syedzayyan/paper_mill_benchmark huggingface dataset:
Analyte sensing with unselectively binding synthetic receptors: virtues of time-resolved supramolecular assays.

The cross-reactivity to many analytes is one major limitation of most synthetic receptors (srs) known so far.Herein, we show that through time-resolved competitive binding assays, even unselectively binding srs can be utilized for analyte distinction and quantification.Furthermore, our methodology has also been applied to analyte mixtures and can be used in a microplate format.

Journal: Chemical communications (Cambridge, England) (2022)
Publication types: Journal Article
Characterization of Patients with Poor Risk for Clinical Outcomes in Adult Symptomatic Lumbar Deformity Surgery.

Study design retrospective review of 159 surgically treated consecutive adult symptomatic lumbar deformity (asld) (65 ± 9 years, female: 94%) from a multicenter database.Objective the aim of this study was to provide a comprehensive analysis of the risk of a poor clinical outcome in asld surgery.Summary of background data poor-risk patients with asld remain poorly characterized.Methods asld was defined as age >40 years with a lumbar curve ≥30° or c7sva ≥5 cm and scoliosis research society 22 (srs22) pain or function 4.Results all srs22 domains were significantly improved after surgery.In total, 21% (n = 34) reported satisfaction ≤3 and 29% (n = 46) reported pain or function ≤3.Poisson regression analysis revealed that frailty (odds ratio [or]: 0.2 [0.1-0.8], p = .03), baseline mental-health (or: 0.6 [0.4-0.9], p = .01) and function (or: 1.9 [1.0-3.6], p 4.0 at 2 years.Conclusion the overall clinical outcome was favorable for asld surgery.Poor-risk patients continue to have inferior outcomes, and alternative treatment strategies are needed to help improve outcomes in this patient population.Recognition and optimization of modifiable risk factors, such as physical function and mental health, and reduced saes may improve overall clinical outcomes of asld surgery.level of evidence: 3.

Journal: Spine (2021)
Publication types: Journal Article
Secondary organizing pneumonia after recovery of mild COVID-19 infection.

A 36-year-old male with diffuse large b-cell lymphoma on maintenance rituximab therapy presented to the emergency department with high fever and fatigue.A chest x-ray showed a lobar infiltrate, 40 days before admission the patient suffered from a mild coronavirus disease 2019 (covid-19) infection and fully recovered.Pcr nasopharyngeal swab was negative for covid-19.Comprehensive biochemical, radiological, and pathological evaluation including 18-fluorodeoxyglucose positron emission tomography with computed tomography and transbronchial lung biopsy found no pathogen or lymphoma recurrence.Treatment for pneumonia with antibiotic and antifungal agents was nonbeneficial.A diagnosis of secondary organizing pneumonia (op) was made after pneumonia migration and a rapid response to corticosteroids.Op secondary to a viral respiratory infection has been well described.Raising awareness for post-covid-19 op has therapeutic and prognostic importance because those patients benefit from steroid therapy.We believe the condition described here is underdiagnosed and undertreated by doctors worldwide.Because of the ongoing global pandemic we are now encountering a new kind of patient, patients that have recovered from covid-19.We hope that this case may contribute to gaining more knowledge about this growing patient population.

Journal: Journal of medical virology (2022)
Publication types: Case Reports;Journal Article
From bench to bedside, via desktop. Recent advances in the application of cutting-edge in silico tools in the research of drugs targeting bromodomain modules.

The discipline of drug discovery has greatly benefited by computational tools and in silico algorithms aiming at rationalization of many related processes, from the stage of early hit identification to the preclinical phases of drug candidate validation.The various methodologies referred to as molecular modeling tools span a broad spectrum of applications, from straightforward approaches such as virtual screening of compound libraries to more advanced techniques involving the precise estimation of free energy upon binding of the candidate drug to its macromolecular target.To this end, we report an overview of specific studies where implementation of such sophisticated modeling algorithms has shown to be indispensable for addressing challenging systems and biological questions otherwise difficult to answer.We focus our attention on the emerging field of bromodomain inhibitors.Bromodomains are small modules involved in epigenetic signaling and currently comprise high-priority targets for developing both drug candidates and chemical probes for basic biomedical research.We attempt a critical presentation of selected cases utilizing cutting-edge in silico methodologies, with our main emphasis being on absolute or relative free energy simulations, on implementation of quantum-mechanics level calculations and on characterization of solvent thermodynamics.We discuss the advantages and strengths as well as the drawbacks and weaknesses of computational tools utilized in those works and we attempt to comment on specific issues related to their integration into the regular medicinal chemistry practice.Our conclusion is that while such methods indeed represent highly promising resources for further advancing the discipline, their application is not always trivial.

