syedzayyan/paper_mill_benchmark huggingface dataset:
Many-Objective Automated Optimization of a Four-Band Antenna for Multiband Wireless Sensor Networks.

This paper describes a new design and an optimization framework for a four-band antenna to be used in wireless sensor networks.The antenna is designed to operate effectively in two open frequency bands (ism-industrial, scientific, medical), 2.4 ghz and 5.8 ghz, as well as in two bands allocated for the fifth-generation (5g) cellular networks, 0.7 ghz and 3.5 ghz.Our initial design was developed using the trial and error approach, modifying a circular disc monopole antenna widely used in ultra wideband (uwb) systems.This initial design covered the three upper bands, but impedance matching within the 700 mhz band was unsatisfactory.The antenna performance was then improved significantly using an optimization algorithm that applies a bi-objective fully-paretian approach to its nine-parameter geometry.The optimization criteria were impedance matching and radiation efficiency.The final design exhibits good impedance matching in all four desired bands with the voltage standing wave ratio (vswr) value below 2 and radiation efficiency of 88%.The simulated antenna performance was verified experimentally.

Journal: Sensors (Basel, Switzerland) (2018)
Publication types: Journal Article
Multivariate analysis of NMR-based metabolomic data.

Nuclear magnetic resonance (nmr) spectroscopy allows for simultaneous detection of a wide range of metabolites and lipids.As metabolites act together in complex metabolic networks, they are often highly correlated, and optimal biological insight is achieved when using methods that take the correlation into account.For this reason, latent-variable-based methods, such as principal component analysis and partial least-squares discriminant analysis, are widely used in metabolomic studies.However, with increasing availability of larger population cohorts, and a shift from analysis of spectral data to using quantified metabolite levels, both more traditional statistical approaches and alternative machine learning methods have become more widely used.This review aims at providing an overview of the current state-of-the-art multivariate methods for the analysis of nmr-based metabolomic data as well as alternative methods, highlighting their strengths and limitations.

Journal: NMR in biomedicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Assessing electrodiagnostic skills among residents and fellows: Relationships between workplace-based assessments using the Electromyography Direct Observation Tool and other measures of trainee performance.

Introduction/aims graduate medical education programs must ensure residents and fellows acquire skills needed for independent practice.Workplace-based observational assessments are informative but can be time- and resource-intensive.In this study we sought to gather "relations-to-other-variables" validity evidence for scores generated by the electromyography direct observation tool (emg-dot) to inform its use as a measure of electrodiagnostic skill acquisition.Methods scores on multiple assessments were compiled by trainees during clinical neurophysiology and electromyography rotations at a large us academic medical center.Relationships between workplace-based emg-dot scores (n = 298) and scores on a prerequisite simulated patient exercise, patient experience surveys (n = 199), end-of-rotation evaluations (n = 301), and an american association of neuromuscular & electrodiagnostic medicine (aanem) self-assessment examination were assessed using pearson correlations.Results among 23 trainees, emg-dot scores assigned by physician raters correlated positively with end-of-rotation evaluations (r = 0.63, p = .001), but emg-dot scores assigned by technician raters did not (r = 0.10, p = .663).When physician and technician ratings were combined, higher emg-dot scores correlated with better patient experience survey scores (r = 0.42, p = .047), but not with simulated patient or aanem self-assessment examination scores.Discussion end-of-rotation evaluations can provide valid assessments of trainee performance when completed by individuals with ample opportunities to directly observe trainees.Inclusion of observational assessments by technicians and patients provides a more comprehensive view of trainee performance.Workplace- and classroom-based assessments provide complementary information about trainee performance, reflecting underlying differences in types of skills measured.

Journal: Muscle & nerve (2022)
Publication types: Journal Article
Biosynthesis of metallic nanoparticles by bacterial cell-free extract.

