Detection and identification of single ribonucleotide monophosphates using a dual in-plane nanopore sensor made in a thermoplastic via replication.

We report the generation of ∼8 nm dual in-plane pores fabricated in a thermoplastic via nanoimprint lithography (NIL). These pores were connected in series with nanochannels, one of which served as a flight tube to allow the identification of single molecules based on their molecular-dependent apparent mobilities (i.e., dual in-plane nanopore sensor). Two different thermoplastics were investigated including poly(methyl methacrylate), PMMA, and cyclic olefin polymer, COP, as the substrate for the sensor both of which were sealed using a low glass transition cover plate (cyclic olefin co-polymer, COC) that could be thermally fusion bonded to the PMMA or COP substrate at a temperature minimizing nanostructure deformation. Unique to these dual in-plane nanopore sensors was two pores flanking each side of the nanometer flight tube (50 × 50 nm, width × depth) that was 10 µm in length. The utility of this dual in-plane nanopore sensor was evaluated to not only detect, but also identify single ribonucleotide monophosphates (rNMPs) by using the travel time (time-of-flight, ToF), the resistive pulse event amplitude, and the dwell time. In spite of the relatively large size of these in-plane pores (∼8 nm effective diameter), we could detect via resistive pulse sensing (RPS) single rNMP molecules at a mass load of 3.9 fg, which was ascribed to the unique structural features of the nanofluidic network and the use of a thermoplastic with low relative dielectric constants, which resulted in a low RMS noise level in the open pore current. Our data indicated that the identification accuracy of individual rNMPs was high, which was ascribed to an improved chromatographic contribution to the nano-electrophoresis apparent mobility. With the ToF data only, the identification accuracy was 98.3%. However, when incorporating the resistive pulse sensing event amplitude and dwell time in conjunction with the ToF and analyzed via principal component analysis (PCA), the identification accuracy reached 100%. These findings pave the way for the realization of a novel chip-based single-molecule RNA sequencing technology.

High Sensitivity Extended Nano-Coulter Counter for Detection of Viral Particles and Extracellular Vesicles.

We present a chip-based extended nano-Coulter counter (XnCC) that can detect nanoparticles affinity-selected from biological samples with low concentration limit-of-detection that surpasses existing resistive pulse sensors by 2-3 orders of magnitude. The XnCC was engineered to contain 5 in-plane pores each with an effective diameter of 350 nm placed in parallel and can provide high detection efficiency for single particles translocating both hydrodynamically and electrokinetically through these pores. The XnCC was fabricated in cyclic olefin polymer (COP) via nanoinjection molding to allow for high-scale production. The concentration limit-of-detection of the XnCC was 5.5 × 103 particles/mL, which was a 1,100-fold improvement compared to a single in-plane pore device. The application examples of the XnCC included counting affinity selected SARS-CoV-2 viral particles from saliva samples using an aptamer and pillared microchip; the selection/XnCC assay could distinguish the COVID-19(+) saliva samples from those that were COVID-19(-). In the second example, ovarian cancer extracellular vesicles (EVs) were affinity selected using a pillared chip modified with a MUC16 monoclonal antibody. The affinity selection chip coupled with the XnCC was successful in discriminating between patients with high grade serous ovarian cancer and healthy donors using blood plasma as the input sample.

DiffN Selection of Tandem Mass Spectrometry Precursors.

Current data-dependent acquisition (DDA) approaches select precursor ions for tandem mass spectrometry (MS/MS) characterization based on their absolute intensity, known as a TopN approach. Low-abundance species may not be identified as biomarkers in a TopN approach. Herein, a new DDA approach is proposed, DiffN, which uses the relative differential intensity of ions between two samples to selectively target species undergoing the largest fold changes for MS/MS. Using a dual nano-electrospray (nESI) ionization source which allows samples contained in separate capillaries to be analyzed in parallel, the DiffN approach was developed and validated with well-defined lipid extracts. A dual nESI source and DiffN DDA approach was applied to quantify the differences in lipid abundance between two colorectal cancer cell lines. The SW480 and SW620 lines represent a matched pair from the same patient: the SW480 cells from a primary tumor and the SW620 cells from a metastatic lesion. A comparison of TopN and DiffN DDA approaches on these cancer cell samples highlights the ability of DiffN to increase the likelihood of biomarker discovery and the decreased probability of TopN to efficiently select lipid species that undergo large fold changes. The ability of the DiffN approach to efficiently select precursor ions of interest makes it a strong candidate for lipidomic analyses. This DiffN DDA approach may also apply to other molecule classes (e.g., other metabolites or proteins) that are amenable to shotgun analyses.

