syedzayyan/paper_mill_benchmark huggingface dataset:
Impact of Relative Dose Intensity of FOLFOX Adjuvant Chemotherapy on Risk of Death Among Stage III Colon Cancer Patients.

The national comprehensive cancer network (nccn) guidelines have recommended tailored chemotherapy for stage iii high-risk (t4 and/or n2) and low-risk (t1-t3 and n1) colon cancer since 2018.Studies have investigated the effect of relative dose intensity (rdi) of folfox on stage iii colon cancer survival, however, none has performed a stratified analysis by risk profiles.This study aims to identify the folfox optimal rdi for high-risk and low-risk stage iii colon cancer patients.Methods data on 407 eligible patients, diagnosed with stage iii colon cancer in 2011 who received folfox, were collected by 8 population-based cancer registries.Multivariable cox model and fine-gray competing risks model were employed to explore optimal rdi defined as the lowest rdi administered without significant differences in either overall or cause-specific death.Results among the 168 high-risk patients, the optimal rdi cut-off was 70% (hr = 1.59 with 95% ci: 0.69-3.66 in overall mortality; hr = 1.24 with 95% ci: 0.42-3.64 in cause-specific mortality when rdi < 70% vs.Rdi ≥ 70%).Among the 239 low-risk patients, none of the evaluated cut-offs were associated with significant differences in risk of death between comparison groups.The lowest assessed rdi was 45%, hr = 0.80; 95% ci: 0.24 to 2.73 for overall mortality and hr = 0.53; 95% ci: 0.06 to 4.95 for cause-specific mortality, when rdi <45% versus rdi ≥45%.Conclusions there is no significant harm on the risk of death when reducing rdi by <30% for high-risk patients.For the low-risk patients, we found that rdi as low as 45% did not significantly affect the risk of death.

Journal: Clinical colorectal cancer (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, U.S. Gov't, P.H.S.
Light-Driven Catalytic Regulation of Enzymes at the Interface with Plasmonic Nanomaterials.

Regulation of enzymes is highly relevant toward orchestrating cell-free and stepwise biotransformations, thereby maximizing their overall performance.Plasmonic nanomaterials offer a great opportunity to tune the functionality of enzymes through their remarkable optical properties.Localized surface plasmon resonances (lspr) can be used to modify chemical transformations at the nanomaterial's surface, upon light irradiation.Incident light can promote energetic processes, which may be related to an increase of local temperature (photothermal effects) but also to effects triggered by generated hotspots or hot electrons (photoelectronic effects).As a consequence, light irradiation of the protein-nanomaterial interface affects enzyme functionality.To harness these effects to finely and remotely regulate enzyme activity, the physicochemical features of the nanomaterial, properties of the incident light, and parameters governing molecular interactions must be optimized.In this perspective, we discuss relevant examples that illustrate the use of plasmonic nanoparticles to control enzyme function through lspr excitation.Finally, we also highlight the importance of expanding the use of plasmonic nanomaterials to the immobilization of multienzyme systems for light-driven regulation of cell-free biosynthetic pathways.Although this concept is living its infancy, we encourage the scientific community to advance in the development of novel light-controlled biocatalytic plasmonic nanoconjugates and explore their application in biosensing, applied biocatalysis, and biomedicine.

Journal: Biochemistry (2021)
Publication types: Journal Article
Superhydrophilic Antireflective Periodic Mesoporous Organosilica Coating on Flexible Polyimide Substrate with Strong Abrasion-Resistance.

