syedzayyan/paper_mill_benchmark huggingface dataset:
Influence of porous tantalum scaffold pore size on osteogenesis and osteointegration: A comprehensive study based on 3D-printing technology.

The emerging role of porous tantalum (ta) scaffold for bone tissue engineering is noticed due to its outstanding biological properties.However, it is controversial which pore size and porosity are more conducive for bone defect repair.In the present work, porous tantalum scaffolds with pore sizes of 100-200, 200-400, 400-600 and 600-800 μm and corresponding porosities of 25%, 55%, 75%, and 85% were constructed, using computer aided design and 3d printing technologies, then comprehensively studied by in vitro and in vivo studies.We found that ta scaffold with pore size of 400-600 μm showed stronger ability in facilitating cell adhesion, proliferation, and osteogenic differentiation in vitro.In vivo tests identified that porous tantalum scaffolds with pore size of 400-600 μm showed better performance of bone ingrowth and integration.In mechanism, computational fluid dynamics analysis proved porous tantalum scaffolds with pore size of 400-600 μm hold appropriate permeability and surface area, which facilitated cell adhesion and proliferation.Our results strongly indicate that pore size and porosity are essential for further applications of porous tantalum scaffolds, and porous tantalum scaffolds with pore size 400-600 μm are conducive to osteogenesis and osseointegration.These findings provide new evidence for further application of porous tantalum scaffolds for bone defect repair.

Journal: Materials science & engineering. C, Materials for biological applications (2021)
Publication types: Journal Article
Dispersion of repolarization increases with cardiac resynchronization therapy and is associated with left ventricular reverse remodeling.

Cardiac resynchronization therapy (crt) reduces ventricular activation times and electrical dyssynchrony, however the effect on repolarization is unclear.In this study, we sought to investigate the effect of crt and left ventricular (lv) remodeling on dispersion of repolarization using electrocardiographic imaging (ecgi).Methods 11 patients with heart failure and electrical dyssynchrony underwent ecgi 1-day and 6-months post crt.Reconstructed epicardial electrograms were used to create maps of activation time, repolarization time (rt) and activation recovery intervals (ari) and calculate measures of rt, ari and their dispersion.Ari was corrected for heart rate (c ari).Results compared to baseline rhythm, lv c ari dispersion was significantly higher at 6 months (28.2 ± 7.7 vs 36.4 ± 7.2 ms; p = 0.03) but not after 1 day (28.2 ± 7.7 vs 34.4 ± 6.8 ms; p = 0.12).There were no significant differences from baseline to crt for mean lv c ari or rt metrics.Significant lv remodeling (>15% reduction in end-systolic volume) was an independent predictor of increase in lv c ari dispersion (p = 0.04) and there was a moderate correlation between the degree of lv remodeling and the relative increase in lv c ari dispersion (r = -0.49) though this was not statistically significant (p = 0.12).Conclusion crt increases lv c ari dispersion, but this change was not fully apparent until 6 months post implant.The effects of crt on lv c ari dispersion appeared to be dependent on lv reverse remodeling, which is in keeping with evidence that the risk of ventricular arrhythmia after crt is higher in non-responders compared to responders.

Journal: Journal of electrocardiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Person-Centered Psychiatry as Dialogical Psychiatry: The Significance of the Therapeutic Stance.

In this article, we present holistic and person-centered perspectives in psychiatry, with the aim of better understanding what a focus on personhood might really mean and what clinical implications it might have.We first introduce classical and philosophical concepts of personhood, in order to then outline person-centered approaches in psychiatry, which mainly focus on the person of the patient.We then argue that, for it to really be person-centered, psychiatry must necessarily also focus on the person of professionals.We thus explore the notion of stance, as the expression of the therapist's personhood.By unpacking the effects that a professional's stance can have on patients, we finally turn to a consideration of the interpersonal sphere.More specifically, we propose clinical considerations on a therapeutic stance that strives to support and to help the person of the patient unfold.Such a stance must - we argue - necessarily be a dialogical one.Drawing on these considerations, we thus claim that a truly person-centered approach in psychiatry must necessarily and automatically be interperson-centered and dialogical.In the concluding remarks, we finally discuss broader societal implications and outline future research perspectives.

Journal: Psychopathology (2022)
Publication types: Journal Article;Review
Unveiling the molecular features, relevant immune and clinical characteristics ofSIGLEC15in thyroid cancer.

