syedzayyan/paper_mill_benchmark huggingface dataset:
Machine Learning Models Predicting Cardiovascular and Renal Outcomes and Mortality in Patients with Hyperkalemia.

Hyperkalemia is associated with increased risks of mortality and adverse clinical outcomes.The treatment of hyperkalemia often leads to the discontinuation or restriction of beneficial but potassium-increasing therapy such as renin-angiotensin-aldosterone inhibitors (raasi) and high-potassium diet including fruits and vegetables.To date, limited evidence is available for personalized risk evaluation in this heterogeneous and multifactorial pathophysiological condition.We developed risk prediction models using extreme gradient boosting (xgb), multiple logistic regression (lr), and deep neural network.Models were derived from a retrospective cohort of hyperkalemic patients with either heart failure or chronic kidney disease stage ≥3a from a japanese nationwide database (1 april 2008−30 september 2018).Studied outcomes included all-cause death, renal replacement therapy introduction (rrt), hospitalization for heart failure (hhf), and cardiovascular events within three years after hyperkalemic episodes.The best performing model was further validated using an external cohort.A total of 24,949 adult hyperkalemic patients were selected for model derivation and internal validation.A total of 1452 deaths (16.6%), 887 rrt (10.1%), 1,345 hhf (15.4%), and 621 cardiovascular events (7.1%) were observed.Xgb outperformed other models.The area under receiver operator characteristic curves (aurocs) of xgb vs.Lr (95% cis) for death, rrt, hhf, and cardiovascular events were 0.823 (0.805−0.841) vs.0.809 (0.791−0.828), 0.957 (0.947−0.967) vs.0.947 (0.936−0.959), 0.863 (0.846−0.880) vs.0.838 (0.820−0.856), and 0.809 (0.784−0.834) vs.0.798 (0.772−0.823), respectively.In the external dataset including 86,279 patients, aurocs (95% cis) for xgb were: death, 0.747 (0.742−0.753); rrt, 0.888 (0.882−0.894); hhf, 0.673 (0.666−0.679); and cardiovascular events, 0.585 (0.578−0.591).Kaplan−meier curves of the high-risk predicted group showed a statistically significant difference from that of the low-risk predicted groups for all outcomes (p < 0.005; log-rank test).These findings suggest possible use of machine learning models for real-world risk assessment as a guide for observation and/or treatment decision making that may potentially lead to improved outcomes in hyperkalemic patients while retaining the benefit of life-saving therapies.

Journal: Nutrients (2022)
Publication types: Journal Article
Prognostic index for estimating the survival benefit of postoperative radiotherapy in pathologic N2 non-small cell lung cancer: A real-world validation study.

S this study aimed to evaluate the effect of postoperative radiotherapy (port) in patients with resected pathologic n2 (p n2) non-small cell lung cancer (nsclc) with different locoregional recurrence (lrr) risks.Materials and methods the primary cohort and validation cohort were retrieved from two independent medical centres.Data for all consecutive patients with completely resected pathologic stage t1-3n2m0 nsclc were analysed.Patients without port in the primary cohort were identified as a training set.Significant prognostic factors for lrr were identified by the fine-gray model to develop a prognostic index (pi) in the training set.Results the primary cohort consisted of 357 patients who met the eligibility criteria (training set, 287 patients without port).The external validation cohort consisted of 1044 patients who met the eligibility criteria (validation set, 711 patients without port).Heavy cigarette smoking history, clinical n2 status (c n2), and the number of positive lymph nodes >4 were identified as independent risk factors.The pi was computed as follows: pi=0.8*smoking history+0.5*c n2+0.7*the number of involved lymph nodes (reference level was assigned the value 1 and risk level the value 2).In the low-risk group (pi score 3), port significantly reduced the risk of lrr and improved os.Conclusions we constructed and validated a pi to predict individually the effect of port in patients with completely resected p n2 nsclc.Patients with a higher pi score can benefit from port in terms of os.

Journal: Lung cancer (Amsterdam, Netherlands) (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Developing a clinical pathway to identify and manage cognitive problems in Multiple Sclerosis: Qualitative findings from patients, family members, charity volunteers, clinicians and healthcare commissioners.

