syedzayyan/paper_mill_benchmark huggingface dataset:
STAMP: A Self-training Student-Teacher Augmentation-Driven Meta Pseudo-Labeling Framework for 3D Cardiac MRI Image Segmentation.

Medical image segmentation has significantly benefitted thanks to deep learning architectures.Furthermore, semi-supervised learning (ssl) has led to a significant improvement in overall model performance by leveraging abundant unlabeled data.Nevertheless, one shortcoming of pseudo-labeled based semi-supervised learning is pseudo-labeling bias, whose mitigation is the focus of this work.Here we propose a simple, yet effective ssl framework for image segmentation-stamp(student-teacher augmentation-driven consistency regularization via meta pseudo-labeling).The proposed method uses self-training (through meta pseudo-labeling) in concert with a teacher network that instructs the student network by generating pseudo-labels given unlabeled input data.Unlike pseudo-labeling methods, for which the teacher network remains unchanged, meta pseudo-labeling methods allow the teacher network to constantly adapt in response to the performance of the student network on the labeled dataset, hence enabling the teacher to identify more effective pseudo-labels to instruct the student.Moreover, to improve generalization and reduce error rate, we apply both strong and weakdata augmentationpolicies, to ensure the segmentor outputs a consistent probability distribution regardless of the augmentation level.Our extensive experimentation with varied quantities of labeled data in the training sets demonstrates the effectiveness of our model in segmenting the left atrial cavity from gadolinium-enhanced magnetic resonance (ge-mr) images.By exploiting unlabeled data with weak and strong augmentation effectively, our proposed model yielded a statistically significant 2.6% improvement(p<0.001)in dice and a 4.4% improvement(p<0.001)in jaccard over other state-of-the-art ssl methods using only 10% labeled data for training.

Journal: Medical Image Understanding and Analysis. Medical Image Understanding and Analysis (Conference) (2022)
Publication types: Journal Article
Fractal fractional analysis of non linear electro osmotic flow with cadmium telluride nanoparticles.

Numerical simulations of non-linear casson nanofluid flow were carried out in a microchannel using the fractal-fractional flow model.The nano-liquid is prepared by dispersing cadmium telluride nanoparticles in common engine oil.Using relative constitutive equations, the system of mathematical governing equations has been formulated along with initial and boundary conditions.Dimensionless variables have been used to obtain the non-dimensional form of the governing equations.The fractal-fractional model has been obtained by employing the fractal-fractional operator of the exponential kernel.As the exact solution of the non-linear fractal-fractional model is very tough to find, therefore the formulated model has been solved numerically via the crank-nicolson scheme.Various plots are generated for the inserted parameters.From the analysis, it has been observed that a greater magnitude of the electro-kinetic parameter slows down the fluid's velocity.It is also worth noting that the fractional and classical models can also be derived from the fractal-fractional model by taking the parameters tend to zero.From the analysis, it is also observed that in response to 0.04 volume fraction of cadmium telluride nanoparticles, the rate of heat transfer (nusselt number) and rate of mass transfer (sherwood number) increased by 15.27% and 2.07% respectively.

Journal: Scientific reports (2022)
Publication types: Journal Article
Locally Advanced Pancreatic Ductal Adenocarcinoma: Challenges and Progress.

Pancreatic ductal adenocarcinoma (pdac) is one of the major causes of death in the western world, and it is estimated to become the second leading cause of tumour-related mortality in the next 10 years.Among pancreatic cancers, ductal adenocarcinomas are by far the most common, characterised by a challenging diagnosis due to the lack of initial and pathognomonic clinical signs.In this scenario, non-metastatic locally advanced pancreatic cancer (lapc) accounts for a large proportion of all new pancreatic ductal adenocarcinoma diagnoses.There is no consensus on a common definition of lapc.Still, it usually includes tumours that are not resectable due to vascular involvement.As of today, treatment is limited, and the prognosis is very unfavourable.Curative-intent surgery remains the gold-standard even if often jeopardized by vascular involvement.Continuing progress in our understanding of lapc genetics and immunology will permit the development of different treatments, targeted or combined, including radiation therapy, hadrontherapy, targeted immunotherapies or new chemotherapies.A multidisciplinary approach combining various fields of expertise is essential in aiming to limit disease progression as well as patient outcome.Using a narrative literature review approach, the manuscript explores the most up-to-date knowledge concerning locally advanced pancreatic ductal adenocarcinoma management.