The groundbreaking research work about siglec15has raised it as a potential promising target in cancer immunotherapy.Unfortunately, the role of siglec15in thyroid carcinoma (thca) remains obscure.Public and home multi-omics data were collected to investigate the role of siglec15in thca in our study.siglec15was upregulated in thca tumor tissue compared to nontumor tissue in both m rna and protein levels; gene set enrichment analysis (gsea) results showed that high siglec15m rna expression was positively correlated to many immune pathways.Results of the examination of immunological landscape characteristics displayed high siglec15m rna expression that mainly positively correlated with a large number of cancer immunity immunomodulators and pathways.In addition, upregulation of siglec15was positively correlated with an enhanced immune score, stromal score, and estimate score.However, higher siglec15m rna also met high immune exhausted status.The majority of cp g methylation sites negatively correlated with siglec15m rna expression.Analysis of clinical characteristics supported increased siglec15expression that was positively correlated with more extrathyroid extension and lymph node metastasis.We observed different single nucleotide variant (snv) and copy number variation (cnv) patterns in high and low siglec15m rna expression subgroups; some vital dna damage repair deficiency scores addressed a negative correlation with siglec15m rna expression.We also found that some commonly used chemotherapy drugs might be suitable for different siglec15m rna expression subgroups.This study highlighted the vital role of siglec15in thca.Targeting siglec15may offer a potential novel therapeutic opportunity for thca patients.However, the detailed exact cellular mechanisms of siglec15in thca still needed to be elucidated by further studies.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article
Antiprotozoal effect of steroid hormone 20-hydroxyecdysone in giardiosis patients.

The world health organization reports that approximately 200 million people are infected with giardia (g.) lamblia worldwide.Taking into account the emergence of resistance and the high toxicity of conventional drugs, research into new strategies to fight against g.Lamblia is increasing.The aim of the study was to assess the antiprotozoal activity of 20-hydroxyecdysone in water sports athletes with giardiosis.A randomized, double-blinded, placebocontrolled clinical study was conducted.Seventy-six athletes with g.Lamblia infection participated in the study and were divided into 20-hydroxyecdysone, metronidazole and placebo groups.Clinical, parasitological, haematological and biochemical analyses were performed.Positive results for antiprotozoal therapy were revealed in the 20-hydroxyecdysone and metronidazole groups.After therapy, elimination of g.Lamblia was observed in 100.0% of the athletes included in the 20-hydroxyecdysone group.However, g.Lamblia was resistant to metronidazole in 4.0% of athletes included in the metronidazole group.A positive clinical response to the therapy occurred in the 20-hydroxyecdysone and metronidazole groups.Our study reveals high antiprotozoal activity of 20-hydroxyecdysone against g.Lamblia.Further clinical studies are necessary to evaluate the antiprotozoal efficacy of 20-hydroxyecdysone.

Journal: Annals of parasitology (2022)
Publication types: Randomized Controlled Trial;Journal Article
Gait speed reference values in community-dwelling older adults - Cross-sectional analysis from the Rotterdam Study.

Gait speed is a simple, inexpensive and clinically useful marker of physical function in older adults.We aimed to establish gait speed reference values for community-dwelling older adults.To this end, we further explored the association of age, sex and height with gait speed.Methods this study included community-dwelling participants aged 50 years and over enrolled in the rotterdam study.Participants completed the gait protocol between 2009 and 2016.The mean gait speed was calculated for age and height groups, stratified by sex.Reference values for gait speed were calculated using a quantile regression model adjusted for sex, the non-linear effects of age and height, as well as the interaction between age and sex plus the interaction between age and height.Results the study population included 4656 dutch participants with a mean (standard deviation) age of 67.7 (9.5) years, comprising 2569 (55.2%) women.The mean height of the participants was 1.69 (0.10) meters and the mean gait speed was 1.20 (0.20) m/s.Gait speed was lower with older age and greater with taller stature, but the effect of height disappeared above the age of 80 years.Sex did not affect gait speed after accounting for age and height.Age-, sex-, and height-specific reference values for gait speed are available for use at speed reference values/.Conclusions we found that height explains the commonly noted difference in usual gait speed between sexes and that neither height nor sex impacts gait speed in the very oldest adults.We developed reference values for usual gait speed in western european community-dwelling older adults.

Journal: Experimental gerontology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Automated selection of mid-height intervertebral disc slice in traverse lumbar spine MRI using a combination of deep learning feature and machine learning classifier.

