syedzayyan/paper_mill_benchmark huggingface dataset:
Basal cell carcinoma with perineural invasion: A prospective study examining subtype, tumor surface diameter, invasion depth, and anatomic site in 3005 consecutive cases.

Basal cell carcinoma (bcc) may present with or without perineural invasion (pni).We reviewed bcc for pni by subtype, microscopic tumor surface diameter, invasion depth, and anatomic site.Method consecutive excisions were prospectively collected in an australian center 2016-2018.Results total cases were 3005 including 40 with pni: 28 in males, 12 in females.Superficial and nodular subtypes had no pni.As the percentage tumor mass of infiltrative bcc increased beyond 90% the presence of pni substantially escalated (or7.0).Comparing pni absent or present the respective maximum mean tumor microscopic surface diameters ranged from (95%ci [9.6-10.0] p < .001) to 11.2 mm (95%ci [9.4-13.0] p = .59).Respective maximum mean invasion depths were from 1.0 mm (95%ci [0.98-1.05] p < .001) to 2.3 mm (95%ci [1.8-2.7] p < .001).Respective maximum mean invasion depths were from 1.0 mm (95%ci [0.98-1.05] p < .001) to 2.3 mm (95%ci [1.8-2.7] p < .001) to 2.3 mm (95%ci[1.8-2.7] p < .001).Males recorded most pni on the scalp, followed by cheek and chin.Patients with more than two bcc cases had a greater proportional pni risk (or3.7).Mean pni nerve diameters were 0.06 mm2(males) and 0.03 mm2(females).Conclusion increases in percentage infiltrative subtype within the tumor mass, microscopic tumor diameter, tumor invasion depth, and bcc cases per patient all recorded more pni.Minimum invasion depths with pni were 1.0 mm on males (nose) and 1.0 mm females (forehead).

Journal: Journal of cutaneous pathology (2020)
Publication types: Journal Article
False aneurysm of the popliteal artery revealing a solitary osteochondroma of the distal femur in an 11-year-old boy.

An 11-year-old boy presented with pain in the right knee, intermittent reverse ischemia of the right foot and paraesthesia of the right toes.An angio-ct showed a false aneurysm of the right superior popliteal artery, and a solitary osteochondroma of the posterior aspect of the distal femur.Excision of the aneurysm and the osteochondroma was performed in two-stages.The patient was clinically well at 1-year follow up.

Journal: Acta chirurgica Belgica (2022)
Publication types: Case Reports;Journal Article
Current smoking predicts inadequate response to methotrexate monotherapy in rheumatoid arthritis patients naïve to DMARDs: Results from a retrospective cohort study.

Identifying predictors of inadequate response to methotrexate (mtx) in rheumatoid arthritis (ra) is key to move from a "trial and error" to a "personalized medicine" treatment approach where patients less likely to adequately respond to mtx monotherapy could start combination therapy at an earlier stage.This study aimed to identify potential predictors of inadequate response to mtx in ra patients naïve to disease modifying anti-rheumatic drugs.data from a real-life cohort of newly diagnosed ra patients starting mtx (baseline, t0) as first-line therapy were analyzed.Outcomes, assessed after 6 months (t1), were defined as failure to achieve a disease activity score 28 (das28) low disease activity (lda) or a good/moderate response to mtx, according to the european league against rheumatism (eular) response criteria.Logistic regression was used to assess the associations between baseline variables and the study outcomes.overall, 294 patients (60.5% females, median age 54.5 years) with a median disease duration of 7.9 months were recruited.At t1, 47.3% of subjects failed to achieve lda, and 29.3% did not have any eular-response.In multivariate analysis, significant associations were observed between no lda and current smoking (adjusted odds ratio [adj or] 1.79, p = .037), female gender (adj or 1.68, p = .048), and higher das28 (adj or 1.31, p = .013); and between no eular-response and current smoking (adj or: 2.04, p = .019), age (adj or: 0.72 per 10-years increases, p = .001), and higher erythrocyte sedimentation rate (adj or: 0.49; p = .020).By contrast, there were no associations between past smoker status and study outcomes.in summary, in our real-life cohort of disease modifying anti-rheumatic drug naïve ra patients, current smoking habit independently predicts inadequate response to mtx.This, together with other independent predictors of response to treatment identified in our study, might assist with personalized monitoring in ra patients.Further studies are required to investigate whether smoking quitting strategies enhance the therapeutic response to mtx.

