Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuro-Immune Modulation Effects of Sacral Nerve Stimulation for Visceral Hypersensitivity in Rats

Background: Visceral hypersensitivity (VH) is one of the underlying pathophysiologies of irritable bowel syndrome. Mast cell overactivation has been found to be one of the main causes of VH. We investigated the effects and mechanisms of actions of sacral nerve stimulation (SNS) on visceral pain in a rodent model of VH. Methods: The VH was established by an intrarectal infusion of AA in 10-day-old pups. Rats were chronically implanted with electrodes for SNS and recording electromyogram (EMG) and electrocardiogram. The acute study was performed in 2-randomized sessions with SNS (14 Hz, 330 μs, 40% motor threshold or MT, 30 min) or sham-SNS. Later on, rats were randomized into SNS/sham-SNS groups and a chronic study was performed with 2 h-daily SNS or sham-SNS for 21 days. Visceromotor reflexes were assessed by abdominal EMG and withdrawal reflex (AWR). Colon tissues were collected to study colonic acetylcholine (ACh), the enteric neurons (ChAT, nNOS, and PGP9.5), mast cells activity [Tryptase, prostaglandins E2 (PGE2), and cyclooxygenases-2 (COX2)] and pain markers [nerve growth factor (NGF) and Sub-P]. Key Results: Sacral nerve stimulation significantly improved visceromotor reflexes assessed by the EMG and AWR, compared with sham-SNS. SNS normalized the protein expressions of ChAT and nNOS and regulated mast cells activity by downregulating Tryptase, COX2, and PGE2. Neonatal AA administration upregulated NGF and Sub-P; chronic SNS significantly decreased these pain biomarkers. Concurrently, chronic SNS increased ACh in colon tissues and vagal efferent activity. Conclusions: Sacral nerve stimulation reduces VH in rats and this ameliorating effect might be attributed to the suppression of mast cell overactivation in the colon tissue via the modulation of autonomic nervous system functions.
Structural Modeling and in planta Complementation Studies Link Mutated Residues of the Medicago truncatula Nitrate Transporter NPF1.7 to Functionality in Root Nodules

Symbiotic nitrogen fixation is a complex and regulated process that takes place in root nodules of legumes and allows legumes to grow in soils that lack nitrogen. Nitrogen is mostly acquired from the soil as nitrate and its level in the soil affects nodulation and nitrogen fixation. The mechanism(s) by which legumes modulate nitrate uptake to regulate nodule symbiosis remain unclear. In Medicago truncatula, the MtNPF1.7 transporter has been shown to control nodulation, symbiosis, and root architecture. MtNPF1.7 belongs to the nitrate/peptide transporter family and is a symporter with nitrate transport driven by proton(s). In this study we combined in silico structural predictions with in planta complementation of the severely defective mtnip-1 mutant plants to understand the role of a series of distinct amino acids in the transporter’s function. Our results support hypotheses about the functional importance of the ExxE(R/K) motif including an essential role for the first glutamic acid of the motif in proton(s) and possibly substrate transport. Results reveal that Motif A, a motif conserved among major facilitator transport (MFS) proteins, is essential for function. We hypothesize that it participates in intradomain packing of transmembrane helices and stabilizing one conformation during transport. Our results also question the existence of a putative TMH4-TMH10 salt bridge. These results are discussed in the context of potential nutrient transport functions for MtNPF1.7. Our findings add to the knowledge of the mechanism of alternative conformational changes as well as symport transport in NPFs and enhance our knowledge of the mechanisms for nitrate signaling.
Interoception Disorder and Insular Cortex Abnormalities in Schizophrenia: A New Perspective Between Psychoanalysis and Neuroscience