Machine-Learning-Guided Discovery of 19F MRI Agents Enabled by Automated Copolymer Synthesis.

Modern polymer science suffers from the curse of multidimensionality. The large chemical space imposed by including combinations of monomers into a statistical copolymer overwhelms polymer synthesis and characterization technology and limits the ability to systematically study structure-property relationships. To tackle this challenge in the context of 19F magnetic resonance imaging (MRI) agents, we pursued a computer-guided materials discovery approach that combines synergistic innovations in automated flow synthesis and machine learning (ML) method development. A software-controlled, continuous polymer synthesis platform was developed to enable iterative experimental-computational cycles that resulted in the synthesis of 397 unique copolymer compositions within a six-variable compositional space. The nonintuitive design criteria identified by ML, which were accomplished by exploring <0.9% of the overall compositional space, lead to the identification of >10 copolymer compositions that outperformed state-of-the-art materials.

Simultaneous fMRI and fast-scan cyclic voltammetry bridges evoked oxygen and neurotransmitter dynamics across spatiotemporal scales.

The vascular contributions of neurotransmitters to the hemodynamic response are gaining more attention in neuroimaging studies, as many neurotransmitters are vasomodulatory. To date, well-established electrochemical techniques that detect neurotransmission in high magnetic field environments are limited. Here, we propose an experimental setting enabling simultaneous fast-scan cyclic voltammetry (FSCV) and blood oxygenation level-dependent functional magnetic imaging (BOLD fMRI) to measure both local tissue oxygen and dopamine responses, and global BOLD changes, respectively. By using MR-compatible materials and the proposed data acquisition schemes, FSCV detected physiological analyte concentrations with high temporal resolution and spatial specificity inside of a 9.4 T MRI bore. We found that tissue oxygen and BOLD correlate strongly, and brain regions that encode dopamine amplitude differences can be identified via modeling simultaneously acquired dopamine FSCV and BOLD fMRI time-courses. This technique provides complementary neurochemical and hemodynamic information and expands the scope of studying the influence of local neurotransmitter release over the entire brain.

A Generalized Potentiostat Adaptor for Multiplexed Electroanalysis.

Electrochemical measurements over an array of electrodes may be accomplished with one of three potentiostat architectures: a single-channel device which averages the signal from a number of interconnected electrodes, a multichannel device with dedicated circuits for each electrode, or a single-channel device with a multiplexer interface to isolate the signal from specific electrodes. Of these three architectures, the use of a multiplexer interface is best suited to facilitate measurements over individual electrodes without the need for large numbers of dedicated potentiostat channels. We present a versatile strategy for the development of flexible printed circuit (FPC) electrode arrays with accompanying multiplexing hardware to interface with single-channel potentiostats. The FPC array was fabricated with 78 individually addressable 0.3 mm diameter gold working electrodes and characterized using optical and scanning electron microscopy, energy dispersive spectroscopy, profilometry, impedance spectroscopy, and cyclic voltammetry to investigate the morphology, elemental composition, height profile, impedance characteristics, and electrochemical response, respectively. Interfacing the FPC array via a simple connector with three 32-channel ADG731 multiplexers permitted electrochemical measurements using single-channel commercial potentiostats. Voltammetric experiments were conducted to demonstrate the reliability, stability, and reproducibility of the FPC array and interfacing hardware. The combination of these devices represents an accessible hardware platform with robust, functionalizable electrodes, a simple connection interface with commercial potentiostats, and a low cost through the use of off-the-shelf components. Our reported strategy holds great promise to facilitate multiplexed electroanalysis in next-generation sensors to increase statistical sample size and multianalyte detection capabilities.

