syedzayyan/paper_mill_benchmark huggingface dataset:
Identification of Prognostic Biomarkers in Patients With Malignant Rhabdoid Tumor of the Kidney Based on mTORC1 Signaling Pathway-Related Genes.

Malignant rhabdoid tumor of the kidney (mrtk) is an infrequent malignant tumor in childhood, accounting for approximately 2% of all childhood kidney tumors.Although the development of current treatments, the overall survival (os) rate of mrtk patients is only 25%.The aim of this research was to explore the prognostic value of genes associated with the m torc1 signaling pathway in mrtk.methods:the transcriptome data of mrtk samples were downloaded from the target database.The 200 genes of hallmark_mtorc1_signaling were downloaded from the molecular signatures database (msig db).Furthermore, we applied gene set variation analysis (gsva) to screen differentially expressed gene sets between the mrtk and normal samples.The 200 genes were combined with differentially expressed genes (degs) identified from differentially expressed gene sets.Then, a gene signature of m torc1 pathway-related genes (m trgs) was constructed in mrtk.The molecular mechanism of prognostic factors in mrtk was further analyzed using gene set enrichment analysis (gsea).The target drugs based on these prognostic factors were explored from the comparative toxicogenomics database (ctd).Moreover, six paired fresh tumor tissues and paraneoplastic tissues from children with mrtk were collected to validate the expressions of p4ha1, mllt11, aurka, and got1 in clinical samples via real-time fluorescence quantitative pcr and western blot.results:a four-gene signature (p4ha1, mllt11, aurka, and got1) related to the m torc1 pathway was developed in mrtk, which divided the mrtk patients into high-risk and low-risk groups.The patients with high-risk scores were strongly associated with reduced os.Receiver operating characteristic (roc) analysis indicated a good prediction performance of the four biomarker signatures.Gsea revealed that the m tor signaling pathway was significantly enriched.The risk score was demonstrated to be an independent predictor for mrtk outcome.According to the correlation of tumor stem cell index and prognostic factors, the target drugs were obtained for the treatment of mrtk patients.Furthermore, the expressions of rt-q pcr and western blot were consistent with rna-sequencing data such that their expressions were significantly elevated in tumor tissues.conclusion:a total of four genes (p4ha1, mllt11, aurka, and got1) were screened as prognostic markers, further providing a new understanding for the treatment of patients with mrtk.

Journal: Frontiers in molecular biosciences (2022)
Publication types: Journal Article
Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary.

Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (aoa) and bacteria (aob).However, the distribution patterns of ammonia-oxidizing microorganisms (aoms) between different habitats in the same area remain unclear.The present study investigated the aoms' abundance and community compositions in both sediment and water habitats of the yellow river estuary.Quantitative pcr (q pcr) revealed that aoa showed significant higher abundance than aob both in sediment and water samples.Aoa and aob abundance distribution trends were consistent in sediment but distinct in water along the sampling sites.Clone library-based analyses showed that aoa sequences were affiliated with nitrososphaera, nitrosopumilus and nitrosotalea clusters.Generally, nitrososphaera was predominant in sediment, while nitrosopumilus and nitrosotalea dominated in water column.Aob sequences were classified into genera nitrosospira and nitrosomonas, and nitrosospira dominated in both habitats.Principal coordinate analysis (pco a) also indicated aoa community structures exhibited significant differences between two habitats, while aob were not.Ammonium and carbon contents were the potential key factors to influence aoms' abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat.These findings increase the understanding of the aoms' distribution patterns in estuarine ecosystems.

Journal: Scientific reports (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Patient satisfaction with anaesthesia services in a tertiary care cancer centre. (SAY study).

And aims patient satisfaction is an important measure of quality of health care.Its assessment leads to a balanced evaluation of the structure, process and outcome of service at an institution.The aim of our study was to assess patient satisfaction with perioperative anaesthesia services provided in our institution and identify factors leading to dissatisfaction which could be preventable or addressed to improve patient care and experience.Material and methods a convenient sample size of 200 patients was accrued after written informed consent.A questionnaire to suit local needs of institute was developed, validated and a language appropriate questionnaire was administered by a trained research nurse 24-48 hours post anaesthesia to accrued patients.Data was summarised in percentages and satisfaction scores were compared across demographic variables using chi square test.Results a total of 96% (192/200) patients were satisfied with the overall interaction with the anaesthetists in the perioperative period; with 99% (198/200) patients being satisfied with acute pain services provided, postoperatively.As regards to recovery room, 96.5% (193/200) patients were satisfied with the services provided.Satisfaction scores of the pre-anaesthetic clinic (pac), pain team and anaesthesia services compared across demographic variables - age, gender and education qualifications were found to be statistically non-significant.Conclusion high rate of patients were satisfied with perioperative anaesthesia care services at our institute.Good and effective preoperative communication with the patient, effective management of postoperative pain and complications significantly contributed towards overall high patient satisfaction.

