syedzayyan/paper_mill_benchmark huggingface dataset:
Antioxidant and Antimicrobial Activity of Algal and Cyanobacterial Extracts: An In Vitro Study.

Algae and cyanobacteria, other than their nutritional value, possess different beneficial properties, including antioxidant and antimicrobial ones.Therefore, they can be considered functional ingredients in animal feed and natural substitutes for antibiotics.The aim of this study was to evaluate the antioxidant and antimicrobial capacity against porcine o138 e.Coli of ascophyllum nodosum, chlorella vulgaris, lithotamnium calcareum, schizochytrium spp.As algal species and arthrospira platensis as cyanobacteria.The antioxidant capacity was determined by abts radical cation decolorization assay testing at three different concentrations (100%; 75%; 50%).The growth inhibition effect of the extracts at concentrations of 25%, 12.5%, 6%, 3% and 1.5% against porcine o138 e.Coli was genetically characterized by pcr to detect the presence of major virulence factors; this was evaluated by following the microdilution bacterial growth method.The abts assay disclosed that ascophyllum nodosum was the compound with the major antioxidant properties (57.75 ± 1.44 percentage of inhibition; p < 0.0001).All the extracts tested showed growth inhibition activity at a concentration of 25%.Among all extracts, a.Nodosum was the most effective, showing a significant growth inhibition of e.Coli; in particular, the log10 cells/m l of e.Coli used as a control resulted in a significantly higher concentration of 25% and 12.5% after 4 h (8.45 ± 0.036 and 7.22 ± 0.025 log10 cells/m l, respectively; p < 0.005).This also suggests a dose-dependent relationship between the inhibitory activity and the concentration.Also, a synergistic effect was observed on antioxidant activity for the combination of ascophyllum nodosum and lithotamnium calcareum (p < 0.0001).Moreover, to determine if this combination could affect the viability of the ipec-j2 cells under the normal or stress condition, the viability and membrane integrity were tested, disclosing that the combination mitigated the oxidative stress experimentally induced by increasing the cell viability.In conclusion, the results obtained highlight that the bioactive compounds of algal species are able to exert antioxidant capacity and modulate o138 e.Coli growth.Also, the combination of ascophyllum nodosum and lithotamnium calcareum species can enhance their bioactivity, making them a promising functional feed additive and a suitable alternative to antibiotics.

Journal: Antioxidants (Basel, Switzerland) (2022)
Publication types: Journal Article
Single-cell analysis of endometriosis reveals a coordinated transcriptional programme driving immunotolerance and angiogenesis across eutopic and ectopic tissues.

Endometriosis is characterized by the growth of endometrial-like tissue outside the uterus.It affects many women during their reproductive age, causing years of pelvic pain and potential infertility.Its pathophysiology remains largely unknown, which limits early diagnosis and treatment.We characterized peritoneal and ovarian lesions at single-cell transcriptome resolution and compared them to matched eutopic endometrium, unaffected endometrium and organoids derived from these tissues, generating data on over 122,000 cells across 14 individuals.We spatially localized many of the cell types using imaging mass cytometry.We identify a perivascular mural cell specific to the peritoneal lesions, with dual roles in angiogenesis promotion and immune cell trafficking.We define an immunotolerant peritoneal niche, fundamental differences in eutopic endometrium and between lesion microenvironments and an unreported progenitor-like epithelial cell subpopulation.Altogether, this study provides a holistic view of the endometriosis microenvironment that represents a comprehensive cell atlas of the disease in individuals undergoing hormonal treatment, providing essential information for future therapeutics and diagnostics.

Journal: Nature cell biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural;Research Support, U.S. Gov't, Non-P.H.S.
Crosstalk between TLR4 and Notch1 signaling in the IgA nephropathy during inflammatory response.