Journal: OncoTargets and therapy (2020)
Publication types: Journal Article;Review
A single Epley manoeuvre can improve self-perceptions of disability (quality of life) in patients with pc-BPPV: A randomised controlled trial in primary care.

Posterior canal benign paroxysmal positional vertigo (pc-bppv) causes physical, functional, and emotional impairment.The treatment is the epley manoeuvre (em).Objective the purpose of the study was to compare the impact of the em and a sham manoeuvre in primary care on self-perceived disability.Design randomised, double-blind, sham-controlled clinical trial conducted in primary care with a follow-up of 1 year.Participants patients aged ≥18 years old diagnosed with pc-bppv according to the dix-hallpike test (dht) were randomised to: interventions: intervention (em) group or a control (sham manoeuvre) group.Main measurements the main study covariates were age, sex, history of depression and anxiety, presence of nystagmus in the dht, patient-perceived disability assessed with the dizziness handicap inventory - screening version (dhi-s).Data were analyzed using bivariate and multivariate mixed tobit analyses.Results overall, 134 patients were studied: 66 in the intervention group and 68 in the control group.Median age was 52 years (interquartile range [iqr], 38.25-68.00 years.Standard deviation, 16.98) and 76.12% of the patients were women.The dht triggered nystagmus in 40.30% of patients.The median total dhi-s score for the overall sample at baseline was 16 (iqr, 8.00-22.00); 16 [iqr, 10.5-24.0] vs 10 [6.0-14.0] for women vs men (p<.001).Patients treated with the em experienced a mean reduction of 2.03 points in dhi-s score over the follow-up period compared with patients in the sham group.Conclusions pc-bppv affects the quality of life of primary care patients.A single em can improve self-perceptions of disability by around 2 points on the dhi-s scale.

Journal: Atencion primaria (2021)
Publication types: Journal Article;Randomized Controlled Trial
Effect of haemolysis on an enzymatic measurement of ethanol.

Introduction we investigated the interference of haemolysis on ethanol testing carried out with the synchron assay kit using an au680 autoanalyser (beckman coulter, brea, usa).Materials and methods two tubes of plasma samples were collected from 20 volunteers.Mechanical haemolysis was performed in one tube, and no other intervention was performed in the other tube.After centrifugation, haemolysed and non-haemolysed samples were diluted to obtain samples with the desired free haemoglobin (hb) values (0, 1, 2, 5, 10 g/l).A portion of these samples was then separated, and ethanol was added to the separated sample to obtain a concentration of 86.8 mmol/l ethanol.After that, these samples were diluted with ethanol-free samples with the same hb concentration to obtain samples containing 43.4, 21.7, and 10.9 mmol/l.Each group was divided into 20 equal parts, and an ethanol test was carried out.The coefficient of variation (cv), bias, and total error (te) values were calculated.Results the te values of haemolysis-free samples were approximately 2-5%, and the te values of haemolysed samples were approximately 10-18%.The bias values of haemolysed samples ranged from nearly - 6.2 to - 15.7%.Conclusions haemolysis led to negative interference in all samples.However, based on the 25% allowable total error value specified for ethanol in the clinical laboratory improvement amendments (clia 88) criteria, the te values did not exceed 25%.Consequently, ethanol concentration can be measured in samples containing free hb up to 10 g/l.

Journal: Biochemia medica (2021)
Publication types: Journal Article
Auditory evoked BOLD responses in awake compared to lightly anaesthetized zebra finches.

Functional magnetic resonance imaging (f mri) is increasingly used in cognitive neuroscience and has become a valuable tool in the study of auditory processing in zebra finches, a well-established model of learned vocal communication.Due to its sensitivity to head motion, most f mri studies in animals are performed in anaesthetized conditions, which might significantly impact neural activity evoked by stimuli and cognitive tasks.In this study, we (1) demonstrate the feasibility of f mri in awake zebra finches and (2) explore how light anaesthesia regimes affect auditory-evoked bold responses to biologically relevant songs.After an acclimation procedure, we show that f mri can be successfully performed during wakefulness, enabling the detection of reproducible bold responses to sound.Additionally, two light anaesthesia protocols were tested (isoflurane and a combination of medetomidine and isoflurane), of which isoflurane alone appeared to be the most promising given the high success rate, non-invasive induction, and quick recovery.By comparing auditory evoked bold responses in awake versus lightly anaesthetized conditions, we observed overall effects of anaesthetics on cerebrovascular reactivity as reflected in the extent of positive and negative bold responses.Further, our results indicate that light anaesthesia has limited effects on selective bold responses to natural versus synthetic sounds.

