syedzayyan/paper_mill_benchmark huggingface dataset:
Metabolic Alterations Induced by Kudingcha Lead to Cancer Cell Apoptosis and Metastasis Inhibition.

Kudingcha is implicated in alleviating metabolic disorders in traditional chinese medicine.However, the role of kudingcha, one of the ligustrum robustum species, in metabolic regulations and its antitumor activity in triple-negative breast cancer (tnbc) remains to be determined.Two breast cancer cell lines and immunocompetent and immunodeficient mice were used to evaluate the therapeutic effects of kudingcha treatment.The production of reactive oxygen species (ros) and glucose uptake were examined by flow cytometry.Metabolic shift was examined by metabonomics and western blot analysis.In this study, we found that aqueous extract of kudingcha dose dependently inhibited cell growth and induced apoptosisin vitroandin vivo.moreover, kudingcha supplementation significantly reduced cancer metastasis.Kudingcha significantly inhibited glycolysis and glutamine metabolism.In addition, we demonstrated that the antitumor effects of kudingcha were dependent on ros production, which was increased by β-oxidation and oxidative phosphorylation.These findings provide a novel potential benefit of kudingcha from targeting the cancer metabolism.

Journal: Nutrition and cancer (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The z-sbDBA, a new concept for a dynamic sheet-based fluence field modulator in x-ray CT.

We present a new concept for dynamic fluence field modulation (ffm) in x-ray computed tomography (ct).The so-called z-aligned sheet-based dynamic beam attenuator (z-sb dba) is developed to dynamically compensate variations in patient attenuation across the fan beam and the projection angle.The goal is to enhance image quality and to reduce patient radiation dose.Methods the z-sb dba consists of an array of attenuation sheets aligned along thezdirection.In neutral position, the array is focused toward the focal spot.Tilting the z-sb dba defocuses the sheets, thus reducing the transmission for larger fan beam angles.The structure of the z-sb dba significantly differs from the previous sheet-based dynamic beam attenuator (sb dba) in two features: (a) the sheets of the z-sb dba are aligned parallel to the detector rows, and (b) the height of the sheets increases from the center toward larger fan beam angles.We built a motor actuated prototype of the z-sb dba integrated into a clinical ct scanner.In experiments, we investigated its feasibility for ffm.We compared the z-sb dba to common ct bowtie filters in terms of the spectral dependency of the transmission and possible image variance distribution in reconstructed phantom images.Additionally, the potential radiation dose saving using z-sb dba for region-of-interest (roi) imaging was studied.Results our experimental results confirm that the z-sb dba can realize variable transmission profiles of the radiation fluence by only small tilts.Compared to the sb dba, the z-sb dba can mitigate some practical and mechanical issues.In comparison to bowtie filters, the spectral dependency is considerably reduced when using the z-sb dba.Likewise, more homogeneous image variance distributions can be attained in reconstructed phantom images.The z-sb dba allows controlling the spatial image variance distribution which makes it suitable for roi imaging.Our comparison on roi imaging reveals skin dose reductions of up to 35% at equal roi image quality by using the z-sb dba.Conclusion our new concept for ffm in x-ray ct, the z-sb dba, was experimentally validated on a clinical ct scanner.It facilitates dynamic ffm by realizing variable transmission profiles across the fan beam angle on a projection-wise basis.This key feature allows for substantial improvements in image quality, a reduction in patient radiation dose, and additionally provides a technical solution for roi imaging.

Journal: Medical physics (2020)
Publication types: Journal Article
Tumor microenvironment involvement in colorectal cancer progressionviaWnt/β-catenin pathway: Providing understanding of the complex mechanisms of chemoresistance.

