syedzayyan/paper_mill_benchmark huggingface dataset:
Screening Emergency Admissions at Risk of Chronic Hepatitis C (SEARCH) to diagnose or 're-diagnose' infections is effective in Australia.

The world health organization has set ambitious viral hepatitis elimination targets; however, difficulties in identifying and engaging patients remain.The emergency visit is an opportunity for enhanced linkage to care (ltc).We assessed the effectiveness of an automated emergency department (ed) screening service in identifying patients with hepatitis c (hcv) and achieving ltc.A retrospective evaluation was undertaken, analysing the first 5000 patients screened through an automatic australian service termed 'screening emergency admissions at risk of chronic hepatitis' (search).Screening was performed for those recommended in the australian national testing policy, specifically overseas born (ob) and aboriginal or torres strait islanders (atsi).Healthcare worker education, patient information materials and opt-out informed consent were used to test sera already collected for biochemistry assays.5000 of 5801 (86.2%) consecutive eligible patients were screened (ob: 4778, atsi: 222) from 14 093 ed presentations.Hcv antibody was positive in 181 patients (3.6%); 51 (1.0%) were hcv rna positive.Of 51 hcv rna-positive patients, 12 were new diagnoses, 32 were 're-diagnoses' (aware but lost to follow-up [ltfu]), and 7 were previously known but treatment contraindicated.Ltc was successful in 38 viraemic patients (7 deceased, 4 ltfu, 1 treatment ineligible and 1 declined).Of rna-negative patients, 75 were previously treated and 49 had presumed spontaneous clearance.Opt-out consent was acceptable to all patients and staff involved.Ed screening can lead to additional diagnosing and 're-diagnosing' of hcv, with high rates of ltc.Opt-out consent and automation removed major obstacles to testing.

Journal: Journal of viral hepatitis (2021)
Publication types: Journal Article
Effects of Rehabilitation on Long-COVID-19 Patient's Autonomy, Symptoms and Nutritional Observance.

Despite significant improvements in covid-19 therapy, many patients still present with persistent symptoms and quality-of-life alterations.The aim of this study was to simultaneously investigate the long-term evolution of autonomy, malnutrition and long-lasting symptoms in people infected with covid-19 and hospitalized in the icu.Method: patients’ clinical characteristics; extent of their loss of autonomy based on “autonomie gérontologie groupes iso-ressources” (ag-gir) classification; nutritional status while following the french and global leadership initiative on malnutrition (glim) recommendations; and symptom evolutions before infection, during hospitalization and rehabilitation, and up to 6 months after returning home were determined in thirty-seven patients.Results: prior to a covid-19 infection, all patients were autonomous, but upon admission to the rehabilitation center (crm), 39% of them became highly dependent.After discharge from the center and 6 months after returning home, only 6 and 3%, respectively, still required considerable assistance.Of these thirty-seven patients, 11% were moderately malnourished and 81% presented with severe malnutrition, with a significant correlation being observed between malnutrition and autonomy (p < 0.05).Except for fatigue, which persisted in 70% of the patients 6 months after discharge from rehabilitation, all other symptoms decreased significantly.Conclusions: this study shows a striking decrease in autonomy associated with malnutrition after hospitalization for a covid-19 infection and a clear beneficial effect from personalized rehabilitation.However, although almost all patients regained autonomy 6 months after returning home, they often still suffer from fatigue.Patient compliance with their nutritional recommendations deserves further improvement, preferably through personalized and persistent follow-up with the patient.

Journal: Nutrients (2022)
Publication types: Journal Article
Cu-catalysed transamidation of unactivated aliphatic amides.

Direct transamidation is gaining prominence as a ground-breaking technique that generates a wide variety of amides without the requirement of acid-amine coupling or other intermediate steps.However, transamidation of unactivated aliphatic amides, on the other hand, has been a long-standing issue in comparison to transamidation of activated amides.Herein, we report a transamidation approach of an unactivated aliphatic amide using a copper catalyst and chlorotrimethylsilane as an additive.In addition, we used transamidation as a tool for selective n-c(o) cleavage and o-c(o) formation to synthesise 2-substituted benzoxazoles and benzothiazoles.The reactions were carried out without using any solvents and offered wide substitution scope.