Cognitive problems are a common and debilitating symptom of multiple sclerosis (ms).Screening and treatment for cognitive problems are recommended, however these are not routinely delivered in uk clinics.We collected and synthesised stakeholder perspectives to develop a care pathway for cognitive problems in ms and produce a logic model, illustrating how this pathway might operate.Methods forty-nine stakeholders, including people with ms and care providers, participated in semi-structured interviews and focus groups.Participants viewed information that illustrated how the pathway might work and provided feedback.Data, transcribed verbatim and analysed using framework analysis, were mapped onto a preliminary logic model and accompanying thematic framework.Results the proposed pathway was perceived as helpful in providing standardised support for a neglected ms symptom.Training packages, online cognitive screening, and triaging decisions were viewed as crucial activities.Shared responsibility, a person-centred approach, and addressing the complexity of cognitive problems were important engagement mechanisms.Allocating time during clinic appointments and within staff workloads were essential resources for implementation.Conclusion our co-constructed ms cognitive screening and management pathway will be evaluated for clinical and cost-effectiveness in a trial.However, in the interim, clinicians can adapt and implement this pathway in their own services and evaluate it locally.

Journal: Multiple sclerosis and related disorders (2021)
Publication types: Journal Article
Kinetic Measurements for Enzyme Immobilization.

Enzyme kinetics is the study of the chemical reactions that are catalyzed by enzymes, with a focus on their reaction rates.The study of an enzyme's kinetics considers the various stages of activity, reveals the catalytic mechanism of this enzyme, correlates its value to assay conditions, and describes how a drug or a poison might inhibit the enzyme.Victor henri initially reported that enzyme reactions were initiated by a bond between the enzyme and the substrate.By 1910, michaelis and menten were advancing their work by studying the kinetics of an enzyme saccharase which catalyzes the hydrolysis of sucrose into glucose and fructose.They published their analysis and ever since the michaelis-menten equation has been used as the standard to describe the kinetics of many enzymes.Unfortunately, soluble enzymes must generally be immobilized to be reused for long times in industrial reactors.In addition, other critical enzyme properties have to be improved like stability, activity, inhibition by reaction products, and selectivity towards nonnatural substrates.Immobilization is by far the chosen process to achieve these goals.although the michaelis-menten approach has been regularly adapted to the analysis of immobilized enzyme activity, its applicability to the immobilized state is limited by the barriers the immobilization matrix places upon the measurement of compounds that are used to model enzyme kinetics.That being said, the estimated value of the michaelis-menten coefficients (e.g., vmax, km) can be used to evaluate effects of immobilization on enzyme activity in the immobilized state when applied in a controlled manner.In this review enzyme activity and kinetics are discussed in the context of the immobilized state, and a few novel protocols are presented that address some of the unique constraints imposed by the immobilization barrier.

Journal: Methods in molecular biology (Clifton, N.J.) (2017)
Publication types: Journal Article;Review
K-Doped Graphitic Carbon Nitride with Obvious Less Electrode Passivation for Highly Stable Electrochemiluminescence and Its Sensitive Sensing Analysis of MicroRNA.

In this study, upon potassium (k) element doping, the electrochemiluminescence (ecl) excitation potential of graphitic carbon nitride (g-c3n4) obviously shifted from -1.57 to -0.74 v.Compared with other reported methods, this work was the first one that could reduce the ecl excitation potential of g-c3n4to below the critical value of -0.9 v.It could more effectively overcome electrode passivation and significantly improve the ecl intensity and stability.Meanwhile, the lower excitation potential could significantly reduce other side reactions caused by high voltage, and the introduction of the k element could obviously increase the water solubility to shorten the preparation time.The apparent decrease of the excitation potential was due to the doping of the k element, which could reduce the band gap, increase the in-plane spacing, and expand π-conjugated systems.Furthermore, using k-doped g-c3n4with highly stable electrochemiluminescence at lower potential as an emitter, a biosensor for micro rna-141 (mi rna-141) sensitive detection was constructed with the assistance of an innovative nicking enzyme-assisted strand displacement amplification (n-sda).Compared to the traditional sda, a nicking enzyme was introduced to obviously improve the utilization rate of the fuel chain and increase the number of cycles, finally resulting in higher signal amplification efficiency.Therefore, the constructed biosensor showed excellent performance in the ultrasensitive detection of mi rna-141 with the limit of detection (lod) being 44.8 a m.This work gave a more effective means to obviously improve the ecl property of g-c3n4caused by electrode passivation and provided a more efficient and convenient detection method for biochemical analysis.