Journal: Journal of anaesthesiology, clinical pharmacology (2022)
Publication types: Journal Article
Impaired microRNA processing in neutrophils from rheumatoid arthritis patients confers their pathogenic profile. Modulation by biological therapies.

The aim of this study was to investigate the micro rna (mi rna) expression pattern in neutrophils from rheumatoid arthritis (ra) patients and its contribution to their pathogenic profile and to analyze the effect of specific autoantibodies or inflammatory components in the regulation of mi rna in ra neutrophils and its modulation by biological therapies.Neutrophils were isolated from paired peripheral blood (pb) and synovial fluid samples of 40 patients with ra and from pb of 40 healthy donors.A mi rna array was performed using n counter technology.Neutrophils from healthy donors were treated in vitrowith antibodies to citrullinated protein antigens isolated from ra patients and tumor necrosis factor-a (tnf-a) or interleukin-6.A number of cytokines and chemokines were analyzed.In vitro treatments of ra-neutrophils with tocilizumab or infliximab were carried out.Transfections with pre-mi rna and dicer downregulation experiments were further performed.Ra-neutrophils showed a global downregulation of mi rna and genes involved in their biogenesis, alongside with an upregulation of various potential m rna targets related to migration and inflammation.Decreased levels of mi rna and dicer correlated with autoimmunity, inflammation and disease activity.Citrullinated protein antigens and tnf-a decreased the expression of numerous mi rna and their biogenesis-related genes, increasing their potential m rna targets.Infliximab reversed those effects.Transfections with pre-mi rna-223, -126 and -148a specifically modulated genes regulating inflammation, survival and migration whereas dicer depletion influenced the inflammatory profile of neutrophils.Taken together ra-neutrophils exhibited a global low abundance of mi rna induced by autoantibodies and inflammatory markers, which potentially contributed to their pathogenic activation.Mi rna biogenesis was significantly impaired in raneutrophils and further associated with a greater downregulation of mi rna mainly related to migration and inflammation in synovial fluid neutrophils.Finally, anti-tnf-a and anti-interleukin-6 receptor treatments can modulate mi rna levels in the neutrophils, minimizing their inflammatory profile.

Journal: Haematologica (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Optimising neurodevelopmental and psychosocial outcomes for survivors with CHD: a research agenda for the next decade.

Neurodevelopmental and psychosocial impairments negatively impact health-related quality of life for survivors with chd and complicate the transition to independent adulthood.Risk for neurodevelopmental and psychosocial impairments is influenced by a complex interplay among genetic, foetal, surgical, perioperative, family, and social factors, requiring a multi-pronged approach to neuroprotection and intervention.To ensure future research can ultimately reduce the burden of chd for individuals, families, and society, the most pressing issues in cardiac neurodevelopment requiring scientific investigation must be identified.through funding from an r13 grant from the national heart, lung, and blood institute of the national institutes of health of the united states of america, the cardiac neurodevelopmental outcome collaborative convened a two-day meeting of international experts in cardiac neurodevelopmental and psychosocial research, clinical care, and health disparities, including patient and family stakeholders, to define the cardiac neurodevelopmental and psychosocial outcomes research agenda for the next decade.Seven multidisciplinary working groups were formed to address key domains crucial to the advancement of cardiac neurodevelopmental and psychosocial outcomes research: 1) foetal brain development and neuroprotection, 2) surgical/perioperative neuroprotection and neurodevelopment, 3) characterization of neurodevelopmental and psychological outcomes, 4) neurodevelopmental and psychosocial intervention, 5) parent mental health and family functioning, 6) neurodevelopmental education, outreach and advocacy, and 7) health disparities and neurodevelopmental outcomes.Working groups identified significant gaps in knowledge and critical questions that must be answered to further knowledge, policy, care, and outcomes.The development of a research agenda in cardiac neurodevelopmental and psychosocial outcomes is critical for informing collaborative initiatives and allocation of funding for research to scientific inquiries of highest value to key stakeholders.

Journal: Cardiology in the young (2021)
Publication types: Journal Article
The Efficacy of Er:YAG Laser-Activated Shock Wave-Enhanced Emission Photoacoustic Streaming Compared to Ultrasonically Activated Irrigation and Needle Irrigation in the Removal of Bioceramic Filling Remnants from Oval Root Canals-An Ex Vivo Study.