The biosynthesis of metallic nanoparticles (mnps), encompassing noble metals, metal oxides, and sulfides, has gained significant attention in recent years due to their unique properties and wide-ranging applications.However, traditional chemical synthesis methods often involve extreme conditions, harsh chemicals, and negative environmental impacts.Consequently, developing a simple, non-toxic, and eco-friendly approach for mnp synthesis is paramount.One promising method that addresses these concerns is using a bacterial cell-free extract (cfe) as a mediator for biosynthesis.Compared with other biosynthesis production methods, the purification process of mnps synthesized using bacterial cfes is much simpler, and cfe production is easier to standardize and reproduce.Bacterial cfes are rich in various biomolecules, including proteins, enzymes, and peptides, which serve as both reducing and oxidizing agents during mnp formation.These biomolecules act as capping agents, contributing to the stability and monodisperse nature of mnps.Using bacterial cfes for mnp synthesis offers several advantages.Firstly, it aligns with eco-friendly practices as a biosynthesis approach.The non-toxic process minimizes environmental damage.Additionally, bacterial cfes are cost-effective, making large-scale production economically viable.This review provides insights into these mechanisms, highlighting the role of cfe biomolecules and their impact on mnp characteristics.It also investigates the correlation between synthesis parameters, morphologies, and physical, chemical, and biological properties, allowing for tailored mnp design through the biosynthesis conditions.Despite its advantages, bacterial cfe-mediated biosynthesis faces challenges.This review addresses these challenges and discusses potential solutions.It also explores future perspectives, emphasizing areas for further investigation and innovation.In summary, using bacterial cfes to synthesize mnps offers significant advantages over other methods.It ensures eco-friendly, non-toxic, and cost-effective production.The review emphasizes the mechanisms and biomolecules involved, showcasing the potential for tailored mnp design.It also addresses challenges and prospects, paving the way for advancements in this field.Furthermore, the originality of this work lies in the exploitation of bacterial cfes as a highly efficient and scalable platform for mnp synthesis.

Journal: Nanoscale (2023)
Publication types: Journal Article;Review
Taxonomic and geographic bias in the genetic study of helminth parasites.

The use of genetic information is now fundamental in parasite taxonomy and systematics, for resolving parasite phylogenies, discovering cryptic species, and elucidating patterns of gene flow among parasite populations.The accumulation of available gene sequences per geographical area or per parasite taxonomic group is likely proportional to species richness, but not without some biases.Certain areas and certain taxonomic groups receive more research effort than others, possibly causing a deficit in the relative number of parasite species being characterized genetically in some areas or taxonomic groups.Here, we use data on the number of parasite records per country or helminth family from the london natural history museum host-parasite database, and matching data on the number of gene sequences available from the national center for biotechnology information (ncbi) gen bank database, to determine how available gene sequences scale with species richness across countries or parasitic helminth families.Our quantitative analysis identified countries/regions of the world and helminth families that have received the most effort in genetic research.More importantly, it allowed us to generate lists (based on residuals from the statistical model) of the 20 countries/regions and the 20 helminth families with the largest deficit in available gene sequences relative to their helminth species richness.We propose these lists as useful guides toward future allocation of effort to maximise advances in parasite biodiscovery, systematics and population structure.

Journal: International journal for parasitology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Does Intense Sexually Transmitted Infection Screening Cause or Prevent Antimicrobial Resistance in Sexually Transmitted Infections? It Depends on One's Underlying Epistemology. A Viewpoint.

Certain authors argue that intensive sexually transmitted infection (sti) screening is a crucial way to reduce sti prevalence and prevent the emergence and spread of antimicrobial resistance (amr) in stis.Others argue the opposite: intense screening in high sti prevalence populations has little effect on prevalence and is likely to select for amr.In this viewpoint, i argue that these radical differences in outlook stem, in part, from different conceptual frameworks of the determinants of sti prevalence and amr.In the absence of strong evidence from randomized controlled trials, our brains interpret the weaker evidence from other sources in different ways, depending on our underlying epistemologies.To illustrate the argument, i contrast a predominantly biomedical individualist conceptual framework with a more ecological conceptual framework.I argue that if one's conceptual framework is based in biomedical individualism, then one is more likely to think that screening reduces sti prevalence and less likely to appreciate the connection between screening, antimicrobial exposure, and amr than perspectives grounded in ecological frameworks.

