syedzayyan/paper_mill_benchmark huggingface dataset:
Accelerated waning of immune responses to a third COVID-19 vaccination in patients with immune-mediated inflammatory diseases.

A 3rd covid-19 vaccination is currently recommended for patients under immunosuppression.However, a fast decline of antibodies against the sars-co v-2 receptor-binding domain (rbd) of the spike protein has been observed.Currently it remains unclear whether immunosuppressive therapy affects kinetics of humoral and cellular immune responses.Methods 50 patients under immunosuppression and 42 healthy controls (hcs) received a 3rddose of an m rna-based vaccine and were monitored over a 12-weeks period.Humoral immune response was assessed 4 and 12 weeks after 3rddose.Antibodies were quantified using the elecsys anti-sars-co v-2 spike immunoassay against the receptor-binding domain (rbd) of the spike protein.Sars-co v-2-specific t cell responses were quantified by ifn-γ elispot assays.Adverse events, including sars-co v-2 infections, were monitored over a 12-week period.Results at week 12, reduced anti-rbd antibody levels were observed in imid patients as compared to hcs (median antibody level 5345 bau/ml [1781-10,208] versus 9650 bau/ml [6633-16,050], p < 0.001).Reduction in relative antibody levels was significantly higher in imid patients as compared to hcs at week 12 (p < 0.001).Lowest anti-rbd antibody levels were detected in imid patients who received biological disease-modifying anti-rheumatic drugs (dmards) or a combination therapy with conventional synthetic and biological dmards.Number of sars-co v-2-specific t cells against wildtype and omicron variants remained stable over 12 weeks in imid patients.No serious adverse events were reported.Conclusion due to a fast decline in anti-rbd antibodies in imid patients an early 4thvaccination should be considered in this vulnerable group of patients.

Journal: Journal of autoimmunity (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Improved Methods for Determination of Petrophysical Properties of Unconventional Tight Rocks Using Particulate Samples.

Drill cuttings are available continuously over the entire depth of any drilled wells.The use of drill cuttings to obtain petrophysical data can add a significant value in formation evaluation.An update to the previous study is presented using nmr and archimedes principle to determine petrophysical properties including porosity, bulk density, and matrix density from drill cuttings of organic-rich mudrock formations.In the original published method, sonication was used to clean and saturate the drill cutting samples.In this improved method, particulate samples were saturated using both sonication and pressure injection methods.The obtained results were compared with accepted lab measurement techniques.Results show that pressure saturation of particulate samples can provide accurate results of petrophysical properties.Obtaining reliable petrophysical data from drill cuttings can provide continuous and quasi-real-time data for the formation evaluation of reservoirs and can effectively reduce costs by reducing or eliminating expensive formation evaluation methods.

Journal: ACS omega (2022)
Publication types: Journal Article
A Tale of Two Mills: Socio-Technological Integration in Meiji Japan, 1868-1912.

Since the 1950s, historians have sought to explain industrial modernization in meiji japan as a model for developing countries.They typically attribute japan's success to single factors such as accumulated knowledge or capital, visionary leadership, or technological choice.This article moves beyond mono-causality to examine technology transfer's role in industrial modernization.Tomioka silk filature and osaka cotton spinning mill make the case that components of industrialization were interrelated and a new socio-technological system was essential for technology transfer to affect a kuhnian-style paradigm shift.Tomioka is an example of ad hoc industrialization, the gradual integration of transferred technologies, and creation of associated regimes leading to a new socio-technological system.In contrast, osaka cotton mill embodies the creation of a new industrial paradigm for japanese industry, demonstrating the essentiality of integrating numerous socio-technological elements such as adapted artifacts, bio-materials, accumulated knowledge, factory management, and geographic location.

Journal: Technology and culture (2022)
Publication types: Journal Article
Prognostic of recurrence and survival in poorly differentiated thyroid cancer.