The existence of disturbances in the perception of somatic states and in the representation of the body with the presence of cœnesthetic hallucinations, of delusional hypochondriac ideas or of dysmorphophobias is a recognized fact in the psychopathology of schizophrenia. Freudian psychoanalytic theory had accorded a privileged place to the alteration of the perception of the body in schizophrenia. Freud had attributed to these phenomena a primary and prodromal role in the psychopathology of psychosis. We propose to look at this theory in a new way, starting from the perspective of recent studies about the role of the insula in the perception and representation of somatic states, since this structure has been identified as underpinning the sense of interoception. The data in the neurobiological literature about abnormalities in the insular cortex in schizophrenia has shown that insula dysfunction could constitute one of the biological substrates of disorders of body perception in schizophrenia, and could be a source of the alteration of the sense of self that is characteristic of this psychiatric pathology. Moreover, this alteration could thus be involved in the positive symptomatology of schizophrenia.
Elicitor Application in Strawberry Results in Long-Term Increase of Plant Resilience Without Yield Loss

For a first step integrating elicitor applications into the current IPM strategy increasing plant resilience against pests, we investigated repeated elicitor treatments in a strawberry everbearer nursery and cropping cycle under glass. During nursery methyl-jasmonate (MeJA), testing induction of defenses with plant bioassays was applied every 3 weeks. Thrips damage and reproduction by spider mites, whitefly and aphids were strongly reduced upon elicitor treatment. Subsequently, we applied MeJA every 3 weeks or based on scouting pests during a whole cropping cycle. Thrips leaf bioassays and LC-MS leaf metabolomics were applied to investigate the induction of defenses. Leaf damage by thrips was lower for both MeJA application schemes compared to the control except for the last weeks. While elicitor treatments after scouting also reduced damage, its effect did not last. Thrips damage decreased from vegetative to mature plants during the cropping cycle. At the end of the nursery phase, plants in the elicitor treatment were smaller. Surprisingly, growth during production was not affected by MeJA application, as were fruit yield and quality. LC-MS leaf metabolomics showed strong induction of vegetative plants decreasing during the maturation of plants toward the end of cultivation. Concurrently, no increase in the JA-inducible marker PPO was observed when measured toward the end of cultivation. Mostly flavonoid and phenolic glycosides known as plant defense compounds were induced upon MeJA application. While induced defense decreased with the maturation of plants, constitutive defense increased as measured in the leaf metabolome of control plants. Our data propose that young, relatively small plant stages lack constitutive defense necessitating an active JA defense response. As plants, mature constitutive defense metabolites seem to accumulate, providing a higher level of basal resistance. Our results have important implications for but are not limited to strawberry cultivation. We demonstrated that repeated elicitor application could be deployed as part of an integrated approach for sustainable crop protection by vertical integration with other management tactics and horizontal integration to control multiple pests concurrently. This approach forms a promising potential for long-term crop protection in greenhouses.
Presurgical Evaluation of Epilepsy Using Resting-State MEG Functional Connectivity

Epilepsy is caused by abnormal electrical discharges (clinically identified by electrophysiological recording) in a specific part of the brain [originating in only one part of the brain, namely, the epileptogenic zone (EZ)]. Epilepsy is now defined as an archetypical hyperexcited neural network disorder. It can be investigated through the network analysis of interictal discharges, ictal discharges, and resting-state functional connectivity. Currently, there is an increasing interest in embedding resting-state connectivity analysis into the preoperative evaluation of epilepsy. Among the various neuroimaging technologies employed to achieve brain functional networks, magnetoencephalography (MEG) with the excellent temporal resolution is an ideal tool for estimating the resting-state connectivity between brain regions, which can reveal network abnormalities in epilepsy. What value does MEG resting-state functional connectivity offer for epileptic presurgical evaluation? Regarding this topic, this paper introduced the origin of MEG and the workflow of constructing source–space functional connectivity based on MEG signals. Resting-state functional connectivity abnormalities correlate with epileptogenic networks, which are defined by the brain regions involved in the production and propagation of epileptic activities. This paper reviewed the evidence of altered epileptic connectivity based on low- or high-frequency oscillations (HFOs) and the evidence of the advantage of using simultaneous MEG and intracranial electroencephalography (iEEG) recordings. More importantly, this review highlighted that MEG-based resting-state functional connectivity has the potential to predict postsurgical outcomes. In conclusion, resting-state MEG functional connectivity has made a substantial progress toward serving as a candidate biomarker included in epileptic presurgical evaluations.
Peri-interventional Triple Therapy With Dabigatran Improves Vasomotion and Promotes Endothelialization in Porcine Coronary Stenting Model

