syedzayyan/paper_mill_benchmark huggingface dataset:
Two-photon AMPK and ATP imaging reveals the bias between rods and cones in glycolysis utility.

In vertebrates, retinal rod and cone photoreceptor cells rely significantly on glycolysis.Lactate released from photoreceptor cells fuels neighboring retinal pigment epithelium cells and müller glial cells through oxidative phosphorylation.To understand this highly heterogeneous metabolic environment around photoreceptor cells, single-cell analysis is needed.Here, we visualized cellular amp-activated protein kinase (ampk) activity and atp levels in the retina by two-photon microscopy.Transgenic mice expressing a hy bret-ampk biosensor were used for measuring the ampk activity.Go-ateam2 transgenic mice were used for measuring the atp level.Temporal metabolic responses were successfully detected in the live retinal explants upon drug perfusion.A glycolysis inhibitor, 2-deoxy-d-glucose (2-dg), activated ampk and reduced atp.These effects were clearly stronger in rods than in cones.Notably, rod ampk and atp started to recover at 30 min from the onset of 2-dg perfusion.Consistent with these findings, ex vivo electroretinogram recordings showed a transient slowdown in rod dim flash responses during a 60-min 2-dg perfusion, whereas cone responses were not affected.Based on these results, we propose that cones surrounded by highly glycolytic rods become less dependent on glycolysis, and rods also become less dependent on glycolysis within 60 min upon the glycolysis inhibition.

Journal: FASEB journal : official publication of the Federation of American Societies for Experimental Biology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Protocol for quantifying the odor detection threshold of mice.

Perceptual measures of odor threshold provide a mechanism to compare sensitivity across species and to gauge stimulus concentrations for functional experiments.Here, we present a protocol to precisely quantify the odor detection threshold of mice.We describe the construction of a head-fixed operant conditioning behavioral rig and provide details of the training and testing procedures.This approach can be used to compare the sensitivity of mice across odorants and to quantify detection differences associated with genetic mutations or pharmacological manipulations.For complete details on the use and execution of this protocol, please refer to johnson et al.(2023),1jennings et al.(2022),2williams and dewan (2020),3and dewan et al.(2018).4.

Journal: STAR protocols (2023)
Publication types: Journal Article
Evaluation of the Clinical, Technical, and Financial Aspects of Cost-Effectiveness Analysis of Artificial Intelligence in Medicine: Scoping Review and Framework of Analysis.

Cost-effectiveness analysis of artificial intelligence (ai) in medicine demands consideration of clinical, technical, and economic aspects to generate impactful research of a novel and highly versatile technology.Objective we aimed to systematically scope existing literature on the cost-effectiveness of ai and to extract and summarize clinical, technical, and economic dimensions required for a comprehensive assessment.Methods a scoping literature review was conducted to map medical, technical, and economic aspects considered in studies on the cost-effectiveness of medical ai.Based on these, a framework for health policy analysis was developed.Results among 4820 eligible studies, 13 met the inclusion criteria for our review.Internal medicine and emergency medicine were the clinical disciplines most frequently analyzed.Most of the studies included were from the united states (5/13, 39%), assessed solutions requiring market access (9/13, 69%), and proposed optimization of direct resources as the most frequent value proposition (7/13, 53%).On the other hand, technical aspects were not uniformly disclosed in the studies we analyzed.A minority of articles explicitly stated the payment mechanism assumed (5/13, 38%), while it remained unspecified in the majority (8/13, 62%) of studies.Conclusions current studies on the cost-effectiveness of ai do not allow to determine if the investigated ai solutions are clinically, technically, and economically viable.Further research and improved reporting on these dimensions seem relevant to recommend and assess potential use cases for this technology.

Journal: JMIR medical informatics (2022)
Publication types: Journal Article;Review
Belowground facilitation and trait matching: two or three to tango?