The prognosis of poorly differentiated thyroid carcinomas (pdtc) defined by the turin criteria is variable.The aim of this study on 51 pdtc patients was to determine clinical, histological and molecular prognostic factors associated with recurrence in patients with localized disease at initial treatment and with overall survival in patients with distant metastases.Of 40 patients for whom next-generation sequencing (ngs) by thyro seq v3 was able to be performed on historical samples, we identified high-risk molecular signature (tert, tp53 mutations) in 24 (60%) cases, intermediate risk signature in 9 (22.5%) cases and low-risk signature in 7 (17.5%) cases.Potentially actionable mutations were identified in 10% of cases.After a median follow-up of 57.5 months, recurrence occurred in 11 (39%) of the 28 patients with localized disease.The american thyroid association (ata) high risk of relapse, high mitotic count, high molecular risk signature and cd163 expression were associated with recurrence (p = 0.009, 0.01, 0.049, 0.03 respectively).After a median follow-up of 49.5 months, thyroid cancer-related death occurred in 53% of the patients with distant metastases.There was no significant prognostic factor associated with death in univariate analysis.However, none of the patients with intermediate ata risk of recurrence and none of the patients with low-risk molecular signature died from the disease.In addition, high molecular-risk signature was associated with the presence of synchronous or metachronous distant metastasis (p = 0.007) and with poor overall survival (p = 0.01).In conclusion, ata risk of relapse and high mitotic count was associated with higher rate of recurrence in localized pdtc.High molecular-risk signature was associated with the presence of distant metastasis and poor overall survival.Further studies are needed to determine if molecular testing adds to ata risk stratification or response to therapy in predicting outcomes.

Journal: Endocrine-related cancer (2022)
Publication types: Journal Article
Clinical outcomes of patients treated with template-based high-dose-rate interstitial brachytherapy boost for post-operative recurrent gynecological malignancies: A retrospective analysis.

To report the clinical outcomes in patients treated with martinez universal perineal interstitial template (mupit)-based interstitial brachytherapy boost for primary and recurrent vault and vaginal cancers, and to perform a comparative analysis with our previously published series of similar patients.Material and methods one hundred and seventeen patients treated between january, 2009 and december, 2015 were evaluated.Descriptive statistics for the patterns of relapse, local recurrence-free survival (lrfs), disease-free survival (dfs), overall survival (os), and late toxicities were carried out.Kaplan-meier curves were used for survival analysis.All variables with the potential to affect outcomes were tested using log-rank test for statistical significance.Results at a median follow-up of 63 months, lrfs, dfs, and os at 3/5 years were 77.1%/74.7%, 61%/52%, and 72.3%/63.1%, respectively.Overall treatment time (ott) of 56 days did not affect outcomes.Bulky tumors and ott > 63 days adversely affected lrfs.Overall treatment time also significantly impacted dfs and os.Grade 3-4 late bladder toxicities were observed in 1.7% patients, and grade 3-4 late rectal toxicities in 5% patients.Compared to our previous series, the outcome in the current series is better in terms of severe late toxicities (5% improvement in rectal toxicity, and 2.7% improvement in bladder toxicity) and os by 10%.This could be attributed to the increasing use of concurrent chemotherapy and relative optimization strategies for organs at risk.Conclusions patients with primary and recurrent vault and vaginal cancers treated with high-dose-rate interstitial brachytherapy boost using mupit resulted in modest clinical outcomes and acceptable late toxicities.Ott was the most important factor affecting the outcomes.

Journal: Journal of contemporary brachytherapy (2022)
Publication types: Journal Article
Lessons learned on recruitment and retention in hard-to-reach families in a phase III randomised controlled trial of preparatory information for children undergoing general anaesthesia.

Recruitment and retention are documented as two of the most difficult elements of conducting clinical trials.These issues are even more challenging in paediatric trials, particularly when the families being recruited and retained are deemed 'hard to reach'.Methods through the authors' own reflection on the conduct of the trial this paper examines recruitment and retention with hard to reach families from the perspective of a recently completed clinical trial on preparatory information for children undergoing general anaesthesia for tooth extractions in which approximately 83% of those approached and eligible agreed to participate.Results the lessons learned for recruitment include: the importance of children's assent; maximising limited resources when screening and approaching potential participants; valuing families' time; and developing effective professional relationships.The retention rate was 83-85.5% at follow up time points up to 3.5 weeks following recruitment, insights into how this was accomplished include: ensuring continuity of care; determination to connect via telephone; valuing families' time; and close monitoring of appointment date changes.Conclusions implications for future paediatric trials with hard to reach families are discussed.Trial registration isrctn18265148 ; nihr portfolio 10,006.Date of registration: 29 november 2013.The trial was registered after commencement but before completion of data collection.