Objective: We evaluated the short and long-term effect of peri-interventional dabigatran therapy on vasomotion, endothelialization, and neointimal formation in a porcine coronary artery stenting model. Background: Stenting of coronary arteries induces local inflammation, impairs vasomotion and delays endothelialization. Methods: Twenty-eight animals underwent percutaneous coronary intervention (PCI) with drug eluting stents. Sixteen pigs started dabigatran therapy 4 days prior to PCI and continued for 4 days post-stenting, while 12 animals served as controls. Post-stenting dual antiplatelet therapy (75 mg clopidogrel and 100 mg aspirin) was continued in both groups until termination. Immediately post-stenting and at day 3 optical coherence tomography (OCT) was performed in all animals, followed by euthanasia of 8 dabigatran and 4 control animals. The remaining pigs (8 of each group) were followed up for 1 month, with control angiography and OCT. Tissue burden (degree of peri-strut structure—thrombus and/or fibrin) was evaluated. After euthanasia coronary arteries were harvested for in-vitro myometry and histology. Results: Thrombin generation was lower (p < 0.001) and tissue burden (0.83 ± 0.98 vs. 3.0 ± 2.45; p = 0.031) was significantly decreased in dabigatran treated animals. After 3 days post-PCI endothelium-dependent vasodilation was significantly improved (77 ± 40% vs. 41 ± 31%, p = 0.02) in dabigatran animals. Neither quantitative angiography nor histomorphometry showed differences between the groups. Endothelialization was faster in the dabigatran group as compared with controls (p = 0.045). Conclusion: Short-term peri-interventional triple therapy with dabigatran, aspirin, and clopidogrel led to an enhanced endothelium dependent vasodilation and faster endothelialization. However, neointimal formation 1-month after stent implantation was comparable between groups.
Resisting Aridification: Adaptation of Sap Conduction Performance in Moroccan Wild Olive Subspecies Distributed Over an Aridity Gradient

In the current context of global change, the increasing frequency and the length of drought periods are testing the resistance capacities of plants of dry habitats. However, although the adaptation of plants to drought has been widely studied, the anatomical features of wood influencing the functional responses of plants to drought are still lacking at the intraspecific level, especially for species with a wide geographical distribution. As a result, we have studied the variation of wood anatomical traits related to sap conduction (i.e., vessel surface area, vessel density, and number of vessels joined by radial file) in two wild olive subspecies distributed in Morocco (i.e., Olea europaea subsp. europaea. var. sylvestris and Olea europaea subsp. maroccana), in relation to various drought conditions. This functional study, based on wood trait measurements of 351 samples from 130 trees and 13 populations, explores potential sap conduction in relation to environmental parameters and as a result, strategies to resist water stress. We found that (1) branch diameter (BD) captured 78% of total wood trait variation, (2) vessel size (SVS) expressed 32% of intraspecific variation according to cambium age, and (3) the positive relationship between SVS and BD could be explained by climate type, vegetation cover changes, and therefore available water resources. Taking into consideration the diameter of the branch as the main factor of anatomical variation, established reaction norms (linear models) at the intrapopulation scale of vessel lumen area according to aridity show for the first time how the functioning of the cambium modulates and controls sap conduction, according to aridity and thus available water resources. They pinpoint the risks incurred by the wild olive tree in the perspective of a dramatic increase in aridity, in particular, the inability of the cambium to produce large enough vessels to efficiently transport sap and irrigate the leaves. Finally, this study opens new and interesting avenues for studying at a Mediterranean scale, the resistance and the vulnerability of wild forms and cultivated varieties of olive to heterogeneous and changing environmental conditions.
Outcomes of Idiopathic Pulmonary Fibrosis Improve with Obesity: A Rural Appalachian Experience