Journal: Organic & biomolecular chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Application of ancillary studies in soft tissue cytology using a pattern-based approach.

The cytologic diagnosis of soft tissue neoplasms has undergone many advances due to the development of numerous useful immunohistochemical markers and molecular assays that target specific molecular alterations.Ancillary tests, when used in conjunction with clinical, radiologic, and cytomorphologic features, allow for more accurate classification and refinement of differential diagnoses of soft tissue neoplasms.Soft tissue tumors encompass a diverse group of tumors showing a wide range of cytomorphologies that can be broadly grouped as lipomatous, myxoid, spindled, pleomorphic, round cell, and epithelioid.This pattern-based classification enables the formation of appropriate differentials; however, entities that share these basic morphologic patterns may vary greatly in their clinical behavior.The breadth of soft tissue tumors that can be diagnosed on cytologic preparations continues to increase with identification of defining molecular alterations that can be detected by conventional means (eg, fluorescence in situ hybridization) or by immunohistochemical surrogates.Furthermore, the emergence of high-throughput molecular techniques (eg, next generation sequencing) has potential roles for additional discovery and diagnostic applications.This review highlights the diagnostic role of ancillary tests in the context of a pattern-based approach to soft tissue cytology.Cancer cytopathol 2018;000:000-000.© 2018 american cancer society.

Journal: Cancer cytopathology (2018)
Publication types: Journal Article;Review
Grayscale medical image segmentation method based on 2D&3D object detection with deep learning.

Grayscale medical image segmentation is the key step in clinical computer-aided diagnosis.Model-driven and data-driven image segmentation methods are widely used for their less computational complexity and more accurate feature extraction.However, model-driven methods like thresholding usually suffer from wrong segmentation and noises regions because different grayscale images have distinct intensity distribution property thus pre-processing is always demanded.While data-driven methods with deep learning like encoder-decoder networks always are always accompanied by complex architectures which require amounts of training data.Methods combining thresholding method and deep learning, this paper presents a novel method by using 2d&3d object detection technologies.First, interest regions contain segmented object are determined with fine-tuning 2d object detection network.Then, pixels in cropped images are turned as point cloud according to their positions and grayscale values.Finally, 3d object detection network is applied to obtain bounding boxes with target points and boxes' bottoms and tops represent thresholding values for segmentation.After projecting to 2d images, these target points could composite the segmented object.Results three groups of grayscale medical images are used to evaluate the proposed image segmentation method.We obtain the io u (dsc) scores of 0.92 (0.96), 0.88 (0.94) and 0.94 (0.94) for segmentation accuracy on different datasets respectively.Also, compared with five state of the arts and clinically performed well models, our method achieves higher scores and better performance.Conclusions the prominent segmentation results demonstrate that the built method based on 2d&3d object detection with deep learning is workable and promising for segmentation task of grayscale medical images.

Journal: BMC medical imaging (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
COVID 19-impact on substance use treatment utilization and provision in South Africa.

