syedzayyan/paper_mill_benchmark huggingface dataset:
Analysis of the Association Among Air Pollutants, Allergenic Pollen, and Respiratory Virus Infection of Children in Guri, Korea During Recent 5 Years.

Concerns about the spread of infectious diseases have increased due to the coronavirus disease pandemic.Knowing the factors that exacerbate or increase the contagiousness of a virus could be a key to pandemic prevention.Therefore, we investigated whether the pandemic potential of infectious diseases correlates with the concentration of atmospheric substances.We also investigated whether environmental deterioration causes an increase in viral infections.Methods pediatric patients (0-18 years old; n = 6,223) were recruited from those hospitalized for aggravated respiratory symptoms at hanyang university guri hospital between january 1, 2015 and december 31, 2019.The number of viral infections was defined as the total number of virus-infected patients hospitalized for respiratory symptoms.We analyzed the association between the number of viral infections/week and the average concentrations of atmospheric substances including particulate matter (pm)10, pm2.5, o3, no2, co, so2, and allergenic pollen) for that week.The cross-correlation coefficient between the weekly measures of pollens and viral infections was checked to determine which time point had the most influence.The association of atmospheric substances in that time, with the number of viral infections/week was investigated using multiple linear regression analysis to identify factors with the greatest influence.Results in spring the tree pollen average concentration one week earlier (t-1) had the greatest correlation with the average virus infection of a given week (t) (ρxy(h) =0.5210).The number of viral infections showed a statistically significant correlation with especially tree pollen concentration of 1 week prior (adj r2=0.2280).O3 concentration was correlated to the number of viral infections within that week (adj r2=0.2552) in spring, and weed pollen and co concentration correlated (adj r2=0.1327) in autumn.Conclusions seasonal co-exposure to air pollutants and allergenic pollens may enhance respiratory viral infection susceptibility in children.Therefore, reducing the concentrations of air pollutants and pollens may help prevent future epidemics.

Journal: Allergy, asthma & immunology research (2022)
Publication types: Journal Article
Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography, NMR Spectroscopy and Molecular Dynamics.

Our understanding of the factors affecting the stability of cyclic d/l peptide (cp) nanotubes remains underdeveloped.In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on cp nanotube stability through x-ray crystallography, nmr spectroscopy and molecular dynamics (md) simulations.We characterise the distinct cp-cp alignments that can form and identify stable and unstable dimers by md simulation.We measure h-bond half-lives of synthesised cps by1h-d exchange experiments and find good correlation with predicted cp-cp stabilities.We find that hydrophobic amino acids improve cp dimer stability but experimentally reduce solubility.Charged amino acids either increase or decrease cp dimer stability depending on the relative orientation and composition of charged groups.X-ray crystal structures are solved for two cps, revealing non-tubular folded conformations.Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.

Journal: Chemistry (Weinheim an der Bergstrasse, Germany) (2021)
Publication types: Journal Article
An Exprimental and Computational Study on the Cl Atom Initiated Photo-Oxidization Reactions of Butenes in the Gas Phase.

Temperature-dependent rate coefficients for the reactions of cl atoms with trans-2-butene and isobutene were measured over the temperature range of 263-363 k using relative rate technique with reference to 1,3-butadiene, isoprene, and 1-pentene.The measured rate coefficients for the reactions of cl atoms with isobutene and trans-2-butene are k r1298k= (3.43 ± 0.11) × 10-10and k r2298k= (3.20 ± 0.04) × 10-10cm3molecule-1s-1, respectively, at 298 k and 760 torr.Measured rate coefficients were used to fit the arrhenius equations, which are obtained to be k r1-exp269-363k= (4.99 ± 0.42) × 10-11exp[(584 ± 26)/t] and k r2-exp269-363k= (1.11 ± 0.3) × 10-10exp[(291 ± 88)/t] cm3molecule-1s-1for isobutene and trans-2-butene, respectively.To understand the reaction mechanism, estimate the contribution of each reaction site, and to complement our experimental results, computational studies were also performed.Canonical variational transition state theory with small curvature tunneling in combination with mp2/6-31g(d), mp2/6-31g(d,p), mp2/6-31+g(d,p), ccsd(t)/cc-pvdz, and qcisd(t)/cc-pvdz level of theories were used to calculate the temperature-dependent rate coefficients over the temperature range of 200-400 k.The effective lifetimes, thermodynamic parameters, and atmospheric implications of the test molecules were also estimated.