Obesity is associated with fibrosis in various tissues, including the liver, heart, kidney, and skin; however, its relation to idiopathic pulmonary fibrosis remains unclear. We systematically identified an idiopathic pulmonary fibrosis cohort at a rural Appalachian academic medical center in accordance with the 2018 American Thoracic Society diagnostic guidelines to describe its association with obesity. Objectives Obesity can be an independent predictor of fibrosis in tissues, including the liver, heart, and skin. We evaluated a rural Appalachian cohort of idiopathic pulmonary fibrosis (IPF) for its relation to obesity. Methods Using American Thoracic Society 2018 diagnostic guidelines, an IPF cohort was systematically identified at an Appalachian academic medical center (2015–2019). The cohort was categorized in subgroups of body mass index (BMI) <30 or BMI ≥30 kg/m2. Demographics, clinical variables, and treatment details were collected retrospectively and evaluated for their associations with obesity. Results In our IPF cohort (N = 138), a usual interstitial pneumonia pattern was less prevalent in the obese group (n = 49) relative to the nonobese group (69% vs 85%, respectively). The obese group was younger (mean age 73.27 ± 9.12 vs 77.97 ± 9.59 years) and had a higher prevalence of hypertension (90% vs 72%), hyperlipidemia (83% vs 68%), diabetes mellitus (47% vs 25%), sleep-disordered breathing (47% vs 25%), chronic pain disorders (28% vs 15%), and deep vein thrombosis (19% vs 7%). An increased proportion of obese-IPF patients was seen at a tertiary or an interstitial lung disease center, with more surgical lung biopsies performed and incident diagnosis (ie, within 6 months of presentation) assigned. Only a minority of patients underwent lung transplantation (3.6%), all of them from the obese-IPF subgroup. Approximately 30% of the total IPF cohort died, with a lower mortality observed in the obese group (35% vs 20%, P = 0.017). An increasing BMI predicted a better survival in the total IPF cohort (BMI 25–29.9, 20–24.9, and <20 had mortality rates of 20%, 47%, and 75%, respectively; P < 0.001). Conclusions Our study represents a first known effort to develop an IPF cohort in a rural Appalachian region. Although they shared an increased burden of comorbidities, the obese subgroup showed less advanced fibrosis with a lower mortality rate relative to nonobese subgroup, suggesting a potential “obesity paradox” in IPF. The study findings significantly advance our understanding of challenges posed by IPF in a rural population that also suffers from an alarming rate of obesity. We highlight the need for the multidisciplinary management of these patients and prospective studies to better define this complex relation.
Racial/Ethnic Disparities in the Incidence of Epithelial Ovarian Cancer in Florida by Histology, 2001–2015: Analysis of Trends

Ovarian cancer incidence has been decreasing in recent decades, with persistent racial/ethnic disparities. Many previous studies have focused on non-Hispanic White and non-Hispanic Black women with relatively fewer including Hispanic women. Florida presents a unique opportunity to evaluate racial/ethnic disparities in health. This article provides an analysis of ovarian cancer incidence trends by race/ethnicity and histology in Florida from 2001 to 2015. Objectives Because the population in Florida is 25.6% Hispanic, it is possible to evaluate the influence of race and ethnicity within clinically relevant subgroups of women with epithelial ovarian cancer (EOC), including histology and tumor grade. This study explores racial/ethnic disparities in the incidence of EOC in Florida by histology and tumor grade. Methods This study is an analysis of the Florida Cancer Database System. All incidence EOC cases from 2001 through 2015 were identified. Age-adjusted incidences were calculated and trends modeled by race/ethnicity and histology using Joinpoint and Poisson regression. Results In total, 80% of the 21,731 women with EOC were White, followed by Hispanic (13.1%) and non-Hispanic Black (7.9%). All races/ethnicities had statistically significant declines in incidence, with non-Hispanic White and non-Hispanic Black women having the steepest declines (annual percentage change −2.5, 95% confidence interval [CI] −5.9 to −2.1 and annual percentage change −2.8, 95% CI −4.8 to −1.5, respectively). A decreased incidence trend across the time period was seen for all subgroups (relative risk 0.97 [95% CI 0.96–0.98], 0.96 [95% CI 0.96–0.99], and 0.98 [95% CI 0.96–0.99] for non-Hispanic White, non-Hispanic Black, and Hispanic). High-grade EOC incidence for all groups did not change with time. Conclusions We found significant declines in the incidence of EOC for all races/ethnicities, but not for high-grade EOC. The observed incidence decline in Hispanic women differs from previous research. More research is needed to understand women the causes of overall racial/ethnic differences and the decline in EOC.
Data Collection and Annotation Pipeline for Social Good Projects