Journal: BMC oral health (2017)
Publication types: Journal Article
Neuroimaging in Dementia: A Brief Review.

Dementia is a clinical syndrome that manifests itself with impairment in cognitive functions owing to various neurodegenerative etiologies causing severe disability in the older population.Although the diagnosis is largely dependent on clinical examination, biomarkers can significantly aid in early diagnosis of dementia, especially in those without any clinical evidence of neurocognitive impairment.These biomarkers can be discovered in cerebrospinal fluid (csf) or can be assessed by neuroimaging.Our goal was to discuss and assess the role of different neuroimaging techniques in the early diagnosis of relatively common etiologies of dementia.We used pub med as search engines to look for helpful articles; most of the sources used were peer reviewed.We discussed the utility of various neuroimaging techniques, such ct, mri, positron emission tomography (pet) scan, and single-photon emission computed tomography (spect), in the diagnosis of dementia.We concluded that various modern neuroimaging techniques prove to be very helpful in early identification, diagnosis, and differentiation between subtypes.However, the actual clinical utility of these tests in terms of their cost-effectivity and availability remains to be seen.Ongoing research is required to further develop biomarkers for early identification and monitor the progression of different etiologies of dementia.

Journal: Cureus (2020)
Publication types: Journal Article;Review
Using ZnCo2O4nanoparticles as the hole transport layer to improve long term stability of perovskite solar cells.

Inorganic metal oxides with the merits of high carrier transport capability, low cost and superior chemical stability have largely served as the hole transport layer (htl) in perovskite solar cells (pscs) in recent years.Among them, ternary metal oxides have gradually attracted attention because of the wide tenability of the two inequivalent cations in the lattice sites that offer interesting physicochemical properties.In this work, zn co2o4nanoparticles (nps) were prepared by a chemical precipitation method and served as the htl in inverted pscs.The device based on the zn co2o4nps htl showed better efficiency of 12.31% and negligible hysteresis compared with the one using pedot:pss film as the htl.Moreover, the device sustained 85% of its initial efficiency after 240 h storage under a halogen lamps matrix exposure with an illumination intensity of 1000 w/m2, providing a powerful strategy to design long term stable pscs for future production.

Journal: Scientific reports (2022)
Publication types: Journal Article
Prevalence of Arrhythmia in Adults after Fontan Operation.

Structural, hemodynamic, and morphological cardiac changes following fontan operation (fo) can contribute to the development of arrhythmias and conduction disorders.Sinus node dysfunction, junction rhythms, tachyarrhythmias, and ventricular arrhythmias (vas) are some of the commonly reported arrhythmias.Only a few studies have analyzed this condition in adults after fo.This study aimed to determine the type and prevalence of arrhythmias and conduction disorders among patients who underwent fo and were under the medical surveillance of the john paul ii hospital in krakow.Data for the study were obtained from 50 fo patients (mean age 24 ± 5.7 years; 28 men (56%)).The median follow-up time was 4 (2-9) years.Each patient received a physical examination, an echocardiographic assessment, and a 24 h electrocardiogram assessment.Bradyarrhythmia was diagnosed in 22 patients (44%), supraventricular tachyarrhythmias in 14 patients (28%), and vas in 6 patients (12%).Six patients required pacemaker implantation, and three required radiofrequency catheter ablation (6%).Arrythmias is a widespread clinical problem in adults after fo.It can lead to serious haemodynamic impairment, and therefore requires early diagnosis and effective treatment with the use of modern approaches, including electrotherapy methods.

Journal: Journal of clinical medicine (2022)
Publication types: Journal Article
Low-Dose Sparse-View HAADF-STEM-EDX Tomography of Nanocrystals Using Unsupervised Deep Learning.

