T cell activation is governed through T cell receptors (TCRs), heterodimers of two sequence-variable chains (often an α and β chain) that synergistically recognize antigen fragments presented on cell surfaces. Despite this, there only exist repositories dedicated to collecting single-chain, not paired-chain, TCR sequence data. We addressed this gap by creating the Observed TCR Space (OTS) database, a source of consistently processed and annotated, full-length, paired-chain TCR sequences. Currently, OTS contains 5.35 million redundant (1.63 million non-redundant), predominantly human sequences from across 50 studies and at least 75 individuals. Using OTS, we identify pairing biases, public TCRs, and distinct chain coherence patterns relative to antibodies. We also release a paired-chain TCR language model, providing paired embedding representations and a method for residue in-filling conditional on the partner chain. OTS will be updated as a central community resource and is freely downloadable and available as a web application.

While the shape of cortical oscillations is increasingly recognised to be physiologically and functionally informative, its relevance to the aging motor system has not been established. We therefore examined the shape of alpha and beta band oscillations recorded at rest, as well as during performance of simple and go/no-go reaction time tasks, in 33 young (23.3 ± 2.9 years, 27 females) and 27 older (60.0 ± 5.2 years, 23 females) adults. The shape of individual oscillatory cycles was characterised using a recently developed pipeline involving empirical mode decomposition, before being decomposed into waveform motifs using principal component analysis. This revealed four principal components that were uniquely influenced by task and/or age. These described specific dimensions of shape and tended to be modulated during the reaction phase of each task. Our results suggest that although oscillation shape is task-dependent, the nature of this effect is altered by advancing age, possibly reflecting alterations in cortical activity. These outcomes demonstrate the utility of this approach for understanding the neurophysiological effects of ageing.

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Exercise is a potent stimulus for combatting skeletal muscle ageing. To study the effects of exercise on muscle in a preclinical setting, we developed a combined endurance-resistance training stimulus for mice called progressive weighted wheel running (PoWeR). PoWeR improves molecular, biochemical, cellular and functional characteristics of skeletal muscle and promotes aspects of partial epigenetic reprogramming when performed late in life (22-24 months of age). In this investigation, we leveraged pan-mammalian DNA methylome arrays and tandem mass-spectrometry proteomics in skeletal muscle to provide detailed information on late-life PoWeR adaptations in female mice relative to age-matched sedentary controls (n = 7-10 per group). Differential CpG methylation at conserved promoter sites was related to transcriptional regulation genes as well as Nr4a3, Hes1 and Hox genes after PoWeR. Using a holistic method of -omics integration called binding and expression target analysis (BETA), methylome changes were associated with upregulated proteins related to global and mitochondrial translation after PoWeR (P = 0.03). Specifically, BETA implicated methylation control of ribosomal, mitoribosomal, and mitochondrial complex I protein abundance after training. DNA methylation may also influence LACTB, MIB1 and UBR4 protein induction with exercise - all are mechanistically linked to muscle health. Computational cistrome analysis predicted several transcription factors including MYC as regulators of the exercise trained methylome-proteome landscape, corroborating prior late-life PoWeR transcriptome data. Correlating the proteome to muscle mass and fatigue resistance revealed positive relationships with VPS13A and NPL levels, respectively. Our findings expose differential epigenetic and proteomic adaptations associated with translational regulation after PoWeR that could influence skeletal muscle mass and function in aged mice. KEY POINTS: Late-life combined endurance-resistance exercise training from 22-24 months of age in mice is shown to improve molecular, biochemical, cellular and in vivo functional characteristics of skeletal muscle and promote aspects of partial epigenetic reprogramming and epigenetic age mitigation. Integration of DNA CpG 36k methylation arrays using conserved sites (which also contain methylation ageing clock sites) with exploratory proteomics in skeletal muscle extends our prior work and reveals coordinated and widespread regulation of ribosomal, translation initiation, mitochondrial ribosomal (mitoribosomal) and complex I proteins after combined voluntary exercise training in a sizeable cohort of female mice (n = 7-10 per group and analysis). Multi-omics integration predicted epigenetic regulation of serine β-lactamase-like protein (LACTB - linked to tumour resistance in muscle), mind bomb 1 (MIB1 - linked to satellite cell and type 2 fibre maintenance) and ubiquitin protein ligase E3 component N-recognin 4 (UBR4 - linked to muscle protein quality control) after training. Computational cistrome analysis identified MYC as a regulator of the late-life training proteome, in agreement with prior transcriptional analyses. Vacuolar protein sorting 13 homolog A (VPS13A) was positively correlated to muscle mass, and the glycoprotein/glycolipid associated sialylation enzyme N-acetylneuraminate pyruvate lyase (NPL) was associated to in vivo muscle fatigue resistance.