High biodiversity increases ecosystem functions; however, belowground facilitation remains poorly understood in this context.Here, we explore mechanisms that operate via 'giving-receiving feedbacks' for belowground facilitation.These include direct effects via root exudates, signals, and root trait plasticity, and indirect biotic facilitation via the effects of root exudates on soil biota and feedback from biota to plants.We then highlight that these two- or three-way mechanisms must affect biodiversity-ecosystem function relationships via specific combinations of matching traits.To tango requires a powerful affinity and harmony between well-matched partners, and such matches link belowground facilitation to the effect of biodiversity on function.Such matching underpins applications in intercropping, forestry, and pasture systems, in which diversity contributes to greater productivity and sustainability.

Journal: Trends in plant science (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.;Review
Application and effect of hybrid grinding techniques on the quality of stone chakkiatta(whole wheat flour) and flat bread.

Industrially packaged whole wheat flour (atta) is manufactured in motorized stonechakkis, which consumes more electric power.Present study is aimed towards evaluating the effect of hybrid grinding technique of wheat using roller mill on its grinding characteristics and quality of chakkiattaandchapatti.Wheat was passed through the pair of first break rolls in mlu 202 with the roll gaps of 1 and 0.9 mm for two different samples.Electrical parameters for grinding energy were compared and the pre-milled wheat was ground in the stonechakki.attaobtained from 2 different variations and control stonechakki attawere compared for physico-chemical, rheological and chapati making quality.Damaged starch increased from 15.25 for controlattato 17.3% for 0.9 mm sample, whereas, farinograph water absorption increased from 75.9 to 78.9% respectively.chapatiswere prepared and sensory studies were carried out.Chapati colour was found to be brighter for 0.9 mm sample.

Journal: Journal of food science and technology (2022)
Publication types: Journal Article
Effect of camel milk in asthmatic children: A double-blind randomized pilot study.

Asthma is one of the prevalent diseases in children.There is some evidence regarding the benefits of camel milk in asthma.The present study was carried out to evaluate the effect of camel milk on asthmatic children.Patients and methods a randomized double-blind pilot study was operated in 2018 in a tertiary center.Sixty children aged more than 6 years with not well-controlled asthma were included.The intervention was consisting of 200-ml camel milk or placebo daily for 2 months.The medication regimen and spirometry parameters were assessed before and after the intervention.Data were analyzed using spss software.Results a total of 57 patients completed the trial.Patients were similar in demographic and baseline characteristics (p &gt; 0.05).There was a significant difference between groups after intervention in use of inhaled corticosteroids (96.7% vs.70.4%, p value = 0.01), short-acting beta-agonists (53.3% vs.29.6%, p value = 0.0001) and long-acting beta-agonists (53.3% vs.40.7%, p value = 0.04) in control and intervention, respectively.The percent of changes in forced expiratory volume (fev1) in the control and intervention groups was 18.54 ± 14.89 and 21.89 ± 17.83, respectively (p = 0.19).The percent of changes in fev1/forced vital capacity (fvc) in the control and intervention groups was 8.11 ± 7.12 and 11.11 ± 8.33, respectively (p = 0.14).Conclusion in our pilot study, some children with asthma may benefit from camel milk.Further studies would be useful to evaluate this hypothesis.

Journal: Pediatric pulmonology (2022)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Putative Activation of the CB1 Cannabinoid Receptors Prevents Anxiety-Like Behavior, Oxidative Stress, and GABA Decrease in the Brain of Zebrafish Submitted to Acute Restraint Stress.

Anxiety disorder is a well-recognized condition observed in subjects submitted to acute stress.Although the brain mechanisms underlying this disorder remain unclear, the available evidence indicates that oxidative stress and gabaergic dysfunction mediate the generation of stress-induced anxiety.Cannabinoids are known to be efficient modulators of behavior, given that the activation of the cannabinoid receptors type-1 (cb1 receptors) induces anxiolytic-like effects in animal models.In the present study, we aimed to describe the effects of the stimulation of the cb1 receptors on anxiety-like behavior, oxidative stress, and the gaba content of the brains of zebrafish submitted to acute restraint stress (ars).The animals submitted to the ars protocol presented evident anxiety-like behavior with increased lipid peroxidation in the brain tissue.The evaluation of the levels of gaba in the zebrafish telencephalon presented decreased levels of gaba in the ars group in comparison with the control.Treatment with acea, a specific cb1 receptor agonist, prevented ars-induced anxiety-like behavior and oxidative stress in the zebrafish brain.Acea treatment also prevented a decrease in gaba in the telencephalon of the animals submitted to the ars protocol.Overall, these preclinical data strongly suggest that the cb1 receptors represent a potential target for the development of the treatment of anxiety disorders elicited by acute stress.