The coronavirus disease 2019 (covid-19) pandemic has impacted people with substance use disorders (suds) worldwide.The aim of this study was to explore, changes in the number of sud treatment episodes provided during the height of the pandemic and, sud treatment providers' perceptions of the impact of covid-19-related restrictions on people with suds and the delivery of sud treatment services in south africa.Methods we used administrative data collected as part of the south african community epidemiology network on drug use (sacendu) project to assess whether the number of treatment episodes changed during the height of covid-19 restrictions.We used data from an online survey of sud treatment providers to assess providers' perceptions of the impact of covid-19 on sud treatment delivery.Eight seven sud facilities were recruited to participate in the online survey.Results sixty-three organisations (out of a total of 86) participated in the survey, yielding a 73.2% response rate.About half (n = 30; 47.6%) of the sample thought the need for sud treatment had remained the same or had increased during the covid-19 lockdown.Half the sample (n = 32; 50.7%) reported decreased availability of sud services during covid-19 lockdowns.Participants believed that the lack of services during covid-19 lockdown impacted negatively on patients that were enrolled in their programmes and on individuals who wished to access the service.Furthermore, changes in service provision seemed to increase patients' anxiety, exacerbate pre-existing mental health problems and in some cases were thought to precipitate relapse.In addition, patient disengagement and attrition from treatment were thought to have increased during this period.Whilst 47.6% (n = 30) of providers agreed with the value of the alcohol ban, 23.8% (n = 15) of providers thought it had unintended negative consequences.Conclusion based on the findings it is evident that sud treatment services in south africa have been significantly affected during the covid-19 pandemic and more severely during the onset of the pandemic.Together with service providers, more effective ways should be sought on how to feasibly expand access to sud treatment for all south africans and enhance the country's preparedness for future health emergencies.

Journal: Substance abuse treatment, prevention, and policy (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The potential effects and mechanisms of hispidulin in the treatment of diabetic retinopathy based on network pharmacology.

Diabetic retinopathy (dr), one of the most common and severe microvascular complication of diabetes mellitus (dm), is mainly caused by diabetic metabolic disorder.So far, there is no effective treatment for dr.Eriocauli flos, a traditional chinese herb, has been used in treating the ophthalmic diseases including dr.However, the active ingredients and molecular mechanisms of eriocauli flos to treat diabetic retinopathy remain elusive.Methods here, the systems pharmacology model was developed via constructing network approach.8 active components which were screened by oral bioavailability (ob ≥ 30%) and drug-likeness (dl ≥ 0.18) and 154 targets were selected from eriocauli flos through tcmsp database.Another 3593 targets related to dr were obtained from genecards, omim, ttd, and drugbank databases.The 103 intersecting targets of dr and eriocauli flos were obtained by draw venn diagram.In addition, protein-protein interaction network was established from string database and the compound-target network was constructed by cytoscape which screened top 12 core targets with cyto nca module.Then the overlapping targets were analyzed by go and kegg enrichment.Moreover, two core targets were selected to perform molecular docking simulation.Subsequently, cck8 assay, rt-pcr and western blotting were applied to further reveal the mechanism of new candidate active component from eriocauli flos in high glucose-induced hrecs.Results the results showed that the overlapping targets by go analysis were enriched in cellular response to chemical stress, response to oxidative stress, response to reactive oxygen species, reactive oxygen species metabolic process and so on.Besides, the overlapping targets principally regulated pathways such as age-rage signaling pathway in diabetic complications, lipid atherosclerosis, fluid shear stress and atherosclerosis, and pi3k-akt signaling pathway.Molecular docking exhibited that vegfa and tnf-α, had good bindings to the great majority of compounds, especially the compound hispidulin.In vitro, hispidulin ameliorated high-glucose induced proliferation by down-regulating the expression of p-erk, p-akt, and vegfa; meanwhile inhibited the m rna levels of tnf-α.Conclusions in this study, through network pharmacology analysis and experimental validation, we found that hispidulin maybe has a potential targeted therapy effect for dr by decreasing the expression of p-akt, p-erk, and vegfa, which resulted in ameliorating the proliferation in hrecs.

Journal: BMC complementary medicine and therapies (2022)
Publication types: Journal Article
Impact of Intermediate Cystic Fibrosis Classification on Parents' Perceptions of Child Vulnerability and Protectiveness.

This cross-sectional, mixed-method study examined factors associated with parent perceptions of child vulnerability and protectiveness in three groups: cystic fibrosis (cf-group, n = 40), intermediate cf classification (i-group, n = 20), and healthy (h-group, n = 50).A composite indicator structural equation (cise) using bayesian estimation tested two mediational models: psychological and biological.Significant results ( p < .05) from the psychological model showed i-group and cf-group parents perceived their children to be more vulnerable than h-group parents but reported lower levels of protectiveness than h-group parents.Perceptions of vulnerability mediated protectiveness for cf- and i-groups.The biological model showed i-group children had significantly less severe genotype and phenotype, and lower sweat chloride levels than the cf-group; i-group parents had lower expectations about children developing cf symptoms.Both models showed negative associations between children's ages and protectiveness.Psychological factors explained perceptions of child vulnerability and protectiveness; biological factors explained protectiveness.Parent perceptions of vulnerability and protectiveness are separate, independent constructs.

