syedzayyan/paper_mill_benchmark huggingface dataset:
Dopamine-dependent effects on basal and glutamate stimulated network dynamics in cultured hippocampal neurons.

Oscillatory activity occurs in cortical and hippocampal networks with specific frequency ranges thought to be critical to working memory, attention, differentiation of neuronal precursors, and memory trace replay.Synchronized activity within relatively large neuronal populations is influenced by firing and bursting frequency within individual cells, and the latter is modulated by changes in intrinsic membrane excitability and synaptic transmission.Published work suggests that dopamine, a potent modulator of learning and memory, acts on dopamine receptor 1-like dopamine receptors to influence the phosphorylation and trafficking of glutamate receptor subunits, along with long-term potentiation of excitatory synaptic transmission in striatum and prefrontal cortex.Prior studies also suggest that dopamine can influence voltage gated ion channel function and membrane excitability in these regions.Fewer studies have examined dopamine's effect on related endpoints in hippocampus, or potential consequences in terms of network burst dynamics.In this study, we record action potential activity using a microelectrode array system to examine the ability of dopamine to modulate baseline and glutamate-stimulated bursting activity in an in vitro network of cultured murine hippocampal neurons.We show that dopamine stimulates a dopamine type-1 receptor-dependent increase in number of overall bursts within minutes of its application.Notably, however, at the concentration used herein, dopamine did not increase the overall synchrony of bursts between electrodes.Although the number of bursts normalizes by 40 min, bursting in response to a subsequent glutamate challenge is enhanced by dopamine pretreatment.Dopamine-dependent potentiation of glutamate-stimulated bursting was not observed when the two modulators were administered concurrently.In parallel, pretreatment of murine hippocampal cultures with dopamine stimulated lasting increases in the phosphorylation of the glutamate receptor subunit glu a1 at serine 845.This effect is consistent with the possibility that enhanced membrane insertion of glu as may contribute to a more slowly evolving dopamine-dependent potentiation of glutamate-stimulated bursting.Together, these results are consistent with the possibility that dopamine can influence hippocampal bursting by at least two temporally distinct mechanisms, contributing to an emerging appreciation of dopamine-dependent effects on network activity in the hippocampus.

Journal: Journal of neurochemistry (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Using Kubelka-Munk reflectance theory to predict optimal pink composite thickness and shade with an opaqued PEEK background for a final gingival color: An in vitro study.

S the aims of this study were to demonstrate and evaluate how kubelka-munk (k-m) reflectance theory is used to adjust the color of the opaqued peek backing and the color and thickness of the resin composite layers in different thicknesses in order to minimize the color difference from a target gingival color.Methods peek specimens were opaqued with either a dark or a light opaquer.Composite resin layers in 3 different colors were fabricated in varying thicknesses.Reflectance of opaqued peek and composite layers was determined using a spectroradiometer.Kubelka-munk (k-m) absorption (k) and scattering (s) coefficients were derived for each material and then k-m reflectance theory was then used to predict the reflectance of each composite disk as layered on each backing.The color of the opaqued peek backings alone and the color of 12 pink composite layers on opaqued peek backings was calculated for the cie d65 illuminant.Composite resins in 3 different color were then bonded to the opaqued peek specimens and color differences of these specimens from the theoretical colors were determined.Results the ∆e00 values ranged from 0.45 to 1.29 units for the bonded pink specimens and the k-m theory.K-m theory was validated as a viable predictor of gingival color using pink composite bonded to opaqued peek background.Significance using k-m theory to predict the gingival color of pink composite bonded to opaqued peek eliminates the need to make many specimens of different thicknesses that would otherwise be required to find an acceptable color match.

Journal: Dental materials : official publication of the Academy of Dental Materials (2022)
Publication types: Journal Article
Cross talk between androgen and Wnt signaling potentially contributes to age-related skeletal muscle atrophy in rats.