Colorectal cancer (crc) continues to be one of the main causes of death from cancer because patients progress unfavorably due to resistance to current therapies.Dysregulation of the wnt/β-catenin pathway plays a fundamental role in the genesis and progression of several types of cancer, including crc.In many subtypes of crc, hyperactivation of the β-catenin pathway is associated with mutations of theadenomatous polyposis coligene.However, it can also be associated with other causes.In recent years, studies of the tumor microenvironment (tme) have demonstrated its importance in the development and progression of crc.In this tumor nest, several cell types, structures, and biomolecules interact with neoplastic cells to pave the way for the spread of the disease.Cross-communications between tumor cells and the tme are then established primarily through paracrine factors, which trigger the activation of numerous signaling pathways.Crucial advances in the field of oncology have been made in the last decade.This minireview aims to actualize what is known about the central role of the wnt/β-catenin pathway in crc chemoresistance and aggressiveness, focusing on cross-communication between crc cells and the tme.Through this analysis, our main objective was to increase the understanding of this complex disease considering a more global context.Since many treatments for advanced crc fail due to mechanisms involving chemoresistance, the data here exposed and analyzed are of great interest for the development of novel and effective therapies.

Journal: World journal of gastroenterology (2022)
Publication types: Journal Article;Review
Rapid multistep kinetic model generation from transient flow data.

Today, the generation of kinetic models is still seen as a resource intensive and specialised activity.We report an efficient method of generating reaction profiles from transient flows using a state-of-the-art continuous-flow platform.Experimental data for multistep aromatic nucleophilic substitution reactions are collected from an automated linear gradient flow ramp with online hplc at the reactor outlet.Using this approach, we generated 16 profiles, at 3 different inlet concentrations and 4 temperatures, in less than 3 hours run time.The kinetic parameters, 4 rate constants and 4 activation energies were fitted with less than 4% uncertainty.We derived an expression for the error in the observed rate constants due to dispersion and showed that such error is 5% or lower.The large range of operational conditions prevented the need to isolate individual reaction steps.Our approach enables early identification of the sensitivity of product quality to parameter changes and early use of unit operation models to identify optimal process-equipment combinationsin silico, greatly reducing scale up risks.

Journal: Reaction chemistry & engineering (2017)
Publication types: Journal Article
Identification and characterization of functional single nucleotide polymorphisms (SNPs) in Axin 1 gene: a molecular dynamics approach.

Wnt signaling pathway has been reported to play crucial role in intestinal crypt formation and deregulation of this pathway is responsible for colorectal cancer initiation and progression.Axin 1, a scaffold protein, play pivotal role in the regulation of wnt/β-catenin signaling pathway and has been found to be mutated in several cancers; primarily in colon cancer.Considering its crucial role, a structural and functional analysis of missense mutations in axin 1 gene was performed in this study.Initially, one hundred non-synonymous single nucleotide polymorphisms in the coding regions of axin 1 gene were selected for in silico analysis.Six variants (g820s, g856s, e830k, l811v, l847v, and r767c) were predicted to be deleterious by combinatorial prediction.Further investigation of structural attributes confirmed two highly deleterious single nucleotide polymorphisms (g820s and g856s).Molecular dynamics simulation demonstrated variation in different structural attributes between native and two highly deleterious axin 1 mutant models.Finally, docking analysis showed variation in binding affinity of mutant axin 1 proteins with two destruction complex members, gsk3β and adenomatous polyposis.The results collectively showed the deleterious effect of the above predicted single nucleotide polymorphisms on the axin 1 protein structure and could prove to be an adjunct in the disease genotype-phenotype correlation studies.

Journal: Cell biochemistry and biophysics (2018)
Publication types: Journal Article
Experiences with Public Health Recommendations for COVID-19: A Qualitative Study of Diverse Mothers with Young Children in the United States.