High-angle annular dark-field (haadf) scanning transmission electron microscopy (stem) can be acquired together with energy dispersive x-ray (edx) spectroscopy to give complementary information on the nanoparticles being imaged.Recent deep learning approaches show potential for accurate 3d tomographic reconstruction for these applications, but a large number of high-quality electron micrographs are usually required for supervised training, which may be difficult to collect due to the damage on the particles from the electron beam.To overcome these limitations and enable tomographic reconstruction even in low-dose sparse-view conditions, here we present an unsupervised deep learning method for haadf-stem-edx tomography.Specifically, to improve the edx image quality from low-dose condition, a haadf-constrained unsupervised denoising approach is proposed.Additionally, to enable extreme sparse-view tomographic reconstruction, an unsupervised view enrichment scheme is proposed in the projection domain.Extensive experiments with different types of quantum dots show that the proposed method offers a high-quality reconstruction even with onlythreeprojection views recorded under low-dose conditions.

Journal: ACS nano (2022)
Publication types: Journal Article
An OmpW-dependent T4-like phage infectsSerratiasp. ATCC 39006.

Serratiasp.Atcc 39006 is a gram-negative bacterium that has been used to study the function of phage defences, such as crispr-cas, and phage counter-defence mechanisms.To expand our phage collection to study the phage-host interaction with serratiasp.Atcc 39006, we isolated the t4-like myovirus lc53 in ōtepoti dunedin, aotearoa new zealand.Morphological, phenotypic and genomic characterization revealed that lc53 is virulent and similar to other serratia,erwiniaand kosakoniaphages belonging to the genus winklervirus.Using a transposon mutant library, we identified the hostomp wgene as essential for phage infection, suggesting that it encodes the phage receptor.The genome of lc53 encodes all the characteristic t4-like core proteins involved in phage dna replication and generation of viral particles.Furthermore, our bioinformatic analysis suggests that the transcriptional organization of lc53 is similar to that of escherichia coliphage t4.Importantly, lc53 encodes 18 t rnas, which likely compensate for differences in gc content between phage and host genomes.Overall, this study describes a newly isolated phage infecting serratiasp.Atcc 39006 that expands the diversity of phages available to study phage-host interactions.

Journal: Microbial genomics (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A cross-sectional survey: Exploring future healthcare workers' intention to use cannabis through extended theory of planned behavior.

Cannabis is the most extensively abused drug, leading to multiple health burdens such as traffic accidents and psychosis.There is a global wave of legalization of recreational and medical cannabis.This study aimed to understand future healthcare workers' intention to use cannabis through extended theory of planned behavior (tpb).An online cross-sectional survey on cannabis, including validated survey tools and questions on demographics, knowledge, and constructs of the tpb was designed, and distributed during virtual classes in late 2020.Responses were obtained from the faculty of medicine of a local university.Nine hundred ninety-six responses were collected, of which 629 were complete and analysed.Age was the only demographic variable associated with cannabis use intention (p= 0.029).Respondents with intention had better knowledge of cannabis.All tpb and additional constructs, including perceived behavioral control (cor = 3.44, 95% ci 2.72-4.35,p< 0.001), descriptive norm (cor = 2.24, 95% ci 1.81-2.77,p< 0.001), injunctive norm (cor = 0.51, 95% ci 0.42-0.61,p< 0.001), attitude (cor = 1.23, 95% ci 1.18-1.28,p< 0.001), knowledge (cor = 1.08, 95% ci 1.03-1.14), and perceived availability (cor = 2.75, 95% ci 2.22-3.40,p< 0.001) were individually associated with intention.In the final multiple logistic regression model adjusted for age, only attitude (aor = 1.19, 95% ci 1.13-1.25,p< 0.001) and perceived availability (p= 0.004) showed statistically significant associations with intention.Descriptive norm (standardized coefficient = 0.570) had better explanatory power than the injunctive norm (standardized coefficient = -0.143) in the model.Perceived behavioral control was associated with intention among respondents with negative to neutral attitudes towards cannabis (aor = 2.48, 95% ci 1.63-3.77,p< 0.001), but not among those with positive attitudes.All tpb constructs positively correlated with the intention to use cannabis.Changing the attitudes and perceived control on cannabis use may be useful in preventing cannabis use.