Superhydrophilic antireflective periodic mesoporous organosilica (pmo) coating was prepared on flexible polyimide substrate via solvent-evaporation-induced self-assembly (seisa) method, in which tetraethoxysilane (teos) and a special bridged silsesquioxane were used as reactants.The bridged silsesquioxane, eg-bsq, was synthesized through the stoichiometric reaction between 3-glycidoxyporpyltrimethoxysilane (gptms) and ethylene diamine (eda).Under the influence of surfactant, teos and eg-bsq co-condensed and enclosed the ordered mesporous in the coating.The results of grazing-incidence small-angle x-ray scattering (gisaxs) and the transmission electron microscope (tem) indicated that the mesopores belonged to a fmmm orthorhombic symmetry structure.With increasing eg-bsq concentration, the mesoporous structure in the pmo coating becomes more and more disordered because silica mesopore walls shrunk or collapsed during calcination and consequently the refractive index of pmo coating became larger.The antireflective (ar) pmo coating showed an optical transmittance of 99.54% on polyimide (pi) much higher than the 88.68% of bare pi.The water contact angle of pmo coating was less than 9.0°, which indicated the ar pmo coating was superhydrophilic.Moreover, the pmo coating showed an excellent mechanical property, the transmittance of the pmo coating displayed a very low loss of 0.1% after abrasion of 25 cycles by cs-10f wearaser.

Journal: ACS applied materials & interfaces (2017)
Publication types: Journal Article
Interference of eltrombopag with bilirubin measurements on the Vitros 5600 analyzer.

Eltrombopag is a thrombopoietin-receptor agonist used to restore platelet count to hemostatic levels in chronic immune thrombocytopenia.The drug has shown to have hepatobiliary adverse effects, but also positive interference with the analytical measurement of bilirubin.Understanding the degree of interference of this drug with bilirubin testing becomes relevant in the clinical management of these patients.Methods eltrombopag at concentrations ranging from 10 to 150 μg/ml was spiked into plasma samples with different baseline concentrations of bilirubin.Total bilirubin, conjugated, and unconjugated bilirubin were measured for each sample using vitros tbili and bu bc slides on the vitros 5600 automated chemistry platform, and interference was assessed.Results plasma samples spiked with eltrombopag yielded falsely elevated bilirubin measurements compared to baseline, with the degree of elevation increasing with greater concentrations of eltrombopag.Bilirubin values were increased relative to baseline across all groups, except in conjugated bilirubin measurements in samples with low baseline conjugated bilirubin.For samples with low total bilirubin at baseline, >100 μg/ml of eltrombopag resulted in an error of >+0.6 mg/dl on the measured total bilirubin.For samples with low unconjugated bilirubin at baseline, the error for the same concentrations was >+0.7 mg/dl.Conclusion our results show that, at supra-physiologically high concentrations, eltrombopag can positively interfere with bilirubin measurements on vitros 5600 platform.

Journal: Journal of clinical laboratory analysis (2021)
Publication types: Journal Article
MUBD-DecoyMaker 2.0: A Python GUI Application to Generate Maximal Unbiased Benchmarking Data Sets for Virtual Drug Screening.

Ligand enrichment assessment based on benchmarking data sets has become a necessity for the rational selection of the best-suited approach for prospective data mining of drug-like molecules.Up to now, a variety of benchmarking data sets had been generated and frequently used.Among them, mubd-hdacs from our prior research efforts was regarded as one of five state-of-the-art benchmarks in 2017 by frontiers in pharmacology.This benchmarking set was generated by one of our unique de-biasing algorithms.It also rendered quite a few other cases of successful applications in recent years, thus is expected to have more impact in modern drug discovery.To make our algorithm amenable to more users, we developed a python gui application called mubd-decoy maker 2.0.Moreover, it has two new additional functional modules, i.E."detect 2d bias" and "quality control".This new gui version had been proved to be easy to use while generate benchmarking data sets of the same quality.Mubd-decoy maker 2.0 is freely available at maker2.0, along with its manual and testcase.

Journal: Molecular informatics (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Medical Image Retrieval via Histogram of Compressed Scattering Coefficients.

The features used in many current medical image retrieval systems are usually low-level hand-crafted features.This limitation may adversely affect the retrieval performance.To address this problem, this paper proposes a simple yet discriminative feature, called histogram of compressed scattering coefficients (hcsc), for medical image retrieval.In the proposed work, the scattering transform, a particular variation of deep convolutional networks, is first performed to yield more abstract representations of a medical image.A projection operation is then conducted to compress the obtained scattering coefficients for efficient processing.Finally, a bag-of-words (bo w) histogram is derived from the compressed scattering coefficients as the features of the medical image.The proposed hcsc takes the advantages of both scattering transform and bo w model.Experiments on three benchmark medical computer tomography image databases demonstrate that hcsc outperforms several state-of-the-art features.

