Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling of synaptic interactions between two brainstem half-centre oscillators that coordinate breathing and swallowing

Respiration and swallowing are vital orofacial motor behaviours that require the coordination of the activity of two brainstem central pattern generators (r-CPG, sw-CPG). Here, we use computational modelling to further elucidate the neural substrate for breathing-swallowing coordination. We progressively construct several computational models of the breathing-swallowing circuit, starting from two interacting half-centre oscillators for each CPG. The models are based exclusively on neuronal nodes with spike-frequency adaptation, having a parsimonious description of intrinsic properties. These basic models undergo a stepwise integration of synaptic connectivity between central sensory relay, sw- and r-CPG neuron populations to match experimental data obtained in a perfused brainstem preparation. In the model, stimulation of the superior laryngeal nerve (SLN, 10s) reliably triggers sequential swallowing with concomitant glottal closure and suppression of inspiratory activity, consistent with the motor pattern in experimental data. Short SLN stimulation (100ms) evokes single swallows and respiratory phase resetting yielding similar experimental and computational phase response curves. Subsequent phase space analysis of model dynamics provides further understanding of SLN-mediated respiratory phase resetting. Consistent with experiments, numerical circuit-busting simulations show that deletion of ponto-medullary synaptic interactions triggers apneusis and eliminates glottal closure during sequential swallowing. Additionally, systematic variations of the synaptic strengths of distinct network connections predict vulnerable network connections that can mediate clinically relevant breathing-swallowing disorders observed in the elderly and patients with neurodegenerative disease. Thus, the present model provides novel insights that can guide future experiments and the development of efficient treatments for prevalent breathing-swallowing disorders. Key points The coordination of breathing and swallowing depends on synaptic interactions between two functionally distinct central pattern generators (CPGs) in the dorsal and ventral brainstem. We model both CPGs as half-centre oscillators with spike-frequency adaptation to identify the minimal connectivity sufficient to mediate physiologic breathing-swallowing interactions. The resultant computational model(s) can generate sequential swallowing patterns including concomitant glottal closure during simulated 10s stimulation of the superior laryngeal nerve (SLN) consistent with experimental data. In silico, short (100 ms) SLN stimulation triggers a single swallow which modulates the respiratory cycle duration consistent with experimental recordings. By varying the synaptic connectivity strengths between the two CPGs and the sensory relay neurons, and by inhibiting specific nodes of the network, the model predicts vulnerable network connections that may mediate clinically relevant breathing-swallowing disorders.
Heat Shock Factor 1 (HSF1) as a new tethering factor for ESR1 supporting its action in breast cancer

Heat shock factor 1 (HSF1), a key regulator of transcriptional responses to proteotoxic stress, was recently linked to estrogen (E2) signaling through ESR1. We found that an HSF1 deficiency could lead to the inhibition of the mitogenic action of E2 in breast cancer cells. The stimulatory effect of E2 on the transcriptome is weaker in HSF1-deficient cells, in part due to the higher basal expression of E2-dependent genes, which correlates with the enhanced binding of unliganded ESR1 to chromatin. HSF1 and ESR1 can cooperate directly in E2-stimulated regulation of transcription, and HSF1 potentiates the action of ESR1 through a mechanism involving chromatin reorganization. Analyses of data from the TCGA database indicate that HSF1 increases the transcriptome diversity in ER-positive breast cancer and can enhance the genomic action of ESR1. Moreover, ESR1 and HSF1 are only prognostic when analyzed together (the worst prognosis for ER−/HSF1high cancers).
Increased mitochondrial activity upon CatSper channel activation is required for sperm capacitation

To fertilize an oocyte, sperm must become hyperactive. However, whether they obtain ATP for hyperactivated motility via glycolysis or mitochondrial respiration is unclear. Here, high-resolution respirometry, flow cytometry, and confocal microscopy experiments revealed that mitochondrial respiration and membrane potential increased during mouse sperm capacitation. Treatment with inhibitors of mitochondrial respiration prevented sperm from hyperactivating and fertilizing an oocyte. Mitochondrial respiration was impaired in sperm from mice lacking the calcium channel CatSper. We developed a method to image mitochondrial calcium in sperm and found that CatSper activation led to increased mitochondrial calcium concentration. Finally, treating sperm with an inhibitor of mitochondrial calcium import impaired mitochondrial function and sperm hyperactivation. Together, our results uncover a new role of sperm mitochondria and reveal a new pathway connecting calcium influx through CatSper to mitochondrial activity and the sperm hyperactivation required to fertilize an oocyte. Summary The source of ATP for sperm hyperactivation is unclear. Ferreira et al. show that mitochondrial activity increases during, and is required for, hyperactivation and fertilization ability. Increased mitochondrial activity depends on calcium influx through the channel CatSper.
Optimizing network neuroscience computation of individual differences in human spontaneous brain activity for test-retest reliability