Journal: Biochemical pharmacology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Design and Application of Mini-libraries of miRNA Probes for an Efficient and Versatile miRNA-mRNA Cross-linking.

Micro rnas constitute a class of endogenous, non-coding rnas that influence various processes within the cell.By base-pairing to partially-complementary sites located in the 3' untranslated region of target messenger rnas, micro rnas participate in post-transcriptional regulation of the majority of human protein-coding genes.Their dysregulation has been related to many pathological processes and diseases.Thus, an in-depth understanding of the micro rna mechanisms of action is crucial.Here, we present a new concept of probe design to achieve an efficient and sequence-independent mi rna-m rna cross-linking.The new strategy is based on the utilization of a controlled mixture of probes for a chosen mi rna, in which a trioxsalen moiety is introduced at the n4-position of a selected cytidine through short oligoethylene glycol-based linkers.In vitro photo-cross-linking experiments with mini-libraries of probes for micro rnas of interest showed variable cross-linking efficiencies, demonstrating a general applicability of the presented approach.

Journal: Chemistry (Weinheim an der Bergstrasse, Germany) (2021)
Publication types: Journal Article
Quality and Safety Analysis of 2,999 Telemedicine Encounters During the COVID-19 Pandemic.

To examine whether telemedicine remains safe and of high quality despite rapid expansion of services by comparing telemedicine encounters before and during the covid-19 pandemic.Methods pre-post study investigating 2,999 telemedicine encounters: february 1, 2020-may 15, 2020, was performed.A total of 2,919 completed visits before and after strict social distancing implementation were analyzed for patient and provider characteristics, encounter characteristics (e.g., history and physical examination), and quality and safety metrics (phone calls ≤ 7 days postvisit, visit-cause-specific hospital admission or mortality ≤ 30 days after visit).Stratified analysis of 3 groups for outcomes (young age, neuromuscular diagnosis, and new encounters) was performed.Results patients ranging from 1 month to 33 years of age were seen.Rural patients were less likely to be seen during the pandemic compared with urban patients (8% vs 90%;p< 0.0001); teaching clinic and specialty clinic encounters increased significantly during the pandemic (8% vs 3%;p= 0.005), and documentation of at least 2 systems on examination was noted significantly more frequently during the pandemic (13% vs 7%;p= 0.009).No deaths were reported.There were no differences before/during the pandemic in safety or telemedicine failure metrics within the entire group and high-risk subgroups.Conclusions despite a markedly and rapidly expanded scope of ambulatory telemedicine care during the covid-19 pandemic, telemedicine remained a safe and high-quality option for pediatric neurology patients.In addition, populations perceived as high risk for telemedicine (the very young, new patients, and those with neuromuscular diagnoses) can benefit from telemedicine visits, particularly when access to in-person care is limited.

Journal: Neurology. Clinical practice (2021)
Publication types: Journal Article
A Comprehensive Survey of Enabling and Emerging Technologies for Social Distancing-Part II: Emerging Technologies and Open Issues.

This two-part paper aims to provide a comprehensive survey on how emerging technologies, e.g., wireless and networking, artificial intelligence (ai) can enable, encourage, and even enforce social distancing practice.In part i, an extensive background of social distancing is provided, and enabling wireless technologies are thoroughly surveyed.In this part ii, emerging technologies such as machine learning, computer vision, thermal, ultrasound, etc., are introduced.These technologies open many new solutions and directions to deal with problems in social distancing, e.g., symptom prediction, detection and monitoring quarantined people, and contact tracing.Finally, we discuss open issues and challenges (e.g., privacy-preserving, scheduling, and incentive mechanisms) in implementing social distancing in practice.As an example, instead of reacting with ad-hoc responses to covid-19-like pandemics in the future, smart infrastructures (e.g., next-generation wireless systems like 6g, smart home/building, smart city, intelligent transportation systems) should incorporate apandemic modein their standard architectures/designs.

Journal: IEEE access : practical innovations, open solutions (2020)
Publication types: Journal Article
High-Mobility Group Box 1 (HMGB1) Induces Migration of Endothelial Progenitor Cell via Receptor for Advanced Glycation End-Products (RAGE)-Dependent PI3K/Akt/eNOS Signaling Pathway.