Implicit visuomotor sequence learning is crucial for acquiring skills that result in automated behaviors. The oscillatory dynamics underpinning this learning process are not well understood. To address this gap, the current study employed electroencephalography with a medium-density array (64 electrodes) to investigate oscillatory activity associated with implicit visuomotor sequence learning in the Serial Reaction Time task. In the task, participants unknowingly learn a series of finger movements. Eighty-five healthy adults participated in the study. Analyses revealed that theta activity at the vertex and alpha/beta activity over the motor areas decreased over the course of learning. No associations between alpha/beta and theta power were observed. These findings are interpreted within a dual-process framework: midline theta activity is posited to regulate top-down attentional processes, whereas beta activity from motor areas underlies the bottom-up encoding of sensory information from movement. From this model, we suggest that during implicit visuomotor sequence learning, top-down processes become disengaged (indicated by a reduction in theta activity), and modality specific bottom-up processes encode the motor sequence (indicated by a reduction in alpha/beta activity).

UNASSIGNED: Acute hemorrhage decreases blood pressure (BP) and sometimes causes hypovolemic shock. At this time, peripheral arteries are supposed to contract and increase peripheral vascular resistance to raise BP. However, there has not been an adequate index of a degree of arterial stiffness. We assessed changes in arterial stiffness during rapid bleeding using new BP-independent vascular indices, aBeta and ifBeta, determined by applying the cardio-ankle vascular index theory to the elastic (aorta) and muscular (common iliac-femoral) arteries, respectively, in rabbits.
UNASSIGNED: Eleven Japanese white male rabbits were fixed at the supine position under pentobarbital anesthesia. Fifteen percent of the total blood volume was depleted at a rate of 2 mL/kg/min for 6 min; 15 min later, the withdrawn blood was re-transfused at the same rate. Pressure waves at the origin of the aorta (oA), distal end of the abdominal aorta (dA), distal end of the left common iliac artery (fA), and flow waves at oA were measured simultaneously. Beta was calculated using the following formula: beta = 2ρ/PP × ln(SBP/DBP) × PWV2, where ρ, SBP, DBP, and PP are blood density, systolic, diastolic, and pulse pressures, respectively. aBeta, ifBeta, and aortic-iliac-femoral beta (aifBeta) were calculated using aPWV, ifPWV, and aifPWV, respectively.
UNASSIGNED: BP declined significantly at oA, dA, and fA during the acute bleeding. aBeta and aifBeta increased significantly from 3.7 and 5.0 before the bleeding (control) to 5.0 (about 34%) and 6.3 (about 26%) on average, while ifBeta decreased significantly from 20.5 before the bleeding to 17.1 (about 17%) after the completion of the bleeding. Reverse reactions of those indices were observed by transfusing the removed blood.
UNASSIGNED: Total arterial stiffness (aifBeta) increased; however, the elastic and muscular arteries stiffened and softened during the bleeding, respectively. These results would give useful diagnostic information during fall in BP.

Parkinson\'s disease (PD) is a progressive neurodegenerative disorder primarily associated with motor dysfunctions. By the time of definitive diagnosis, about 60% of dopaminergic neurons have already been lost; moreover, even if dopaminergic drugs are highly effective in symptoms control, they only help maintaining a near-healthy condition when started as soon as possible. Therefore, interest in identifying early biomarkers of PD has grown in recent years, especially using neurophysiological techniques such as electroencephalography (EEG). This study aims to investigate brain complexity differences in PD patients compared to healthy controls, focusing on the beta band using approximate entropy (ApEn) analysis of resting-state EEG recordings. Sixty participants were recruited, including 25 PD patients and 35 healthy elderly subjects, matched for age and gender. EEG were recorded for each participant and ApEn values were computed in the beta 1 (13-20 Hz) and beta 2 (20-30 Hz) frequency bands for each EEG-channel and for ROIs. PD patients showed statistically lower ApEn values compared to controls in both beta 1 and beta 2 bands. Regarding electrodes analysis, beta 1 band alterations were found in frontocentral areas, while beta 2 band alterations were observed in centroparietal and frontocentral areas. Considering ROIs, statistically lower ApEn values for PD patients has been reported in central and parietal ROIs in the beta 2 band. Complexity reduction in these areas may underlie beta oscillatory activity dysfunction, reflecting impaired cortical mechanisms associated with motor dysfunction in PD. The results suggest that ApEn analysis of resting EEG activity may serve as a potential tool for early PD detection. Further studies are necessary to validate this approach in PD diagnosis and rehabilitation planning.