A rapidly emerging application of network neuroscience in neuroimaging studies has provided useful tools to understand individual differences in intrinsic brain function by mapping spontaneous brain activity, namely intrinsic functional network neuroscience (ifNN). However, the variability of methodologies applied across the ifNN studies - with respect to node definition, edge construction, and graph measurements-makes it difficult to directly compare findings and also challenging for end users to select the optimal strategies for mapping individual differences in brain networks. Here, we aim to provide a benchmark for best ifNN practices by systematically comparing the measurement reliability of individual differences under different ifNN analytical strategies using the test-retest design of the Human Connectome Project. The results uncovered four essential principles to guide ifNN studies: 1) use a whole brain parcellation to define network nodes, including subcortical and cerebellar regions, 2) construct functional networks using spontaneous brain activity in multiple slow bands, 3) optimize topological economy of networks at individual level, 4) characterise information flow with specific metrics of integration and segregation. We built an interactive online resource of reliability assessments for future ifNN (ibraindata.com/research/ifNN). AUTHOR SUMMARY It is an essential mission for neuroscience to understand the individual differences in brain function. Graph or network theory offer novel methods of network neuroscience to address such a challenge. This article documents optimal strategies on the test-retest reliability of measuring individual differences in intrinsic brain networks of spontaneous activity. The analytical pipelines are identified to optimize for highly reliable, individualized network measurements. These pipelines optimize network metrics for high inter-individual variances and low inner-individual variances by defining network nodes with whole-brain parcellations, deriving the connectivity with spontaneous high-frequency slow-band oscillations, constructing brain graphs with topology-based methods for edge filtering, and favoring multi-level or multi-modal metrics. These psychometric findings are critical for translating the functional network neuroscience into clinical or other personalized practices requiring neuroimaging markers.
A short report on optimization of nucleic acid probes by DNA microarray synthesis and next generation sequencing

Introduction Recent development in oligonucleotide synthesis and DNA sequencing technologies have facilitated advancements for application of the human genome sequencing project into the clinics and routine research thus advance human health and our understanding of human biology. Examples are exome sequencing (1), CRISPR genome editing (2) and MPRA (3,4). Aside from analysis of liquid biopsies, sample-derived cell lines, tissue imaging and investigation of molecular events in situ (5, 6, 7) also provides a means to retrieve biological information however argument on specificity from the secondary labels. Present study built on previous work on utilizing several molecular biology tools, such as restriction enzymes (9) and rolling circle amplification (RCA) for enhancing signal-to-noise ratio in a detection assay (8) – a novel probe-type 2fold probe is developed to generate a single strand circular reporter molecule upon target recognition and multi-step enzymatic conversion. We specifically investigated probe performance by varying a 9-nt sequence within the stem structure at single nucleotide resolution and in library fashion.
Rpl24Bst mutation suppresses colorectal cancer by promoting eEF2 phosphorylation via eEF2K

Increased protein synthesis supports the rapid proliferation associated with cancer. The Rpl24Bst mutant mouse reduces the expression of the ribosomal protein RPL24 and has been used to suppress translation and limit tumorigenesis in multiple mouse models of cancer. Here we show that Rpl24Bst also suppresses tumorigenesis and proliferation in a model of colorectal cancer with two common patient mutations, Apc and Kras. In contrast to previous reports, Rpl24Bst mutation has no effect on ribosomal subunit abundance but suppresses translation elongation through phosphorylation of eEF2, reducing protein synthesis by 40% in tumour cells. Ablating eEF2 phosphorylation in Rpl24Bst mutant mice by inactivating its kinase, eEF2K, completely restores the rates of elongation and protein synthesis. Furthermore, eEF2K activity is required for the Rpl24Bst mutant to suppress tumorigenesis. This work demonstrates that elevation of eEF2 phosphorylation is an effective means to suppress colorectal tumorigenesis with two driver mutations. This positions translation elongation as a therapeutic target in colorectal cancer, as well as other cancers where the Rpl24Bst mutation has a tumour suppressive effect in mouse models.
Effects of Normoxia, Hyperoxia, and Mild Hypoxia on Macro-Hemodynamics and the Skeletal Muscle Microcirculation in Anesthetised Rats