Journal: Frontiers in behavioral neuroscience (2020)
Publication types: Journal Article
Survey of Airborne Microorganisms in an Arcade-Type Traditional Market in Anseong, South Korea.

We aimed to analyze airborne microorganisms and assess air quality, temperature, and relative humidity at “j” market, an arcade-type traditional market in anseong (south korea).Measurements were taken 16 times, twice per quarter (january, april, july, and october), at both the entrance and intersection of the market in 2020.The concentrations of airborne bacteria and fungi at the entrance and intersection were highest in october and lowest in april; however, they were below the recommended indoor levels (airborne bacteria: <800 cfu/m3, airborne fungi: <500 cfu/m3) in january (second measurement) and april (first and second measurements).The concentrations of microbes during the first measurement in january and both measurements in july and october exceeded the allowed limits.The concentration of microorganisms exceeded the acceptable levels at relative humidity ≥60%.At all time points, except during the eighth survey, when the microorganisms were too numerous to count, microbial concentrations were higher at the intersection than at the entrance.It was confirmed that the microorganisms detected in this experiment were 26 species of bacteria and 21 species of fungi.Three of the four species of bacteria and fungi detected in more than 50% of the 16 experimental results were pathogenic.Our findings suggest that air purification systems must be installed in the market to improve sanitary conditions.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
EGCG overcomes gefitinib resistance by inhibiting autophagy and augmenting cell death through targeting ERK phosphorylation in NSCLC.

Several egfr-tyrosine kinase inhibitors (tkis), such as gefitinib (gef), have been used as effective clinical therapies for patients with non-small cell lung cancer (nsclc).However, due to acquired resistance, the efficacy of gef treatment is severely blocked.Our preliminary study found that epigallocatechin gallate (egcg) in combination with gef could work synergistically to increase the sensitivity to gef in nsclc, but the mechanisms responsible for this have not been completely defined.Purpose in our present study, we devoted to investigate the synergistic effects of combined egcg and gef treatment and the importance of autophagy and erk signaling pathway in overcoming acquired drug resistance to gef in nsclc.Methods we evaluated the synergistic effects of combined egcg and gef treatment through in vitro cell proliferation/viability assays and in vivo xenograft studies, respectively.Autophagic flux was assessed by gfp-microtubule-associated protein 1 light chain 3 (lc3) plasmid transfection and western blot detection of autophagy-related proteins.Besides, the role of erk on acquired resistance was validated with a erk inhibitor.Results we discovered that egcg can synergize with gef to inhibit the proliferation of gef-resistant nsclc cells and suppress tumor growth in a xenograft mouse model.The underlying mechanisms of synergism were investigated, and the results showed that co-treatment with gef and egcg could inhibit gef-induced autophagy and erk phosphorylation.Consistently, the expression of lc3-ii/i and atg5 were inhibited, whereas the expression of p62 was enhanced in egcg and gef combination treatment groups.Further, inhibition of autophagy in gef-resistant a549 cells could augment cell death.Conclusion in conclusion, egcg overcomes gef resistance by inhibiting autophagy and augmenting cell death through targeting erk pathway in nsclc.Gef and egcg combination therapy may be an effective strategy to overcome acquired resistance in nsclc.

Journal: OncoTargets and therapy (2019)
Publication types: Journal Article
LncRNA HOXB-AS3 promotes growth, invasion and migration of epithelial ovarian cancer by altering glycolysis.