Journal: IEEE journal of biomedical and health informatics (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Comparing estrogen-based hormonal contraceptives and hormone therapy on bone mineral density in women with premature ovarian insufficiency: a systematic review.

Importance premature ovarian insufficiency (poi) is a condition associated with estrogen deficiency which leads to decreased bone mineral density and an increased risk of osteoporosis and fractures.Estrogen-based hormone therapy is an integral component of treatment; however, to date the ideal hormone formulation for optimizing bone health has not been established.Objective to assess the effects of estrogen-based oral contraceptives (ocp) versus hormone therapy (ht) on bone mineral density (bmd) in women with poi.Evidence review a systematic review of ovid medline, embase, cochrane library, and web of science databases was conducted from conception until december 2020.Randomized controlled trials (rcts) and observational studies that met inclusion criteria were included in the analysis.Risk of bias was assessed with the newcastle-ottawa quality assessment scale for cohort studies and the cochrane risk of bias for rcts.The study protocol was registered with the international prospective register of systematic reviews and adheres to the preferred reporting items for systematic reviews and meta-analysis.Findings our search yielded 1,227 studies; 3 rcts and 2 observational cohort studies met inclusion criteria and were included in our study.The largest subpopulation was turner syndrome (n = 625), followed by idiopathic poi (n = 146).Of the four studies that assessed changes in bmd, two studies reported a significant increase in lumbar spine bmd with ht compared with ocp (+0.050 g/cm2, p < 0.025; +0.019 g/cm2, p < 0.01), one study found similar improvement in lumbar spine bmd across treatments (ht -0.003 g/cm2, p = 0.824), and one study did not directly compare treatments.Effects on bone turnover markers were inconsistent across three studies that evaluated this outcome.Conclusions and relevance this is the first systematic review to include studies that directly compared ocp and ht on bone outcomes in poi.While two studies reported increased lumbar spine bmd with ht, this result was not consistently found across studies.There were important differences in poi etiology, treatment regimens and formulations, and risk of bias was high in many of the studies.These results indicate future, larger-scale trials are needed to further understand the optimal hormone therapy for bone density in poi.

Journal: Menopause (New York, N.Y.) (2022)
Publication types: Journal Article;Systematic Review
Increasing Fusobacterium infections with Fusobacterium varium, an emerging pathogen.

Infections caused by fusobacterium species are rare; however serious infections with complications or mortality may occur occasionally.We conducted a retrospective study to investigate the clinical features of patients with fusobacterium infections and the differences between infections caused by the species f.Necrophorum, f.Nucleatum, and f.Varium.Additionally, we attempted to identify risk factors for fusobacterium-associated mortality.This study included all patients at a large tertiary care teaching hospital in south korea with fusobacterium infections from january 2006 to april 2021.Demographic, clinical, laboratory, and outcome data were analyzed.Multiple logistic regression analysis was performed to assess the risk factors for in-hospital mortality associated with f.Nucleatum and f.Varium infections.We identified 272 patients with fusobacterium infections during the study period.The number of fusobacterium cases has increased recently, with f.Varium infections markedly increasing since 2016 and causing a significant proportion of infections.Patients with f.Varium infections were older and had a higher proportion of nosocomial infections than the other groups.The f.Nucleatum and f.Varium groups showed higher in-hospital mortality than the f.Necrophorum group.Through logistic regression analysis, apache ii score and serum albumin level were considered risk factors for in-hospital mortality.Apache ii score was positively correlated with age, red cell distribution width, and serum blood urea nitrogen, and negatively correlated with serum albumin level.Infections caused by fusobacterium species are increasing.F.Varium causes a significant proportion of severe infections.

Journal: PloS one (2022)
Publication types: Journal Article
Crystalline-Amorphous Ni2P4O12/NiMoOxNanoarrays for Alkaline Water Electrolysis: Enhanced Catalytic Activity via In Situ Surface Reconstruction.

