syedzayyan/paper_mill_benchmark huggingface dataset:
An assessment of the quality of optical coherence tomography image acquisition.

Optical coherence tomography (oct) provides excellent image resolution, however oct optimal acquisition is essential but could be challenging owing to several factors.We sought to assess the quality of oct pullbacks and identify the causes of suboptimal image acquisition.We evaluated 784 (404 pre-pci; 380 post-pci) coronary pullbacks from an anonymized oct database from our cardiovascular imaging core laboratory.Imaging of the region-of-interest (roi-lesion or stented segment plus references) was incomplete in 16.1% pullbacks, caused by pullback starting too proximal (63.7%), inappropriate pullback length (17.1%) and pullback starting too distal (11.4%).The quality of image acquisition was excellent in 36.3% pullbacks; whereas 4% pullbacks were unanalyzable.Pullback quality was most commonly affected by poor blood displacement from inadequate contrast volume (27.4%) or flow (25.6%), followed by artifacts (24.1%).Acquisition mode was 'high-resolution' (54 mm) in 74.4% and 'survey' (75 mm) in 25.6% of cases.The 54 mm mode was associated with incomplete roi imaging (p = 0.020) and inadequate contrast volume (p = 0.035).We observed a substantial frequency of suboptimal image acquisition and identified its causes, most of which can be addressed with minor modifications during the procedure, ultimately improving patient outcomes.

Journal: The international journal of cardiovascular imaging (2020)
Publication types: Journal Article;Multicenter Study
Recent progress in antibody-based therapeutics for triple-negative breast cancer.

Introduction triple-negative breast cancer (tnbc) is a subtype of severely aggressive breast cancer that lacks the expression of oestrogen receptor (er), progesterone receptor and human epidermal growth factor receptor 2 (her2) and is highly metastatic and related to a poor prognosis.Current standard treatments are still limited to systemic chemotherapy, radiotherapy, and surgical resection.More effective treatments are urgently needed.Areas covered the immunogenicity of tnbc has provided opportunities for the development of targeted immunotherapy.In this review, we focus on the recent development in antibody-based drug modalities, including angiogenesis inhibitors, immune checkpoint inhibitors, antibody-drug conjugates, immunoconjugates, t cell-redirecting bispecific antibodies and car-t cells, and their mechanisms of action in tnbc.Expert opinion at present, the treatment of tnbc is still a major challenge that needs to be addressed.Novel immunotherapies are promising opportunities for improving the management of this aggressive disease.

Journal: Expert opinion on drug delivery (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Subacute Cardiac Tamponade in a COVID-19 Patient Despite Negative Testing.

Covid-19 infection has been documented to cause a wide range of symptoms including cardiac complications.We present a case of subacute cardiac tamponade in a patient infected with covid-19 in the absence of respiratory symptoms; we also review the current literature on this rare sequela.Our patient is a 67-year-old man who presented to the hospital due to intermittent chest pain for three weeks.Covid-19 polymerase chain reaction (pcr) testing was negative two times.He had an outpatient echocardiogram that showed a moderate pericardial effusion about a week prior to the hospital presentation.On admission, a repeat echocardiogram showed a large pericardial effusion with tamponade physiology.Pericardiocentesis did not reveal a clear etiology of the hemorrhagic effusion but four days later, the patient was found to be positive for covid-19 infection without any clear respiratory illness.Given the absence of other etiology and negative workup, cardiac tamponade was attributed to pericardial inflammation from this virus and our patient improved with colchicine and steroids.We, therefore, advise providers to consider covid-19 as a cause of hemorrhagic, cryptogenic cardiac tamponade despite negative covid-19 testing.We also review 42 additional reported cases of cardiac tamponade in patients infected with covid-19.Covid-19 can cause cardiac tamponade even in the absence of pulmonary disease.This case and literature review highlight tamponade as a rare complication of covid-19 and should be considered in the differential of any acute deterioration in this patient population.

Journal: Cureus (2022)
Publication types: Case Reports;Journal Article
Role for 2D image generated 3D face models in the rehabilitation of facial palsy.