We sought to determine whether age-related gastrocnemius muscle mass loss was associated with parallel decrements in androgen receptor (ar) or select wnt signaling markers.To test this hypothesis, serum-free and total testosterone (test) and gastrocnemius ar and wnt signaling markers were analyzed in male fischer 344 rats that were 3, 6, 12, 18, and 24 mo (mo) old ( n = 9 per group).Free and total test was greatest in 6 mo rats, and ar protein and wnt5 protein levels linearly declined with aging.There were associations between wnt5 protein levels and relative gastrocnemius mass ( r = 0.395, p = 0.007) as well as ar and wnt5 protein levels (r = 0.670, p < 0.001).We next tested the hypothesis that wnt5 affects muscle fiber size by treating c2c12-derived myotubes with lower (75 ng/ml) and higher (150 ng/ml) concentrations of recombinant wnt5a protein.Both treatments increased myotube size ( p < 0.05) suggesting this ligand may affect muscle fiber size in vivo.We next tested if wnt5a protein levels were androgen-modulated by examining 10-mo-old male fischer 344 rats ( n = 10-11 per group) that were orchiectomized and treated with testosterone-enanthate (test-e); trenbolone enanthate (tren), a nonaromatizable synthetic testosterone analogue; or a vehicle (orx only) for 4 wk.Interestingly, test-e and tren treatments increased wnt5a protein in the androgen-sensitive levator ani/bulbocavernosus muscle compared with orx only ( p < 0.05).To summarize, aromatizable and nonaromatizable androgens increase wnt5a protein expression in skeletal muscle, age-related decrements in muscle ar may contribute wnt5a protein decrements, and our in vitro data imply this mechanism may contribute to age-related muscle loss.New & noteworthy results from this study demonstrate androgen and wnt5 protein expression decrease with aging, and this may be a mechanism involved with age-related muscle loss.

Journal: Journal of applied physiology (Bethesda, Md. : 1985) (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.

S gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear.We examined the human gut microbiome's functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the meta cardis cohort.We focused on the role of b vitamins and b7/b8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.Design we performed metagenomic analyses in 1545 subjects from the meta cardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice.Results severe obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes.We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue.In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels.Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice.Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and b vitamins, while limiting weight gain and glycaemic deterioration.Conclusion strategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.Trial registration number nct02059538.

Journal: Gut (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A theoretical investigation into gallic acid pyrolysis.

Thermodynamic and kinetic information on the first two steps of gallic acid pyrolysis, a decarboxylation followed by a dehydrogenation, is obtained based on density functional theory and quantum chemistry.For the kinetics, transition states are identified with the help of the climbing image nudged elastic band method.Both reactions exhibit two transition states.One of them is related to the rotation of oh groups, and the other one is related to the breaking and forming of bonds.The gallic acid pyrolysis as a whole is judged to be endothermal, and it changes from endergonic to exergonic between 500 and 750 k.The second reaction, the dehydrogenation of pyrogallol, is identified as the rate-determining step of gallic acid pyrolysis, with reaction rate constants below 1 s-1for temperatures below 1250 k.

Journal: Journal of computational chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Let's Agree to Disagree on Operative versus Nonoperative (LADON) treatment for proximal humerus fractures: Study protocol for an international multicenter prospective cohort study.

The proximal humerus fracture is a common injury, but the optimal management is much debated.The decision for operative or nonoperative treatment is strongly influenced by patient specific factors, regional and cultural differences and the preference of the patient and treating surgeon.The aim of this study is to compare operative and nonoperative treatment of proximal humerus fractures for those patients for whom there is disagreement about optimal management.Methods and analysis this protocol describes an international multicenter prospective cohort study, in which all patients of 18 years and older presenting within three weeks after injury with a radiographically diagnosed displaced proximal humerus fracture can be included.Based on patient characteristics and radiographic images several clinical experts advise on the preferred treatment option.In case of disagreement among the experts, the patient can be included in the study.The actual treatment that will be delivered is at the discretion of the treating physician.The primary outcome is the quick dash score at 12 months.Propensity score matching will be used to control for potential confounding of the relation between treatment modality and quick dash scores.Discussion the ladon study is an international multicenter prospective cohort study with a relatively new methodological study design.This study is a "natural experiment" meaning patients receive standard local treatment and surgeons perform standard local procedures, therefore high participation rates of patients and surgeons are expected.Patients are only included after expert panel evaluation, when there is proven disagreement between experts, which makes this a unique study design.Through this inclusion process, we create two comparable groups whom received different treatments and where expert disagree about the already initiated treatment.Since we are zooming in on this particular patient group, confounding will be largely mitigated.Internationally the treatment of proximal humerus fractures are still much debated and differs much per country and hospital.This observational study with a natural experiment design will create insight into which treatment modality is to be preferred for patients in whom there is disagreement about the optimal treatment strategy.Trial registration registered in netherlands trial register nl9357 and swiss trial register ch 2020-00961;

Journal: PloS one (2022)
Publication types: Clinical Trial;Journal Article;Multicenter Study;Research Support, Non-U.S. Gov't
Evaluation of Zhilong Huoxue Tongyu capsule in the treatment of acute cerebral infarction: A systematic review and meta-analysis of randomized controlled trials.