Water electrolysis affords a promising approach to large-scale hydrogen yield, but its efficiency is restrained by the sluggish water dissociation kinetics.Here, an efficient bifunctional electrocatalyst of in situ formed crystalline nickel metaphosphate on amorphous ni mo oxnanoarrays supported on nickel foam (c-ni2p4o12/a-ni mo ox/nf) for both hydrogen evolution reaction (her) and oxygen evolution reaction (oer) in alkaline solution is reported.The c-ni2p4o12/a-ni mo ox/nf can deliver a current density of 10 m a cm-2at a low potential of 78 m v for her, and a current density of 20 m a cm-2at an overpotential of 250 m v for oer.Moreover, it only requires a small cell voltage of 1.55 v at 10 m a cm-2for robust water splitting with outstanding long-term durability over 84 h.Various spectroscopic studies reveal that in situ surface reconstruction is crucial for the enhanced catalytic activity, where c-ni2p4o12/a-ni mo oxis transformed into c-ni2p4o12/a-ni mo o4during the her process, and into c-ni2p4o12/a-ni ooh in the oer process.This work may provide a new strategy for uncovering the catalytic mechanism of crystalline-amorphous catalysts.

Journal: Small (Weinheim an der Bergstrasse, Germany) (2022)
Publication types: Journal Article
Identification of Optimal Urinary Biomarkers of Synthetic Cannabinoids BZO-HEXOXIZID, BZO-POXIZID, 5F-BZO-POXIZID, and BZO-CHMOXIZID for Illicit Abuse Monitoring.

The continuous introduction of new synthetic cannabinoid (sc) subtypes and analogues remains a major problem worldwide.Recently, a new "oxizid" generation of scs surfaced in seized materials across various countries.Hence, there is an impetus to identify urinary biomarkers of the oxizids to detect their abuse.Methods we adapted our previously reported two-pronged approach to investigate the metabolite profiles and disposition kinetics of 4 oxizid analogues, namely, bzo-hexoxizid (mda-19), bzo-poxizid (5c-mda-19), 5f-bzo-poxizid (5f-mda-19), and bzo-chmoxizid (chm-mda-19).First, bottom-up in vitro incubation experiments comprising metabolite identification, metabolic stability, and reaction phenotyping were performed using human liver microsomes and recombinant human cytochrome p450 enzymes.Second, top-down analysis of authentic urine samples from drug abusers was performed to corroborate the in vitro findings and establish a panel of urinary biomarkers.Results a total of 42 to 51 metabolites were detected for each oxizid, and their major metabolic pathways included n-alkyl and phenyl hydroxylation, oxidative defluorination (for 5f-bzo-poxizid), oxidation to ketone and carboxylate, amide hydrolysis, and n-dealkylation.The oxizids were metabolically unstable, mainly metabolized by cytochromes p3a4, p3a5, and p2c9, and demonstrated mechanism-based inactivation of cytochrome p3a4.Integrating with the results of 4 authentic urine samples, the parent drug and both n-alkyl and phenyl mono-hydroxylated metabolites of each oxizid were determined as suitable urinary biomarkers.Conclusions drug enforcement agencies worldwide may apply these biomarkers in routine monitoring procedures to identify abusers and counter the escalation of oxizid abuse.

Journal: Clinical chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Heat Stress and Feed Restriction Distinctly Affect Performance, Carcass and Meat Yield, Intestinal Integrity, and Inflammatory (Chemo)Cytokines in Broiler Chickens.