Journal: The journal of physical chemistry. A (2017)
Publication types: Journal Article
Analysis and Design Methodology of RF Energy Harvesting Rectifier Circuit for Ultra-Low Power Applications.

This paper reviews and analyses the design of popular radio frequency energy harvesting systems and proposes a method to qualitatively and quantitatively analyze their circuit architectures using new square-wave approximation method.This approach helps in simplifying design analysis.Using this analysis, we can establish no load output voltage characteristics, upper limit on rectifier efficiency, and maximum power characteristics of a rectifier.This paper will help guide the design of rf energy harvesting rectifier circuits for radio frequency identification (rfids), the internet of things (io ts), wearable, and implantable medical device applications.Different application scenarios are explained in the context of design challenges, and corresponding design considerations are discussed in order to evaluate their performance.The pros and cons of different rectifier topologies are also investigated.In addition to presenting the popular rectifier topologies, new measurement results of these energy harvester topologies, fabricated in 65nm, 130nm and 180nm cmos technologies are also presented.

Journal: IEEE open journal of circuits and systems (2022)
Publication types: Journal Article
Ligand-Directed GPCR Antibody Discovery.

Developing affinity reagents recognizing and modulating g-protein coupled receptors (gpcr) function by traditional animal immunization or in vitro screening methods is challenging.Some anti-gpcr antibodies exist on the market, but the success rate of development is still poor compared with antibodies targeting soluble or peripherally anchored proteins.More importantly, most of these antibodies do not modulate gpcr function.The current pipeline for antibody development primarily screens for overall affinity rather than functional epitope recognition.We developed a new strategy utilizing natural ligand affinity to generate a library of antibody variants with an inherent bias toward the active site of the gpcr.Instead of using phage libraries displaying antibodies with random cdr sequences at polymorphism sites observed in natural immune repertoire sequences, we generated focused antibody libraries with a natural ligand encoded within or conjugated to one of the cdrs or the n-terminus.To tailor antibody binding to the active site, we limited the sequence randomization of the antibody in regions holstering the ligand while leaving the ligand-carrying part unaltered in the first round of randomization.With hits from the successful first round, the second round of randomization of the ligand-carrying part was then performed to eliminate the bias of the ligand.Based on our results on three different gpcr targets, the proposed pipeline will enable the rapid generation of functional antibodies (both agonists and antagonists) against high-value targets with poor function epitope exposures including gpcr, channels, transporters as well as cell surface targets whose binding site is heavily masked by glycosylation.

Journal: Methods in molecular biology (Clifton, N.J.) (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Prevalence, symptom burden and under-diagnosis of chronic obstructive pulmonary disease in Polish lung cancer screening population: a cohort observational study.

S lung cancer screening using low-dose ct may be not effective without considering the presence of comorbidities related to chronic smoking.The aim of the study was to establish the prevalence of chronic obstructive pulmonary disease (copd) in group of phighlight the potential benefits atients participating in the largest polish lung cancer screening programme moltest-bis and attempt to confirm the necessity of combined lung cancer and copd screening.Design cohort, prospective study.Setting medical university of gdańsk, poland participants: the study included 754 participants in lung cancer screening trial from the pomeranian region, aged 50-70 years old, current and former smokers with a smoking history ≥30 pack-years.Primary and secondary outcome measures questionnaire, physical examination, anthropometric measurements, spirometry test before and after inhaled bronchodilator (400 μg of salbutamol) results: obstructive disorders were diagnosed in 186 cases (103 male and 83 female).In the case of 144 participants (19.73%), copd was diagnosed.Only 13.3% of participants with copd were known about the disease earlier.According to classification of airflow limitation 55.6% of diagnosed copd were in global initiative for chronic obstructive lung disease (gold) 1 (mild), 38.9% in gold 2 (moderate), 4.9% in gold 3 (severe) and 0.7% in gold 4 (very severe) stage.Women with recognition of copd were younger than men (63.7 vs 66.3 age) and they smoked less cigarettes (41.1 vs 51.9 pack-years).Conclusions prevalence of copd in polish lung cancer screening cohort is significant.The copd in this group is remarkably under-diagnosed.Most diagnosed copd cases were in the initial stage of advancement.This early detection of airflow limitation highlights the potential benefits arising from combined oncological-pulmonary screening.nkbbn.