Journal: Scientific reports (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Resubclassification and clinical management for Barcelona Clinic Liver Cancer Stage C hepatocellular carcinoma.

Patients with barcelona clinic liver cancer stage c (bclc-c) hepatocellular carcinoma (hcc) can be markedly heterogeneous with varying prognosis.This study aims to establish a new subclassification system for bclc-c hcc to better predict overall survival (os) and to tailor therapy.Methods we retrospectively studied 1856 bclc-c hcc patients between 2006 and 2017 from e-da hospital, taiwan (n = 622, training cohort), kaohsiung medical university hospital, taiwan (n = 774, taiwan validation cohort), and stanford university medical center and mayo clinic (united states), hanyang university hospital (south korea), and ogaki municipal hospital (japan) to make up the international validation cohort (n = 460).Results in the training cohort, significant factors associated with os were largest tumor size ≥ 10 cm, extrahepatic spread, macrovascular invasion, and child-pugh class, which provided the basis, together with aged ≥ 75 years, for the substaging, through c0 to c4, of bclc-c hcc patients.The median os for substages c0, c1, c2, c3, and c4 were 43.8 months (95% confidence interval [ci] 32.2-53.7), 20.6 months (ci 14.1-25.9), 11.5 months (ci 8.02-14.1), 5.7 months (ci 4.02-5.98), and 3.2 months (ci 2.41-3.59), respectively, (p < 0.05).Os remained distinct among the proposed substages in the taiwan validation cohort as well as the international validation cohort.The distinction between the substages persisted in subgroup analysis by substage combined with treatment modality.In substage c0-c3, patients receiving hcc curative therapy had a significantly better median os than those receiving sorafenib or palliative therapy.Conclusion our new substaging system provides more precise prognosis to better tailor therapy for bclc-c hcc patients.

Journal: Hepatology international (2021)
Publication types: Journal Article
Vaginal Secretion Epithelium Count as a Prognostic Indicator of High Abundance of Ureaplasmas in Women with a Normal Nugent Score.

Genital tract ureaplasma infections are associated with numerous complications, ranging from inflammation, through infertility, to problematic pregnancy.In the course of ureaplasma infection, the risk of human papillomavirus infection increases.Diagnostic tests for urea-plasma infections are not always carried out, especially in women with the normal nugent test results.The study attempts to check whether it is possible to find a prognostic indicator that could suggest a high abundance of ureaplasmas (≥ 104cfu/ml) at the stage of the initial examination of vaginal discharge.Such a prognostic factor could qualify women for further tests to detect infections with these atypical bacteria.Six hundred twenty-seven white women with a score of 0-3 on the nugent scale were tested, including 322 patients with a high abundance of ureaplasmas (≥ 104cfu/ml) and 305 who tested negative for these bacteria.Ureaplasma infections were detected statistically significant in women who had few or no epithelial cells in the genital swab specimens compared to the results obtained for women with numerous or very numerous epithelial cells (p< 0.001).The risk of the high density of ureaplasmas was 38.7% higher with fewer or no epithelial cells than with high numbers.In patients aged 18-40 years with few or no epithelial cells, a high density of ureaplasmas (≥ 104cfu/ml) was observed significantly more frequently (p= 0.003).Determining the number of epithelial cells in gram-stained slides may be the prognostic indicator of ureaplasma infection.Testing for genital ureaplasma infection should be considered, especially in women of childbearing age (18-40 years), even if the nugent test value is normal and p h ≤ 4.6.

Journal: Polish journal of microbiology (2022)
Publication types: Journal Article
Causal Discovery in Linear Non-Gaussian Acyclic Model With Multiple Latent Confounders.