Ig a nephropathy (ig an) is an immune complex-mediated disease involved in the kidney disease.Recent studies have revealed that notch signaling-related genes are aberrantly expressed in various cell types and maybe associate with inflammation-induced carcinogenesis.The aim of our study was to investigate the function of notch1 in the inflammatory response of ig an.Methods the expression of notch1, jagged1 and nicd1 in 52 ig an renal tissues and 20 control renal tissues was first determined using quantitative real-time pcr and western blot.Elisa was then used to estimate the inflammatory response of human podocytes to lps.Nf-κb activity was measured using dual-luciferase reporter assay.Activation of notch1 and nf-κb signaling pathway was assessed using western blot.Results the expression of notch1, nicd1 and jagged1 was significantly higher in ig an renal tissues than control renal tissues (p < 0.05).Lps treatment resulted in an obvious increase of mcp-1, il-8 and phosphorylated nf-κb p65 in podocytes polymeric ig a (p ig a) ig an group compared to control group (p < 0.05 for all).Activated notch1 and its target genes, hes1 and hey1 were also enhanced upon lps stimulation.Silencing of notch1 signaling with inhibitor dapt, nf-κb activation and lps-induced inflammatory response were obviously attenuated, whereas notch1 activator jagged1 could markedly restore nf-κb activity and lps-induced inflammatory response (p < 0.05 for all).Conclusions crosstalk between tlr4 and notch1 signaling regulates the inflammatory response in the ig an and maybe plays an important role in the progression of ig an.

Journal: International urology and nephrology (2018)
Publication types: Journal Article
Metal complexes as optical probes for DNA sensing and imaging.

Transition and lanthanide metal complexes have rich photophysical properties that can be used for cellular imaging, biosensing and phototherapy.One of the applications of such luminescent compounds is the detection and visualisation of nucleic acids.In this brief review, we survey the recent literature on the use of luminescent metal complexes (including re i, ru ii, os ii, ir iii, pt ii, eu iiiand tb iii) as dna optical probes, including examples of compounds that bind selectively to non-duplex dna topologies such as quadruplex, i-motif and dna mismatches.We discuss the applications of metal-based luminescent complexes in cellular imaging, including time-resolved microscopy and super-resolution techniques.Their applications in biosensing and phototherapy are briefly mentioned in the relevant sections.

Journal: Current opinion in chemical biology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Towards the Development of AgoKirs: New Pharmacological Activators to Study Kir2.x Channel and Target Cardiac Disease.

Inward rectifier potassium ion channels (ik1-channels) of the kir2.x family are responsible for maintaining a stable negative resting membrane potential in excitable cells, but also play a role in processes of non-excitable tissues, such as bone development.Ik1-channel loss-of-function, either congenital or acquired, has been associated with cardiac disease.Currently, basic research and specific treatment are hindered by the absence of specific and efficient kir2.x channel activators.However, twelve different compounds, including approved drugs, show off-target ik1activation.Therefore, these compounds contain valuable information towards the development of agonists of kirchannels, ago kirs.We reviewed the mechanism of ik1channel activation of these compounds, which can be classified as direct or indirect activators.Subsequently, we examined the most viable starting points for rationalized drug development and possible safety concerns with emphasis on cardiac and skeletal muscle adverse effects of ago kirs.Finally, the potential value of ago kirs is discussed in view of the current clinical applications of potentiators and activators in cystic fibrosis therapy.

Journal: International journal of molecular sciences (2020)
Publication types: Journal Article;Review
Anterior Translocation of the Right Pulmonary Artery to Relieve Bronchial Compression in Truncus Arteriosus With Interrupted Aortic Arch.

We report an anterior translocation of the right pulmonary artery procedure to relieve severe left bronchial obstruction that was caused by right pulmonary artery stent placement in a 1-year-old patient with truncus arteriosus and interrupted aortic arch.After neonatal repair, the patient re-presented with severe truncal valve regurgitation, right pulmonary artery stenosis, and severe biventricular dysfunction, which was treated with truncal valve repair and right pulmonary artery plasty.The patient suffered from left bronchial compression from right pulmonary artery stent placement, which was successfully treated by the translocation procedure.Bronchial stenosis was successfully relieved by the translocation procedure.Indications, advantages, and disadvantages of this procedure are discussed.