Abnormalities and defects that can cause lumbar spinal stenosis often occur in the intervertebral disc (ivd) of the patient's lumbar spine.Their automatic detection and classification require an application of an image analysis algorithm on suitable images, such as mid-sagittal images or traverse mid-height intervertebral disc slices, as inputs.Hence the process of selecting and separating these images from other medical images in the patient's set of scans is necessary.However, the technological progress in making this process automated is still lagging behind other areas in medical image classification research.In this paper, we report the result of our investigation on the suitability and performance of different approaches of machine learning to automatically select the best traverse plane that cuts closest to the half-height of an ivd from a database of lumbar spine mri images.This study considers images features extracted using eleven different pre-trained deep convolution neural network (dcnn) models.We investigate the effectiveness of three dimensionality-reduction techniques and three feature-selection techniques on the classification performance.We also investigate the performance of five different machine learning (ml) algorithms and three fully connected (fc) neural network learning optimizers which are used to train an image classifier with hyperparameter optimization using a wide range of hyperparameter options and values.The different combinations of methods are tested on a publicly available lumbar spine mri dataset consisting of mri studies of 515 patients with symptomatic back pain.Our experiment shows that applying the support vector machine algorithm with a short gaussian kernel on full-length image features extracted using a pre-trained dense net201 model is the best approach to use.This approach gives the minimum per-class classification performance of around 0.88 when measured using the precision and recall metrics.The median performance measured using the precision metric ranges from 0.95 to 0.99 whereas that using the recall metric ranges from 0.93 to 1.0.When only considering the l3/l4, l4/l5, and l5/s1 classes, the minimum f1-scores range between 0.93 to 0.95, whereas the median f1-scores range between 0.97 to 0.99.

Journal: PloS one (2022)
Publication types: Journal Article
Safety assessment of compliant, highly invasive, lipid A-altered, O-antigen-defected Salmonella strains as prospective vaccine delivery systems.

In the present study, two prospective salmonella delivery strains, jol2782 and jol2837, were developed by gene deletions of lon and cpx r, which are related to cellular adhesion and intracellular survival.Additionally, sif a deletion was introduced for jol2782, which confers immune susceptibility and improves antigen delivery.Similarly, the rfa l deletion and lpx e substitution for pag l were accomplished in jol2837 to reduce virulence and endotoxicity.Thus, enhanced adhesion and invasion and reduced intracellular survival were attained.Furthermore, aspartic acid auxotrophic (asd) was deleted to impose darwinian selection on retention of the foreign antigen-expressing plasmid.Both delivery strains induced sufficient cytokine expression, but the level was significantly lower than that of the wild-type strain; the lowest cytokine expression was induced by the jol2837 strain, indicating reduced endotoxicity.In parallel, ig g production was significantly enhanced by both delivery strains.Thus, the innate and adaptive immunogenicity of the strains was ensured.The environmental safety of these strains was ascertained through faecal dissemination assays.The nonpathogenicity of these strains to the host was confirmed by body weight monitoring, survival assays, and morphological and histological assessments of the vital organs.The in vitro assay in murine and human cell lines and in vivo safety assessments in mice suggest that these novel strains possess safety, invasiveness, and immunogenicity, making them ideal delivery strains.Overall, the results clearly showed that strain jol2782 with sif a deletion had higher invasiveness, demonstrating superior vaccine deliverability, while jol2837 with lpx e substitution for pag l and rfa l deletion had outstanding safety potential with drastically abridged endotoxicity.

Journal: Veterinary research (2022)
Publication types: Journal Article
Neuroprotective activity ofUlmus pumilaL. in Alzheimer's disease in rats; role of neurotrophic factors.

Alzheimer's disease (ad) is one of the most prevalent neurodegenerative disorders which affects the hippocampus and cortical neurons leading to impairment of cognitive ability.Treatment of ad depends mainly on acetylcholinesterase inhibitors, however, a novel therapeutic approach is introduced based on the maintenance of neuronal viability and functionality exerted through neurotrophic factors.In the current study,ulmus pumila l.Leaves alcoholic extract was investigated for its neuroprotective activity in al cl3-induced ad in rats.Rats were orally treated with al cl3(17 mg/kg) for 4 weeks followed by u.Pumilaextract (150 mg/kg b.wt.) for another 6 weeks.Treatment of neuro-intoxicated rats with u.Pumilaextract resulted in a significant regulation in neurotrophic factors; brain derived neurotrophic factor and transforming growth factor-β and pro-inflammatory cytokine; tnf.It also induced an elevation in serum levels of monoamine neurotransmitters; norepinephrine, dopamine and serotonin and a decline in brain acetlycholinesterase activity.u.Pumilaextract also showed potent antioxidant activity as indicated by the declined malondialdehyde and elevated reduced glutathione, catalase and super oxide dismutase levels in ad rats' brains.Histological improvement was detected in the cerebral cortex, the hippocampus and striatum of the treated rats.the phytochemical analysis of u.Pumilaextract revealed high contents of flavonoids and phenolics and the major compounds were isolated and chemically characterized.Additionally,u.Pumilaextract and the isolated compounds exerted a prominent activity inin-vitroacetylcholinesterase inhibition assay with kaempferol-3-o-β-glucoside being the most potent compound showing ic50of 29.03 ± 0.0155 μm.A molecular docking study indicated high affinity of kaempferol-3-o-β-robinobioside on acetylcholine esterase binding site with estimated binding free energy of -8.26 kcal/mol.