Resting Cerebral Blood Flow After Exercise Training in Mild Cognitive Impairment.

BACKGROUND: Exercise training has been associated with greater cerebral blood flow (CBF) in cognitively normal older adults (CN). Alterations in CBF, including compensatory perfusion in the prefrontal cortex, may facilitate changes to the brain's neural infrastructure. OBJECTIVE: To examine the effects of a 12-week aerobic exercise intervention on resting CBF and cognition in CN and those with mild cognitive impairment (MCI). We hypothesized individuals with MCI (versus CN) would exhibit greater whole brain CBF at baseline and that exercise would mitigate these differences. We also expected CBF changes to parallel cognitive improvements. METHODS: Before and after a 12-week exercise intervention, 18 CN and 17 MCI participants (aged 61-88) underwent aerobic fitness testing, neuropsychological assessment, and an MRI scan. Perfusion-weighted images were collected using a GE 3T MR system. Repeated measures analyses of covariance were used to test within- and between-group differences over time, followed by post-hoc analyses to examine links between CBF changes and cognitive improvement. RESULTS: At baseline, individuals with MCI (versus CN) exhibited significantly elevated perfusion in the left insula. Twelve weeks of aerobic exercise reversed this discrepancy. Additionally, exercise improved working memory (measured by the Rey Auditory Verbal Learning Test) and verbal fluency (measured by the Controlled Oral Word Association Test) and differentially altered CBF depending on cognitive status. Among those with MCI, decreased CBF in the left insula and anterior cingulate cortex was associated with improved verbal fluency. CONCLUSIONS: Exercise training alters CBF and improves cognitive performance in older adults with and without cognitive impairment. Future studies must evaluate the mediating effects of CBF on the association between exercise training and cognition.

An implantable multimodal sensor for oxygen, neurotransmitters, and electrophysiology during spreading depolarization in the deep brain.

Brain tissue injury is often accompanied by spreading depolarization (SD) events, marked by widespread cellular depolarization and cessation of neuronal firing. SD recruits viable tissue into the lesion, making it a focus for intervention. During SD, drastic fluctuations occur in ion gradients, extracellular neurotransmitter concentrations, cellular metabolism, and cerebral blood flow. Measuring SD requires a multimodal approach to capture the array of changes. However, the use of multiple sensors can inflict tissue damage. Here, we use carbon-fiber microelectrodes to characterize several aspects of SD with a single, minimally invasive sensor in the deep brain region of the nucleus accumbens. Fast-scan cyclic voltammetry detects large changes in oxygen, which reflect the balance between cerebral blood flow and energy consumption, and also supraphysiological release of electroactive neurotransmitters (i.e., dopamine). We verify waves of SD with concurrent single-unit or DC potential electrophysiological recordings. The single-unit recordings reveal bursts of action potentials followed by inactivity. The DC potentials exhibit a slow negative voltage shift in the extracellular space indicative of wide-spread cellular depolarization. Here, we characterize the multiple modalities of our sensor and demonstrate its utility for improved SD recordings.

Neural effects of cognitive control load on auditory selective attention.

Whether and how working memory disrupts or alters auditory selective attention is unclear. We compared simultaneous event-related potentials (ERP) and functional magnetic resonance imaging (fMRI) responses associated with task-irrelevant sounds across high and low working memory load in a dichotic-listening paradigm. Participants performed n-back tasks (1-back, 2-back) in one ear (Attend ear) while ignoring task-irrelevant speech sounds in the other ear (Ignore ear). The effects of working memory load on selective attention were observed at 130-210ms, with higher load resulting in greater irrelevant syllable-related activation in localizer-defined regions in auditory cortex. The interaction between memory load and presence of irrelevant information revealed stronger activations primarily in frontal and parietal areas due to presence of irrelevant information in the higher memory load. Joint independent component analysis of ERP and fMRI data revealed that the ERP component in the N1 time-range is associated with activity in superior temporal gyrus and medial prefrontal cortex. These results demonstrate a dynamic relationship between working memory load and auditory selective attention, in agreement with the load model of attention and the idea of common neural resources for memory and attention.

Flexible software platform for fast-scan cyclic voltammetry data acquisition and analysis.