Journal: World journal for pediatric & congenital heart surgery (2022)
Publication types: Case Reports;Journal Article
A Novel Evaluation Model for a Mixed-Reality Surgical Navigation System: Where Microsoft HoloLens Meets the Operating Room.

Holo lens-based mixed-reality surgical navigation system (mr-sns) technology has made great progress.However, the methodology for evaluating users' perceptions concerning the safety, comfort, and efficiency of mr-sns is still in its infancy.This study was intended to develop a method to systematically evaluate an existing mr-sns system during actual clinical applications.This method differs from other existing methods currently used in industry, education, and device maintenance.Based on analytical hierarchy process theory and ergonomics evaluation methods, in this article, we propose a novel multicriteria evaluation model for a holo lens-based mr-sns.The model includes factors such as comfort, safety, and effectiveness, and is performed in an actual clinical application.A comprehensive experimental platform and scoring system that can analyze all indicators was built.The validation test showed no statistically significant differences in the accuracy of the 3 different movement patterns (p= .95,p> .05).However, the static pattern showed the best accuracy.In addition, no significant difference (p= .68,p> .05) in accuracy was found under 4 kinds of illuminance.A comparison of the results of this evaluation model and the input from experts who use the holo lens-based mr-sns in hospitals, indicated that this model has good precision (100%), recall (80%), and f1-measure (88.89%).The results highlighted the full efficacy of the proposed model in determining whether this system can be used in clinical trials to provide indicators for preliminary ex ante feasibility studies.This article describes the lessons learned from conducting this evaluation study of mr-sns as part of the design process.

Journal: Surgical innovation (2020)
Publication types: Evaluation Study;Journal Article
Enforcing Extended Porphyrin J-Aggregate Stacking in Covalent Organic Frameworks.

The potential of covalent organic frameworks (cofs) for realizing porous, crystalline networks with tailored combinations of functional building blocks has attracted considerable scientific interest in the fields of gas storage, photocatalysis, and optoelectronics.Porphyrins are widely studied in biology and chemistry and constitute promising building blocks in the field of electroactive materials, but they reveal challenges regarding crystalline packing when introduced into cof structures due to their nonplanar configuration and strong electrostatic interactions between the heterocyclic porphyrin centers.A series of porphyrin-containing imine-linked cofs with linear bridges derived from terephthalaldehyde, 2,5-dimethoxybenzene-1,4-dicarboxaldehyde, 4,4'-biphenyldicarboxaldehyde and thieno[3,2- b]thiophene-2,5-dicarboxaldehyde, were synthesized, and their structural and optical properties were examined.By combining x-ray diffraction analysis with density-functional theory (dft) calculations on multiple length scales, we were able to elucidate the crystal structure of the newly synthesized porphyrin-based cof containing thieno[3,2- b]thiophene-2,5-dicarboxaldehyde as linear bridge.Upon cof crystallization, the porphyrin nodes lose their 4-fold rotational symmetry, leading to the formation of extended slipped j-aggregate stacks.Steady-state and time-resolved optical spectroscopy techniques confirm the realization of the first porphyrin j-aggregates on a > 50 nm length scale with strongly red-shifted q-bands and increased absorption strength.Using the cof as a structural template, we were thus able to force the porphyrins into a covalently embedded j-aggregate arrangement.This approach could be transferred to other chromophores; hence, these cofs are promising model systems for applications in photocatalysis and solar light harvesting, as well as for potential applications in medicine and biology.

Journal: Journal of the American Chemical Society (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Design, synthesis and evaluation of tryptophan analogues as tool compounds to study IDO1 activity.