High-mobility group box1 (hmgb1) is a cytokine that has been demonstrated to have an important role in inducing migration and homing of endothelial progenitor cells (epcs) in the process of neovascularization during wound healing, but its specific mechanism remains elusive.The aim of this study was to investigate the effects of the hmgb-rage axis in epc migration, as well as the underlying molecular mechanism responsible for these effects.Material and methods epcs were isolated from the mice and identified using flow cytometry and fluorescence staining.The effect of hmgb1 on the activity of epcs was detected using the cell counting kit-8 (cck-8).Then, the migration of epcs was detected by scratch wound-healing and cell migration assay.No levels were analyzed by elisa.The expression of p-pi3k, p-akt, and p-e nos was determined by western blot analysis.Rage expression was measured by quantitative reverse transcription polymerase chain reaction (q rt-pcr) and western blot analysis.F-actin was assessed by fluorescent staining.Results the results showed that hmgb1 induced a concentration-dependent migration of epcs, and the migration was rage-dependent.The migration could be almost completely blocked by pi3k inhibitors and e nos inhibitor.Hmgb1-rage upregulated the expression of p-akt, p-e nos, and p-erk.We also demonstrated that the mek/erk signaling pathway is not involved in the epc migration induced by hmgb1-rage.Conclusions these data demonstrate that hmgb1 activates rage and induces pi3k/akt/e nos signaling transduction pathway activation to promote epc migration.Therefore, the hmgb1-rage axis plays an important role in the epc migration process and may become a potential target in wound healing.

Journal: Medical science monitor : international medical journal of experimental and clinical research (2019)
Publication types: Journal Article
Homing peptide combined with DNAzyme-based ELISA-like assay for highly specific and sensitive detection of fibrin.

A highly sensitive and specific elisa-like chemiluminescence method for detection of fibrin has been developed.In the sensing platform, the homing peptide (creka), as recognition molecule, which can specially recognize the fibrin on microtiter plate, combined with g-quadruplex-based dnazyme to form the probe of g-quadruplex-hemin dnazyme-creka.After the sample solution was coated on the plates, the probe was crosslinked with fibrin through the interaction of creka and fibrin.Finally, luminol-h2o2chemiluminesecence (cl) reaction was exploited for quantitative analysis of fibrin.The liner range for fibrin detection was from 0.112 pmol l-1to 5.6 pmol l-1with the detection limit of fibrin as low as 0.04 pmol l-1, based on a signal-to-noise ratio (s/n) of 3.Furthermore, on the basis of the high amplification efficiency of the rolling circle amplification (rca) reaction, the method enabled to analyze fibrin with a detection limit corresponding to 0.06 fmol l-1, whose sensitivity increased 3 orders of magnitude than that of above method in the absence of rca reaction.In particular, combined with the separation and washing steps of elisa, the proposed method possessed higher selectivity, high-throughput and low cost, which shows promise for applications in clinical diagnosis.

Journal: Talanta (2022)
Publication types: Journal Article
Predicting secondary surgery after operative fixation of olecranon fractures: a model using data from 800 patients.

High rates of secondary surgery after fixation of olecranon fractures have been reported.Identification of risk factors can aid surgeons to reduce complications leading to additional surgical procedures.Methods olecranon fractures treated at seven hospitals from 2007 to 2017 were identified, and the radiographs were classified.Isolated, displaced olecranon fractures treated operatively with tension band wiring (tbw) or precontoured plate fixation (pf) were reviewed.Adjusted risk factors for secondary surgery were analyzed, and a multivariable predictive model for secondary surgery was built.Results after the initial review of 1259 olecranon fractures, 800 isolated, displaced olecranon fractures met the inclusion and exclusion criteria.The distribution of two-part and multifragmented fractures was equal.Tbw was used in 636 patients and pf in 164 patients.Multifragmentation was a significant variable influencing preference for pf.Secondary surgery was performed in 41% patients and symptomatic hardware removal was the most frequent primary indication.In both the tbw and pf group, the rates of major complications leading to secondary surgery were 13% (p= .96).The adjusted risk of secondary surgery was lower with increasing age (odds ratio by 10 years increments, 0.74; 95% confidence interval, 0.68-0.80,p< .01).Compared with pf, tbw with transcortical k-wires (odds ratio, 2.06; 95% confidence interval, 1.36-3.14;p< .01) and tbw with intramedullary k-wires (odds ratio, 4.32; 95% confidence interval, 2.16-8.86,p< .01) had significantly higher adjusted risk of secondary surgery.Conclusion surgeons preferred to use pf in younger patients and multifragmented fractures.Patients should be counseled that secondary surgery is common after surgical fixation of olecranon fractures.Symptomatic hardware removal was the most frequently reported reason for secondary surgery and more frequent after tbw.When using tbw, intramedullary k-wire positioning should be avoided.The rate of major complications leading to secondary surgery was similar in the tbw and pf groups.Overall, the risk of subsequent secondary surgery was higher in younger patients and patients treated with tbw.

Journal: JSES international (2021)
Publication types: Journal Article
Robotic Surgery as Applied to Functional and Reconstructive Urology.