Objectives: Excessive oxygen (O2) administration may have a negative impact on tissue perfusion by inducing vasoconstriction and oxidative stress. We aimed to evaluate the effects of different inhaled oxygen fractions (FiO2) on macro-hemodynamics and microvascular perfusion in a rat model. Methods: Isoflurane-anesthetised spontaneously breathing male Wistar rats were equipped with arterial (carotid artery) and venous (jugular vein) catheters and tracheotomy, and randomized into three groups: normoxia (FiO2 21%, n = 6), hyperoxia (FiO2 100%, n = 6) and mild hypoxia (FiO2 15%, n = 6). Euvolemia was maintained by infusing Lactate Ringer solution at 10 ml/kg/h. At hourly intervals for 4 h we collected measurements of: mean arterial pressure (MAP); stroke volume index (SVI), heart rate (HR), respiratory rate (by means of echocardiography); arterial and venous blood gases; microvascular density, and flow quality (by means of sidestream dark field videomicroscopy on the hindlimb skeletal muscle). Results: MAP and systemic vascular resistance index increased with hyperoxia and decreased with mild hypoxia (p < 0.001 in both cases, two-way analysis of variance). Hyperoxia induced a reduction in SVI, while this was increased in mild hypoxia (p = 0.002). The HR increased under hyperoxia (p < 0.05 vs. normoxia at 3 h). Cardiax index, as well as systemic O2 delivery, did not significantly vary in the three groups (p = 0.546 and p = 0.691, respectively). At 4 h, microvascular vessel surface (i.e., the percentage of tissue surface occupied by vessels) decreased by 29 ± 4% in the hyperoxia group and increased by 19 ± 7 % in mild hypoxia group (p < 0.001). Total vessel density and perfused vessel density showed similar tendencies (p = 0.003 and p = 0.005, respectively). Parameters of flow quality (microvascular flow index, percentage of perfused vessels, and flow heterogeneity index) remained stable and similar in the three groups. Conclusions: Hyperoxia induces vasoconstriction and reduction in skeletal muscle microvascular density, while mild hypoxia has an opposite effect.
Biological complexity facilitates tuning of the neuronal parameter space

The electrical and computational properties of neurons in our brains are determined by a rich repertoire of membrane-spanning ion channels and elaborate dendritic trees. However, the precise reason for this inherent complexity remains unknown. Here, we generated large stochastic populations of biophysically realistic hippocampal granule cell models comparing those with all 15 ion channels to their reduced but functional counterparts containing only 5 ion channels. Strikingly, valid parameter combinations in the full models were more frequent and more stable in the face of perturbations to channel expression levels. Scaling up the numbers of ion channels artificially in the reduced models recovered these advantages confirming the key contribution of the actual number of ion channel types. We conclude that the diversity of ion channels gives a neuron greater flexibility and robustness to achieve target excitability. Significance statement Over the course of billions of years, evolution has led to a wide variety of biological systems. The emergence of the more complex among these seems surprising in the light of the high demands of searching for viable solutions in a correspondingly high-dimensional parameter space. In realistic neuron models with their inherently complex ion channel composition, we find a surprisingly large number of viable solutions when selecting parameters randomly. This effect is strongly reduced in models with fewer ion channel types but is recovered when inserting additional artificial ion channels. Because concepts from probability theory provide a plausible explanation for this improved distribution of valid model parameters, we propose that this may generalise to evolutionary selection in other complex biological systems. In brief Studying ion channel diversity in neuronal models we show how robust biological systems may evolve not despite but because of their complexity. Highlights 15 channel model of hippocampal granule cells (GCs) reduces to 5 ion channels without loss of spiking behaviour. But knocking out ion channels can be compensated only in the full model. Random sampling leads to ~ 6% solutions in full but only ~ 1% in reduced model. Law of large numbers generalises our observations to other complex biological systems.
A universal pocket in fatty acyl-AMP ligases ensures redirection of fatty acid pool away from coenzyme A-based activation

Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4’-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3’, 5’-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organisations. The universal distribution of FAALs suggests they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.
Panacea: a hyperpromiscuous antitoxin protein domain for the neutralisation of diverse toxin domains