Despite the increased availability of vaccines, masking and social distancing remain important strategies to mitigate covid-19 transmission.This qualitative study aimed to better understand experiences navigating public health recommendations to slow the spread of covid-19 among economically and ethnically diverse mothers with young children.Methods mothers of preschoolers (n=25) were recruited from project eat 2010-2018 (eating and activity over time) longitudinal cohort.Participants completed a virtual semi-structured interview about their experiences during covid-19.Interview transcripts were coded using deductive and inductive content analysis and analyzed using thematic analysis to identify themes.Results the first identified theme, "selective adherence to recommendations" included subthemes highlighting how social distancing was more challenging than mask wearing, family and children were primary reasons for reduced adherence, and concern for the wellbeing of others influenced adherence.The second theme, "personal experiences and relationships were important determinants of perceived severity of the virus and critical aspects of desired support," included subthemes on feelings of uncertainty, personal experiences with the virus, and desired community supports.Participants felt stressed and confused about what information to trust.Personal experiences with covid-19 influenced perceptions of its seriousness, and mothers were more confident about following recommendations when they them from trusted medical professionals and desired for communities to work together.Conclusions how findings among this diverse population of mothers can help inform future public health messaging and policies throughout the remainder of this pandemic, its aftermath, and future public health emergencies, in which masking and social distancing will be needed, are discussed.

Journal: Journal of communication in healthcare (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Nocardamine-Dependent Iron Uptake inPseudomonas aeruginosa: Exclusive Involvement of the FoxA Outer Membrane Transporter.

Iron is a key nutrient for almost all living organisms.Paradoxically, it is poorly soluble and consequently poorly bioavailable.Bacteria have thus developed multiple strategies to access this metal.One of the most common consists of the use of siderophores, small compounds that chelate ferric iron with very high affinity.Many bacteria are able to produce their own siderophores or use those produced by other microorganisms (exosiderophores) in a piracy strategy.pseudomonas aeruginosaproduces two siderophores, pyoverdine and pyochelin, and is also able to use a large panel of exosiderophores.We investigated the ability of p.Aeruginosato use nocardamine (noca) and ferrioxamine b (dfob) as exosiderophores under iron-limited planktonic growth conditions.Proteomic and rt-q pcr approaches showed induction of the transcription and expression of the outer membrane transporter fox a in the presence of noca or dfob in the bacterial environment.Expression of the proteins of the heme- or pyoverdine- and pyochelin-dependent iron uptake pathways was not affected by the presence of these two tris-hydroxamate siderophores.55fe uptake assays usingfox amutants showed ferri-noca to be exclusively transported by fox a, whereas ferri-dfob was transported by fox a and at least one other unidentified transporter.The crystal structure of fox a complexed with noca-fe revealed very similar siderophore binding sites between noca-fe and dfob-fe.We discuss iron uptake by hydroxamate exosiderophores in p.Aeruginosacells in light of these results.

Journal: ACS chemical biology (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Insight into the pilot-scale fed-batch fermentation for production ofEnterococcus faeciumCW3801 using molasses-based medium.

Enterococcussp.Has been used as starters in food fermentation due to their probiotic and antimicrobial properties in food biopreservation.The antimicrobial properties were mainly contributed by the bacteriocin called enterocin.Hence, the availability of a cost-effective pilot-scale cultivation conditions is a necessity for the production of probiotic bacteria.This study aims to investigate optimization of medium composition using sugarcane molasses as a carbon source using response surface methodology and the potential use of fed-batch cultivation for improvement of the cell viability of enterococcus faecium cw3801 for the use as a probiotic starter culture.Two feeding strategies (ramp and constant) were applied in fed-batch cultivation for enhancement of the production of e.Faeciumin a 2-l stirred tank bioreactor using the optimized medium and scaled up to a 15-l bioreactor.Optimized fermentation medium which comprised of 10% (v/v) of molasses and 10 g/l of yeast extract at p h 7 yielded maximum cell viability of 29.4 × 1011cfu/m l with 3900 au/m l of bacteriocin-like inhibitory substances (blis) activity.In the fed-batch, the cell viability (8.4 × 1013) and dry cell weight (6.34 g/l) reached the highest in optimized medium when the ramp (stepwise) feeding was applied.In scaling up to 15-l bioreactor, the growth of e.Faeciumwas achieved at 2.3 × 1013cfu/m l with the dry cell weight of 5.28 g/l under the same condition.The blis in 15-l bioreactor was 6% higher than the 2-l bioreactor.This study demonstrated that molasses and yeast extract are good feedstock for the growth of e.Faecium.The e.Faecium,a non-vancomycin resistant enterococcus (vre) was successfully produced by a fed-batch cultivation approach and scaled up to a 15-l bioreactor using a ramp feeding strategy.Results from this study revealed that the fed-batch cultivation using molasses-based medium has industrial potential for the production of probiotics.