Over the last several decades, fast-scan cyclic voltammetry (FSCV) has proved to be a valuable analytical tool for the real-time measurement of neurotransmitter dynamics in vitro and in vivo. Indeed, FSCV has found application in a wide variety of disciplines including electrochemistry, neurobiology, and behavioral psychology. The maturation of FSCV as an in vivo technique led users to pose increasingly complex questions that require a more sophisticated experimental design. To accommodate recent and future advances in FSCV application, our lab has developed High Definition Cyclic Voltammetry (HDCV). HDCV is an electrochemical software suite that includes data acquisition and analysis programs. The data collection program delivers greater experimental flexibility and better user feedback through live displays. It supports experiments involving multiple electrodes with customized waveforms. It is compatible with transistor-transistor logic-based systems that are used for monitoring animal behavior, and it enables simultaneous recording of electrochemical and electrophysiological data. HDCV analysis streamlines data processing with superior filtering options, seamlessly manages behavioral events, and integrates chemometric processing. Furthermore, analysis is capable of handling single files collected over extended periods of time, allowing the user to consider biological events on both subsecond and multiminute time scales. Here we describe and demonstrate the utility of HDCV for in vivo experiments.

Acute and subacute changes in neural activation during the recovery from sport-related concussion.

To study the natural recovery from sports concussion, 12 concussed high school football athletes and 12 matched uninjured teammates were evaluated with symptom rating scales, tests of postural balance and cognition, and an event-related fMRI study during performance of a load-dependent working memory task at 13 h and 7 weeks following injury. Injured athletes showed the expected postconcussive symptoms and cognitive decline with decreased reaction time (RT) and increased RT variability on a working memory task during the acute period and an apparent full recovery 7 weeks later. Brain activation patterns showed decreased activation of right hemisphere attentional networks in injured athletes relative to controls during the acute period with a reversed pattern of activation (injured > controls) in the same networks at 7 weeks following injury. These changes coincided with a decrease in self-reported postconcussive symptoms and improved cognitive test performance in the injured athletes. Results from this exploratory study suggest that decreased activation of right hemisphere attentional networks mediate the cognitive changes and postconcussion symptoms observed during the acute period following concussion. Conversely, improvement in cognitive functioning and postconcussive symptoms during the subacute period may be mediated by compensatory increases in activation of this same attentional network.

Semantic memory functional MRI and cognitive function after exercise intervention in mild cognitive impairment.

Mild cognitive impairment (MCI) is associated with early memory loss, Alzheimer's disease (AD) neuropathology, inefficient or ineffective neural processing, and increased risk for AD. Unfortunately, treatments aimed at improving clinical symptoms or markers of brain function generally have been of limited value. Physical exercise is often recommended for people diagnosed with MCI, primarily because of its widely reported cognitive benefits in healthy older adults. However, it is unknown if exercise actually benefits brain function during memory retrieval in MCI. Here, we examined the effects of exercise training on semantic memory activation during functional magnetic resonance imaging (fMRI). Seventeen MCI participants and 18 cognitively intact controls, similar in sex, age, education, genetic risk, and medication use, volunteered for a 12-week exercise intervention consisting of supervised treadmill walking at a moderate intensity. Both MCI and control participants significantly increased their cardiorespiratory fitness by approximately 10% on a treadmill exercise test. Before and after the exercise intervention, participants completed an fMRI famous name discrimination task and a neuropsychological battery, Performance on Trial 1 of a list-learning task significantly improved in the MCI participants. Eleven brain regions activated during the semantic memory task showed a significant decrease in activation intensity following the intervention that was similar between groups (p-values ranged 0.048 to 0.0001). These findings suggest exercise may improve neural efficiency during semantic memory retrieval in MCI and cognitively intact older adults, and may lead to improvement in cognitive function. Clinical trials are needed to determine if exercise is effective to delay conversion to AD.

Perceptual demand modulates activation of human auditory cortex in response to task-irrelevant sounds.