The metabolism of l-tryptophan to n-formyl-l-kynurenine by indoleamine-2,3-dioxygenase 1 (ido1) is thought to play a critical role in tumour-mediated immune suppression.Whilst there has been significant progress in elucidating the overall enzymatic mechanism of ido1 and related enzymes, key aspects of the catalytic cycle remain poorly understood.Here we report the design, synthesis and biological evaluation of a series of tryptophan analogues which have the potential to intercept putative intermediates in the metabolism of 1 by ido1.Functionally-relevant binding to ido1 was demonstrated through enzymatic inhibition, however no ido1-mediated metabolism of these compounds was observed.Subsequent tm-shift analysis shows the most active compound, 17, exhibits a distinct profile from known competitive ido1 inhibitors, with docking studies supporting the hypothesis that 17 may bind at the recently-discovered sisite.These findings provide a start-point for development of further mechanistic probes and more potent tryptophan-based ido1 inhibitors.

Journal: RSC chemical biology (2021)
Publication types: Journal Article
Netarsudil for the Treatment of Open-Angle Glaucoma and Ocular Hypertension: A Literature Review.

To evaluate netarsudil's role as first-line therapy for the treatment of open-angle glaucoma (oag) and ocular hypertension (oht).Data sources a literature search utilizing medline and cinahl was performed usingnetarsudiland ar-13324as keywords.Studies published from january 1970 to september 2020 were eligible.Study selection and data extraction for inclusion, articles were required to be published in english and participants enrolled in phase i, ii, or iii clinical trials.Articles were excluded if netarsudil was coformulated with another medication.Preclinical research, case reports, case series, review articles, citations without an abstract, and newsletters were excluded.Literature review the search retrieved 97 unique citations; 90 results were excluded, and 7 studies were included for analysis.Relevance to patient care and clinical practice in all, 20 years elapsed between the food and drug administration's approvals of distinct medications to treat oag.Existing first-line therapies target the uveoscleral pathway, which is responsible for a small amount of aqueous humor outflow.Rho kinase inhibitors target the trabecular pathway, which is responsible for 90% of aqueous humor outflow; thus, rho kinase inhibitors may significantly reduce intraocular pressure and improve clinical outcomes for patients with oag or oht.Conclusions evidence demonstrates that netarsudil is inferior to prostaglandin analogues and noninferior to topical β-blockers in the treatment of oag and oht.Hyperemia is a common adverse drug reaction, which often resolves after medication discontinuation.Additional phase iii clinical trials and evidence-based guidelines are necessary to determine netarsudil's position in oag and oht management.

Journal: The Annals of pharmacotherapy (2021)
Publication types: Journal Article;Review
Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital.

S mdr bacteria have become a prevailing health threat worldwide.We here aimed to use optical dna mapping (odm) as a rapid method to trace nosocomial spread of bacterial clones and gene elements.We believe that this method has the potential to be a tool of pivotal importance for mdr control.Methods twenty-four escherichia coli samples of st410 from three different wards were collected at an ethiopian hospital and their plasmids were analysed by odm.Plasmids were specifically digested with cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging.The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria.Results odm demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the esbl gene bla ctx-m-15, suggesting clonal spread.The results correlate perfectly with core genome (cg)mlst data, where bacteria with the same plasmid also had very similar cg mlst profiles.Conclusions odm is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes.Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread.We propose that plasmid typing can be a useful tool to identify clonal spread of mdr bacteria.Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.

Journal: The Journal of antimicrobial chemotherapy (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Comparing the effectiveness of vitamin D plus iron vs vitamin D on depression scores in anemic females: Randomized triple-masked trial.