The outcome for patients diagnosed with facial palsy has been shown to be linked to rehabilitation.Dense 3d morphable models have been shown within the computer vision to create accurate representations of human faces even from single 2d images.This has the potential to provide feedback to both the patient and medical expert dealing with the rehabilitation plan.It is proposed that a framework for the creation and measuring of patient facial movement consisting of a hybrid 2d facial landmark fitting technique which shows better accuracy in testing than current methods and 3d model fitting.

Journal: Healthcare technology letters (2017)
Publication types: Journal Article
Rigidly Fused Spiro-Conjugated π-Systems.

Spiro-fused π-systems have gained considerable attention for their application as semiconductors in molecular electronics.Here, a synopsis regarding recent breakthroughs in ladderized spirobifluorenes and indeno-spirobifluorenes, along with further spiro-condensed heteroatomic hydrocarbons with donor-acceptor moieties, is provided.Additionally, an extended range of rigid spirobifluorene polymers and specific doubly linked spiro-systems with partial chiral character is discussed.The diverse applications of the aforementioned structures are thoroughly evaluated.

Journal: ChemPlusChem (2021)
Publication types: Journal Article;Review
Endometriosis infiltrating the pelvic floor muscles with histopathological correlation-A case report.

We report the case of a 29-year-old woman with deep infiltrating endometriosis who underwent robotic nerve-sparing surgery for resection of all visible lesions infiltrating pelvic and extrapelvic sites.Painful symptoms included severe dysmenorrhea, menstrual dyschezia and stranguria, with no improvement in response to hormonal treatment.The location on physical examination of a painful retrocervical nodule was identified by magnetic resonance imaging to be infiltrating the right parametrium/paracervix.During surgery, this nodule was recognized as an important retrocervical/rectovaginal lesion infiltrating the pelvic floor (i.e.Levator ani and coccygeus), and was histopathologically confirmed as endometriosis infiltrating the skeletal pelvic floor muscles.A pubmed search of the medline database in march (2019) found no publication reporting histopathologic confirmation of endometriosis infiltrating the pelvic floor muscles.

Journal: The journal of obstetrics and gynaecology research (2019)
Publication types: Case Reports;Journal Article
'Virtual' Action Research: Two examples.

Action research is the predominant approach for organisational inquiry, but it comes in many guises and in some cases ends up as all action and no research.A common feature of all action research is the necessity to meet stakeholders in person in order to gain an understanding 'from within', this is particularly the case where 'soft' action research is the basis of the inquiry.In this paper first, we reflect, briefly, upon the history of action research and second, upon the lessons leant from the outcomes from two projects.The first project was conducted 'virtually', between a college in the usa and one in the uk and the second undertaken during the disruption caused by the restrictions arising from the covid-19 pandemic.The experiences gained from these two 'virtual' action research projects and the lessons learnt are of interest to both the 'traditional' and 'soft' action research community.

Journal: Systemic practice and action research (2022)
Publication types: Journal Article
Distance Between Home and the Admitting Hospital and Its Effect on Survival of Low Socioeconomic Status Population WithStaphylococcus aureusBacteremia.

Bacteremia is the presence of bacteria in the bloodstream.The objective of this study was to determine the relationship between low socioeconomic status (ses) and the epidemiology, process of care, and outcomes of patients with staphylococcus aureusbacteremia (sab).Methods we conducted a multicenter, retrospective, cohort study that evaluated adult patients with sab in 3 los angeles county hospitals from july 15, 2012, through may 31, 2018.We determined ses (low ses, intermediate ses, and high ses) for each patient and compared sociodemographic and epidemiologic characteristics, management of care received by patients with sab (ie, process of care), and outcomes.We used a cox proportional hazards model to determine predictors of 30-day mortality for each ses group.Results of 915 patients included in the sample, 369 (40%) were in the low-ses group, 294 (32%) in the intermediate-ses group, and 252 (28%) in the high-ses group.Most significant predictors of 30-day mortality in the cox proportional hazards model were admission to an intensive care unit (hazard ratio [hr] = 9.04; 95% ci, 4.26-19.14), pitt bacteremia score ≥4 indicating critical illness (hr = 4.30; 95% ci, 2.49-7.44), having ≥3 comorbidities (hr = 2.05; 95% ci, 1.09-3.85), and advanced age (hr = 1.03; 95% ci, 1.01-1.05).Distance between home and admitting hospital affected mortality only in the low-ses group (hr = 1.02; 95% ci, 1.00-1.02).Conclusions ses did not independently affect the outcome of sab; however, the farther the patient's residence from the hospital, the greater the negative effect on survival in a low-ses population.Our findings underscore the need to develop multipronged, targeted public health efforts for populations that have transportation barriers to health care.