Journal: Sexually transmitted diseases (2020)
Publication types: Journal Article
Blueberry anthocyanin extracts protect against Helicobacter pylori-induced peptic epithelium injuries both in vitro and in vivo: the key role of MAPK/NF-κB pathway.

Anthocyanins are well-characterized by anti-oxidative and anti-inflammatory potentials.Peptic ulcers contribute to the development of severe gastric disorders.In the current study, the effects of blueberry anthocyanin extracts (be) on the helicobacter pylori lipopolysaccharide (lps)-induced peptic epithelium injures were assessed and the associated mechanism driving the effects was explored by focusing on mapk/nf-κb pathway.Methods peptic injures were induced in a mouse model using lps plus ligation method and then the mice were treated with be.Then changes in gastric histology, inflammatory response, and mapk/nf-κb axis were detected.To reveal the role of mapk/nf-κb axis in the effects of be, human gastric epithelial cells (hgecs) were further subjected to co-treatment of be, lps, and mapk activator.Results the assays of mouse model showed that be attenuated gastric epithelial injuries by improving epithelial structure and suppressing gastric inflammatory response, which was associated with the inhibition of mapk/nf-κb axis.In in vitro assays, be suppressed viability and production of cytokines, and induced apoptosis in lps-treated hgecs.The re-activation of mapk pathway counteracted the effects of be by re-inducing cell viability and suppressing cell apoptosis.Conclusions the protective effects of be against lps-induced injuries in mouse stomach depended on the inhibition of both mapk pathway and the downstream nf-κb signaling.

Journal: European journal of nutrition (2022)
Publication types: Journal Article
Modification of Thin Film Composite Membrane by Chitosan-Silver Particles to Improve Desalination and Anti-Biofouling Performance.

Reverse osmosis (ro) desalination is a technology that is commonly used to mitigate water scarcity problems; one of its disadvantages is the bio-fouling of the membranes used, which reduces its performance.In order to minimize this problem, this study prepared modified thin film composite (tfc) membranes by the incorporation of chitosan-silver particles (cs-ag) of different molecular weights, and evaluated them in terms of their anti-biofouling and desalination performances.The cs-ag were obtained using ionotropic gelation, and were characterized by fourier transform infrared spectroscopy (ftir), high-resolution scanning electron microscopy (hr-sem), energy-dispersive x-ray spectroscopy (edx), thermogravimetric analysis (tga) and dynamic light scattering (dls).The modified membranes were synthetized by the incorporation of the cs-ag using the interfacial polymerization method.The membranes (mcs-ag) were characterized by fourier transform infrared spectroscopy (ftir), atomic force microscopy (afm) and contact angle.Bactericidal tests by total cell count were performed using bacillus halotolerans mcc1, and anti-adhesion properties were confirmed through biofilm cake layer thickness and total organic carbon (%).The desalination performance was defined by permeate flux, hydraulic resistance, salt rejection and salt permeance by using 2000 and 5000 mg l-1of na cl.The mcs-ag-l presented superior permeate flux and salt rejection (63.3% and 1% higher, respectively), as well as higher bactericidal properties (76% less in total cell count) and anti-adhesion capacity (biofilm thickness layer 60% and total organic carbon 75% less, compared with the unmodified membrane).The highest hydraulic resistance value was for mcs-ag-m.In conclusion, the molecular weight of cs-ag significantly influences the desalination and the antimicrobial performances of the membranes; as the molecular weight decreases, the membranes' performances increase.This study shows a possible alternative for increasing membrane useful life in the desalination process.