The removal of filling material is important for successful root canal retreatment.The aim of the study was to compare the efficiency of two activated irrigation techniques, the shock wave-enhanced emission photoacoustic streaming (sweeps) mode of the er:yag laser and ultrasonically activated irrigation (uai) and a conventional syringe-needle technique (sni), in the removal of bioceramic sealer/gutta-percha during conventional retreatment in oval root canals.The study sample consisted of distal root canals of 42 extracted human mandibular molars, which were prepared using a pro taper next system up to size 40/0.06 and filled with bioceramic sealer using a single-cone obturation technique.The teeth were then re-treated with a reciproc blue rb40 file and 3% sodium hypochlorite solution.The prepared teeth were randomly divided into three groups (n = 14 per group) and subjected to one of the three irrigation methods.Micro-ct scans were performed at different stages to assess the amount of filling material after each retreatment phase.The results of the study showed that all the tested irrigation techniques reduced a statistically significant amount of the remnant filling material at retreatment (p < 0.05), and there were no statistically significant differences in efficacy between the three methods.All tested techniques had similar efficacy in the removal of the remaining filling remnants.

Journal: Bioengineering (Basel, Switzerland) (2022)
Publication types: Journal Article
Women's reproductive behaviour and perspectives on fertility, and their modifying factors, in a Turkish province with a high fertility rate.

S population growth is an important public health problem with economic, social, cultural and political consequences.The aim of the study was to determine the reproductive behaviour and perspectives on fertility of women in sanliurfa, the city with the highest fertility rate in turkey.Methods the quantitative dimension of the study was carried out using a mixed methods approach in which 300 women were interviewed and a questionnaire was completed; the qualitative dimension was carried out through in-depth individual interviews with 14 women, using a semi-structured interview form.Analysis of the qualitative data was done using a content analysis technique.Results the median number of children was three (range 0-10).Women with no or a low level of education tended to have a greater number of children.Preference for a particular sex of child was one reason behind the higher number of children.These two factors were main causes of an increased number of children.Women with no or a low level of education (odds ratio [or] 9.1) and women who expressed a preference for a male child (or 5.9) had more children compared with other women.Participants regarded a male child as more valuable than a female child and that having many children strengthened the family.Parents regarded their sons as insurance for their old age.Having an induced abortion was perceived as a sin.Conclusion the results showed that cultural norms and values significantly affected fertility rates.

Journal: The European journal of contraception & reproductive health care : the official journal of the European Society of Contraception (2021)
Publication types: Journal Article
Left and right ventricular longitudinal strains are associated with poor outcome in COVID-19: a systematic review and meta-analysis.

This systematic review and meta-analysis aimed to assess whether ventricular longitudinal strain can be used as a prognostication tool in patients with coronavirus disease 2019 (covid-19).Methods systematic literature searches of pub med, embase, and europe pmc databases were performed on 16 november 2020.Left ventricular global longitudinal strain (lv-gls) refers to lv contraction measurement using the speckle tracking-based method refers to the mean of strain values of the rv free wall (three segments) measured using echocardiography.The main outcome was poor outcome, defined as a composite of mortality and severe covid-19.Results seven studies comprising of 612 patients were included in meta-analysis.Six studies have mortality as their outcome, and 1 study has severity as their outcome.Patients with poor outcome have lower lv-gls (smd 1.15 (0.57, 1.72), p < 0.001; i270.4%).Each 1% decrease in lv-gls was associated with 1.4x increased risk of poor outcome (or 1.37 (1.12, 1.67), p = 0.002; i248.8%).Patients with poor outcome have lower rv-ls (smd 1.18 (0.91, 1.45), p < 0.001; i20%).Each 1% decrease in rv-ls was associated with 1.3x increased risk of poor outcome (or 1.25 (1.15, 1.35), p < 0.001; i211.8%).Subgroup analysis showed that for every 1% decrease in lv-gls and rv-ls is increased mortality with or of 1.30 (1.12, 1.50) and or of 1.24 (1.14, 1.35), respectively.Conclusion this study shows that lower lv-gls and rv-ls measurements were associated with poor outcome in patients with covid-19.Trial registration prospero crd42020221144.

Journal: Journal of intensive care (2021)
Publication types: Journal Article
The role of repetition in narcissism and self-sacrifice: A Freudian Kleinian reflection on the person's foundational love of the other.

Through reexamination of freud's thinking on the "compulsion to repeat", including detailed study of his beyond the pleasure principle(1920), this paper brings to the fore a central tension in freud's thinking on the roles narcissism and love in his foundational view of the person.While freud conceptualizes the person as self-serving, aiming primarily to maximize personal satisfaction in accordance with the "pleasure principle," he develops an alternative view of the person as primarily loving, desiring to truly encounter the other and reality, even if painful, and guilty when he fails to do so (largely because of conflicting narcissistic/destructive aims).This basic loving desire is associated with eros and the life instincts, which, counter to what is commonly thought, is what freud ultimately posits as lying beyond the pleasure principle.From this perspective, narcissistic pleasures become associated with death.The paper goes on to show how while freud struggled to conceptually ground the view of the person as contending with his desire to love and inevitable inner obstacles to it, kleinian psychoanalysis takes this view as basic and develops it further.One significant development finds expression in ideas on how the desire to love is not only non-narcissistic, but, rather, is self-sacrificing.Clinical implications are noted.