In the visual modality, perceptual demand on a goal-directed task has been shown to modulate the extent to which irrelevant information can be disregarded at a sensory-perceptual stage of processing. In the auditory modality, the effect of perceptual demand on neural representations of task-irrelevant sounds is unclear. We compared simultaneous ERPs and fMRI responses associated with task-irrelevant sounds across parametrically modulated perceptual task demands in a dichotic-listening paradigm. Participants performed a signal detection task in one ear (Attend ear) while ignoring task-irrelevant syllable sounds in the other ear (Ignore ear). Results revealed modulation of syllable processing by auditory perceptual demand in an ROI in middle left superior temporal gyrus and in negative ERP activity 130-230 msec post stimulus onset. Increasing the perceptual demand in the Attend ear was associated with a reduced neural response in both fMRI and ERP to task-irrelevant sounds. These findings are in support of a selection model whereby ongoing perceptual demands modulate task-irrelevant sound processing in auditory cortex.

The effect of movement rate and complexity on functional magnetic resonance signal change during pedaling.

We used functional magnetic resonance imaging (fMRI) to record human brain activity during slow (30 RPM), fast (60 RPM), passive (30 RPM), and variable rate pedaling. Ten healthy adults participated. After identifying regions of interest, the intensity and volume of brain activation in each region was calculated and compared across conditions (p < .05). Results showed that the primary sensory and motor cortices (S1, M1), supplementary motor area (SMA), and cerebellum (Cb) were active during pedaling. The intensity of activity in these areas increased with increasing pedaling rate and complexity. The Cb was the only brain region that showed significantly lower activity during passive as compared with active pedaling. We conclude that M1, S1, SMA, and Cb have a role in modifying continuous, bilateral, multijoint lower extremity movements. Much of this brain activity may be driven by sensory signals from the moving limbs.

Does physical activity influence semantic memory activation in amnestic mild cognitive impairment?

The effect of physical activity (PA) on functional brain activation for semantic memory in amnestic mild cognitive impairment (aMCI) was examined using event-related functional magnetic resonance imaging during fame discrimination. Significantly greater semantic memory activation occurred in the left caudate of High- versus Low-PA patients, (P=0.03), suggesting PA may enhance memory-related caudate activation in aMCI.

Detecting changes in human cerebral blood flow after acute exercise using arterial spin labeling: implications for fMRI.

The use of arterial spin labeling to measure cerebral blood flow (CBF) after acute exercise has not been reported. The aims of this study were to examine: (1) the optimal inversion time to detect changes in CBF after acute exercise and (2) if acute exercise alters CBF in the motor cortex at rest or during finger-tapping. Subjects (n=5) performed 30 min of moderate intensity exercise on an electronically braked cycle ergometer (perceived exertion 'somewhat hard'). Before and after exercise, relative CBF was measured using multiple inversion time (TI) pulsed arterial spin labeling (PASL). Two multiple TI runs were obtained at rest and during 4 Hz finger-tapping. Four inversion times (675, 975, 1275, and 1,575 ms) were acquired per run, with 20 interleaved pairs of tag and control images per inversion time (320 s run). The results indicated that global CBF increased approximately 20% following exercise, with significant differences observed at an inversion time of 1,575 ms (p<.05). Finger-tapping induced CBF in the motor cortex significantly increased from before to after exercise at TI=1,575 ms (p<.01). These findings suggest changes in human cerebral blood flow that result from acute moderate intensity exercise can be detected afterwards using PASL at 3T with an inversion time of 1,575 ms. The effect of prior acute exercise to increase motor cortex CBF during the performance of a motor task suggests future use of indices of functional activation should account for exercise-induced changes in cardio-pulmonary physiology and CBF.

Upper limb function and brain reorganization after constraint-induced movement therapy in children with hemiplegia.

OBJECTIVE: The aims of this study were to (1) investigate the effectiveness of CIMT for children with hemiplegia, (2) determine the feasibility of using fMRI for describing brain activity patterns before and after CIMT and (3) describe changes in brain reorganization after CIMT in children with hemiplegia using fMRI. DESIGN: Before and after study with one group. METHODS: Ten children aged 7-14 years (M = 11.0, SD = 2.5) with hemiplegia received CIMT over a 2-week period using a before and after design. Clinical measures included the Melbourne Assessment of Unilateral Upper Limb Function, upper limb kinematics and parent questionnaire. Children were measured with fMRI before and after CIMT. RESULTS: Findings showed that CIMT may be effective at improving upper limb function in some, but not all children; those children with a moderate degree of impairment seemed to benefit the most. fMRI findings correlated moderately with clinical measures. CONCLUSION: Although unique challenges with fMRI data collection exist for this population, it provides potentially valuable information to better understand mechanisms of change after interventions such as CIMT.