Journal: Journal of family nursing (2019)
Publication types: Comparative Study;Journal Article;Research Support, Non-U.S. Gov't
Circulating Protein Biomarkers for Prognostic Use in Patients with Advanced Pancreatic Ductal Adenocarcinoma Undergoing Chemotherapy.

Patients with advanced pancreatic ductal adenocarcinoma (pdac) have a dismal prognosis.We aimed to find a prognostic protein signature for overall survival (os) in patients with advanced pdac, and to explore whether early changes in circulating-protein levels could predict survival.We investigated 92 proteins using the olink immuno-oncology panel in serum samples from 363 patients with advanced pdac.Protein panels for several survival cut-offs were developed independently by two bioinformaticians using lasso and ridge regression models.Two panels of proteins discriminated patients with os 2 years.Index i (csf-1, il-6, pdcd1, tnfrsf12a, trail, tweak, and ca19-9) had aucs of 0.99 (95% ci: 0.98−1) (discovery cohort) and 0.89 (0.74−1) (replication cohort).For index ii (cxcl13, il-6, pdcd1, and tnfrsf12a), the corresponding aucs were 0.97 (0.93−1) and 0.82 (0.68−0.96).Four proteins (angpt2, il-6, il-10, and tnfrsf12a) were associated with survival across all treatment groups.Longitudinal samples revealed several changes, including four proteins that were also part of the prognostic signatures (csf-1, cxcl13, il-6, tnfrsf12a).This study identified two circulating-protein indices with the potential to identify patients with advanced pdac with very short os and with long os.

Journal: Cancers (2022)
Publication types: Journal Article
Actual Racial/Ethnic Disparities in COVID-19 Mortality for the Non-Hispanic Black Compared to Non-Hispanic White Population in 35 US States and Their Association with Structural Racism.

Introduction while the increased burden of covid-19 among the black population has been recognized, most attempts to quantify the extent of this racial disparity have not taken the age distribution of the population into account.In this paper, we determine the black-white disparity in covid-19 mortality rates across 35 states using direct age standardization.We then explore the relationship between structural racism and differences in the magnitude of this disparity across states.Methods using data from the centers for disease control and prevention, we calculated both crude and age-adjusted covid-19 mortality rates for the non-hispanic white and non-hispanic black populations in each state.We explored the relationship between a state-level structural racism index and the observed differences in the racial disparities in covid-19 mortality across states.We explored the potential mediating effects of disparities in exposure based on occupation, underlying medical conditions, and health care access.Results relying upon crude death rate ratios resulted in a substantial underestimation of the true magnitude of the black-white disparity in covid-19 mortality rates.The structural racism index was a robust predictor of the observed racial disparities.Each standard deviation increase in the racism index was associated with an increase of 0.26 in the ratio of covid-19 mortality rates among the black compared to the white population.Conclusions structural racism should be considered a root cause of the black-white disparity in covid-19 mortality.Dismantling the long-standing systems of racial oppression is critical to adequately address both the downstream and upstream causes of racial inequities in the disease burden of covid-19.

Journal: Journal of racial and ethnic health disparities (2022)
Publication types: Journal Article
Treatment of Complications Due to Fuchs Heterochromic Iridocyclitis (FHI) - a Case Report.