Journal: Analytical chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Paeoniflorin alleviates the progression of retinal vein occlusion via inhibiting hypoxia inducible factor-1α/vascular endothelial growth factor/STAT3 pathway.

Retinal vein occlusion (rvo) is a severe retinal vascular disease involving several complications, leading to weakening of vision and even blindness.Globally, over 16 million patients with rvo were found in the middle-aged population.Paeoniflorin (pf), a monomer of taohong siwu decoction, was reported to exhibit many pharmacological activities including anti-inflammatory, antioxidant, cardioprotective, and neuroprotective effects.However, the effect of pf on the progression of rvo remains unclear.In the current study, cck8 assay was performed to investigate the cell viability.In addition, transwell assay and western blot were used to measure cell invasion and protein expression, respectively.Moreover, a mouse model of oxygen-induced dischemic retinopathy (oir) was established.We found pf was able to inhibit the migration and angiogenesis of human retinal capillary endothelial cells under normoxia.Additionally, pf notably prevented hypoxia-induced angiogenesis of human retinal capillary endothelial cells via inhibiting hypoxia-inducible factor-1α (hif-1α)/vascular endothelial growth factor (vegf)/stat3 pathway.Eventually, pf significantly alleviated the retinal lesions in the mouse with oir.All in all, pf was able to alleviate the progression of retinal vein occlusion via inhibiting hif-1α/vegf/stat3 pathway.These findings might provide some theoretical knowledge for exploring novel effective treatment for patients with rvo.

Journal: Bioengineered (2022)
Publication types: Journal Article
A C-terminally truncated form of β-catenin acts as a novel regulator of Wnt/β-catenin signaling in planarians.

Β-catenin, the core element of the wnt/β-catenin pathway, is a multifunctional and evolutionarily conserved protein which performs essential roles in a variety of developmental and homeostatic processes.Despite its crucial roles, the mechanisms that control its context-specific functions in time and space remain largely unknown.The wnt/β-catenin pathway has been extensively studied in planarians, flatworms with the ability to regenerate and remodel the whole body, providing a 'whole animal' developmental framework to approach this question.Here we identify a c-terminally truncated β-catenin (β-catenin4), generated by gene duplication, that is required for planarian photoreceptor cell specification.Our results indicate that the role of β-catenin4 is to modulate the activity of β-catenin1, the planarian β-catenin involved in wnt signal transduction in the nucleus, mediated by the transcription factor tcf-2.This inhibitory form of β-catenin, expressed in specific cell types, would provide a novel mechanism to modulate nuclear β-catenin signaling levels.Genomic searches and in vitro analysis suggest that the existence of a c-terminally truncated form of β-catenin could be an evolutionarily conserved mechanism to achieve a fine-tuned regulation of wnt/β-catenin signaling in specific cellular contexts.

Journal: PLoS genetics (2017)
Publication types: Journal Article
A Study on Dislocation Mechanisms of Toughening in Cu-Graphene Nanolayered Composite.

We investigated the role of graphene interfaces in strengthening and toughening of the cu-graphene nanocomposite by a combination ofin situtransmission electron microscopy (tem) deformation and molecular dynamics (md) simulations.in situ tem directly showed that dislocation plasticity is strongly confined within single cu grains by the graphene interfaces and grain boundaries.The weak cu-graphene interfacial bonding induces stress decoupling, which results in independent plastic deformation of each cu layer.As confirmed by the md simulation, the localized deformation made by such constrained dislocation plasticity results in the nucleation and growth of voids at the graphene interface, which acts as a precursor for crack.The graphene interfaces also effectively block crack propagation promoted by easy delamination of cu layers dissipating the elastic strain energy.The toughening mechanisms revealed by the present study will provide valuable insights into the optimization of the mechanical properties of metal-graphene nanolayered composites.