Journal: Membranes (2022)
Publication types: Journal Article
Portuguese adaptation and validation of a patient-reported experience measure for patients with rheumatoid arthritis: A protocol study.

There is a growing attention to patient-reported experience measures in assessing the quality of care in patient-centered care models.A specific patient-reported experience measure for patients with rheumatoid arthritis (ra) has been developed in the united kingdom-commissioning for quality in rheumatoid arthritis patient-reported experience measure.This patient-reported experience measure might be feasible to be used in portugal, yet an adaptation and validation process is needed.Therefore, the aims of this study will be to translate and cross-culturally adapt the portuguese version of the commissioning for quality in rheumatoid arthritis patient-reported experience measure, evaluate its content and face validity through a qualitative approach, and evaluate its psychometric properties through a clinical field testing.Methods this study is based on a multimethod approach combining qualitative and quantitative approaches.This study will include patients with ra from a single rheumatology center.Three sequential phases are planned: commissioning for quality in rheumatoid arthritis patient-reported experience measure translation and cultural adaptation, commissioning for quality in rheumatoid arthritis patient-reported experience measure content and face validity assessed through 2 focus groups with at least 10 patients, and the commissioning for quality in rheumatoid arthritis patient-reported experience measure field testing through a cross-sectional study with 50 patients.Conclusions by involving patients with ra in the validation and implementation of the commissioning for quality in rheumatoid arthritis patient-reported experience measure, we expect to demonstrate the usefulness of this specific patient-reported experience measure to improve health care provided to patients with ra.

Journal: Porto biomedical journal (2022)
Publication types: Journal Article
An ultrasensitive label-free electrochemical impedimetric immunosensor for vascular endothelial growth factor based on specific phage via negative pre-screening.

As a vascular growth regulator, vascular endothelial growth factor (vegf) exerts significant biological roles through specific binding to its receptors on the vascular endothelial cells.Vegf165 is generally referenced as a potential therapeutic target of many malignant tumors.In this study, a negative pre-screening strategy with structurally analogous members of vegf121, vegfc and vegfd was first proposed for vegf165 biopanning, aiming at significantly improving the specificity of the selected phage monoclones.Indirect elisa experiment showed that the phage monoclone expressing peptide spfllrm demonstrates excellent affinity and specificity.Then a vegf165 electrochemical impedimetric spectroscopy (eis) immunosensor was constructed by above specific phage modified electrode.After optimizing the experimental conditions, the as-explored eis immunosensor had a linear range of 0.5-1000 pg/m l with the limit of detection of 0.15 pg/m l vegf165.In addition, the developed phage-based eis immunosensor was applied to satisfactorily detect vegf165 in human serum samples.Considering its ultra-sensitivity, good selectivity, batch reproducibility and stability, the screened selective phage-based eis sensor is envisioned potential application in diagnosis and therapy.

Journal: Analytica chimica acta (2022)
Publication types: Journal Article
SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19.

Over the past two years, the severe acute respiratory syndrome coronavirus 2 (sars-co v-2) has caused hundreds of millions of infections, resulting in an unprecedented pandemic of coronavirus disease 2019 (covid-19).As the virus spreads through the population, ongoing mutations and adaptations are being discovered.There is now substantial clinical evidence that demonstrates the sars-co v-2 variants have stronger transmissibility and higher virulence compared to the wild-type strain of sars-co v-2.Hence, development of vaccines against sars-co v-2 variants to boost individual immunity has become essential.However, current treatment options are limited for covid-19 caused by the sars-co v-2 variants.In this review, we describe current distribution, variation, biology, and clinical features of covid-19 caused by sars-co v-2 variants (including alpha (b.1.1.7 lineage) variant, beta (b.1.351 lineage) variant, gamma (p.1 lineage) variant, delta (b.1.617.2 lineage) variant, and omicron (b.1.1.529 lineage) variant and others.In addition, we review currently employed vaccines in clinical or preclinical phases as well as potential targeted therapies in an attempt to provide better preventive and treatment strategies for covid-19 caused by different sars-co v-2 variants.