Low levels of 25-hydroxyvitamin d (25(oh)d) have been related to depression and anxiety.It seems that anemia is associated with vitamin d deficiency.We aimed to evaluate the effects of iron-vitamin d co-supplementation versus vitamin d alone on depression scores in anemic females with low levels of serum 25-hydroxyvitamin d.methods:this randomized controlled trial was conducted on eighty premenopausal females who were recruited between may 2015 and october 2015 from primary health care centers.Women with anemia and low concentrations of 25(oh)d were randomized to either 1000 iu/d vitamin d plus 27 mg/d iron (d-fe) or vitamin d plus placebo supplements (d-p) for 12 weeks.Depressive and anxious symptoms were evaluated with the beck depression inventory (bdi) with subscales 1-13 and 14-21 and beck anxiety inventory (bai).To compare the groups, mann-whitney or chi-squared tests were used and within groups comparison was performed using wilcoxon signed ranks test.The study was registered on www.clinicaltrial.org as nc 01876563.results:the serum concentrations of 25(oh)d were increased significantly in both groups at the end of the study.In both groups, there was a significant improvement in total bdi, the bdi subscale, and the bai scores (p 0.05).conclusion:although the potential positive effect of vitamin d on mental health was evident, iron plus vitamin d co-supplementation did not demonstrate any significant benefits over vitamin d alone, neither in depression score reduction nor anxiety symptoms.

Journal: Medical journal of the Islamic Republic of Iran (2019)
Publication types: Journal Article
Multiple Exon Skipping in the Duchenne Muscular Dystrophy Hot Spots: Prospects and Challenges.

Duchenne muscular dystrophy (dmd), a fatal x-linked recessive disorder, is caused mostly by frame-disrupting, out-of-frame deletions in thedystrophin(dmd) gene.Antisense oligonucleotide-mediated exon skipping is a promising therapy for dmd.Exon skipping aims to convert out-of-frame m rna to in-frame m rna and induce the production of internally-deleted dystrophin as seen in the less severe becker muscular dystrophy.Currently, multiple exon skipping has gained special interest as a new therapeutic modality for this approach.Previous retrospective database studies represented a potential therapeutic application of multiple exon skipping.Since then, public dmd databases have become more useful with an increase in patient registration and advances in molecular diagnosis.Here, we provide an update on dmdgenotype-phenotype associations using a global dmd database and further provide the rationale for multiple exon skipping development, particularly for exons 45−55 skipping and an emerging therapeutic concept, exons 3−9 skipping.Importantly, this review highlights the potential of multiple exon skipping for enabling the production of functionally-corrected dystrophin and for treating symptomatic patients not only with out-of-frame deletions but also those with in-frame deletions.We will also discuss prospects and challenges in multiple exon skipping therapy, referring to recent progress in antisense chemistry and design, as well as disease models.

Journal: Journal of personalized medicine (2018)
Publication types: Journal Article;Review
Layer-specific activation in human primary somatosensory cortex during tactile temporal prediction error processing.

The human brain continuously generates predictions of incoming sensory input and calculates corresponding prediction errors from the perceived inputs to update internal predictions.In human primary somatosensory cortex (area 3b), different cortical layers are involved in receiving the sensory input and generation of error signals.It remains unknown, however, how the layers in the human area 3b contribute to the temporal prediction error processing.To investigate prediction error representation in the area 3b across layers, we acquired layer-specific functional magnetic resonance imaging (f mri) data at 7t from human area 3b during a task of index finger poking with no-delay, short-delay and long-delay touching sequences.We demonstrate that all three tasks increased activity in both superficial and deep layers of area 3b compared to the random sensory input.The f mri signal was differentially modulated solely in the deep layers rather than the superficial layers of area 3b by the delay time.Compared with the no-delay stimuli, activity was greater in the deep layers of area 3b during the short-delay stimuli but lower during the long-delay stimuli.This difference activity features in the superficial and deep layers suggest distinct functional contributions of area 3b layers to tactile temporal prediction error processing.The functional segregation in area 3b across layers may reflect that the excitatory and inhibitory interplay in the sensory cortex contributions to flexible communication between cortical layers or between cortical areas.

Journal: NeuroImage (2022)
Publication types: Journal Article;Research Support, N.I.H., Intramural;Research Support, Non-U.S. Gov't