Development of an MR safe reach and grasp movement evaluation system to study brain activation patterns after stroke.

An MR safe apparatus is important for the for monitoring of tasks in the magnetic resonance (MR) environment. This paper describes the development of an MR safe movement evaluation system to measure the hand grasp and elbow flexion/extension movements. The system will be used to monitor motor performance in the fMRI environment and assess functional and motor impairment level pre and post robot-assisted therapy.

A novel technique for examining human brain activity associated with pedaling using fMRI.

Advances in neural imaging technologies, such as functional magnetic resonance imaging (fMRI), have made it possible to obtain images of human brain activity during motor tasks. However, technical challenges have made it difficult to image the brain during multijoint lower limb movements like those involved in locomotion. We developed an MR compatible pedaling device and recorded human brain activity associated with rhythmic, alternating flexion and extension of the lower extremities. Ten volunteers pedaled at 30 RPM while recording fMRI signals in a GE 3T short bore MR scanner. We utilized a block design consisting of 3 runs of pedaling, each lasting 4 min. In a single run, subjects pedaled for 30 s and then rested for 30 s. This sequence was repeated 4 times. Conventional fMRI processing techniques, that correlate the entire BOLD signal with standard model, did not extract physiologically meaningful signal, likely due to magnetic field distortion caused by leg movement. Hence, we examined only the portion of the blood-oxygen-level dependent (BOLD) signal during movement-free periods. This technique takes advantage of the delayed nature of the BOLD signal and fits the falling portion of the signal after movement has stopped with a standard model. Using this approach, we observed physiologically plausible brain activity patterns associated with pedaling in the primary and secondary sensory and motor cortices and the cerebellum. To our knowledge, this is the first time that human brain activity associated with pedaling has been recorded with fMRI. This technique may be useful for advancing our understanding of supraspinal control of locomotor-like movements in health and disease.

Inhibitory control test is a simple method to diagnose minimal hepatic encephalopathy and predict development of overt hepatic encephalopathy.

OBJECTIVES: To compare inhibitory control test (ICT), a simple/rapid test of attention, to a standard psychometric battery (SPT) to diagnose minimal hepatic encephalopathy (MHE) and predict development of overt hepatic encephalopathy (OHE) in cirrhotic patients. METHODS: Fifty nonalcoholic cirrhotics and 50 age/educational-status-matched controls were given ICT and SPT in the same sitting. Performance impaired beyond two standard deviations of controls was considered MHE in cirrhotics. ICT results (lure/target response and lures/person) were compared between controls and cirrhotics and within cirrhotics with/without MHE. Receiver-operating characteristic analysis was used to study ICT for MHE diagnosis. Twenty subjects were administered SPT and ICT twice to assess test-retest reliability. All cirrhotics were followed routinely for the development of OHE. RESULTS: Cirrhotics performed worse than controls on SPT and ICT. Using SPT, 39 cirrhotics had MHE. ICT was administered faster than SPT (15 vs 37 min). Cirrhotics with MHE had significantly higher lure (28%vs 3%) and lower target response (91%vs 96%) compared with those without MHE. Lure/person >5 had 90% sensitivity/specificity for MHE diagnosis. AUC for receiver-operating characteristic for lures alone was 95.8%. Lure and target responses were highly correlated (r= 0.9) between sessions showing high test-retest reliability. Five (10%) patients developed OHE on f/u of 26 +/- 10 months; all five had been diagnosed with MHE using ICT and SPT. None of the five patients with discordant results on SPT and ICT developed OHE. CONCLUSIONS: ICT has good sensitivity/specificity for MHE diagnosis, is reliable and is equivalent to SPT for predicting OHE development.