Fuchs heterochromic iridocyclitis is a chronic, unilateral iridocyclitis characterized by iris heterochromia.The gradual progression of the disease leads to the development of cataracts, glaucoma, and, occasionally, vitreous infiltration.The trigger for inflammation of the iris and ciliary body is still unknown.There are several as yet unconfirmed theories about the mechanism of occurrence, including toxoplasma gondii infection, immune dysfunction, infiltration of sensitized lymphocytes, and chronic herpes virus infection.Objective the aim of this article is to present a case of fuchs heterochromic iridocyclitis with complications in form of glaucoma and dense cataract in a female patient during a standard ophthalmologic exam in our clinic.The next aim is to show a proper algorithm of treatment in form of carbonic anhydrase inhibitors antiglaucoma medication, cataract surgery with implantation of the intraocular lens, yag laser capsulothomy.Case report a 55-year-old patient reports to our clinic for an examination.She was informed 7 years ago by her ophthalmologist that her lack of vision in the right eye is irreparable.Ophthalmological examination as well as a positive torch test (elevation of ig g for toxoplasma gondii) lead to a diagnosis of fuchs heterochromic iridocyclitis with complications of glaucoma and dense cataract.Antiglaucoma drops are prescribed, phaco surgery is performed on the right eye with implantation of the intraocular lens, and yag laser capsulotomy in the follow ups.There was a significant improvement of the visual acuity from light sensation with uncertain projection of the same on the right eye, to 0,5-0,6 snellen scale.We also educated the patient of her disease as well as the importance of her treatment and follow up consultations.Conclusion due to the insidious nature of this condition, along with a mild chronic course, most patients with fhi are not aware of the subtle changes that occur in their eyes.One of the most serious complications of fhi is secondary glaucoma, which can cause permanent vision loss in patients.The main cause of poor vision in patients with fhi is caused by cataract formation, with a prevalence of 23% to 90.7%.We placed special emphasis on educating the patient about her condition and the long-term and importance of regular check-ups to prevent possible recurrent or new complications.

Journal: Acta informatica medica : AIM : journal of the Society for Medical Informatics of Bosnia & Herzegovina : casopis Drustva za medicinsku informatiku BiH (2022)
Publication types: Case Reports;Journal Article
Design, Synthesis, and Characterization of I-BET567, a Pan-Bromodomain and Extra Terminal (BET) Bromodomain Oral Candidate.

Through regulation of the epigenome, the bromodomain and extra terminal (bet) family of proteins represent important therapeutic targets for the treatment of human disease.Through mimicking the endogenous n-acetyl-lysine group and disrupting the protein-protein interaction between histone tails and the bromodomain, several small molecule pan-bet inhibitors have progressed to oncology clinical trials.This work describes the medicinal chemistry strategy and execution to deliver an orally bioavailable tetrahydroquinoline (thq) pan-bet candidate.Critical to the success of this endeavor was a potency agnostic analysis of a data set of 1999 thq bet inhibitors within the gsk collection which enabled identification of appropriate lipophilicity space to deliver compounds with a higher probability of desired oral candidate quality properties.Sar knowledge was leveraged via free-wilson analysis within this design space to identify a small group of targets which ultimately delivered i-bet567 (27), a pan-bet candidate inhibitor that demonstrated efficacy in mouse models of oncology and inflammation.

Journal: Journal of medicinal chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Directional dependence of the plasmonic gain and nonreciprocity in drift-current biased graphene.

Here, we investigate the nonreciprocal propagation and amplification of surface plasmons in drift-current biased graphene, using both galilean and relativistic-type doppler shift transformations of the graphene's conductivity.Consistent with previous studies, both conductivity models predict strongly nonreciprocal propagation of surface plasmons due to the drag effect caused by the drifting electrons.In particular, the galilean doppler shift model leads to stronger spectral asymmetries in the plasmon dispersion with regimes of unidirectional propagation.Remarkably, it is shown that both conductivity models predict regimes of nonreciprocal plasmon amplification in a wide angular sector of in-plane directions when the drift-current biased graphene sheet is coupled to a plasmonic substrate (namely, si c), with the plasmon amplification rate being substantially higher for the relativistic doppler shift model.

Journal: Nanophotonics (Berlin, Germany) (2022)
Publication types: Journal Article