Heading aims lnc rna hoxb-as3 is proved as an oncogene in tumors.Herein, we determine the function and mechanism of hoxb-as3 in epithelial ovarian cancer (eoc) cells.Materials and methods chi-square test, kaplan-meier (km) analysis and cox regression analysis were used to analyze the clinicopathological features of hoxb-as3 in eoc patients.Cck8, transwell and wound healing assay were used to test the function of hoxb-as3.Luciferase reporter assay, western blot and glycolysis rate assay were used for further mechanistic studies.Key findings hoxb-as3 was abundantly expressed in eoc tissues, and higher levels of hoxb-as3 in eoc patients were significantly associated with disease status and overall survival status.Eoc patients with high levels of hoxb-as3 had strikingly shorter disease-free survival (dfs) and overall survival (os) times than those with low levels.Hoxb-as3 also might as an independent prognostic factor.Further study revealed knockdown of hoxb-as3 significantly inhibited the proliferation, invasion and migration of eoc cells.Mechanistic investigations suggested that knockdown of hoxb-as3 could decrease lactate dehydrogenase a (ldha) expression and the extracellular acidification rate (ecar) by sponging mi r-378a-3p.Significance to our knowledge, this is the first study to suggest that hoxb-as3 could crosstalk with mi rna in the cytoplasm and alter glycolysis in cancer cells.Our results improve our understanding of the mechanism of hoxb-as3 and suggest that hoxb-as3 can act as a predictor of os and a target for eoc therapies.

Journal: Life sciences (2021)
Publication types: Journal Article
Methylation profiles of global LINE-1 DNA and the GSTP1 promoter region in children exposed to lead (Pb).

Lead (pb) exposure has adverse health effects and altered dna methylation may contribute to pb toxicity.Line-1 is an interspersed repeated dna that is used as a surrogate marker for estimating genomic dna methylation levels, and gstp1 is an isozyme that detoxifies xenobiotics like pb, and its expression is inhibited by methylation.Thus, to assess the effects of pb exposure on global hypomethylation and gene-specific promoter hypermethylation, we examined dna methylation at line-1 repetitive elements and the gstp1 promoter region.Blood samples were obtained from children (n = 123) living in pb-polluted areas (as exposed children) and children (n = 63) living in pb-unpolluted areas (as control children) in kabwe, zambia.Icp-ms was used to determine blood lead levels (blls), and pyrosequencing and a fluorescence-based polymerase chain reaction assay were used to determine levels of line-1 methylation and gstp1 promoter methylation, respectively.Inverse association was found between blls and line-1 methylation (β = - 0.046,p= 0.006).The highest quartile of bll had significant hypomethylation of line-1 (pfor trend = 0.03), suggesting the higher the bll, the lower line-1 methylation.Gstp1 methylation levels did not differ significantly between the two areas (p= 0.504), nor was it associated with pb poisoning risk (or = 1.03,p= 0.476), indicating gstp1 methylation may not be a reliable biomarker of pb exposure in healthy people.Therefore, pb-related health problems could result from global dna methylation changes due to high blls.

Journal: Epigenetics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Predictive modeling of groundwater nitrate pollution and evaluating its main impact factors using random forest.

Groundwater quality in plains and basins of arid and semi-arid regions with increased agriculture and urbanization development faces severe nitrate pollution, which is affected by both climate and anthropogenic activities.Here, shallow groundwater nitrate concentrations in the yinchuan region in central yinchuan plain were modeled during 2000, 2005, 2010, and 2015 using random forest.Multiple spatial environment factors were taken as predictor variables.The relative importance of these factors was also calculated using the constructed model.Remote sensing and gis methods were used to compile various environmental factors to generate training and test sets for training and validation of the random forest model.Mean absolute error (mae), root mean square error (rmse), and coefficient of determination (r2) between the observed and predicted groundwater nitrate concentrations were used to measure the model performance.As indicated by these metrics, the random forest model for groundwater nitrate prediction was performed well.The relative importance of the predictor variables computed by the model indicated groundwater nitrate was mainly affected by the distance to the yellow river, meteorological elements (precipitation, evaporation, and mean air temperature), and water level elevation.Additionally, urban and arable land were the two land use/land cover types that mainly influenced groundwater nitrate concentration in the yinchuan region, of which urban land was more influential than arable land as a result of intense expansion of urban land from 2000 to 2015.Overall, the current study provides an approach to integrate multiple environmental factors for groundwater quality study and is also significant for sustainable groundwater management in the yinchuan region.