Journal: Medicine (2021)
Publication types: Journal Article
The effect of a zirconia primer on the shear bond strength of Y-TZP ceramic to three different core materials by using a self-adhesive resin cement.

Considering the importance of bond strength of zirconia ceramic to different core materials, this study aimed to evaluate the effect of a new zirconia primer, a mixture of organophosphate and carboxylic acid monomers, on the bond strength of zirconia to three core materials cemented with a self-adhesive resin cement.Materials and methods the study was done on 36 disk-shaped zirconia specimens in the case (receiving new zirconia primer) and control groups (n= 18) and three core material subgroups (n= 6) (amalgam, nickel-chromium [ni-cr], and composite resin).A self-adhesive resin-based luting agent bonded the two parts together.The shear bond strength was tested and the facture modes were determined.Two-way anova and tukey's honestly significant difference tests were used for data analyses (α = 0.05).Results zirconia primer could not significantly increase the bond strength of zirconia ceramic to different core materials (p= 0.754).Composite resin and amalgam cores showed significantly higher bond strength than ni-cr core (p= 0.001).On using zirconia primer, 100% of failures of composite resin cores were cohesive inside the core material, 75% in amalgam core and 100% in ni-cr core were adhesive.Conclusions the use of new zirconia primer based on organophosphate/carboxylic acid monomers could not enhance the bond strength of zirconia ceramic to different core materials.The bond strength of zirconia to amalgam and composite resin cores was higher than that to ni-cr core material.

Journal: Journal of Indian Prosthodontic Society (2019)
Publication types: Journal Article
Quantitative volumetric analysis of the Golgi apparatus following X-ray irradiation by super-resolution 3D-SIM microscopy.

To obtain quantitative volumetric data for the golgi apparatus after ionizing radiation (ir) using super-resolution three-dimensional structured illumination (3d-sim) microscopy.Normal human retinal pigment epithelial (rpe) cells were irradiated with x-rays (10 gy), followed by immunofluorescence staining of the golgi marker rcas1.3d-sim imaging was performed using delta vision omx version 4 and soft wo rx 6.1.Polygon rendering and spot signal identification were performed using imaris 8.1.2.Differences between groups were assessed by welch's t test.Rcas1 signals in untreated cells were located adjacent to nuclei and showed a reticular morphology.Upon ir, the area of rcas1 signals expanded while retaining the reticular morphology.Polygon rendering imaging revealed that the volume of rcas1 at 48 h post-ir was greater than that for unirradiated cells (93.7 ± 19.0 μm3vs.33.0 ± 4.2 μm3, respectively; p < 0.001): a 2.8-fold increase.Spot signal imaging showed that the number of rcas1 spot signals post-ir was greater than that for unirradiated cells [3.4 ± 0.8 (× 103) versus 1.3 ± 0.2 (× 103), respectively; p < 0.001]: a 2.7-fold increase.This is the first study to report quantitative volumetric data of the golgi apparatus in response to ir using super-resolution 3d-sim microscopy.

Journal: Medical molecular morphology (2021)
Publication types: Journal Article
Combination of Goniothalamin and Sol-Gel-Derived Bioactive Glass 45S5 Enhances Growth Inhibitory ActivityviaApoptosis Induction and Cell Cycle Arrest in Breast Cancer Cells MCF-7.