Causal discovery from observational data is a fundamental problem in science.Though the linear non-gaussian acyclic model (li ngam) has shown promising results in various applications, it still faces the following challenges in the data with multiple latent confounders: 1) how to detect the latent confounders and 2) how to uncover the causal relations among observed and latent variables.To address these two challenges, we propose a hybrid causal discovery method for the li ngam with multiple latent confounders (mlcli ngam).First, we utilize the constraint-based method to learn the causal skeleton.Second, we identify the causal directions, by conducting regression and independence tests on the adjacent pairs in the causal skeleton.Third, we detect the latent confounders with the help of the maximal clique patterns raised by the latent confounders and reconstruct the causal structure with latent variables.Theoretical results show the correctness and efficiency of the algorithms.We conduct extensive experiments on synthetic and real data, which illustrates the efficiency and effectiveness of the proposed algorithms.

Journal: IEEE transactions on neural networks and learning systems (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Immunoglobulin A anti-phospholipid antibodies in Swedish cases of systemic lupus erythematosus: associations with disease phenotypes, vascular events and damage accrual.

Immunoglobulin (ig) g- and ig m-class anti-cardiolipin antibodies (a cl) and lupus anti-coagulant (la) are included in the 1997 update of the american college of rheumatology (acr-97) systemic lupus erythematosus (sle) criteria.Despite limited evidence, ig a-a cl and ig a anti-β2-glycoprotein-i (anti-β2gpi) were included in the 2012 systemic lupus international collaborating clinics criteria.The present study aimed to evaluate ig g-/ig a-/ig m-a cl and anti-β2gpi occurrence in relation to disease phenotype, smoking habits, pharmacotherapy, anti-phospholipid syndrome (aps) and organ damage among 526 swedish sle patients meeting acr-97.Patients with rheumatoid arthritis (n = 100), primary sjögren's syndrome (n = 50) and blood donors (n = 507) served as controls.Anti-phospholipid antibodies (a pl) were analysed by fluoroenzyme-immunoassays detecting a cl/anti-β2gpi.Seventy-six (14%) sle cases fulfilled the sydney aps-criteria, and ≥ 1 a cl/anti-β2gpi isotype (ig g/ig a/ig m) occurred in 138 sle patients (26%).Forty-five (9%) of the sle cases had ig a-a cl, 20 of whom (4%) lacked ig g-/ig m-a cl.Seventy-four (14%) tested positive for ig a anti-β2gpi, 34 (6%) being seronegative regarding ig g/ig m anti-β2gpi.Six (1%) had aps manifestations but were seropositive regarding ig a-a cl and/or ig a anti-β2gpi in the absence of ig g/ig m-a pl and la.Positive la and ig g-a pl tests were associated with most aps-related events and organ damage.Exclusive ig a anti-β2gpi occurrence associated inversely with caucasian ethnicity [odds ratio (or) = 0·21, 95% confidence interval (ci) = 0·06-0·72) and photosensitivity (or = 0·19, 95% ci = 0·05-0·72).Nephritis, smoking, la-positivity and statin/corticosteroid-medication associated strongly with organ damage, whereas hydroxychloroquine-medication was protective.In conclusion, ig a-a pl is not rare in sle (16%) and ig a-a pl analysis may have additional value among sle cases with suspected aps testing negative for other isotypes of a pl and la.

Journal: Clinical and experimental immunology (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effects of renal denervation therapy on cardiac function and malignant arrhythmia in patients with reduced left ventricular ejection fraction and narrow QRS complexes treated with implantable cardioverter defibrillator.