Journal: Vaccines (2022)
Publication types: Journal Article;Review
Airway management in the adult patient with an unstable cervical spine.

Of review the ideal airway management of patients with unstable spinal injury presents a perennial challenge for anaesthesiologists.With competing interests, potentially catastrophic complications, and a scarcity of evidence to support common practices, it is an area rich with dogma and devoid of data.This review seeks to highlight recent evidence that improves our assurance that what we do to manage the airway in the unstable cervical spine is supported by data.Recent findings the increasing range of available technology for intubation provides important opportunities to investigate the superiority (or otherwise) of various techniques - and a chance to challenge accepted practice.Long-held assumptions regarding spinal immobilisation in the context of airway management may require refinement as a true base of evidence develops.Summary video laryngoscopy may replace direct laryngoscopy as the default technique for endotracheal intubation in patients with suspected or confirmed spinal instability.Immobilisation of the unstable cervical spine, manually or with rigid cervical collars, is increasingly controversial.It may be that hard collars are used in specific circumstances, rather than as universal precaution in the future.there are no recent data of significantly high quality to warrant wholesale changes to recommended airway management practice and in the absence of new information, limiting movement (in the suspected or confirmed unstable cervical spine) remains the mainstay of clinical practice advice.

Journal: Current opinion in anaesthesiology (2021)
Publication types: Journal Article;Review
Human Galectin-9 Potently Enhances SARS-CoV-2 Replication and Inflammation in Airway Epithelial Cells.

The severe acute respiratory syndrome coronavirus 2 (sars-co v-2) pandemic has caused a global economic and health crisis.Recently, plasma levels of galectin-9 (gal-9), a β-galactoside-binding lectin involved in immune regulation and viral immunopathogenesis, were reported to be elevated in the setting of severe covid-19 disease.However, the impact of gal-9 on sars-co v-2 infection and immunopathology remained to be elucidated.Here, we demonstrate that gal-9 treatment potently enhances sars-co v-2 replication in human airway epithelial cells (aecs), including primary aecs in air-liquid interface (ali) culture.Gal-9-glycan interactions promote sars-co v-2 attachment and entry into aecs in an ace2-dependent manner, enhancing the binding affinity of the viral spike protein to ace2.Transcriptomic analysis revealed that gal-9 and sars-co v-2 infection synergistically induce the expression of key pro-inflammatory programs in aecs including the il-6, il-8, il-17, eif2, and tnfα signaling pathways.Our findings suggest that manipulation of gal-9 should be explored as a therapeutic strategy for sars-co v-2 infection.Importance covid-19 continues to have a major global health and economic impact.Identifying host molecular determinants that modulate sars-co v-2 infectivity and pathology is a key step in discovering novel therapeutic approaches for covid-19.Several recent studies have revealed that plasma concentrations of the human β-galactoside-binding protein galectin-9 (gal-9) are highly elevated in covid-19 patients.In this study, we investigated the impact of gal-9 on sars-co v-2 pathogenesisex vivoin airway epithelial cells (aecs), the critical initial targets of sars-co v-2 infection.Our findings reveal that gal-9 potently enhances sars-co v-2 replication in aecs, interacting with glycans to enhance the binding between viral particles and entry receptors on the target cell surface.Moreover, we determined that gal-9 accelerates and exacerbates several virus-induced pro-inflammatory programs in aecs that are established signature characteristics of covid-19 disease and sars-co v-2-induced acute respiratory distress syndrome (ards).Our findings suggest that gal-9 is a promising pharmacological target for covid-19 therapies.

Journal: bioRxiv : the preprint server for biology (2022)
Publication types: Preprint;Journal Article