucidating how the healthy central nervous system (CNS) differentially encodes objective stimulus intensity and subjective experiences of pain perception may offer key insights into the central mechanisms contributing to chronic pain. Functional MRI (fMRI) combined with controlled noxious stimulation provides a powerful means to explore neural representations of nociception and pain perception. Here, we applied noxious heat at three intensities (46 {degrees}C, 47 {degrees}C, 48 {degrees}C, 8 trials each randomized) to the right forearm of 28 healthy women during simultaneous spinal cord-brain fMRI to investigate how distributed corticospinal activity and connectivity encode stimulus intensity and subjective pain. Activity increased with stimulus temperature across regions involved in pain processing--including somatosensory, motor, prefrontal, insular, and subcortical areas--as well as in the ipsilateral dorsal and ventral spinal cord. Spinal- brain functional connectivity was observed between the right dorsal horn and pain-related brain regions such as primary and secondary somatosensory cortex, insula, anterior cingulate cortex, thalamus, and periaqueductal gray, and was positively associated with individual pain ratings. Using representational similarity analysis (RSA), we found that multivoxel activation patterns in the brain and spinal cord, as well as corticospinal connectivity patterns, reliably tracked stimulus temperature, while only subsets of cortical regions (e.g., insula, sensorimotor, and frontal cortices) encoded subjective pain. Notably, spinal cord representations were primarily organized by stimulus temperature rather than perceived pain intensity. These findings demonstrate that simultaneous spinal cord-brain fMRI combined with multivariate modeling can identify sensory and perceptual components of nociceptive processing across the neuroaxis. Such approaches advance mechanistic understanding of pain and may inform the development of CNS-based biomarkers for chronic pain assessment and intervention.

neuroscience↗

Task-Based Spinal fMRI using a Median Nerve Stimulation Reveals Functional Alterations in Degenerative Cervical Myelopathy

Functional spinal cord MRI (fMRI) is an emerging technique for evaluating sensorimotor responses in both healthy and disease states. However, degenerative cervical myelopathy (DCM), a non-traumatic, age-related pathology characterized by spinal cord compression, often leads to motor and sensory impairments that make standard task-based fMRI paradigms challenging to perform or execute. To overcome this, we implemented an fMRI paradigm using direct electrical stimulation to the median nerve to evoke neural responses in both motor and sub-motor spinal cord pathways. In this study, 23 DCM and 23 aged-matched healthy controls (HC) underwent two task-based spinal cord fMRI sessions with direct, median nerve stimulation to the right upper limb. Motor thresholds were determined on an individual basis by a thumb/finger twitching, and sub-motor thresholds were set to be 15% underneath motor with no visible twitching. Blood Oxygenation Level Depended (BOLD) signals were analyzed across the C5-C8 cervical spinal cord segments. HCs demonstrated increased activation during motor vs sub-motor stimulation (1155 vs 496 voxels; +7.1%), whereas DCM patients showed reduction in activation with higher stimulation (1028 vs 1220 voxels; -2.2%). This activation pattern was consistent across the cervical spinal segments, with HCs peaking at C7 (sub-motor: 328 voxels, motor: 608 voxels), which is consistent with median nerve input for forearm and hand. While DCM responses were altered, with sub-motor differentially maximized at C6 (406 voxels) and abnormal recruitment at C5 (112 voxels) and C8 (198 voxels). Spatially, HC responses were focused in the gray matter (GM) and bilateral, whereas DCM responses showed reduced GM localization and were more ipsilateral. Furthermore, we saw spikes in sub-motor DCM deactivation at the overall (3032 voxels) and C6 root level (1500 voxels) that were greater than the other conditions. This study demonstrates the feasibility and effectiveness of median nerve stimulation as a task-based paradigm for assessing spinal cord function in those with spinal cord compression. Group level differences between DCM patients and age-matched HCs showed spatial and quantitatively distinct patterns across stimulation thresholds and spinal segments. Our findings suggest disrupted sub-motor and motor activation in the DCM group, highlighting the use of this approach as a functional biomarker to capture disease specific alterations.