Combination of natural products with chemically synthesised biomaterials as cancer therapy has attracted great interest lately.Hence, this study is aimed at investigating the combined effects of goniothalamin and bioactive glass 45s5 (gtn-bg) and evaluating their anticancer properties on human breast cancer cells mcf-7.Methods the bg 45s5 was prepared using the sol-gel process followed by characterisation using psa, bet, sem/eds, xrd, and ftir.The effects of gtn-bg on the proliferation of mcf-7 were assessed by mtt, presto blue, and scratch wound assays.The cell cycle analysis, annexin-fitc assay, and activation of caspase-3/7, caspase-8, and caspase-9 assays were determined to further explore its mechanism of action.Results the synthesised bg 45s5 was classified as a fine powder, having a rough surface, and contains mesopores of 12.6 nm.Eds analysis revealed that silica and calcium elements are the primary components of bg powders.Both crystalline and amorphous structures were detected with 73% and 27% similarity to na2ca2(si2o7) and hydroxyapatite, respectively.The combination of gtn-bg was more potent than gtn in inhibiting the proliferation of mcf-7 cells.G0/g1 and g2/m phases of the cell cycle were arrested by gtn and gtn-bg.The percentage of viable cells in gtn-bg treatment was significantly lower than that in gtn.In terms of activation of initiator caspases for both extrinsic and intrinsic apoptosis pathways, caspase-8 and caspase-9 were found more effective in response to gtn-bg than gtn.Conclusion the anticancer effect of gtn in mcf-7 cells was improved when combined with bg.The findings provide significant insight into the mechanism of gtn-bg against mcf-7 cells, which can potentially be used as a novel anticancer therapeutic approach.

Journal: BioMed research international (2022)
Publication types: Journal Article
Epigenetic regulation of T cells by Polycomb group proteins.

T cells are critical for pathogen elimination, tumor surveillance, and immunoregulation.The development, activation, and differentiation of cd8 and cd4 t lymphocytes are a set of complex and dynamically regulated events that require epigenetic control.The polycomb group (pc g) proteins are a family of diverse and evolutionarily conserved epigenetic modulators fundamentally involved in several mechanisms of gene regulation.Pc g proteins can assemble into distinct repressor complexes, the two most understood being the polycomb repressor complex (prc)1 and prc2, which control chromatin structure mainly through posttranslational modifications of histones.In this review, we will summarize the most recent findings regarding the diverse roles performed by pc g proteins in t cell biology.We will focus on prc1 and prc2 contribution to the regulation of t cell development in the thymus, cd4 t cell differentiation in helper or regulatory phenotypes and cd8 t cell fate commitment in the context of infections and cancer, highlighting the known mechanisms and knowledge gaps that still need to be addressed.

Journal: Journal of leukocyte biology (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
MRI Dynamic Contrast Imaging of Oral Cavity and Oropharyngeal Tumors.

In the past decade, dynamic contrast-enhanced magnetic resonance imaging has had an increasing role in assessing the microvascular characteristics of various tumors, including head and neck cancer.Dynamic contrast-enhanced magnetic resonance imaging allows noninvasive assessment of permeability and blood flow, both important parametric features of tumor hypoxia, which is in turn a marker for treatment resistance for head and neck cancer.in this article we will provide a comprehensive review technique in evaluating tumor proliferation and application of its parameters in differentiating between various tumor types of the oral cavity and how its parameters can correlate between epidermal growth factor receptor and human papillomavirus which can have an implication in patient's overall survival rates.we will also review how the parameters of this method can predict local tumor control after treatment and compare its efficacy with other imaging modalities.Lastly, we will review how its parameters can be used prospectively to identify early complications from treatment.

Journal: Topics in magnetic resonance imaging : TMRI (2021)
Publication types: Journal Article;Review
Outer Retinal Assessment Using Spectral-Domain Optical Coherence Tomography in Patients With Alzheimer's and Parkinson's Disease.

To investigate outer retinal parameters among patients with various chronic neurodegenerative disorders by using spectral-domain coherence tomography (oct) in a prospective cross-sectional cohort study.Methods a total of 132 participants were enrolled following a comprehensive diagnostic evaluation with neurologic, neuropsychology, and magnetic resonance imaging volumetric evaluations.Participants were 50 years or older, either diagnosed with alzheimer's disease (ad) dementia, amnestic mild cognitive impairment (mci), non-ad dementia, parkinson's disease (pd), or age- and sex-matched controls.All participants underwent a macular cube scan for both eyes by using the cirrus 4000 hd-oct (zeiss, oberkochen, germany).The oct image with the best quality was selected for further analysis.Outer retinal parameters including ellipsoid zone mapping and outer nuclear layer metrics were evaluated with a novel software platform.Results one hundred twenty-four eyes of 124 participants with ad dementia (24 eyes), amnestic mci (22 eyes), non-ad dementia (20 eyes), pd (22 eyes), and age- and sex-matched controls (36 eyes) were included in the analysis.Eight eyes were excluded either due to the presence of macular disease or poor quality of the oct image.The mean ages of participants were 65.9 ± 8.9 years.The outer retinal thickness measures did not show any statistical significance between the groups.However, ellipsoid zone to retinal pigment epithelium volume correlated with cognitive testing scores in all study participants.Conclusions there were no identifiable differences in the outer retinal metrics across neurodegenerative disease groups and controls.The relationship between the degree of cognitive impairment and ellipsoid zone to retinal pigment epithelium volume warrants further study.