Journal: Chemosphere (2022)
Publication types: Journal Article
A randomized, placebo-controlled clinical development program exploring the use of litoxetine for treating urinary incontinence.

S to investigate the safety and efficacy of litoxetine, a serotonin reuptake inhibitor, in treating urinary incontinence (ui) and mixed urinary incontinence (mui).Methods two randomized, double-blind, placebo-controlled clinical trials (rct1 and rct2) were conducted.Rct1, which included 196 women aged 18-75 with mui randomized 1:1:1:1 to receive 10, 20, or 40 mg litoxetine or placebo orally twice daily (bid) for 12 weeks, investigated the efficacy (including changes in patient reported outcomes) and safety of litoxetine compared to placebo.Rct2, which included 82 men and women aged 18-70 with any ui type randomly assigned 2:1 to receive 30 mg litoxetine or placebo orally bid for 8 weeks including a 2 week dose titration period, investigated the safety (including psychiatric safety) and efficacy of litoxetine compared to placebo.Efficacy was measured as the change in number of incontinence episodes per week and assessed using an analysis of covariance with missing data imputed by predictive mean matching.Safety was assessed by adverse events (aes) and physical examinations and analyzed using descriptive statistics.Results the 30-mg and placebo groups in rct2 showed no difference in frequency of aes, and litoxetine reduced the number of incontinence episodes per week compared to placebo.Although rct1 suffered an unexpectedly high placebo response, and therefore did not meet the primary efficacy endpoint, 71% of participants receiving 40 mg litoxetine reported a clinically meaningful improvement in the king's health questionnaire.Conclusions litoxetine may be a safe, effective and well-tolerated treatment for patients with ui.

Journal: Neurourology and urodynamics (2021)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Exploration of spatial clustering in maternal health continuum of care across districts of India: A geospatial analysis of demographic and health survey data.

Introduction the continuum of care (co c) throughout pregnancy, delivery and post-delivery has recently been highlighted as an integrated intervention programme for maternal, new-born, and child health.Existing literature suggests the importance of continuum of care (co c) for improved maternal and child health outcomes.However due to unavailability of data at the lowest administrative levels, literature on spatial pattern of uptake of full co c is lacking.The present study attempts to focus on the spatial analysis of co c in maternal health care in india.Data and methods the study is based on the fourth round of national family health survey data conducted in 2015-16 in india.The outcome variable used is maternal health continuum of care which includes- at least 4 anc visits, delivery through skilled birth attendant and postnatal check-up within 48 hours of delivery.Univariate and bivariate local indicator of spatial association (lisa) maps have been generated to show the spatial pattern of co c across 640 districts in india.We also employed spatial regression techniques to explore the determinants of co c.Findings percentage of women who followed full co c was observed to be least for east kameng (0.0%) district of arunachal pradesh and highest in north goa district (90.4%).Majority of districts where uptake of full co c was more than 80 percent were found concentrated in southern region on india.Equivalently, findings indicated a strong spatial clustering of full co c with high-high clusters mostly concentrated in southern districts.Low-low district clusters are concentrated in the states of uttar pradesh, bihar and madhya pradesh.For complete co c the global moran's i is 0.73 indicating the spatial dependence.The spatial regression analysis suggested that modern contraceptive use, meeting with health worker, urbanization and secondary or above education for women have positive impact on the utilisation of co c.Conclusion the spatial pattern indicates district level clustering in uptake of co c among women.The study suggests policymakers and stakeholders to implement comprehensive interventions at sub-regional levels for ensuring the completion of co c for women which acts as a preventive measure for adverse outcomes such as-maternal and child mortality.

Journal: PloS one (2022)
Publication types: Journal Article