Zhilong huoxue tongyu capsule (zl) is a chinese patent medicine and used for the treatment of acute cerebral infarction (aci) and its clinical application has gradually been widely recognized in china.However, the effects of zl for patients with aci have never been systematically evaluated.Purpose a systematic review and meta-analysis was performed to evaluate the efficacy of zl in aci.Study design a systematic review and meta-analysis of randomized clinical trials (rcts).Materials and methods a systematic review and meta-analysis were performed in accordance with the preferred reporting items for systematic reviews and meta-analyses guidelines.The comprehensive literature search was accomplished in 6 electronic databases to find relevant randomized controlled trials from their inception until october 31, 2020.The cochrane handbook for systematic reviews of interventions was used for methodological quality and independent evaluation.Review manager 5.3 was used to analyze all the data obtained.The clinical effective rate (cer) was the primary outcome, and the national institutes of health stroke score (nihss), barthel index (bi), and modified rankin scale (mrs) were the secondary outcomes.Results seven clinical studies recruiting 571 eligible patients were included in this meta-analysis.The results of meta-analysis suggested that compared with conventional treatment alone, zl combined with conventional treatment significantly improved cer (rr = 1.20, 95% ci: 1.12-1.29, p < 0.00001), decrease national institutes of health stroke scale score (nihss) (md = -2.60, 95% ci: -3.41-1.79, p < 0.00001), barthel index (bi) (md = -9.75, 95% ci: 7.15-12.36, p < 0.00001) and modified rankin scale (mrs) (md = -0.57, 95% ci: -0.84-0.30, p < 0.00001).There were no reported adverse events in the studies.Most results were robust and the quality of evidence was from moderate to low.Conclusion zl combined with conventional treatment can improve the short-term outcomes of aci patients, indicating zl is a promising treatment choice for aci and may be used as adjunctive treatment to the conventional treatment of aci.However, due to the limitations of included clinical trials, high-quality clinical trials with longer follow-ups are still needed to further assess the effectiveness and safety of zl for aci patients.

Journal: Phytomedicine : international journal of phytotherapy and phytopharmacology (2021)
Publication types: Journal Article;Meta-Analysis;Systematic Review
In situinvestigation of the formation mechanism ofα-Bi2Rh nanoparticles in polyol reductions.

The synthesis of intermetallic phases formed from elements with very different melting points is often time and energy consuming, and in extreme cases the evaporation of a reactant may even prevent formation completely.An alternative, facile synthesis approach is the reduction of metal salts in the polyol process, which requires only moderate temperatures and short reaction times.In addition, the starting materials for this procedure are readily available and do not require any special treatment to remove or prevent passivation layers, for example.Although the formation of intermetallic particlesviathe polyol process is an established method, little attention has been paid to the mechanism behind it.However, it is precisely a deeper understanding of the underlying mechanisms that would enable better and more targeted synthesis planning and product design.Taking the well-known formation of bi2rh particles from bi(no3)3and various rhodium salts in ethylene glycol as an example, we studied the chemical process in detail.We investigated the effects of anion type and p h on the polyol reaction.The reaction was also probed byin situ x-ray diffraction using synchrotron radiation.Products, intermediates and solutions were characterized by x-ray and electron diffraction, electron microscopy and optical spectroscopy.In the first step, co-reduction of the metal cations leads to bi rh.Only with increasing reaction temperature, the remaining bismuth cations in the solution are reduced and incorporated into the bi rh particles, leading to a gradual transition from bi rh toα-bi2rh.

Journal: Dalton transactions (Cambridge, England : 2003) (2022)
Publication types: Journal Article
Latent CMV Infection Is Associated With Lower Influenza Virus-Specific Memory T-Cell Frequencies, but Not With an Impaired T-Cell Response to Acute Influenza Virus Infection.

Latent infection with cytomegalovirus (cmv) is assumed to contribute to the age-associated decline of the immune system.Cmv induces large changes in the t-cell pool and may thereby affect other immune responses.Cmv is expected to impact especially older adults, who are already at higher risk of severe disease and hospitalization upon infections such as influenza virus (iav) infection.Here, we investigated the impact of cmv infection on iav-specific cd8+t-cell frequencies in healthy individuals (n=96) and the response to iav infection in older adults (n=72).Iav-specific memory t-cell frequencies were lower in healthy cmv+older individuals compared to healthy cmv-older individuals.Upon acute iav infection, cmv serostatus or cmv-specific antibody levels were not negatively associated with iav-specific t-cell frequencies, function, phenotype or t-cell receptor repertoire diversity.This suggests that specific t-cell responses upon acute iav infection are not negatively affected by cmv.In addition, we found neither an association between cmv infection and inflammatory cytokine levels in serum during acute iav infection nor between cytokine levels and the height of the iav-specific t-cell response upon infection.Finally, cmv infection was not associated with increased severity of influenza-related symptoms.In fact, cmv infection was even associated with increased iav-specific t-cell responses early upon acute iav infection.In conclusion, although associated with lower frequencies of memory iav-specific t cells in healthy individuals, cmv infection does not seem to hamper the induction of a proper t-cell response during acute iav infection in older adults.