This study was conducted to distinguish the effects of heat stress (hs) and feed intake (fi) on broiler chicken's physiological responses.Day-old male cobb 500 broilers (n= 672) were allocated to three treatments: (1) control (ctl): birds raised under normal temperature (23°c) from day 29 to 42; (2) cyclic heat stress (chs): birds exposed to high temperatures (8 h/day at 35°c; from 9:30 am to 5:30 pm) from day 29 to 42; (3) pair-fed (pf): birds raised under thermoneutral condition but fed the same amount of feed as chs from day 29 to 42.On day 42, 15 birds/pen were processed, to measure carcass and meat yields.To measure blood parameters and gut integrity (using fluorescein isothiocyanate-dextran), on day 42, chs birds were sampled before (pre-chs) and 2 h after (post-chs) the temperature increased.Furthermore, after sampling ctl birds, they were exposed to 2h heat and sampled (acute heat stress, ahs).Data were analyzed using one-way anova (jmp pro15) and significance between treatments identified by lsd (p< 0.05).Bw and relative carcass yield were significantly higher in ctl compared to chs and pf.Compared to chs, pf had significantly higher bw and lower relative carcass yield.Breast yield was significantly higher for ctl and pf, while leg quarters and wings yield were significantly lower compared to chs.Gut barrier integrity was significantly altered in post-chs and ahs compared to ctl.M rna abundances of tumor necrosis factor-α, c-c motif chemokine ligand-20, heat shock protein (hsp)-27, and hsp70were significantly higher in post-chs and ahs compared to ctl.Ahs had significantly higher m rna abundances of card domain containing (nlrc)-3and nlrc5inflammasomes, and lower superoxide dismutase (sod)-1and sod2abundance compared with ctl.Pf had significantly higher liver weight (% bw) compared to all other groups; while abdominal fat was significantly higher in pre-chs compared to ctl, pf, and ahs.Together, these data indicate that the negative effects of hs are partially due to reduced fi.However, the negative effect of hs on gut integrity, average daily gain, feed conversion ratio, and meat yield are direct and independent of the reduced fi during the hs.Thus, warrant investigating the underlying mechanisms in future research.

Journal: Frontiers in physiology (2021)
Publication types: Journal Article
Continuing Pharmacy Education: Exploring the Status and Future Prospects in Nepal.

Continuing pharmacy education (cpe) is an educational way for pharmacy professionals to develop competency in providing quality pharmaceutical care to patients.The cpe program helps maintain up-to-date knowledge and skills, increase the professionalism of pharmacists, and positively impact patient health outcomes.However, the concept and practice of cpe are still in their infancy in nepal.Nepal's conventional pharmacy education system involves didactic lectures focusing more on theoretical learning than practical and experiential approaches, leading to the generation of pharmacists theoretically knowledgeable but practically non-competent to deliver pharmaceutical care services in independent practice settings.Additionally, in the absence of cpe, the professionals might miss updated information on new therapies, technologies, and approaches in patient management.The community and hospital pharmacies in nepal are often business-oriented rather than service, and may not even be staffed by pharmacists, so the cpe programs are rarely conducted for the pharmacy professionals.Hence, the present commentary aimed to explore the status of cpe and its barriers or challenges in implementation and to suggest solutions in nepal.

Journal: Advances in medical education and practice (2022)
Publication types: Journal Article
VE-cadherin RGD motifs promote metastasis and constitute a potential therapeutic target in melanoma and breast cancers.

We have investigated the role of vascular-endothelial (ve)-cadherin in melanoma and breast cancer metastasis.We found that ve-cadherin is expressed in highly aggressive melanoma and breast cancer cell lines.Remarkably, inactivation of ve-cadherin triggered a significant loss of malignant traits (proliferation, adhesion, invasion and transendothelial migration) in melanoma and breast cancer cells.These effects, except transendothelial migration, were induced by the ve-cadherin rgd motifs.Co-immunoprecipitation experiments demonstrated an interaction between ve-cadherin and α2β1 integrin, with the rgd motifs found to directly affect β1 integrin activation.Ve-cadherin-mediated integrin signaling occurred through specific activation of src, erk and jnk, including akt in melanoma.Knocking down ve-cadherin suppressed lung colonization capacity of melanoma or breast cancer cells inoculated in mice, while pre-incubation with ve-cadherin rgd peptides promoted lung metastasis for both cancer types.Finally, an in silico study revealed the association of high ve-cadherin expression with poor survival in a subset of melanoma patients and breast cancer patients showing low cd34 expression.These findings support a general role for ve-cadherin and other rgd cadherins as critical regulators of lung and liver metastasis in multiple solid tumours.These results pave the way for cadherin-specific rgd targeted therapies to control disseminated metastasis in multiple cancers.

Journal: Oncotarget (2017)
Publication types: Journal Article