neuroscience↗

Mapping Hand Function with Simultaneous Brain-Spinal Cord Functional MRI

INTRODUCTIONHand motor control depends on intricate brain-spinal cord interactions that regulate muscle activity. Hand function can be disrupted by injury to the brain, spinal cord, and peripheral nerves leading to weakness and impaired coordination. Functional MRI (fMRI) can map motor-related neural activity and potentially characterize the mechanisms underlying hand weakness and diminished coordination. Although brain motor control has been extensively studied, spinal cord mechanisms remain less explored. Here we use simultaneous brain-spinal cord fMRI to map neural activity related to hand strength and dexterity across the central nervous system using force matching and finger tapping tasks. This study pioneers the use of simultaneous brain-spinal cord fMRI to comprehensively map hand function, offering novel insights into coordinated motor processing across the central nervous system. METHODSWe performed simultaneous brain-spinal cord fMRI in 28 right-handed healthy volunteers (age: 40.0 {+/-} 13.8 years, 14 females, 14 males) using a 3T GE SIGNA Premier scanner equipped with a 21-channel head-neck coil. Participants performed a force-matching task at 10%, 20%, and 30% of maximum voluntary contraction using a hand dynamometer. For the finger tapping task, participants completed button-presses at 1 Hz with a 5-button response pad for three task levels: single-digit response with the second digit only (low), single-digit response with all digits in a sequential order (medium), single-digit response with all digits in a random order (high). Visual cues and feedback were provided during the tasks. Brain and spinal cord images were processed separately using FSL and the Spinal Cord Toolbox, with motion correction, physiological noise filtering, and spatial normalization to standard templates. Subject level activity maps were generated and entered into group level analyses to explore both activations and deactivations. For the brain, we used a mixed effect design with a voxelwise threshold of Z score > 3.10 and cluster threshold of p < 0.05. For the spinal cord, we used a fixed effect design with a voxelwise threshold of Z score > 1.64 and cluster threshold of p < 0.05. Region of interest (ROI) analyses were conducted to examine localized changes in activation across task levels RESULTSBoth tasks elicited activation in motor and sensory regions of the brain and spinal cord, with graded responses in the left primary motor (M1), left primary sensory (S1) cortex, and right spinal cord gray matter across task levels. Deactivation of the right M1 and S1 was also present for both tasks. Deactivation of the left spinal cord gray matter was present in the high task level of the force matching task. The ROI analysis findings complemented the group level activity maps. DISCUSSIONOur study provides a detailed map of brain-spinal cord interactions in hand function, revealing graded neural activation and inhibition patterns across motor and sensory regions. Interhemispheric inhibition, reflected in right M1 deactivation, likely restricts extraneous motor output during unilateral tasks. For force matching, the deactivation of the left ventral and dorsal horns of the spinal cord, provides the first evidence that the inhibition of motor areas during a unilateral motor task extends to the spinal cord. Whether this inhibition results from direct descending modulation from the brain or interneuronal inhibition in the cord remains to be interrogated. These findings expand our understanding of central motor control mechanisms and could inform rehabilitation strategies for individuals with motor impairments. CONCLUSIONSOur simultaneous brain-spinal cord fMRI approach provides novel insights into the neural coordination of hand function, enhancing our understanding of motor control and its modulation. This approach may offer a foundation for studying motor dysfunction in conditions such as stroke, spinal cord injury, and neurodegenerative diseases.

neuroscience↗

EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data

Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Preprocessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.

neuroscience↗

Zea mays genotype influences microbial and viral rhizobiome community structure

Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two different genotypes of Zea mays parviglumis and Z. mays genotype B73 in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as apply 16S rRNA gene amplicon sequencing and genome resolved metagenomics to identify the rhizobiome microbial and viral community. Our results demonstrate that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both, the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n =7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vMAG) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbor genes capable of contributing to carbon cycling in the rhizosphere.