Journal: Nano letters (2022)
Publication types: Journal Article
A novel in-situ Raman spectroscopic cell for aqueous geochemistry at the solid-liquid interface.

In-situ raman spectroscopy has the potential to be a powerful technique for monitoring geochemical reactions at a solid-liquid interface in real time.In this article, we present the development and testing of an in-situ raman spectroscopic cell, which can be used for reaction systems at moderate temperatures and pressure [<1000 psi (6.89 mpa), <100 °c, relevant to subsurface geologic systems] and can hold samples large enough for chemical mapping of heterogeneous rock surfaces.The system is validated by measuring the temperature-dependent conversion of gypsum to calcite over time.Near total conversion of gypsum to calcite on the mineral surface took 29 hours at room temperature and 150 minutes at 100 °c, corresponding to an 11.6-fold increase in the conversion rate.We anticipate that this cell can be an important tool in quantifying the rates of carbon mineralization relevant to geologic carbon sequestration, particularly for the elevated rates recently observed in mafic/ultramafic rocks.

Journal: The Review of scientific instruments (2023)
Publication types: Journal Article
Pathological outcomes and biochemical recurrence-free survival after radical prostatectomy for high-risk prostate cancer in the Indian population.

Introduction we analyzed the biochemical recurrence-free survival (brfs) of patients with high-risk prostate cancer (hrca p) as per the d'amico classification undergoing radical prostatectomy (rp) at our center.We aimed to determine whether the number and type of risk factors (c t2c-t3b, prostate-specific antigen >20 ng/ml, gleason score >7) are associated with biochemical recurrence (bcr) in hrca p patients undergoing rp in the indian population.Methods between 2006 and 2017, 192 patients underwent rp (open rp [orp], laparoscopic rp [lrp], and robotic rp [rrp]) at our center, of which 109 had d'amico hr disease.Preoperative, postoperative, and pathological outcome data were analyzed for patients with hr disease as per the d'amico classification.Subgroups were formed to determine whether an increasing number of risk factors (1, 2, or 3) were associated with poorer oncological results and early bcr.The kaplan-meier method with log-rank test was used to test the difference in brfs between the groups.Univariate and multivariate analyses were done to find significant variable against bcr.Results according to the d'amico criteria, 109 patients had hr, 63 patients had intermediate-risk, and 19 patients had low-risk disease.These 109 patients with hr disease were analyzed in our study (50 rrp, 33 orp, and 26 lrp).A total of 59 (54.1%) patients had one hr factor (1hr), 44 (40%) had two hr factors (2hr), and 6 (5.5%) had three hr factors (3hr).The mean follow-up for our patient population was 21.5 ± 19 months (median 18 months; range, 0-108).Overall, the 2-year and 5-year brfs was 45% and 35%, respectively (mean brfs 46 ± 6 months).Two-year brfs was 63%, 23%, and 22%, respectively, for 1hr, 2hr, and 3hr (logrank,p< 0.0001).The prognostic substratification based on the three risk factors was significantly predictive for adverse pathologic features and oncologic outcomes.Conclusion substratification based on the three well-defined criteria leads to a better identification of the more aggressive cancers and prediction of need for additional treatment modalities.Localized hrca p includes a heterogeneous population of patients with variable oncological outcomes.

Journal: Indian journal of urology : IJU : journal of the Urological Society of India (2018)
Publication types: Journal Article
Is ABA the exogenous vector of interplant drought cuing?