Journal: Investigative ophthalmology & visual science (2018)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Two Archaeal Metagenome-Assembled Genomes from El Tatio Provide New Insights into the Crenarchaeota Phylum.

A phylogenomic and functional analysis of the first two crenarchaeota mags belonging to el tatio geysers fields in chile is reported.A soil sample contiguous to a geothermal activity exposed lagoon of el tatio was used for shotgun sequencing.Afterwards, contigs were binned into individual population-specific genomes data.A phylogenetic placement was carried out for both mag 9-5tat and mag 47-5tat.Then functional comparisons and metabolic reconstruction were carried out.Results showed that both mag 9-5tat and mag 47-5tat likely represent new species in the genus thermoproteusand the genus sulfolobus, respectively.These findings provide new insights into the phylogenetic and genomic diversity for archaea species that inhabit the el tatio geysers field and expand the understanding of the crenarchaeota phylum diversity.

Journal: Genes (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
SEC61G Promotes Cervical Cancer Proliferation by Activating MAPK Signaling Pathway.

The abnormal expression of sec61g plays an important role in the development of various tumors.This study explored the effects of sec61g on mapk signaling pathway and proliferation of cervical cancer (cc) cells.Methods sh rna was used to inhibit the expression of sec61g and ed u to observe its effect on the proliferation of cc cell si ha.The effect of sec61g on invasion was evaluated by transwell assay.Tcga database was used to analyze the influence of high or low sec61g expression level on the overall survival of cc patients.Western blot was used to detect the expressions of sec61g, p-raf1, raf1, p-mek1/2, mek1/2, and p-erk1/2 in cells.Si ha cells overexpressing sec61g (si ha-sec61g) and control group (si ha-mock) were subcutaneously implanted in nude mice.The tumor growth curve was measured at the specified time points between si ha-sec61g and si ha-mock.The inhibitory effect of gefitinib on sec61g was further evaluated.Results in patients with cc, high sec61g expression predicted poor prognosis.Silencing sec61g inhibited proliferation and invasion of cc cells in vitro.Overexpression of sec61g can promote the proliferation and invasion of cc cells in vitro.Meanwhile, overexpression of sec61g promoted the proliferation of cc xenografts.Knocking down sec61g can inhibit mapk signaling pathway.Gefitinib can inhibit cc proliferation and tumor growth by sec61g.Conclusion sec61g is highly expressed in cc and has poor prognosis.Inhibition of sec61g expression can effectively inhibit the growth and proliferation of human cc cells.The mechanism may be related to the inhibition of mapk signaling pathway.

Journal: Disease markers (2022)
Publication types: Journal Article
Biomimetic facile synthesis of zinc oxide and copper oxide nanoparticles from Elaeagnus indica for enhanced photocatalytic activity.

The present study focused on synthesizing zn o nanoparticles (nps) and cu o nps using elaeagnus indica leaf extract as reducing and stabilizing agents using zn(o2cch3)2and cu2so4, respectively, for the first time.We have confirmed the formation of aggregated zn o nps and cu o nps with phytochemicals by various spectral analyses and electron microscopy studies.The size of synthesized zn o nps and cu o nps were in the range of 20-30 nm and 30-40 nm, respectively.The antimicrobial activity of zn o nps at 75 μg concentration is superior against salmonella typhimurium, klebsiella pneumonia, bacillus subtilis, staphylococcus epidermidis, and aspergillus niger.While cu o nanoparticles with 75 μg concentration effectively inhibited s.Typhimurium, b.Subtilis, s.Epidermidis, and a.Niger.Phytochemicals and reactive oxygen species generated by the prepared nps may account for the antimicrobial effects observed.The photodegradation of methylene blue by zn o nps and cu o nps was 91% and 76%, respectively, for 6 h of sunlight exposure.Cu o nps and zn o nps have different intrinsic properties and phytochemical compositions; hence zn o nps photodegrade faster than cu o nps even though zn o has higher bandgap energy than cu o.Consequently, cu o and zn o nps produced from e.Indica leaf extract might be utilized as antimicrobials and photocatalysts in the future.