microbiology↗

Effects of variability in manually contoured spinal cord masks on fMRI co-registration and interpretation

Functional magnetic resonance imaging (fMRI) of the human spinal cord (SC) is a unique non-invasive method for characterizing neurovascular responses to stimuli. Group-analysis of SC fMRI data involves co-registration of subject-level data to standard space, which requires manual masking of the cord and may result in bias of group-level SC fMRI results. To test this, we examined variability in SC masks drawn in fMRI data from 21 healthy participants from a completed study mapping responses to sensory stimuli of the C7 dermatome. Masks were drawn on temporal mean functional image by eight raters with varying levels of neuroimaging experience, and the rater from the original study acted as a reference. Spatial agreement between rater and reference masks was measured using the Dice Similarity Coefficient, and the influence of rater and dataset was examined using ANOVA. Each raters masks were used to register functional data to the PAM50 template. Gray matter-white matter signal contrast of registered functional data was used to evaluate the spatial normalization accuracy across raters. Subject- and group-level analyses of activation during left- and right-sided sensory stimuli were performed for each raters co-registered data. Agreement with the reference SC mask was associated with both rater (F(7,140) = 32.12, P < 2x10-16,{eta} 2 = 0.29) and dataset (F(20,140) = 20.58, P < 2x10-16,{eta} 2 = 0.53). Dataset variations may reflect image quality metrics: the ratio between the signal intensity of spinal cord voxels and surrounding cerebrospinal fluid was correlated with DSC results (p<0.001). As predicted, variability in the manually-drawn masks influenced spatial normalization, and GM:WM contrast in the registered data showed significant effects of rater and dataset (rater: F(8,160) = 23.57, P < 2x10-16,{eta} 2 = 0.24; dataset: F(20,160) = 22.00, P < 2x10-16,{eta} 2 = 0.56). Registration differences propagated into subject-level activation maps which showed rater-dependent agreement with the reference. Although group-level activation maps differed between raters, no systematic bias was identified. Increasing consistency in manual contouring of spinal cord fMRI data improved co-registration and inter-rater agreement in activation mapping, however our results suggest that improvements in image acquisition and post-processing are also critical to address.

neuroscience↗

Evaluation and Optimization of Motion Correction in Spinal Cord fMRI Preprocessing

Motion correction is an essential step in the preprocessing of functional magnetic resonance imaging (fMRI) data, improving the temporal signal to noise ratio (tSNR) and removing unwanted variance. Because of the characteristics of the spinal cord (non-rigidity, surrounded by moving organs), motion correction becomes especially challenging. We compared the efficiency of different motion correction protocols and suggest a preferred method for spinal cord fMRI data. Here we acquired gradient-echo echo-planar-imaging axial lumbar spinal cord fMRI data during painful mechanical stimulation of the left lower extremity of 15 healthy volunteers on a 3T scanner. We compared multiple motion correction techniques: 2D and 3D FLIRT realignment with and without slice-wise regulation, SliceCorr (implemented in the Spinal Cord Toolbox) and proposed a method 3D FLIRT in addition to Slice Regulation (SLiceReg) along the spinal cord. TSNR, image entropy, DVARS, image Sum of Absolute Differences and number of activated voxels in the spinal cord from GLM analysis to evaluate the performance of multiple motion correction procedures. The tSNR and DVARS 3D FLIRT + SLiceReg were significantly improved over other realignment methods (p<0.001). In comparison, tSNR=14.20{+/-}0.02 and DVARS=165.77{+/-}1.54 were higher than other methods. Additionally, the number of activated voxels of the statistical map in our suggested method was higher than the other realignment methods (p<0.05). Our results illustrated the proposed motion correction algorithm that integrated 3D motion correction and 2D slicewise regularization along spinal cord curvature could improve subject-level processing outputs by reducing the effects of motions. Our proposed protocols can improve subject-level analysis, especially in lumbar region that suffers from involuntary motions and signal loss due to susceptibility effect more than other spinal cord regions.

neuroscience↗