Journal: Public health reports (Washington, D.C. : 1974) (2022)
Publication types: Journal Article;Multicenter Study
Obesity-driven prepartal hepatic lipid accumulation in dairy cows is associated with increased CD36 and SREBP-1 expression.

We investigated the hypothesis that obesity in dairy cows enhanced expression of proteins involved in hepatic fatty acid uptake and metabolism.Sixteen holstein-friesian close-up cows were divided into 2 equal groups based on their body condition score (bcs) as optimal (3.25≤bcs≤3.5) and high (4.0≤bcs≤4.25).Intravenous glucose tolerance test (gtt) and liver biopsies were carried out at day 10 before calving.Blood samples were collected before (basal) and after glucose infusion, and glucose, insulin and non-esterified fatty acid (nefa) levels were determined at each sample point.In addition, β-hydroxybutyrate and triglycerides levels were measured in the basal samples.The liver biopsies were analyzed for total lipid content and protein expression of insulin receptor beta (irβ), fatty acid translocase (fat/cd36) and sterol regulatory element-binding protein-1 (srebp-1).Basal glucose and insulin were higher in high-bcs cows, which coincided with higher circulating triglycerides and hepatic lipid content.Clearance rate and auc for nefa during gtt were higher in optimal-bcs cows.The development of insulin resistance and fatty liver in obese cows was paralleled by increased hepatic expression of the irβ, cd36 and srebp-1.These results suggest that increased expression of hepatic cd36 and srebp-1 is relevant in the obesity-driven lipid accumulation in the liver of dairy cows during late gestation.

Journal: Research in veterinary science (2016)
Publication types: Journal Article
miRCarta: a central repository for collecting miRNA candidates.

The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications.Especially for mi rnas, one class of small non-coding rnas, many algorithms have been developed to predict new candidates from next-generation sequencing data.While the amount of publications describing novel mi rna candidates keeps steadily increasing, the current gold standard database for mi rnas - mi rbase - has not been updated since june 2014.As a result, publications describing new mi rna candidates in the last three to five years might have a substantial overlap of candidates without noticing.With mi rcarta we implemented a database to collect novel mi rna candidates and augment the information provided by mi rbase.In the first stage, mi rcarta is thought to be a highly sensitive collection of potential mi rna candidates with a high degree of analysis functionality, annotations and details on each mi rna.We added-besides the full content of the mi rbase-12,857 human mi rna precursors to mi rcarta.Users can match their own predictions to the entries of mi rcarta to reduce potential redundancies in their studies.Mi rcarta provides the most comprehensive collection of human mi rnas and mi rna candidates to form a basis for further refinement and validation studies.The database is freely accessible at

Journal: Nucleic acids research (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
An update on the incidence of perioperative outcomes after carotid endarterectomy, stratified by type of preprocedural neurologic symptom.