Journal: Frontiers in public health (2022)
Publication types: Journal Article
Protein interaction network analysis of mTOR signaling reveals modular organization.

The mammalian target of rapamycin (m tor) is a serine-threonine kinase that acts as a central mediator of translation and plays important roles in cell growth, synaptic plasticity, cancer, and a wide range of developmental disorders.The signaling cascade linking lipid kinases (phosphoinositide 3-kinases), protein kinases (akt), and translation initiation complexes (eifs) to m tor has been extensively modeled, but does not fully describe m tor system behavior.Here, we use quantitative multiplex coimmunoprecipitation to monitor a protein interaction network (pin) composed of 300+ binary interactions among m tor-related proteins.Using a simple model system of serum-deprived or fresh-media-fed mouse 3t3 fibroblasts, we observed extensive pin remodeling involving 27+ individual protein interactions after 1 h, despite phosphorylation changes observed after only 5 min.Using small molecule inhibitors of phosphoinositide 3-kinase, akt, m tor, mek and erk, we define subsets of the pin, termed "modules", that respond differently to each inhibitor.Using primary fibroblasts from individuals with overgrowth disorders caused by pathogenic pik3ca or mtor variants, we find that hyperactivation of m tor pathway components is reflected in a hyperactive pin.Our data define a "modular" organization of the m tor pin in which coordinated groups of interactions respond to the activation or inhibition of distinct nodes, and demonstrate that kinase inhibitors affect the modular network architecture in a complex manner, inconsistent with simple linear models of signal transduction.

Journal: The Journal of biological chemistry (2023)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Enantioselective construction of the 8-azabicyclo[3.2.1]octane scaffold: application in the synthesis of tropane alkaloids.

The 8-azabicyclo[3.2.1]octane scaffold is the central core of the family of tropane alkaloids, which display a wide array of interesting biological activities.As a consequence, research directed towards the preparation of this basic structure in a stereoselective manner has attracted attention from many research groups worldwide across the years.Despite this, most of the approaches rely on the enantioselective construction of an acyclic starting material that contains all the required stereochemical information to allow the stereocontrolled formation of the bicyclic scaffold.As an alternative, there are a number of important methodologies reported in which the stereochemical control is achieved directly in the same transformation that generates the 8-azabicyclo[3.2.1]octane architecture or in a desymmetrization process starting from achiral tropinone derivatives.This review compiles the most relevant achievements in these areas.

Journal: Organic & biomolecular chemistry (2021)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Monolayer Fullerene Networks as Photocatalysts for Overall Water Splitting.

Photocatalytic water splitting can produce hydrogen in an environmentally friendly way and provide alternative energy sources to reduce global carbon emissions.Recently, monolayer fullerene networks have been successfully synthesized [hou et al.nature2022,606, 507], offering new material candidates for photocatalysis because of their large surface area with abundant active sites, feasibility to be combined with other 2d materials to form heterojunctions, and the c60cages for potential hydrogen storage.However, efficient photocatalysts need a combination of a suitable band gap and appropriate positions of the band edges with sufficient driving force for water splitting.In this study, i employ semilocal density functional theory and hybrid functional calculations to investigate the electronic structures of monolayer fullerene networks.I find that only the weakly screened hybrid functional, combined with time-dependent hartree-fock calculations to include the exciton binding energy, can reproduce the experimentally obtained optical band gap of monolayer c60.All the phases of monolayer fullerene networks have suitable band gaps with high carrier mobility and appropriate band edges to thermodynamically drive overall water splitting.In addition, the optical properties of monolayer c60are studied, and different phases of fullerene networks exhibit distinct absorption and recombination behavior, providing unique advantages either as an electron acceptor or as an electron donor in photocatalysis.

Journal: Journal of the American Chemical Society (2022)
Publication types: Journal Article