Journal: BMJ open (2022)
Publication types: Journal Article;Observational Study;Research Support, Non-U.S. Gov't
Tethered Cord Syndrome Associated With Lumbar Lipomyelomeningocele: A Case Report.

The objective is to describe a rare case of lumbar lipomyelomeningocele presenting as progressive urinary incontinence.Lipomyelomeningocele is a type of closed spinal dysraphism typically presenting as a lipomatous mass contiguous with a neural defect above the gluteal crease.Tethered cord syndrome is defined as symptoms and signs caused by excessive spinal cord tension from an abnormally low conus medullaris, with an abnormally thick filum terminale attached to the lower sacral region.A 19-year-old male with no remarkable medical history presented with low back pain and urinary incontinence for the past one year.On physical exam patient had normal motor strength, sensory testing to all modalities was intact.The rectal tone was normal, and no saddle anesthesia was noted.Mri lumbar spine revealed lumbar lipomyelomeningocele with associated tethered cord syndrome.The patient underwent tethered cord release surgery with lipoma excision.Pathology of the soft tissue showed fibrovascular tissue and mature adipose tissue consistent with lipoma.The majority of cases of tethered cord syndrome are related to spinal dysraphism, a rare pediatric syndrome.It is potentially treatable if caught early, and mri can help with an accurate diagnosis of the condition.Older adults are more likely to present with urological and neurological complaints.Surgical un-tethering is indicated in patients with progressive symptoms.In our case, the only presenting symptom was urinary incontinence, and the neurological exam was normal other than lower lumbar paraspinal tenderness.

Journal: Cureus (2022)
Publication types: Case Reports;Journal Article
Plasma-induced nanoparticle aggregation for stratifying COVID-19 patients according to disease severity.

Stratifying patients according to disease severity has been a major hurdle during the covid-19 pandemic.This usually requires evaluating the levels of several biomarkers, which may be cumbersome when rapid decisions are required.In this manuscript we show that a single nanoparticle aggregation test can be used to distinguish patients that require intensive care from those that have already been discharged from the intensive care unit (icu).It consists of diluting a platelet-free plasma sample and then adding gold nanoparticles.The nanoparticles aggregate to a larger extent when the samples are obtained from a patient in the icu.This changes the color of the colloidal suspension, which can be evaluated by measuring the pixel intensity of a photograph.Although the exact factor or combination of factors behind the different aggregation behavior is unknown, control experiments demonstrate that the presence of proteins in the samples is crucial for the test to work.Principal component analysis demonstrates that the test result is highly correlated to biomarkers of prognosis and inflammation that are commonly used to evaluate the severity of covid-19 patients.The results shown here pave the way to develop nanoparticle aggregation assays that classify covid-19 patients according to disease severity, which could be useful to de-escalate care safely and make a better use of hospital resources.

Journal: Sensors and actuators. B, Chemical (2022)
Publication types: Journal Article
Induced antigen-binding polyreactivity in human serum IgA.

Previous studies have shown that polyreactive antibodies play an important role in the frontline defense against the dissemination of pathogens in the pre-immune host.Interestingly, antigen-binding polyreactivity can not only be inherent, but also acquired post-translationally.The ability of individual monoclonal ig g and ig e antibodies to acquire polyreactivity following contact with various agents that destabilize protein structure (urea, low p h) or have a pro-oxidative potential (heme, ferrous ions) has been studied in detail.However, to the best of our knowledge this property of human ig a has previously been described only cursorily.In the present study pooled human serum ig a and two human monoclonal ig a antibodies were exposed to buffers with acidic p h, to free heme or to ferrous ions, and the antigen-binding behavior of the native and modified ig a to viral and bacterial antigens were compared using immunoblot and elisa.We observed a dose-dependent increase in reactivity to several bacterial extracts and to pure viral antigens.This newly described property of ig a may have therapeutic potential as has already been shown for pooled ig g with induced polyreactivity.