Journal: Environmental research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Phylogenetic and Phenotypic Analyses of a Collection of Food and Clinical Listeria monocytogenes Isolates Reveal Loss of Function of Sigma B from Several Clonal Complexes.

To understand the molecular mechanisms that contribute to the stress responses of the important foodborne pathogen listeria monocytogenes, we collected 139 strains (meat,n= 25; dairy,n= 10; vegetable,n= 8; seafood,n= 14; mixed food,n= 4; and food processing environments,n= 78), mostly isolated in ireland, and subjected them to whole-genome sequencing.These strains were compared to 25 irish clinical isolates and 4 well-studied reference strains.Core genome and pan-genome analysis confirmed a highly clonal and deeply branched population structure.Multilocus sequence typing showed that this collection contained a diverse range of strains from l.Monocytogenes lineages i and ii.Several groups of isolates with highly similar genome content were traced to single or multiple food business operators, providing evidence of strain persistence or prevalence, respectively.Phenotypic screening assays for tolerance to salt stress and resistance to acid stress revealed variants within several clonal complexes that were phenotypically distinct.Five of these phenotypic outliers were found to carry mutations in thesig boperon, which encodes the stress-inducible sigma factor sigma b.Transcriptional analysis confirmed that three of the strains that carried mutations insig b,rsb v, orrsb uhad reduced sig b activity, as predicted.These strains exhibited increased tolerance to salt stress and displayed decreased resistance to low p h stress.Overall, this study shows that loss-of-function mutations in thesig boperon are comparatively common in field isolates, probably reflecting the cost of the general stress response to reproductive fitness in this pathogen.importancethe bacterial foodborne pathogen listeria monocytogenes frequently contaminates various categories of food products and is able to cause life-threatening infections when ingested by humans.Thus, it is important to control the growth of this bacterium in food by understanding the mechanisms that allow its proliferation under suboptimal conditions.In this study, intraspecies heterogeneity in stress response was observed across a collection consisting of mainly irish l.Monocytogenes isolates.Through comparisons of genome sequence and phenotypes observed, we identified three strains with impairment of the general stress response regulator sig b.Two of these strains are used widely in food challenge studies for evaluating the growth potential of l.Monocytogenes.Given that loss of sig b function is associated with atypical phenotypic properties, the use of these strains in food challenge studies should be re-evaluated.

Journal: Applied and environmental microbiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Phylogenetic and comparative analyses of Hydnora abyssinica plastomes provide evidence for hidden diversity within Hydnoraceae.

To date, plastid genomes have been published for all but two holoparasitic angiosperm families.However, only a single or a few plastomes represent most of these families.Of the approximately 40 genera of holoparasitic angiosperms, a complete plastid genome sequence is available for only about half.In addition, less than 15 species are currently represented with more than one published plastid genome, most of which belong to the orobanchaceae.Therefore, a significant portion of the holoparasitic plant plastome diversity remains unexplored.This limited information could hinder potential evolutionary pattern recognition as well as the exploration of inter- and intra-species plastid genome diversity in the most extreme holoparasitic angiosperms.Results here, we report the first plastomes of kenyan hydnora abyssinica accessions.The plastomes have a typical quadripartite structure and encode 24 unique genes.Phylogenetic tree reconstruction recovers the kenyan accessions as monophyletic and together in a clade with the namibian h.Abyssinica accession and the recently published h.Arabica from oman.Hydnora abyssinica as a whole however is recovered as non-monophyletic, with h.Arabica nested within.This result is supported by distinct structural plastome synapomorphies as well as pairwise distance estimates that reveal hidden diversity within the hydnora species in africa.Conclusion we propose to increase efforts to sample widespread holoparasitic species for their plastid genomes, as is the case with h.Abyssinica, which is widely distributed in africa.Morphological reinvestigation and further molecular data are needed to fully investigate the diversity of h.Abyssinica along the entire range of distribution, as well as the diversity of currently synonymized taxa.

Journal: BMC ecology and evolution (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't