Journal: The International journal of psycho-analysis (2020)
Publication types: Journal Article
Resistant Protein: Forms and Functions.

Several global health risks are related to our dietary lifestyle.As a consequence of the overconsumption of ultra-processed and highly digestible protein (150-200% of the recommended value), excess dietary proteins reach the colon, are hydrolysed to peptides and amino acids by bacterial proteases and fermented to various potentially toxic end products.A diet reformulation strategy with reduced protein content in food products appears to be the most effective approach.A potential approach to this challenge is to reduce food digestibility by introducing resistant protein into the diet that could positively influence human health and gut microbiome functionality.Resistant protein is a dietary constituent not hydrolysed by digestive enzymes or absorbed in the human small intestine.The chemical conformation and the amino acid composition strictly influence its structural stability and resistance to in vivo proteolysis and denaturation.Responding to the important gap in our knowledge regarding the digestibility performance of alternative proteins, we hypothesise that resistant proteins can beneficially alter food functionality via their role in improving metabolic properties and health benefits in human nutrition, similar to fibres and resistant starches.A multidisciplinary investigation of resistant protein will generate tremendous scientific impact for other interlinked societal, economic, technological and health and wellbeing aspects of human life.

Journal: Foods (Basel, Switzerland) (2022)
Publication types: Journal Article
Korean Red Ginseng Improves Astrocytic Mitochondrial Function by Upregulating HO-1-Mediated AMPKα-PGC-1α-ERRα Circuit after Traumatic Brain Injury.

Heme oxygenase-1 (ho-1) exerts beneficial effects, including angiogenesis and energy metabolism via the peroxisome proliferator-activating receptor-γ coactivator-1α (pgc-1α)-estrogen-related receptor α (errα) pathway in astrocytes.However, the role of korean red ginseng extract (krge) in ho-1-mediated mitochondrial function in traumatic brain injury (tbi) is not well-elucidated.We found that ho-1 was upregulated in astrocytes located in peri-injured brain regions after a tbi, following exposure to krge.Experiments with pharmacological inhibitors and target-specific si rnas revealed that ho-1 levels highly correlated with increased amp-activated protein kinase α (ampkα) activation, which led to the pgc-1α-errα axis-induced increases in mitochondrial functions (detected based on expression of cytochrome c oxidase subunit 2 (mtco2) and cytochrome c as well as o2consumption and atp production).Knockdown of errα significantly reduced the p-ampkα/ampkα ratio and pgc-1α expression, leading to ampkα-pgc-1α-errα circuit formation.Inactivation of ho by injecting the ho inhibitor sn(iv) protoporphyrin ix dichloride diminished the expression of p-ampkα, pgc-1α, errα, mtco2, and cytochrome c in the krge-administered peri-injured region of a brain subjected to tbi.These data suggest that krge enhanced astrocytic mitochondrial function via a ho-1-mediated ampkα-pgc-1α-errα circuit and consequent oxidative phosphorylation, o2consumption, and atp production.This circuit may play an important role in repairing neurovascular function after tbi in the peri-injured region by stimulating astrocytic mitochondrial biogenesis.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article
Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns.

Small ruminant lentiviruses (srlvs) cause a multisystemic chronic wasting disease in sheep across much of the world.Srlv subtype a2 is prevalent in north america and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes.In sheep, the ovine transmembrane protein 154 (tmem154) gene is associated with srlv susceptibility.Ewes with at least one copy of tmem154encoding a full-length protein with glutamate at position 35 (e35; haplotypes 2 and 3), are highly susceptible to srlv infection while ewes with any combination of tmem154haplotypes which encodes lysine (k35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so.A2 subgroups 1 and 2 are associated with host tmem154genotypes; subgroup 1 with the k35/k35 genotype and subgroup 2 with the e35/e35 genotype.methods:the goals of this study were to analyze sequence variation within and among srlv subtype a2 subgroups 1 and 2 and to identify genome-scale recombination patterns.This was done using full-length assemblies of virus samples.results:consensus viral genomes were assembled for 23 infected sheep, including animals of assorted tmem154genotypes comprised of haplotypes 1, 2, or 3.Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional sub-structure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes.Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined genomes.conclusions:the viral subgroup framework developed to classify srlv consensus genomes along a continuum of recombination suggests that animals with the tmem154e35/k35 genotype may represent a reservoir for producing viral genomes representing recombination between a2 subgroups 1 and 2.

Journal: F1000Research (2020)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.