Journal: Immunobiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Assessment of Thigh MRI Radiomics and Clinical Characteristics for Assisting in Discrimination of Juvenile Dermatomyositis.

Magnetic resonance imaging (mri) is an important non-invasive examination in the early diagnosis of juvenile dermatomyositis (jdm).We aimed to evaluate the feasibility of radiomics to establish a quantitative analysis of mri images.Radiomics and machine learning were used to retrospectively analyze mri t2 fat suppression sequences and relevant clinical data.The model associated with radiomics features was established using a cohort of patients who underwent thigh mri at the children's hospital from june 2014 to september 2021.In total, 75 patients with jdm and 75 control children were included in the training cohort (n= 102) and validation cohort (n= 48).The independent factors including lower muscle strength (or, 0.75; 95% ci, 0.59-0.90), higher creatine kinase (ck) level (or, 1.65; 95% ci, 1.20-2.38), and higher radiomics score (or, 2.30; 95% ci, 1.63-3.62) were associated with a clinical diagnosis of jdm.The combined model achieved good discrimination performance compared the radiomics score model under linear discriminant analyses in the training cohort (auc, 0.949; 95% ci, 0.912-0.986 vs.Auc, 0.912; 95% ci, 0.858-0.967;p= 0.02) and in the validation cohort (auc, 0.945; 95% ci, 0.878-1 vs.Auc, 0.905; 95% ci, 0.812-0.998;p= 0.03).The combined model showed the diagnostic value was not weaker than the biopsy (auc, 0.950; 95% ci, 0.919-0.981,n= 150 vs.Auc, 0.952; 95% ci, 0.889-1,n= 72;p= 0.95) and electromyogram (emg) (auc, 0.950; 95% ci, 0.919-0.981 vs.Auc, 0.900; 95% ci, 0.852-0.948;p= 0.10) among all the patients.The combination of radiomics features extracted from the mri and non-invasive clinical characteristics obtained a pronounced discriminative performance to assist in discriminating jdm.

Journal: Journal of clinical medicine (2022)
Publication types: Journal Article
Myeloperoxidase Levels in Pericardial Fluid Is Independently Associated with Postoperative Atrial Fibrillation after Isolated Coronary Artery Bypass Surgery.

Postoperative atrial fibrillation (poaf) is the most common complication after surgery for atherosclerotic cardiovascular disease (ascvd) and leads to extended hospital stays and increased mortality.Myeloperoxidase (mpo) in postoperative pericardial drainage fluid is associated with an increased risk of poaf; however, the correlations between mpo in intraoperative pericardial fluid and poaf remain largely unknown.The aim of the study was to evaluate whether mpo is associated with poaf.Methods a total of 97 patients with no history of atrial arrhythmia who had undergone coronary artery bypass surgery (cabg) were identified.We prospectively measured the levels of mpo in intraoperative pericardial fluid and blood using the human magnetic luminex assay.Then, the occurrence of atrial fibrillation was continuously observed by postoperative ecg and telemetry strips until discharge.Results our data showed that poaf occurred in 24 of 97 patients (24.74%).Mpo levels in blood were higher in the poaf group than the sr group (p= 0.064).Patients with poaf had significantly higher intraoperative pericardial fluid mpo levels than patients who remained in sr (p= 0.021).There was no significant correlation between pericardial fluid mpo levels and blood mpo levels (r = -0.47,p= 0.770).In a multivariable logistic regression model, pericardial fluid mpo levels were significantly associated with a higher risk of poaf (odds ratio = 1.016, 95% confidence interval, 1.001-1.031;p= 0.031).Conclusions higher intraoperative pericardial fluid mpo levels are linked with poaf in patients undergoing cabg.This finding provides insight into a possible mechanism of mpo in pericardial fluid increase susceptibility to developing poaf in patients undergoing cabg.