Context in recent years, there has been a rapid uptake in the use of laparoscopic and robotic surgery within urological oncological surgery.There is now growing interest in applying these surgical techniques to functional and reconstructive urology (fru).Objective to provide an overview of the use of robotic surgery within the sphere of functional and reconstructive urology and discuss the research needs and the likely role of robotic technology in future.Evidence acquisition a pub med-based literature review performed in march 2019 identified all articles published regarding the use of robotic surgery within fru for the reconstruction of the upper tracts, bladder, bladder neck, pelvic floor, and urinary sphincter; creation of urinary diversion; and repair of genitourinary fistulae.Evidence synthesis there is a need to study the robotic approach in carefully designed prospective studies to better establish safety and clinical efficacy as well as the economic viability as compared with laparoscopic and open approaches.Conclusions the use of the robotic minimally invasive approach has many potential advantages; however, there is a need for a high level of technical expertise and experience, especially in some of the complex and technically challenging scenarios often seen within fru.Surgeons should ensure that they have received sufficient training in not only the surgical principles of fru, but also the assessment, management, and follow-up of patients.Moreover, it is imperative not to compromise important surgical steps.Patient summary in this report, we looked into the use of robotic technologies in the treatment of functional and reconstructive problems of the urinary tract.We found that the robotic approach has not yet been evaluated in prospective clinical studies in this field.There is a need for carefully designed prospective studies to establish the safety and efficacy of robotic surgeries.

Journal: European urology focus (2019)
Publication types: Journal Article;Review
The Role of Urotensin-II in Obesity and Metabolic Syndrome in Pediatric Population.

Urotensin-ii (u-ii) is a short cyclic peptide that is widely recognized as one of the most potent vasoconstrictors.U-ii plays a role in the pathophysiology of ms, participating in the development of essential hypertension, insulin resistance, hyperglycemia, and a proinflammatory state.Methods this study comprised 52 obese children and adolescents with a body mass index (bmi) z score > 2, aged 10 to 18 years.Serum levels of u-ii were assessed using an enzyme-linked immunosorbent assay along with other standard biochemical parameters.Results elevated serum levels of u-ii were recorded in the group of obese subjects with ms when compared with the group of obese subjects without ms (4.99 (8.97-3.16) vs.4.17 (5.17-2.03) ng/m l, median and iqr,p= 0.026).Furthermore, a subgroup of study subjects with high blood pressure had significantly higher u-ii levels in comparison with the normotensive subgroup (4.98 (7.19-3.22) vs.3.32 (5.06-1.97) ng/m l,p= 0.027), while the subgroup with a positive family history of high blood pressure had significantly higher u-ii levels when compared with subjects who had a negative family history of elevated blood pressure (5.06 (6.83-4.45) vs.3.32 (6.13-2.21) ng/m l,p= 0.039).Conclusions to the best of the author's knowledge, this is the first study on the levels of u-ii in obese children and adolescents, including a possible link to ms.

Journal: Children (Basel, Switzerland) (2022)
Publication types: Journal Article
Are patients with cognitive impairment fit to fly? Current evidence and practical recommendations.

The worldwide prevalence of dementia is increasing and represents a major public health concern.In the last decades, air travel services have undergone an impressive expansion and one of ten passengers is aged 65 years and older.While air travel can be stressful at all ages and health conditions, older individuals with cognitive impairment carry a greater risk for air-travel-related complications.Consequently, demands to general practitioners for assessing their older patient's fitness to fly are increasing.Methods we conducted a search of the literature in pub med on the impact of in-flight environmental changes on passengers with cognitive impairment and possible resulting complications.This set the base for a discussion on pharmacological and non-pharmacological interventions aimed at preventing in-flight complications in this vulnerable population.Results while our research strategy identified a total of 11 articles related to older age and air travel, only three focused on passengers with cognitive impairment.Our literature review showed that the airplane environment may lead to a large spectrum of symptoms in passengers of all age groups.However, passengers with cognitive impairment due to neurodegenerative diseases are at increased risk for experiencing the most extreme symptoms such as acute confusional state.Non-pharmacological and pharmacological interventions at different stages of the travel process (before, during and after) can help prevent complications in this vulnerable population.Conclusion the decision to let a patient with cognitive impairment fly requires a solid understanding of the in-flight environmental changes and their impact on older patients with cognitive impairment.Moreover, a sound weighing of the risks and benefits while considering different aspects of the patient's history is demanded.In this regard, the role of the treating physicians and caregivers is essential along with the support of the medical department of the airline.

Journal: Journal of travel medicine (2021)
Publication types: Journal Article;Review
Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities.

Kelps are dominant primary producers in temperate coastal ecosystems.Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota.Here, we investigated the bacterial community associated with the kelp laminaria hyperborea during its accumulation and degradation on the seafloor.Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation.Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession.Initially, dominant genera (hellea, litorimonas, granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as bacteroidia members which responded within 4 weeks.Acidimicrobiia, especially members of the sva0996 marine group, colonized the degrading kelp biomass after 11 weeks.These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders.In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles.Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.

Journal: Environmental microbiology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't