Journal: Preparative biochemistry & biotechnology (2022)
Publication types: Journal Article
How can we improve investigation, prevention and treatment for recurrent urinary tract infections - ICI-RS 2018.

Recurrent urinary tract infection (r uti) is a chronic condition and has a significant impact on health-related quality of life.The commonly used definition for r uti is greater than three episodes in a year or more than two in 6 months.Current diagnostic methods have been used worldwide for over five decades, despite well evidenced criticism.Enhanced culture techniques demonstrate that the microbiome of the bladder is far more complex than previously thought and begs a reappraisal of our current testing.Treatment of r uti is based on a small number of antibiotic trials with some evidence showing a reduction in the number of positive cultures, but one must be cautious in interpreting the results and weigh against the risk of generation of antimicrobial resistance (amr).Aim the international consultation on incontinence-research society think tank reviewed the literature with a view to improving investigation, prevention and treatment of r uti.Methods a multidisciplinary team of experts were invited to present evidence regarding the current diagnostic methods, recent advances related to bladder biome mapping and current treatment strategies, including antibiotic and nonantibiotic options.Current guidelines regarding antibiotic stewardship and concerns regarding amr were discussed.Discussion outcome of the think tank discussions are summarised with a set of recommendations to inform future research.Particular consideration is given to bacterial survival in the bladder after treatment as well as defects in urothelial barrier function which may play a significant part in the failure to eradicate uti.

Journal: Neurourology and urodynamics (2019)
Publication types: Journal Article;Review
Orbital Sarcoidosis Masquerading as Late Postoperative Blepharoplasty Complication: A Case Report.

Orbital sarcoid is a rare entity and may be the first manifestation of systemic sarcoidosis.We report a case of orbital sarcoidosis where diagnosis was complicated by a history of lower eyelid blepharoplasty.The patient presented with progressive swelling of the left lower eyelid, which was assumed to be a late complication of her surgery.After failing multiple treatments, mri orbits was obtained and revealed an enhancing lesion in the left orbit inseparable from the lacrimal gland and inferior oblique muscle.Biopsy showed noncaseating granulomatous inflammation, and the patient was eventually diagnosed with sarcoidosis.

Journal: Ophthalmic plastic and reconstructive surgery (2022)
Publication types: Case Reports;Journal Article
Low-Temperature Synthesis of Boron Nitride as a Large-Scale Passivation and Protection Layer for Two-Dimensional Materials and High-Performance Devices.

Two-dimensional materials (2dms) with extraordinary electronic and optical properties have attracted great interest in optoelectronic applications.Due to their atomically thin feature, 2dm-based devices are generally sensitive to oxygen and moisture in ambient air, and thus, practical application of durable 2dm-based devices remains challenging.Here, we report a novel strategy to directly synthesize amorphous bn film on various 2dms and field-effect transistor (fet) devices at low temperatures by conventional chemical vapor deposition.The wafer-scale bn film with controllable thickness serves as a passivation and heat dissipation layer, further improving the long-term stability, the resistance to laser irradiation, and the antioxidation performance of the underneath 2dms.In particular, the bn capping layer could be deposited directly on a wse2fet at low temperature to achieve a clean and conformal interface.The high performance of the bn-capped wse2device is realized with suppressed current fluctuations and 10-fold enhanced carrier mobility.The transfer-free amorphous bn synthesis technique is simple and applicable to various 2dms grown on arbitrary substrates, which shows great potential for applications in future two-dimensional electronics.

Journal: ACS applied materials & interfaces (2022)
Publication types: Journal Article
Viral reservoirs in elite controllers of HIV-1 infection: Implications for HIV cure strategies.