Perioperative complications after carotid endarterectomy (cea) have decreased over time.Therefore, we aimed to provide an update on 30-day outcomes after cea, stratified by type of preprocedural neurologic symptom.Methods we included all ceas from the targeted vascular module of the american college of surgeons national surgical quality improvement program (acs-nsqip, 2011-2015) and stratified patients based on type of preprocedural neurologic symptom, that is, asymptomatic, ocular transient ischemic attack (tia), hemispheric tia, and stroke.We compared 30-day outcomes across the groups, with 30-day stroke/death as our primary endpoint.Results of 16,739 cea patients, 9784 were asymptomatic (58%).Among the 6955 symptomatic patients, 1216 (17%) had a preprocedural ocular tia, 2635 (38%) a preprocedural hemispheric tia, and 3104 (45%) a preprocedural stroke.Preprocedural stroke patients had higher 30-day stroke/death rates compared with those with a preprocedural hemispheric tia, or ocular tia, or asymptomatic patients (5.0% vs 3.3%, 1.9%, and 1.8%, respectively; all p < .001), primarily owing to differences in perioperative 30-day stroke rates, with 4.1% vs 2.5%, 1.4%, and 1.3%, respectively (all p < .001).Conclusions among symptomatic cea patients, those with a preprocedural stroke had a high perioperative 30-day stroke/death rate, compared with those patients with either a preprocedural hemispheric or ocular tia.Therefore, the common stratification applied to cea patients, which groups all symptomatic patients, should be avoided, especially as the relative proportion of symptomatic patients with a preprocedural stroke vs those with a hemispheric or ocular tia will affect the overall outcome for all symptomatic patients after cea.

Journal: Journal of vascular surgery (2018)
Publication types: Comparative Study;Journal Article;Research Support, N.I.H., Extramural
Wavefront shaping for forward scattering.

Aberrations and scattering limit the ability of optical microscopy to penetrate deep tissues.Adaptive optics (ao) is a very effective technique to correct for smooth aberrations.Wavefront shaping (wfs) techniques, on the other hand, compensate both scattering and aberrations and have guaranteed convergence even for finding high-dimensional corrections.However, if it is known in advance that the required corrections should be smooth, wfs is suboptimal because it does not use this a priori information.Here, we combine the best of ao and wfs by introducing a wfs method that takes into account the smoothness of the required correction.Our method is numerically stable and robust against noise, and it can find the corrections for multiple targets simultaneously.We experimentally confirmed that this method outperforms existing wfs techniques, especially in forward scattering samples.

Journal: Optics express (2022)
Publication types: Journal Article
Primer and Historical Review on Rapid Cardiac CINE MRI.

Acceleration is an important consideration when imaging moving organs such as the heart.Not only does acceleration enable motion-free scans but, more importantly, it lies at the heart of capturing the dynamics of cardiac motion.For over three decades, various ingenious approaches have been devised and implemented for rapid cine mri suitable for dynamic cardiac imaging.Virtually all techniques relied on acquiring less data to reduce acquisition times.Parallel imaging was among the first of these innovations, using multiple receiver coils and mathematical algorithms for reconstruction; acceleration factors of 2 to 3 were readily achieved in clinical practice.However, in the context of imaging dynamic events, further decreases in scan time beyond those provided by parallel imaging were possible by exploiting temporal coherencies.This recognition ushered in the era of k-t accelerated mri, which utilized predominantly statistical methods for image reconstruction from highly undersampled k-space.Despite the successes of k-t acceleration methods, however, the accuracy of reconstruction was not always guaranteed.To address this gap, mr physicists and mathematicians applied compressed sensing theory to ensure reconstruction accuracy.Reconstruction was, indeed, more robust, but it required optimizing regularization parameters and long reconstruction times.To solve the limitations of all previous methods, researchers have turned to artificial intelligence and deep neural networks for the better part of the past decade, with recent results showing rapid, robust reconstruction.This review provides a comprehensive overview of key developments in the history of cine mri acceleration, and offers a unique and intuitive explanation behind the techniques and underlying mathematics.level of evidence: 5technical efficacy stage: 1.

Journal: Journal of magnetic resonance imaging : JMRI (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Genomic epidemiology and characterisation of penicillin-sensitiveStaphylococcus aureusisolates from invasive bloodstream infections in China: an increasing prevalence and higher diversity in genetic typing be revealed.