Journal: Journal of clinical medicine (2022)
Publication types: Journal Article
Integrating family therapy into exposure-based CBT for a Spanish patient with obsessive scrupulosity.

Obsessive-compulsive symptom profiles vary widely among individuals and may be affected by cultural backgrounds.In the case of scrupulosity, moral and religious principles are the target of obsessive-compulsive symptoms.Cognitive biases and beliefs have special relevance in the origin and maintenance of obsessive scrupulosity.In addition, rigid and exaggerated beliefs about morality are held by these patients.Moral and religious principles are mainly transmitted by family.These influences may be more prominent in cultures, such as the spanish culture, where family and religion are important values for individuals.The authors describe the treatment of a spanish patient with obsessive scrupulosity.Family therapy strategies were integrated into exposure-based cbt in order to facilitate the modification of beliefs, behaviors, and pathological family relationships.The patient exhibited clinically significant improvements in ocd symptoms.Findings from this case show the need for individualized interventions that take into consideration cultural, social, and family factors.

Journal: Bulletin of the Menninger Clinic (2018)
Publication types: Case Reports;Journal Article
Human NAIP/NLRC4 and NLRP3 inflammasomes detect Salmonella type III secretion system activities to restrict intracellular bacterial replication.

Salmonella enterica serovar typhimurium is a gram-negative pathogen that uses two distinct type iii secretion systems (t3sss), termed salmonella pathogenicity island (spi)-1 and spi-2, to deliver virulence factors into the host cell.The spi-1 t3ss enables salmonella to invade host cells, while the spi-2 t3ss facilitates salmonella's intracellular survival.In mice, a family of cytosolic immune sensors, including naip1, naip2, and naip5/6, recognizes the spi-1 t3ss needle, inner rod, and flagellin proteins, respectively.Ligand recognition triggers assembly of the naip/nlrc4 inflammasome, which mediates caspase-1 activation, il-1 family cytokine secretion, and pyroptosis of infected cells.In contrast to mice, humans encode a single naip that broadly recognizes all three ligands.The role of naip/nlrc4 or other inflammasomes during salmonella infection of human macrophages is unclear.We find that although the naip/nlrc4 inflammasome is essential for detecting t3ss ligands in human macrophages, it is partially required for responses to infection, as salmonella also activated the nlrp3 and casp4/5 inflammasomes.Importantly, we demonstrate that combinatorial naip/nlrc4 and nlrp3 inflammasome activation restricts salmonella replication in human macrophages.In contrast to spi-1, the spi-2 t3ss inner rod is not sensed by human or murine naips, which is thought to allow salmonella to evade host recognition and replicate intracellularly.Intriguingly, we find that human naip detects the spi-2 t3ss needle protein.Critically, in the absence of both flagellin and the spi-1 t3ss, the naip/nlrc4 inflammasome still controlled intracellular salmonella burden.These findings reveal that recognition of salmonella spi-1 and spi-2 t3sss and engagement of both the naip/nlrc4 and nlrp3 inflammasomes control salmonella infection in human macrophages.

Journal: PLoS pathogens (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Warfarin Dosing Requirement According to Body Mass Index.

Introduction many factors affect the required dose of warfarin, including body weight, which is mentioned only in a few studies.Our study was conducted using body mass index (bmi) to assess the requirements for warfarin dosing.Methods a retrospective study was conducted that included adults who used warfarin for more than three months, with at least two consecutive international ratio (inr) readings within the therapeutic range.Results over 301 patients were included; the 20% higher dose of warfarin was required in obese patients than normal bmi and overweight patients (32.2 ± 15.2 vs.27.4 ±17.3 and 26.8 ± 12.7; p=0.013, respectively).Conclusion obese patients required a higher dose than other patients, which should be considered when initiating or adjusting the warfarin dose.

Journal: Cureus (2020)
Publication types: Journal Article