Vast amounts of data are generated during crisis events through both formal and informal sources, and this data can be used to make a positive impact in all phases of crisis events. However, collecting and annotating data quickly and effectively in the face of crises is a challenging task. Crises require quick, robust, and efﬁcient annotation to best respond to unfolding events. Data must be accessed and aggregated across different platforms and sources, and annotation tools must be able to utilize this data effectively. This work describes an architecture built for rapid collection and annotation of data from multiple sources which can then be built into machine learning and data analysis models. We extract data from social media via multiple systems for Twitter data collection, as well as building architecture for the collection of news articles from diverse sources. These can then be input into the INCEpTION annotation framework, which has been adapted to allow for easy management of multiple annotators, aiming to improve functionality to facilitate the application of citizen science. This allows us to rapidly prototype new annotation schema across a diverse array of data sources, which can then be deployed for machine learning. As a use case, we explore annotation of COVID-19 related Tweets and news articles for case prediction.
The Ryanodine Receptor as a Sensor for Cellular Environments in Muscles

The ryanodine receptor (RyR) is a Ca2+ release channel in the sarcoplasmic reticulum of skeletal and cardiac muscles and plays a key role in excitation-contraction coupling. The activity of the RyR is regulated by many intracellular factors such as divalent cations (Ca2+ and Mg2+), nucleotides, associated proteins, and reactive oxygen species. Since these intracellular factors change depending on the condition of the muscle, e.g., exercise, fatigue, or disease states, the RyR channel activity will be altered accordingly. In this review, we describe how the RyR channel is regulated under various conditions and discuss the possibility that the RyR acts as a sensor for change in the cellular environment of muscles.
Rapid melting and revitrification as an approach to microsecond time-resolved cryo-electron microscopy

Proteins typically undergo dynamics on the microsecond to millisecond timescale, which is much faster than the time resolution of cryo-electron microscopy. Here, we propose a novel approach for microsecond time-resolved cryo-electron microscopy that involves melting a cryo specimen in situ with a laser beam. The sample remains liquid for the duration of the laser pulse, offering a tunable time window in which the dynamics of embedded particles can be induced in a liquid environment. After the laser pulse, the sample vitrifies, trapping particles in their transient configurations. As a proof of principle, we study the disassembly of particles after they incur
Lifelong Learning Maxent for Suggestion Classification

Suggestion classification for opinion data is defined as identifying a given utterance by suggestion or non-suggestion class. In this paper, we introduce a method called LLMaxent which is the solution for the cross-domain suggestion classification. LLMaxent is a lifelong machine learning approach using maximum entropy (Maxent). In the course of lifelong learning, the drawn knowledge from the past tasks is retained and supported for the future learning. From that, we build a classifier by using labelled data in existed domains for suggestion classification in a new domain. The experimental results show that the proposed novel model can improve the performance of cross-domain suggestion classification. This is one of the preliminary research in lifelong machine learning using Maxent. Its effect is not only for suggestion classification but also for cross-domain text classification in general.