Journal: Frontiers in immunology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Oversizing Increases Pacemaker Implantation Rate After Sutureless Minimally Invasive Aortic Valve Replacement.

Cardiac conduction system disturbances potentially leading to permanent pacemaker implantation are significant postoperative complications after aortic valve replacement.The aim of this study was to assess the impact of sutureless prosthetic valve oversizing on permanent pacemaker implantation rate.Methods this multicenter retrospective study included 306 patients who underwent minimally invasive aortic valve replacement with the perceval sutureless valve.Oversizing was determined by the implanted valve size indexed to body surface area.Data were analyzed with a multivariable logistic regression model.Results this study confirmed excellent postoperative results for minimally invasive aortic valve replacement with right anterior minithoracotomy approach and rapid deployment sutureless valves.Mortality rate was 1%.Eighteen (5.9%) patients received a new permanent pacemaker.Multivariable logistic regression model (p= 0.05) found oversizing as significant risk factor (p= 0.017) for permanent postoperative pacemaker implantation independent of patient age.There was a significant negative correlation between the indexed implanted valve size and the mean and peak postoperative transvalvular gradients (p< 0.001).Conclusions oversizing of sutureless prosthetic aortic valves is a risk factor for postoperative permanent pacemaker implantation.Proper sizing of perceval is important to avoid complications and ensure optimal valve performance.

Journal: Innovations (Philadelphia, Pa.) (2020)
Publication types: Journal Article;Multicenter Study
Physics approach to the variable-mass optimal-transport problem.

Optimal transport (ot) has become a discipline by itself that offers solutions to a wide range of theoretical problems in probability and mathematics with applications in several applied fields such as imaging sciences, machine learning, and in data sciences in general.The traditional ot problem suffers from a severe limitation: its balance condition imposes that the two distributions to be compared be normalized and have the same total mass.However, it is important for many applications to be able to relax this constraint and allow for mass creation and/or destruction.This is true, for example, in all problems requiring partial matching.In this paper, we propose an approach to solving a generalized version of the ot problem, which we refer to as the discrete variable-mass optimal-transport (vmot) problem, using techniques adapted from statistical physics.Our first contribution is to fully describe this formalism, including all the proofs of its main claims.In particular, we derive a strongly concave effective free-energy function that captures the constraints of the vmot problem at a finite temperature.From its maximum we derive a weak distance (i.e., a divergence) between possibly unbalanced distribution functions.The temperature-dependent ot distance decreases monotonically to the standard variable-mass ot distance, providing a robust framework for temperature annealing.Our second contribution is to show that the implementation of this formalism has the same properties as the regularized ot algorithms in time complexity, making it a competitive approach to solving the vmot problem.We illustrate applications of the framework to the problem of partial two- and three-dimensional shape-matching problems.

Journal: Physical review. E (2021)
Publication types: Journal Article
Kappa-opioid receptor-dependent changes in dopamine and anxiety-like or approach-avoidance behavior occur differentially across the nucleus accumbens shell rostro-caudal axis.

Neural circuit engagement within the nucleus accumbens (nac) shell is implicated in the regulation of both negative and positive affect.Classically, the dynorphin/kappa opioid receptor (kor) system in the nac was believed to promote aversion, while dopamine was viewed as interacting with reward behavior, and kor activation was known to inhibit dopamine release.Recently, however, both the kor and dopamine systems have, separately, been shown to have differential effects across the rostro-caudal axis of the nac shell on hedonic responses.Whether or not this is due to interactions between kors and dopamine, and if it extends to anxiety-like or approach-avoidance behaviors, remains to be determined.In this study, we examined in rats the relationship between the kor and dopamine systems in both the rostral and caudal nac shell using ex vivo fast scan cyclic voltammetry and the impact of kor activation on affective behavior using exploration-based tasks.We report here that activation of kors in the caudal nac shell significantly inhibits dopamine release, stimulates rearing behavior in a novel environment, increases anxiety-like or avoidance behavior, and reduces locomotor activity.In contrast, activation of kors in the rostral nac shell inhibits dopamine release to a lesser extent and instead reduces anxiety-like behavior or increases approach behavior.Taken together, these results indicate that there is heterogeneity across the rostro-caudal axis of the nac shell in the effects of kor stimulation on affective behaviors, and they suggest that this might be due to differences in kor control over dopamine release.

Journal: Neuropharmacology (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural