syedzayyan/paper_mill_benchmark huggingface dataset:
Zeolitic imidazolate framework-8 as a dispersive solid phase extraction sorbent for simultaneous determination of 145 pesticide residues in polyphenol-rich plants.

Many plants have a high polyphenol content, which causes the matrix effect and makes the analysis of trace pesticide residues highly challenging.A common approach to improving matrix effects is to purify pesticides through the use of sorbents, but this requires a combination of multiple sorbents and extensive use.Zeolitic imidazolate framework-8 is widely used for pesticide analysis due to its high porosity, large specific surface area, and versatility.Here, we established and validated a modified quick, easy, cheap, effective, rugged, and safe method based on a zeolitic imidazolate framework-8 that was used to test the removal ability for polyphenols.To this end, 145 pesticide residues in peppermint, perilla, fennel, and mulberry leaves were analyzed by the modified method coupled with liquid chromatography with tandem mass spectrometry.The mean recoveries of all pesticide residues were in the range of 74.3-103.7%, with mean relative standard deviations ≤9.1% at spiked concentrations of 1, 10, 50, and 100 μg/kg for mulberry leaves.The limits of quantitation of the method ranged from 1 to 50 μg/kg.This study offers a reliable approach for the accurate quantitative analysis of various trace substances in the polyphenol-rich plants.

Journal: Journal of separation science (2022)
Publication types: Journal Article
Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures.

Fentanyl is one of the most common opioid analgesics administered to patients undergoing surgery or for chronic pain management.While the side effects of chronic fentanyl abuse are recognized (e.g., addiction, tolerance, impairment of cognitive functions, and inhibit nociception, arousal, and respiration), it remains poorly understood what and how changes in brain activity from chronic fentanyl use influences the respective behavioral outcome.Here, we examined the functional and molecular changes to cortical neural network activity following sub-chronic exposure to two fentanyl concentrations, a low (0.01 μm) and high (10 μm) dose.Primary rat co-cultures, containing cortical neurons, astrocytes, and oligodendrocyte precursor cells, were seeded in wells on either a 6-well multi-electrode array (mea, for electrophysiology) or a 96-well tissue culture plate (for serial endpoint bulk rna sequencing analysis).Once networks matured (at 28 daysin vitro), co-cultures were treated with 0.01 or 10 μm of fentanyl for 4 days and monitored daily.Only high dose exposure to fentanyl resulted in a decline in features of spiking and bursting activity as early as 30 min post-exposure and sustained for 4 days in cultures.Transcriptomic analysis of the complex cultures after 4 days of fentanyl exposure revealed that both the low and high dose induced gene expression changes involved in synaptic transmission, inflammation, and organization of the extracellular matrix.Collectively, the findings of thisin vitrostudy suggest that while neuroadaptive changes to neural network activity at a systems level was detected only at the high dose of fentanyl, transcriptomic changes were also detected at the low dose conditions, suggesting that fentanyl rapidly elicits changes in plasticity.

Journal: Frontiers in toxicology (2022)
Publication types: Journal Article
Multi-Robot 2.5D Localization and Mapping Using a Monte Carlo Algorithm on a Multi-Level Surface.

Most indoor environments have wheelchair adaptations or ramps, providing an opportunity for mobile robots to navigate sloped areas avoiding steps.These indoor environments with integrated sloped areas are divided into different levels.The multi-level areas represent a challenge for mobile robot navigation due to the sudden change in reference sensors as visual, inertial, or laser scan instruments.Using multiple cooperative robots is advantageous for mapping and localization since they permit rapid exploration of the environment and provide higher redundancy than using a single robot.This study proposes a multi-robot localization using two robots (leader and follower) to perform a fast and robust environment exploration on multi-level areas.The leader robot is equipped with a 3d lidar for 2.5d mapping and a kinect camera for rgb image acquisition.Using 3d lidar, the leader robot obtains information for particle localization, with particles sampled from the walls and obstacle tangents.We employ a convolutional neural network on the rgb images for multi-level area detection.Once the leader robot detects a multi-level area, it generates a path and sends a notification to the follower robot to go into the detected location.The follower robot utilizes a 2d lidar to explore the boundaries of the even areas and generate a 2d map using an extension of the iterative closest point.The 2d map is utilized as a re-localization resource in case of failure of the leader robot.

Journal: Sensors (Basel, Switzerland) (2021)
Publication types: Journal Article
Enhancing Rearing of European Seabass (Dicentrarchus labrax) in Aquaponic Systems: Investigating the Effects of Enriched Black Soldier Fly (Hermetia illucens) Prepupae Meal on Fish Welfare and Quality Traits.

Within the modern aquaculture goals, the present study aimed to couple sustainable aquafeed formulation and culturing systems.Two experimental diets characterized by 3 and 20% of fish meal replacement with full-fat spirulina-enriched black soldier fly (hermetia illucens) prepupae meal (hpm3 and hpm20, respectively) were tested on european seabass (dicentrarchus labrax) juveniles during a 90-day feeding trial performed in aquaponic systems.The experimental diets ensured 100% survival and proper zootechnical performance.No behavioral alterations were evidenced in fish.Histological and molecular analyses did not reveal structural alterations and signs of inflammation at the intestinal level, highlighting the beneficial role on gut health of bioactive molecules typical of hpm or derived from the enriching procedure of insects' growth substrate with spirulina.Considering the quality traits, the tested experimental diets did not negatively alter the fillet's fatty acid profile and did not compromise the fillet's physical features.In addition, the results highlighted a possible role of spirulina-enriched hpm in preserving the fillet from lipid oxidation.Taken together, these results corroborate the use of sustainable ingredients (spirulina-enriched hpm) in aquaponic systems for euryhaline fish rearing.

Journal: Animals : an open access journal from MDPI (2023)
Publication types: Journal Article
Light-Guided Percutaneous Neck Rejuvenation With Division of Platysma Bands and Suture Suspension: A Multicenter Retrospective Study.

Traditional invasive suture suspension techniques have proven efficacy and durability.A previously described percutaneous placement of a neck suspension suture with light guidance has transformed this into a minimally invasive technique.This novel technique provides a major advance for minimally invasive neck rejuvenation.Objectives the authors sought to describe their experience with light-guided percutaneous neck rejuvenation over the past 4.5 years, including technique, patient selection, safety profile, and expected outcomes.Methods data were retrospectively reviewed for all patients who underwent the procedure with 5 surgeons across 4 aesthetic plastic surgery practices from january 2018 through may 2022.Inclusion criteria were mild to moderate neck laxity, prominent anterior platysma bands, and desire to improve neck contour.Patients undergoing concurrent skin incision >5 mm (ie, open rhytidectomy or platysmaplasty) were excluded.Results a total of 391 patients meeting criteria were identified during the study period.No hematomas were documented.Four patients (1%) developed infection at the suture site, 1 resolving on antibiotics and 3 requiring suture removal.Eighteen (4.6%) developed recurrent platysmal bands, and 7 (1.8%) had residual loose skin.Four (1%) experienced transient marginal mandibular neuropraxia.Mean length of follow-up time was 240 days.Conclusions light-guided percutaneous suture suspension is a safe and viable option for improving neck contours.Although it does not address extensive skin laxity or excess submental fat, it can be combined with energy-based tissue tightening, submental liposuction, or skin excision.In selected patients, this minimally invasive procedure provides predictable results with a low risk of complications.Level of evidence: 3

Journal: Aesthetic surgery journal (2023)
Publication types: Multicenter Study;Journal Article
Distinguishing the pros and cons of metabolic reprogramming in oncolytic virus immunotherapy.

Oncolytic viruses (ovs) represent a class of cancer immunotherapies that rely on hijacking the host cell factory for replicative oncolysis and eliciting immune responses for tumor clearance.An increasing evidence suggests that the metabolic state of tumor cells and immune cells is a putative determinant of the efficacy of cancer immunotherapy.However, how therapeutic intervention with ovs affects metabolic fluxes within the tumor microenvironment (tme) remains poorly understood.Herein, we review the complexities of metabolic reprogramming involving the effects of viruses and their consequences on tumor cells and immune cells.We highlight the inherent drawback of oncolytic virotherapy, namely that treatment with ovs inevitably further exacerbates the depletion of nutrients and the accumulation of metabolic wastes in the tme, leading to a metabolic barrier to antitumor immune responses.We also describe targeted metabolic strategies that can be used to unlock the therapeutic potential of ovs.

Journal: International journal of cancer (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Third-generation cephalosporin (3GC) resistance and its association with Extra-intestinal pathogenic Escherichia coli (ExPEC). Focus on broiler carcasses.

The worldwide spread of extra-intestinal pathogenic escherichia coli (ex pec), together with the antimicrobial resistance linked with extended-spectrum β-lactamases (esbls) and plasmid-mediated amp c β-lactamases (p amp cs) are pressing threats for public health.This study aimed to investigate the presence of ex pec genes in third-generation cephalosporin (3 gc)-resistant e.Coli and to study their distribution in broiler carcasses at the slaughterhouse after the chilling process.To this purpose, isolates from a collection of 3 gc-resistant e.Coli from carcasses of broilers originating from twelve broiler farms and three production chains were investigated.Several multivariate statistical approaches were adopted to elucidate the relationships among features.Phylogroup f was predominant in all broiler batches and was mainly associated with bla temand esbl genes but less correlated to ex pec genes.Another remarkable finding was the predominance of ex pec strains assigned to uncommon phylogroups, such as b2, d, e and clade i, commonly found into the environment.This study represents a first step for a comprehensive characterization of ex pec genes harboured by 3 gc-resistant e.Coli.These findings may be valuable for the identification of potential risks associated to broiler carcasses as source of uncommon e.Coli phylogroups.

Journal: Food microbiology (2022)
Publication types: Journal Article
A prospective randomized trial to compare the effectiveness of zero calorie carbonated drink and water as a solvent in sodium phosphate for colonoscopy.

S to compare the effectiveness of zero-calorie soft drink and plain water as a solvent for sodium phosphate in terms of good palatability and better patient tolerance.Methods the randomised controlled trial was conducted from may to december 2019 at the dowites operation theatre endoscopy suite, surgical unit 3, civil hospital karachi, and comprised patients aged >18 years of either gender undergoing colonoscopy for screening and non-emergency/non-urgent colorectal diseases.The patients were randomised into group a, which was assigned to take sodium phosphate in water, and group b, which was assigned to take sodium phosphate in zero-calorie soft drink.Bowel preparation was assessed by the consultant during endoscopy.Outcome variables, such as bowel cleanliness, palatability, tolerance of solution, adverse effects, and willingness to repeat the preparation, were evaluated in both groups.Data was analysed using spss 21.Results of the 162 patients, there were 81(50%) in each of the two groups.There were 124(76.5%) males and the overall mean age was 43±8.66 years.The palatability score was significant (p=0.01) for group b compared to group a.Due to better palatability and tolerance, 64(79%) patients in group b took the preparation in <6 hours.Conclusions use of zero-calorie soft drink was found to be a better option for colonoscopic preparation compared to plain water.Rct registration clinical trial unit (www.clinicaltrials.gov), nct04316858.

Journal: JPMA. The Journal of the Pakistan Medical Association (2022)
Publication types: Journal Article;Randomized Controlled Trial
Treatment of gingival class I or class II recession using subepithelial connective tissue graft and acellular dermal matrix allograft.

The present randomized control was conducted clinically to evaluate the effectiveness of acellular dermal matrix allograft (adma) and subepithelial connective tissue graft (sctg) in combination with coronally positioned flap (cpf) in the treatment of miller's class i and ii multiple gingival recession in aesthetic areas.A total of 20 patients aged between 18 to 40 years were selected for this study, meeting all the criteria for inclusion.10 patients were treated with adma and 10 patients with sctg in combination with cpf.Various clinical parameters were assessed viz.Probing pocket depth (ppd), clinical attachment level (cal), gingival recession height (rh) and width of keratinized gingiva (wkg) at baseline and 6 months after surgery.The mean rh at baseline in the control and test groups was 3.05 ±0 .55(mean± sd) and 2.60 ±.99 respectively.At 3 months the mean rh was found to be 1.60±0.74 and 1.05 ± .60 in the control and test group respectively.The mean percentage of root coverage (mrc%) at 6 months in the control and test group was 65.69 ±26.52 (mean± sd) and 65.54 ±.9.16 respectively but no statistically significant difference was seen between the two groups.The results of the study suggest that the combination of both subepithelial connective tissue graft and acellular dermal matrix graft with a coronally positioned flap can produce an equivalent amount of esthetic root coverage.

Journal: Bioinformation (2022)
Publication types: Journal Article
Malignant Rhabdoid Tumor, an Aggressive Tumor Often Misclassified as Small Cell Variant of Hepatoblastoma.

The clinical management of pediatric liver tumors involves stratification into risk groups.One previously defined, high-risk group of hepatoblastomas is the small cell undifferentiated variant.In light of molecular studies showing smarcb1deletion in these tumors, it is now recognized that most small cell, undifferentiated liver tumors represent an aggressive unrelated tumor-the malignant rhabdoid tumor (mrt).smarcb1is a member of the chromatin remodeling swi/snf complex and encodes the ini1 protein.The histologic diagnosis of mrt is currently based on ini1 negative immunoreactivity and the presence of rhabdoid morphology.Ini1-negative small cell liver tumors lacking classic rhabdoid morphology are often misclassified as small cell undifferentiated hepatoblastomas (scud-hb), according to the current classification.Pediatric liver tumors diagnosed between 2003-2017 as scud-hb (four cases) or mrt (two cases) were identified from the columbia university pathology department archives.All tumors were associated with normal or low serum alpha fetoprotein levels, and showed an absence of immunohistochemical staining of hepatocellular markers (hep-par1, arginase) and loss of ini1 staining.Two cases were initially diagnosed as mrt, one with prominent rhabdoid morphology, the other with predominant small cell morphology.The remaining four cases with small cell morphology were classified as scud-hb.Ancillary molecular studies confirmed the loss of smarcb1, supporting the diagnosis of mrt in all cases, proving morphology an unreliable criterion.It is critical to eliminate the term ini1-negative hepatoblastoma from the current classification scheme, and classify ini1-negative tumors as mrt, particularly since high-risk hb-chemotherapy regimens are not effective for treating mrt.

Journal: Cancers (2019)
Publication types: Journal Article
Atomic partial charge predictions for furanoses by random forest regression with atom type symmetry function.

Furanoses that are components for many important biomolecules have complicated conformational spaces due to the flexible ring andexo-cyclic moieties.Machine learning algorithms, which require descriptors as structural inputs, can be used to efficiently compute conformational adaptive (ca) charges to capture the electrostatic potential variations caused by the conformational changes in the molecular mechanics (mm) calculations.In the present study, we introduced atom type symmetry function (atsf) developed based on atom centered symmetry function (acsf) for describing conformations for furanoses, in which atoms were categorized by atom types defined by their properties or connectivity in classic molecular mechanics (mm) force field parameters to generate a suitable coordinate size.Random forest regression (rfr) models with atsf showed improvements for predicting ca charges and dipole moments for furanoses compared to those with acsf and atom name symmetry functions where atoms were categorized by their unique atom names.The ca charges predicted by rfr models with atsf showed more comparable reproductions of the carbohydrate-water and carbohydrate-protein interactions computed with resp charges individually derived from qm calculations than the ensemble-averaged atomic charge sets commonly employed in molecular mechanics force fields, suggesting that the predicted ca charges were capable of including electrostatic variations in their dynamic charge values.Improvements by atsf showed that categorizing atoms by atom types introduced chemical structural perceptions to descriptors and produced a suitable coordinate size in atsf to capture key structural features for furanoses.This categorizing scheme also allows atsf to be readily adopted by other biomolecules thanks to the broad implementations of mm force fields.

Journal: RSC advances (2020)
Publication types: Journal Article
Comparative effectiveness of interventional therapeutic modalities for unresectable hepatocellular carcinoma: A systematic review and network meta-analysis.

It is unclear whether hepatic artery infusion chemotherapy (haic) or transcatheter arterial chemoembolization (tace) is more efficient in the combination therapy of hepatocellular carcinoma (hcc).Head-to-head comparisons among haic-related therapies are lacking.For this network meta-analysis, pub med, embase and cochrane library databases were searched up to april 1, 2022.Randomized controlled trials (rcts) were eligible if they evaluated the use or prolongation of tace or haic in patients with advanced hcc and reported or collected survival data.A network meta-analysis was performed to synthesize data and make direct and indirect comparisons between treatments.Hazard ratios (hrs) with 95% confidence intervals (cis) were calculated to explore the efficacy of various treatment options on overall survival (os), odds ratios (ors) with 95% ci were used for overall response rate (orr), whereas risk ratios (rrs) with 95% ci were used for serious adverse events (saes).The analysis of 7 trials including a total of 1,073 patients found that sorafenib with haic-oxaliplatin improved survival (hr=0.33, 95% ci: 0.25-0.44); the orr was also improved in patients treated with sorafenib plus haic-oxaliplatin and sorafenib plus pf-haic (or=22.18, 95% ci: 10.69-52.56; and or=2.72, 95% ci: 1.43-5.36, respectively).The incidence of liver injury was elevated in patients treated with sorafenib plus tace (or=5.93, 95% ci: 2.70-15.41).However, no differences in the incidences of other saes were identified among the treatment groups.The present meta-analysis provides preliminary evidence for the comparative safety and efficacy of haic and tace combined with sorafenib, and indicates the dominance of haic-oxaliplatin in hcc interventional therapy.However, high-quality rcts are required to further confirm the efficacy of haic-oxaliplatin.The present study has been registered with prospero (registration no.Crd42021288497).

Journal: Oncology letters (2022)
Publication types: Journal Article
Deep-Learning-Based Hemoglobin Concentration Prediction and Anemia Screening Using Ultra-Wide Field Fundus Images.

Anemia is the most common hematological disorder.The purpose of this study was to establish and validate a deep-learning model to predict hgb concentrations and screen anemia using ultra-wide-field (uwf) fundus images.methods:the study was conducted at peking union medical college hospital.Optos color images taken between january 2017 and june 2021 were screened for building the dataset.Asmodel_uwf using uwf images was developed.Mean absolute error (mae) and area under the receiver operating characteristics curve (auc) were used to evaluate its performance.Saliency maps were generated to make the visual explanation of the model.results:asmodel_uwf acquired the mae of the prediction task of 0.83 g/dl (95%ci: 0.81-0.85 g/dl) and the auc of the screening task of 0.93 (95%ci: 0.92-0.95).Compared with other screening approaches, it achieved the best performance of auc and sensitivity when the test dataset size was larger than 1000.The model tended to focus on the area around the optic disc, retinal vessels, and some regions located at the peripheral area of the retina, which were undetected by non-uwf imaging.conclusion:the deep-learning model asmodel_uwf could both predict hgb concentration and screen anemia in a non-invasive and accurate way with high efficiency.

Journal: Frontiers in cell and developmental biology (2022)
Publication types: Journal Article
Effects of Deep Eutectic Solvents on cellulosic fibres and paper properties: Green "chemical" refining.

This work aims to study the effects of deep eutectic solvents (des) on cellulosic fibre structure.A focus was made on the induced fibrillation phenomena which could facilitate the further production of microfibrillated cellulose.Three des of different p h (acid, neutral and alkaline), namely betaine hydrochloride-urea, choline chloride-urea and choline chloride-monoethanolamine, were tested.Eucalyptus and cotton pulps were used to investigate the effects of des on both hemicelluloses and cellulose.Interestingly, cellulose was esterified during acidic des treatment.Moreover, an internal and external fibrillation occurred with des treatment without a great extent of modification in terms of chemical composition, crystallinity and degree of polymerisation.Compared to enzymatic hydrolysis (used as a conventional pre-treatment for cellulose microfibrillation), des have significantly enhanced the mechanical properties of resulting papers.To conclude, des treatment can be considered as a soft and green "chemical" refining that could be applied as a pre-treatment for cellulose microfibrillation.

Journal: Carbohydrate polymers (2022)
Publication types: Journal Article