Many countries have reported increasing rates of penicillin-susceptible methicillin-sensitive staphylococcus aureus(mssa-pens).To date, there is relatively little known about the current situation and molecular characteristics of mssa-pensin china.In this study, we carried out a laboratory-based multi-region retrospective study to investigate the genomic epidemiology and characterisation of mssa-pensisolated from invasive bloodstream infections (bsis) across 17 provinces.The prevalence of mssa-pensisolates increased significantly over the 6-year period, with the proportion increasing from 3.51% in 2014-8.80% in 2019, an average relative increase of 22.14% per year (95% confidence interval 9.67%-34.61%, p for trend <0.001), suggesting that china is experiencing a resurgence of mssa-pens.Phylogenetic analysis showed a higher strain diversity occurred; the most frequent clonal complexes (ccs) identified were cc188 (17.14%), cc398 (15.71%) and cc5 (15.71%).Over half of mssa-pensstrains were pan-susceptible, with erythromycin the most frequent resistance observed.Moreover, 25 isolates were identified as immune evasion cluster negative, including cc15, cc188 and cc1, and 6 strains encoded the panton-valentine leucocidin gene.Importantly, virulence assays showed that mssa-pensexhibited a level of virulence comparable to that of penicillin-resistant mssa (mssa-penr), indicating that more-sensitive strains should not be mistaken for lacking aggressiveness invivo.Furthermore, 11 of these isolates were confirmed asbla zpositive but phenotype sensitive, with different amino acid changes inbla z.Our data support the recommendation to clinicians regarding the usage of penicillin in invasive bsis caused by mssa-pens, which might create a novel opportunity for better antimicrobial stewardship in the future.

Journal: Emerging microbes & infections (2022)
Publication types: Journal Article
Nephropathic cystinosis in Poland: a 40-year retrospective study.

Introduction nephropathic cystinosis (nc) is a rare, autosomal recessive disorder leading to lysosomal accumulation of cystine.It is caused by mutations in the ctns gene encoding a cystine cotransporter cystinosin.The infantile (inc) and juvenile (jnc) forms are distinguished.The former, responsible for 95% of cases, is characterized by development of renal fanconi syndrome, end-stage kidney disease (eskd), and extrarenal complications.A therapy with cysteamine significantly improves outcomes.There are limited data on nc in the central eastern european countries.Objectives we aimed to evaluate the prevalence, genetic background, and clinical course of nc in the polish population.Patients and methods we performed a retrospective analysis of data of all identified nc patients in poland.Results between 1982 and 2017, 15 patients with nc (13 icn, 2 jcn) were identified.The most common mutations of the ctns gene were c.18_c.21del gact and c.681+1g>a, whereas only 2 patients carried the 57 kb deletion.The majority (11/13) of inc patients with limited access to the cysteamine therapy developed eskd at a median age of 11 years and 9 of them received kidney transplants.Three inc patients died at a median age of 24 years.In contrast, 2 inc patients treated adequately present normal kidney function and growth at the age of 13 and 11 years.Two jnc patients presented a milder course.Conclusions the prevalence of nc in poland is much lower than in the western countries and its molecular background appears to be different.The unfavorable course in the majority of inc patients was caused by a limited access to the cysteamine treatment.

Journal: Polish archives of internal medicine (2022)
Publication types: Journal Article
Comparison of astigmatic correction with and without limbal marking during small-incision lenticule extraction.

To compare clinical outcomes after correction of moderate to high astigmatism through small-incision lenticule extraction (smile) with and without limbal marking.Setting tianjin eye hospital, tianjin, china.Design prospective randomized comparative case series.Methods this prospective randomized control study included 240 unilateral eyes of 240 patients who underwent smile with astigmatism of more than 0.75 diopters (d).The eyes were randomly assigned to a marked group (120 eyes) or an unmarked control group (120 eyes).Manifest refraction was observed at the 3-month follow-up timepoint and evaluated using a vector analysis.Results postoperative astigmatism differed statistically significantly in the marked group (-0.08 ± 0.15 d) and the control group (-0.16 ± 0.24 d) at 3 months ( p = .001), and correction index, index of success, angle of error (absolute value), and magnitude of error were also significantly better in the marked group ( p < .05).There was a significant positive correlation between index of success and angle of error (absolute value) ( p < .001).Conclusions limbal marking-based manual compensation prior to smile was associated with a statistically significant reduction in undercorrection and error of axis in cases of moderate to high astigmatism, although the magnitude of the difference was small.

Journal: Journal of cataract and refractive surgery (2022)
Publication types: Journal Article;Randomized Controlled Trial