We have recently demonstrated that root cuing from drought-stressed plants increased the survival time of neighboring plants under drought, which came at performance costs under benign conditions.The involvement of abscisic acid (aba) was implicated from additional experiments in which interplant drought cuing was greatly diminished in aba-deficient plants.Here, we tested the hypothesis that aba is the exogenous vector of interplant drought cuing.pisum sativumplants were grown in rows of three split-root plants.One of the roots of the first plant was subjected to either drought of benign conditions in one rooting vial, while its other root shared its rooting vial with one of the roots of an unstressed neighbor, which in turn shared its other rooting vial with an additional unstressed neighbor.One hour after subjecting one of the roots of the first plant to drought, aba concentrations were 106% and 145% higher around its other root and the roots of its unstressed neighbor, compared to their respective unstressed controls; however, the absolute concentrations of aba found in the rooting media were substantially low.The results may indicate that despite its involvement in interplant drought and the commonly observed exchange of aba between drought-stressed plants and their rhizospheres, aba is not directly involved in exogenous interplant drought cuing.However, previous studies have shown that even minute concentrations of aba in the rhizosphere can prevent aba leakage from roots and thus to significantly increase endogenous aba levels.In addition, under drought conditions, plants tend to accumulate aba, which could markedly increase internal aba concentrations over time and aba concentrations in close proximity to the root surface might be significantly greater than estimated from entire rooting volumes.Finally, phaseic acid, an aba degradation product, is known to activate various aba receptors, which could enhance plant drought tolerance.It is thus feasible that while the role of aba is limited, its more stable degradation products could play a significant role in interplant drought cuing.Our preliminary findings call for an extensive investigation into the identity and modes of operation of the exogenous vectors of interplant drought cuing.

Journal: Plant signaling & behavior (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Nursing students' classroom climate perceptions: A longitudinal study.

As a versatile and dynamic process, classroom climate directly affects the learning levels of students and their quality of life while in school.Objectives the study was conducted to explore and compare nursing students' perceptions of classroom climate throughout four years of university education and to evaluate the influencing factors.Design and settings the longitudinal study was conducted between 2017 and 2020 in the nursing department of a university in turkey.Participants the study was carried out with 134 nursing students who enrolled in their first year and agreed to participate in the study.Methods the data were collected at the end of the fall semester of each of the four years using the student information form and the classroom climate inventory.Results the mean score of students' perceptions of classroom climate was 2.88 ± 0.83 for all academic years.The classroom climate inventory mean scores of fourth-year students were statistically significantly higher than their scores in the first and third years (p = 0.000).The students' classroom climate levels were statistically significantly affected by the positive classroom communication among students in all academic years in a positive direction.Statistically significant effective factors in students' classroom climate perceptions by year were as follows: the sense of belongingness to the class in the second and third years (although significantly lower in the first year), socio-cultural activities organized at school the second and fourth years (p < 0.05), instructors' attitudes supporting classroom communication in the first year, and opportunities supporting communication in the school environment in the fourth year (p < 0.05).Conclusions students' perception of the classroom climate was moderate overall and affected by positive classroom communication among students in all academic years.School administrators and educators can develop strategies and organize activities to increase positive communication in the classroom.

Journal: Nurse education today (2022)
Publication types: Journal Article
Pegvaliase dosing in adults with PKU: Requisite dose for efficacy decreases over time.

Novel pharmaceutical therapies such as pegvaliase, phenylalanine ammonia lyase (pal), have enhanced disease control for many individuals with phenylketonuria (pku).We present a retrospective chart review to assess pegvaliase doses over time in individuals followed at the boston children's hospital pal clinic, including those who started pegvaliase in a clinical trial ("trial patients") and those who started after drug came to market ("post-market patients").Trial patients were on pegvaliase an average of 4.8 years longer, and their mean current pegvaliase dose was 126 ± 92 compared to 223 ± 147 mg/week for post-market patients (p = 0.0155), suggesting that the pegvaliase dose for target efficacy may decrease over time in adults with pku.In post-market patients, we demonstrated a significant, inverse correlation with dose change and number of weeks from response (r = -0.46, p = 0.046).The entire cohort showed significant variability in terms of time to achieve a therapeutic response, response dose, and current dose.Our data suggest that patients tolerate a reduction in pegvaliase dose over time while maintaining efficacy.This is a clinically meaningful finding as it indicates that patients may reduce number of weekly injections over time on pegvaliase.

Journal: Molecular genetics and metabolism (2022)
Publication types: Journal Article