Elite controllers are hiv-1 positive subjects who control viral replication without antiretroviral therapy.Many of these subjects have replication-competent virus and thus represent a model of a functional cure.Peripheral cd4+ t cells in these subjects have small reservoirs with a low frequency of intact proviruses.Furthermore, recent studies suggest that many of these intact proviruses are disproportionally integrated at sites that have limited transcriptional activity raising the possibility that replication-competent viruses do not replicate because they are in a "blocked and locked" state.However, this feature is probably a consequence rather than a cause of elite control.Additionally, evolution of plasma virus has been detected in many elites suggesting that there continues to be ongoing viral replication in other compartments.While exceptional elite controllers with very limited viral reservoirs have recently been described, more work is needed to determine whether these patients have achieved a sterilizing cure.

Journal: EBioMedicine (2020)
Publication types: Journal Article;Review
CLEC12B Is a Melanocytic Gene Regulating the Color of the Skin.

Pigmentation of the human skin is a complex process regulated by many genes.However, only a few have a profound impact on melanogenesis.Transcriptome analysis of pigmented skin compared with analysis of vitiligo skin devoid of melanocytes allowed us to unravel clec12b as a melanocytic gene.We showed that clec12b, a c-type lectin receptor, is highly expressed in melanocytes and that its expression is decreased in dark skin compared with that in white skin.Clec12b directly recruits and activates shp1 and shp2 through its immunoreceptor tyrosine-based inhibitory motif domain and promotes cre-binding protein degradation, leading to the downregulation of the downstream mitf pathway.Clec12b ultimately controls melanin production and pigmentation in vitro and in a model of reconstructed human epidermis.The identification of clec12b in melanocytes shows that c-type lectin receptors exert function beyond immunity and inflammation.It also provides insights into the understanding of melanocyte biology and regulation of melanogenesis.

Journal: The Journal of investigative dermatology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
TELEmedicine for EPIlepsy Care (TELE-EPIC): protocol of a randomised, open controlled non-inferiority clinical trial.

Introduction epilepsy is a chronic condition requiring consistent follow-up aimed at seizure control, and monitoring of anti-seizure medication (asm) levels and side effects.Telemedicine (tm) offers invaluable support to patient follow-up, guaranteeing the prompt availability of a team of experts for persons with epilepsy (pwe) widely distributed across the country.Although many health institutions have endorsed the use of tm, robust data on effectiveness, safety and costs of tm applied to epilepsy are lacking.Telemedicine for epilepsy care (tele-epic) will evaluate the effectiveness of video consultation (vc) via tm compared with usual care (uc) for the monitoring of pwe (tele-epic_rct).Moreover, tele-epic will apply an innovative volumetric absorptive microsampling (vams) device for quantitation of asm through finger prick blood sampling as an alternative to venipuncture sampling (tele-epic_vams).Methods and analysis tele-epic_rct is a multicentre, open, pragmatic two-arm randomised controlled trial prospectively including adult and paediatric outpatients with established diagnosis of epilepsy consecutively attending the epilepsy centres of bologna and rome, respectively.The primary outcome is the non-inferiority of vc on seizure control compared with uc after an 18-month follow-up.Secondary outcomes are adherence to treatment, asm-related adverse events, quality of life, mood disorders, patient and caregiver satisfaction, safety and costs.Tele-epic_vams is a cross-validation study for blood asm quantitation through a novel, vams-based device, comparing (1) vams versus plasma samples (reference standard method); and (2) nurse-collected versus self-collected blood by vams device.Ethics and dissemination the study has been approved by the local ethics committee (349-2019-sper-auslbo).Complete information about the state of project, relevant events and results will be regularly updated on the project's webpage on clinical trials.gov.The project's results and data on the potential impact of tm in epilepsy will be disseminated on social media.A closeout meeting will be convened for the communication and dissemination of the project, highlighting its main achievements and impacts.Trial registration number nct04496310.

Journal: BMJ open (2021)
Publication types: Clinical Trial Protocol;Journal Article;Research Support, Non-U.S. Gov't