Journal: Heliyon (2020)
Publication types: Journal Article
DCE-DForest: A Deep Forest Model for the Prediction of Anticancer Drug Combination Effects.

Drug combinations have recently been studied intensively due to their critical role in cancer treatment.Computational prediction of drug synergy has become a popular alternative strategy to experimental methods for anticancer drug synergy predictions.In this paper, a deep learning model called dce-dforest is proposed to predict the synergistic effect of drug combinations.To sufficiently extract drug information, the paper leverages bert (bidirectional encoder representations from transformers) to encode the drug and the deep forest to model the nonlinear relationship between the drugs and cell lines.The experimental results on the synergy datasets demonstrate that the proposed method consistently shows superior performance over the other machine learning models.

Journal: Computational and mathematical methods in medicine (2022)
Publication types: Journal Article
Eating Behaviors in Early Childhood (1-5 Years) and Their Association With Sociodemographic Characteristics in Turkey.

Eating problems are common in childhood and being seen in 25%-45% of healthy children.The period following the first year of life up to five years is when eating problems are most frequently reported and also when the child acquires eating habits.Several studies have shown that eating behavior is affected by the family environment, and by parental eating habits and modes of feeding their children.The purpose of this study was to investigate the eating behavior characteristics of children in early childhood, to determine the frequency of problematic eating behaviors, and to compare these with the family's sociodemographic characteristics.The study consisted of 255 children aged 1-5 years, with no chronic disease, presenting to i̇zmir tepecik education and research hospital child health and diseases department general pediatric clinics between february and april, 2017, together with their parents.In the study, 39 questions were asked to parents related to children's demographic characteristics and eating behaviour.Problematic eating behavior was present in 43.9% of the study group.Analysis identified feeding bottle use, feeding with the use of an assistant object, eating lasting longer than half an hour, and the child not feeding itself as the most frequent eating problems.Malnutrition was present in 104 (65.8%) of the children with problematic eating behavior.Examination of unhealthy eating behavior in the light of the study findings showed no significant association between eating behaviors and variables such as type and time of delivery, maternal education level, maternal employment status, maternal age, or the number of children in the family.In terms of nutrition status, turkey appears to exhibit problems associated with both developed and developing countries.Public nutrition in turkey fluctuates significantly depending on the region, the season, socioeconomic levels, and differences between urban and rural settlements.Early-onset of eating-related problems can have a negative effect on children's subsequent physical, emotional, and social development.Determination in the early period of eating problems seen in children and investigation of the causes thereof is important in terms of identifying a potential solution.It is important to work with the family to that end, and for children to be followed-up by pediatricians at regular intervals.

Journal: Cureus (2021)
Publication types: Journal Article
Classification Accuracy of Hepatitis C Virus Infection Outcome: Data Mining Approach.

The dataset from genes used to predict hepatitis c virus outcome was evaluated in a previous study using a conventional statistical methodology.Objective the aim of this study was to reanalyze this same dataset using the data mining approach in order to find models that improve the classification accuracy of the genes studied.Methods we built predictive models using different subsets of factors, selected according to their importance in predicting patient classification.We then evaluated each independent model and also a combination of them, leading to a better predictive model.Results our data mining approach identified genetic patterns that escaped detection using conventional statistics.More specifically, the partial decision trees and ensemble models increased the classification accuracy of hepatitis c virus outcome compared with conventional methods.Conclusions data mining can be used more extensively in biomedicine, facilitating knowledge building and management of human diseases.

Journal: Journal of medical Internet research (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Successful endoscopic removal of foreign body lacerating into the duodenum.

Video 1the endoscope was advanced under direct visualization to the third part of the duodenum.A foreign body consistent with a ballpoint pen was identified in the duodenum.The sharp end of the pen formed a deep laceration through the second portion of the duodenum.The blunt end of the pen was ulcerated into the third portion of the duodenum with 2 additional pressure ulcers located in close proximity.Removal of the pen was first attempted using a snare without success.The foreign body was then successfully removed with a rat tooth.The second portion of the duodenum showed minimal oozing with contained deep laceration.The third portion of the duodenum showed 2 pressure ulcers.

Journal: VideoGIE : an official video journal of the American Society for Gastrointestinal Endoscopy (2022)
Publication types: Journal Article