Toxin-Antitoxin (TA) gene pairs are ubiquitous in microbial chromosomal genomes and plasmids, as well as bacteriophages. They act as regulatory switches, with the toxin limiting the growth of bacteria and archaea by compromising diverse essential cellular targets, and the antitoxin counteracting the toxic effect. To uncover previously uncharted TA diversity across microbes and bacteriophages, we analysed the conservation of genomic neighbourhoods using our computational tool FlaGs (for Flanking Genes), which allows high-throughput detection of TA-like operons. Focussing on the widespread but poorly experimentally characterised antitoxin domain DUF4065, our in silico analyses indicated that DUF4065-containing proteins serve as broadly distributed antitoxin components in putative TA-like operons with dozens of different toxic domains with multiple different folds. Given the versatility of DUF4065, we have renamed the domain to Panacea (and proteins containing the domain, PanA) after the Greek goddess of universal remedy. We have experimentally validated nine PanA-neutralised TA pairs. While the majority of validated PanA-neutralised toxins act as translation inhibitors or membrane disruptors, a putative nucleotide cyclase toxin from a Burkholderia prophage compromises replication and translation, as well as inducing RelA-dependent accumulation of the nucleotide alarmone (p)ppGpp. We find that Panacea-containing antitoxins form a complex with their diverse cognate toxins, characteristic of the direct neutralisation mechanisms employed by Type II TA systems. Finally, through directed evolution we have selected PanA variants that can neutralise non-cognate TA toxins, thus experimentally demonstrating the evolutionary plasticity of this hyperpromiscuous antitoxin domain. Significance Toxin-antitoxin systems are enigmatic and diverse elements of bacterial and bacteriophage genomes. We have uncovered remarkable versatility of an antitoxin protein domain, that has evolved to neutralise dozens of different toxin domains. We find that antitoxins carrying this domain – Panacea – form complexes with their cognate toxins, indicating a direct neutralisation mechanism, and that Panacea can be evolved to neutralise a non-cognate and non-homologous toxin with just two amino acid substitutions. This raises the possibility that this domain could be an adaptable universal, or semi-universal protein neutraliser with significant biotechnological and medical potential.
Hepatic Metastasis in Newly Diagnosed Esophageal Cancer: A Population-Based Study

Background The hepatic metastasis pattern of esophageal cancer (EC) has not been fully explored. The primary objective of this study was to explore the predictors of esophageal cancer with hepatic metastasis (ECHM) at the time of diagnosis. In addition, we also analyzed the factors affecting ECHM prognosis. Methods We used the Surveillance, Epidemiology and End Result (SEER) database to identify ECHM patients at the time of initial diagnosis. The ECHM predictors were identified using multivariate logistic regression. Multivariate Cox regression and competing survival risk analyses were performed to identify factors associated with all-cause mortality and EC-specific mortality of ECHM, respectively. Results A total of 10,965 eligible EC patients were identified in the SEER database between 2010 and 2016, of which 1,197 were ECHM patients, accounting for 10.9% of the entire cohort. In the whole cohort, eight ECHM predictors (age, primary site, grade, histology type, T staging, N staging, insurance status, and number of extrahepatic metastatic sites) were determined using multivariate logistic regression analysis. Multivariate Cox regression and multivariate competing survival risks models confirmed that the male sex, advanced age, squamous cancer, and multiple extrahepatic metastasis increased the risk of both all-cause and EC-specific mortality, whereas chemotherapy and chemotherapy plus radiotherapy significantly reduced the risk of both. Conclusions This study explored population-level predictors of hepatic metastasis at the time of EC diagnosis and analyzed the clinical characteristics affecting the prognosis in ECHM patients. These findings may provide clinicians with a reference for the screening and treatment of hepatic metastasis in EC.
Benchmarking the Extent and Speed of Reperfusion: First Pass TICI 2c-3 Is a Preferred Endovascular Reperfusion Endpoint

Background and Purpose: End-of-procedure substantial reperfusion [modified Treatment in Cerebral Ischemia (mTICI) 2b-3], the leading endpoint for thrombectomy studies, has several limitations including a ceiling effect, with recent achieved rates of ~90%. We aimed to identify a more optimal definition of angiographic success along two dimensions: (1) the extent of tissue reperfusion, and (2) the speed of revascularization. Methods: Core-lab adjudicated TICI scores for the first three passes of EmboTrap and the final all-procedures result were analyzed in the ARISE II multicenter study. The clinical impact of extent of reperfusion and speed of reperfusion (first-pass vs. later-pass) were evaluated. Clinical outcomes included 90-day functional independence [modified Rankin Scale (mRS) 0–2], 90-day freedom-from-disability (mRS 0–1), and dramatic early improvement [24-h National Institutes of Health Stroke Scale (NIHSS) improvement ≥ 8 points]. Results: Among 161 ARISE II subjects with ICA or MCA M1 occlusions, reperfusion results at procedure end showed substantial reperfusion in 149 (92.5%), excellent reperfusion in 121 (75.2%), and complete reperfusion in 79 (49.1%). Reperfusion rates on first pass were substantial in 81 (50.3%), excellent reperfusion in 62 (38.5%), and complete reperfusion in 44 (27.3%). First-pass excellent reperfusion (first-pass TICI 2c-3) had the greatest nominal predictive value for 90-day mRS 0–2 (sensitivity 58.5%, specificity 68.6%). There was a progressive worsening of outcomes with each additional pass required to achieve TICI 2c-3. Conclusions: First-pass excellent reperfusion (TICI 2c-3), reflecting rapid achievement of extensive reperfusion, is the technical revascularization endpoint that best predicted functional independence in this international multicenter trial and is an attractive candidate for a lead angiographic endpoint for future trials. Clinical Trial Registration: http://www.clinicaltrials. gov, identifier NCT02488915.