The purpose of this study was to explore the effects of renal denervation (rdn) on cardiac function and malignant arrhythmia in patients with reduced left ventricular ejection fraction (hfr ef) and narrow qrs treated with an implantable cardioverter defibrillator (icd).methods:a total of 20 eligible hfr ef patients [left ventricular ejection fraction (lvef) <40%] and narrow qrs complexes (qrs duration <120 ms) were randomized into either the icd plus rdn group or the icd only group during 17 april 2014 to 22 november 2016.Clinical data, including clinical characteristics, blood biochemistry, b-type natriuretic peptide, echocardiographic indexes, 6-min walk distance (6mwd), new york heart association (nyha) classification, and count of icd discharge events before and after the operation were analyzed.Patients were followed up for up to 3 years post icd or icd plus rdn.results:baseline clinical data were comparable between the two groups.Higher lvef (%) (mixed model repeated measure,p= 0.0306) (39.50% ± 9.63% vs.31.20% ± 4.52% at 1 year; 41.57% ± 9.62% vs.31.40% ± 8.14% at 3 years), systolic blood pressure (p= 0.0356), and longer 6mwd (p< 0.0001) as well as reduction of nyha classification (p< 0.0001) were evidenced in the icd plus rdn group compared to icd only group during follow-up.Patients in the icd plus rdn group experienced fewer icd discharge events (2 vs.40) and decreased diuretic use; rehospitalization rate (30% vs.100%,p= 0.0031) and cardiogenic mortality rate (0% vs.50%,p= 0.0325) were also significantly lower in the icd plus rdn group than in the icd only group during follow-up.conclusion:icd implantation plus rdn could significantly improve cardiac function and cardiac outcome as well as increase exercise capacity compared to icd only for hfr ef patients with narrow qrs complexes.

Journal: Frontiers in physiology (2022)
Publication types: Journal Article
Application of Dual-Enhanced Surface-Enhanced Raman Scattering Probe Technology in the Diagnosis of Tumor Cells in Vitro.

With the development of precision medicine, antigen/antibody-targeted therapy has brought great hope to tumor patients; however, the migration of tumor cells, especially a small number of cells flowing into blood or other tissues, remains a clinical challenge.In particular, it is difficult to use functional gold nanomaterials for targeted clinical tumor diagnosis while simultaneously obtaining stable and highly sensitive raman signals.Therefore, we developed a detection method for functional au nanostars (au nss) with dual signal enhancement that can specifically track location and obtain high-intensity surface-enhanced raman scattering (sers) signals.First, au nss with specific optical properties were synthesized and functionalized.The raman dye 4-mercapto-hydroxybenzoic acid and polyethylene glycol were coupled with the tumor marker, epidermal growth factor receptor, to obtain the targeted sers probes.In addition, a detection chip was prepared for raman detection with physical enhancement, exhibiting a 40-times higher signal intensity than that of quartz glass.This study combines physical enhancement and sers enhancement technologies to achieve dual enhancement, enabling the detection of a highly sensitive and stable raman signal; this has potential clinical value for antigen/antibody-targeted tumor diagnosis and treatment.

Journal: Molecules (Basel, Switzerland) (2022)
Publication types: Journal Article
Harnessing the Multistability of Kresling Origami for Reconfigurable Articulation in Soft Robotic Arms.

This study examines a biology-inspired approach of using reconfigurable articulation to reduce the control requirement for soft robotic arms.We construct a robotic arm by assembling kresling origami modules that exhibit predictable bistability.By switching between their two stable states, these origami modules can behave either like a flexible joint with low bending stiffness or like a stiff link with high stiffness, without requiring any continuous power supply.In this way, the robotic arm can exhibit pseudo-linkage kinematics with lower control requirements and improved motion accuracy.A unique advantage of using origami as the robotic arm skeleton is that its bending stiffness ratio between stable states is directly related to the underlying kresling design.Therefore, we conduct extensive parametric analyses and experimental validations to identify the optimized kresling pattern for articulation.The results indicate that a higher angle ratio, a smaller resting length at contracted stable state, and a large number of polygon sides can offer more significant and robust bending stiffness tuning.Based on this insight, we construct a proof-of-concept, tendon-driven robotic arm consisting of three modules and show that it can exhibit the desired reconfigurable articulation behavior.Moreover, the deformations of this manipulator are consistent with kinematic model predictions, which validate the possibility of using simple controllers for such compliant robotic systems.

Journal: Soft robotics (2022)
Publication types: Journal Article
SARS-CoV-2 and COVID-19: revisiting the most important research questions.

In february 2020, we highlighted the top nine important research questions on sars-co v-2 and covid-19 concerning virus transmission, asymptomatic and presymptomatic virus shedding, diagnosis, treatment, vaccine development, origin of virus and viral pathogenesis.These and related questions are revisited at the end of 2021 to shed light on the roadmap of bringing an end to the pandemic.

Journal: Cell & bioscience (2021)
Publication types: Journal Article