The relationship between brainwave oscillations and Attention-Deficit/Hyperactivity Disorder (ADHD)-related cognitive challenges is a trending proposition in the field of Cognitive Neuroscience. Studies suggest the role of brainwave oscillations in the symptom expressions of ADHD-diagnosed children. Intervention studies have further suggested the scope of brain stimulation techniques in improving cognition. The current manuscript explored the effect of changes in the brainwaves post-sensory entrainment on cognitive performance of children. We calculated each participant\'s brainwave difference and ratios of theta, alpha, and beta power after the entrainment sessions. Further, we explored possible correlations between these values and the psychometric scores. The beta resting state showed the strongest association with selective attention performance of all participants. Theta-beta ratio (TBR) showed an inverse correlation with selective attention and working memory performances. The theta frequency was associated with decreased working performance in children without ADHD. Our findings also suggest a predominant role of TBR than the theta-alpha ratio in determining the cognitive performance of children with ADHD. The individual differences in the entrainment reception were attributed to the participant\'s age, IQ, and their innate baseline frequencies. The implications of our findings can initiate substantiating brainwave-based entrainment sessions as a therapeutic modality to improve cognition among children.

Parkinson\'s disease (PD) is a progressive neurological disorder that is typically characterized by a range of motor dysfunctions, and its impact extends beyond physical abnormalities into emotional well-being and cognitive symptoms. The loss of dopaminergic neurons in the substantia nigra pars compacta (SNc) leads to an array of dysfunctions in the functioning of the basal ganglia (BG) circuitry that manifests into PD. While active research is being carried out to find the root cause of SNc cell death, various therapeutic techniques are used to manage the symptoms of PD. The most common approach in managing the symptoms is replenishing the lost dopamine in the form of taking dopaminergic medications such as levodopa, despite its long-term complications. Another commonly used intervention for PD is deep brain stimulation (DBS). DBS is most commonly used when levodopa medication efficacy is reduced, and, in combination with levodopa medication, it helps reduce the required dosage of medication, prolonging the therapeutic effect. DBS is also a first choice option when motor complications such as dyskinesia emerge as a side effect of medication. Several studies have also reported that though DBS is found to be effective in suppressing severe motor symptoms such as tremors and rigidity, it has an adverse effect on cognitive capabilities. Henceforth, it is important to understand the exact mechanism of DBS in alleviating motor symptoms. A computational model of DBS stimulation for motor symptoms will offer great insights into understanding the mechanisms underlying DBS, and, along this line, in our current study, we modeled a cortico-basal ganglia circuitry of arm reaching, where we simulated healthy control (HC) and PD symptoms as well as the DBS effect on PD tremor and bradykinesia. Our modeling results reveal that PD tremors are more correlated with the theta band, while bradykinesia is more correlated with the beta band of the frequency spectrum of the local field potential (LFP) of the subthalamic nucleus (STN) neurons. With a DBS current of 220 pA, 130 Hz, and a 100 microsecond pulse-width, we could found the maximum therapeutic effect for the pathological dynamics simulated using our model using a set of parameter values. However, the exact DBS characteristics vary from patient to patient, and this can be further studied by exploring the model parameter space. This model can be extended to study different DBS targets and accommodate cognitive dynamics in the future to study the impact of DBS on cognitive symptoms and thereby optimize the parameters to produce optimal performance effects across modalities. Combining DBS with rehabilitation is another frontier where DBS can reduce symptoms such as tremors and rigidity, enabling patients to participate in their therapy. With DBS providing instant relief to patients, a combination of DBS and rehabilitation can enhance neural plasticity. One of the key motivations behind combining DBS with rehabilitation is to expect comparable results in motor performance even with milder DBS currents.

BACKGROUND: Despite substantial progress in investigating its psychophysical complexity, tinnitus remains a scientific and clinical enigma. The present study, through an ecological and multidisciplinary approach, aims to identify associations between electroencephalographic (EEG) and psycho-audiological variables.
METHODS: EEG beta activity, often related to stress and anxiety, was acquired from 12 tinnitus patients (TIN group) and 7 controls (CONT group) during an audio cognitive task and at rest. We also investigated psychological (SCL-90-R; STAI-Y; BFI-10) and audiological (THI; TQ12-I; Hyperacusis) variables using non-parametric statistics to assess differences and relationships between and within groups.
RESULTS: In the TIN group, frontal beta activity positively correlated with hyperacusis, parietal activity, and trait anxiety; the latter is also associated with depression in CONT. Significant differences in paranoid ideation and openness were found between groups.
CONCLUSIONS: The connection between anxiety trait, beta activity in the fronto-parietal cortices and hyperacusis provides insights into brain functioning in tinnitus patients, offering quantitative descriptions for clinicians and new multidisciplinary treatment hypotheses.