syedzayyan/paper_mill_benchmark huggingface dataset:
Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders.

The development of new sequencing technologies in the post-genomic era has accelerated the identification of causative mutations of several single gene disorders.Advances in cell and animal models provide insights into the underlining pathogenesis, which facilitates the development and maturation of new treatment strategies.The progress in biochemistry and molecular biology has established a new class of therapeutics-the short rnas and expressible long rnas.The sequences of therapeutic rnas can be optimized to enhance their stability and translatability with reduced immunogenicity.The chemically-modified rnas can also increase their stability during intracellular trafficking.In addition, the development of safe and high efficiency carriers that preserves the integrity of therapeutic rna molecules also accelerates the transition of rna therapeutics into the clinic.For example, for diseases that are caused by genetic defects in a specific protein, an effective approach termed "protein replacement therapy" can provide treatment through the delivery of modified translatable m rnas.Short interference rnas can also be used to treat diseases caused by gain of function mutations or restore the splicing aberration defects.Here we review the applications of newly developed rna-based therapeutics and its delivery and discuss the clinical evidence supporting the potential of rna-based therapy in single-gene neurological disorders.

Journal: Biomedicines (2022)
Publication types: Journal Article;Review
Safety of the endovascular aneurysm repair procedure: real-world evidence using interrupted-time series analysis.

S in taiwan, endovascular aneurysm repair for treating abdominal aortic aneurysms (aaa) was introduced in 2004 and became reimbursable in february 2010.We evaluated the real-world practice and safety of endovascular aneurysm repair in taiwan.Methods patients who underwent repair operations for aaa (open or endovascular) from 2000 to 2016 were enrolled (n = 11485).Outcome statistics (during the index hospitalization: length of stay, rate of ischaemic bowel disease and 30-day mortality; after discharge: 30-day readmission rate, 2-year mortality, 2-year reintervention rate and 2-year paraplegia rate) were calculated for each half-year cohort.Propensity score-based stabilized weights were used to balance covariates among each half-year cohort.Interrupted time-series analysis was then performed.Results the elective and emergency ratio of aaa repair was 50:50 from 2000 to 2004 and became 60:40 from 2010 to 2016.The half-year rate of endovascular aneurysm repair was 0% in 2000 to 2004/06, 83.16% in 2010 and 98.1% in 2016.Interrupted time series analysis revealed that after endovascular aneurysm repair became reimbursable, both elective and emergency groups had a reduction in length of stay (-4.2 days, p < 0.0001; -1.5 days, p = 0.0928) and 30-day mortality (-5.22%, p = 0.0702; -7.76%, p = 0.0086) but a significant increase in the reintervention rate (5.05%, p = 0.0031; 4.36%, p = 0.0097).Conclusions endovascular aneurysm repair was predominantly used in treating aaas after it was reimbursed in taiwan.Endovascular aneurysm repair is efficacious regarding short-term outcomes but increased the 2-year reintervention rate in both groups.

Journal: European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery (2022)
Publication types: Journal Article
Role of JNK in the Regulation of Xenobiotic Metabolizing Function of Hepatocytes.

We studied the role of jnk in the regulation of the metabolism of xenobiotic venlafaxine by liver cells under in vitro conditions.The inhibitory role of this protein kinase in the biotransformation of this psychotropic agent by hepatocytes was demonstrated.Jnk inhibitor added to the liver homogenate containing antidepressant enhanced and accelerated the formation of the only pharmacologically active venlafaxine metabolite o-desmethylvenlafaxine in the cell suspension.The results show the promise of studying modifiers of activity of intracellular signaling molecules (in particular, mitogen-activated protein kinases) to develop a fundamentally new approach to control the transformation of xenobiotics and to create a new class of pharmaceutical, target regulators of drugs metabolism.

Journal: Bulletin of experimental biology and medicine (2021)
Publication types: Journal Article
Single Day Outdoor Photometric Stereo.

Photometric stereo (ps) under outdoor illumination remains a challenging, ill-posed problem due to insufficient variability in illumination.Months-long capture sessions are typically used in this setup, with little success on shorter, single-day time intervals.In this paper, we investigate the solution of outdoor ps over a single day, under different weather conditions.First, we investigate the relationship between weather and surface reconstructability in order to understand when natural lighting allows existing ps algorithms to work.Our analysis reveals that partially cloudy days improve the conditioning of the outdoor ps problem while sunny days do not allow the unambiguous recovery of surface normals from photometric cues alone.We demonstrate that calibrated ps algorithms can thus be employed to reconstruct lambertian surfaces accurately under partially cloudy days.Second, we solve the ambiguity arising in clear days by combining photometric cues with prior knowledge on material properties, local surface geometry and the natural variations in outdoor lighting through a cnn-based, weakly-calibrated ps technique.Given a sequence of outdoor images captured during a single sunny day, our method robustly estimates the scene surface normals with unprecedented quality for the considered scenario.Our approach does not require precise geolocation and significantly outperforms several state-of-the-art methods on images with real lighting, showing that our cnn can combine efficiently learned priors and photometric cues available during a single sunny day.

Journal: IEEE transactions on pattern analysis and machine intelligence (2021)
Publication types: Journal Article
Fluorescent "Turn-Off" Detection of Fluoride and Cyanide Ions Using Zwitterionic Spirocyclic Meisenheimer Compounds.

Stable zwitterionic spirocyclic meisenheimer compounds were synthesized using a one-step reaction between picric acid and diisopropyl (zw1) or dicyclohexyl (zw3) carbodiimide.A solution of these compounds displays intense orange fluorescence upon uv or visible light excitation, which can be quenched or "turned-off" by adding a mole equivalent amount of f-or cn-ions in acetonitrile.Fluorescence is not quenched in the presence of other ions such as cl-, br-, i-, no2-, no3-, or h2po4-.These compounds can therefore be utilized as practical colorimetric and fluorescent probes for monitoring the presence of f-or cn-anions.

Journal: Molecules (Basel, Switzerland) (2017)
Publication types: Journal Article
Neurosurgery in a patient with severe hemophilia B: an experience using eftrenonacog alfa as perioperative management.

Extended half-life fix (ehl-fix) concentrates have been developed with the purpose of reducing the frequency of infusions in patients with severe or moderate hemophilia b.We describe the case of a 63-year-old patient with severe hemophilia b (s hb) treated with fix-fc fusion protein (r fixfc) who underwent neurosurgery.

Journal: Clinical case reports (2022)
Publication types: Case Reports;Journal Article
Ageing impacts phenotypic flexibility in an air-acclimated amphibious fish.

The ability to tolerate environmental change may decline as fishes age.We tested the hypothesis that ageing influences the scope for phenotypic flexibility in the mangrove rivulus (kryptolebias marmoratus), an amphibious fish that transitions between two vastly different environments, water and land.We found that older fish (4-6 years old) exhibited marked signs of ageing; older fish were reproductively senescent, had reduced fin regenerative capacity and body condition, and exhibited atrophy of both oxidative and glycolytic muscle fibers relative to younger adult fish (1-2 years old).However, age did not affect routine o2consumption.We then acclimated adult fish (1-6 years) to water (control) or air for 10 days to assess the scope for phenotypic flexibility in response to terrestrial exposure.In support of our hypothesis, we found that older air-acclimated fish had a diminished scope for gill remodeling relative to younger fish.We also found that older fish exhibited poorer terrestrial locomotor performance relative to younger adult fish, particularly when acclimated to air.Our results indicate that ageing diminishes skeletal muscle integrity and locomotor performance of amphibious fishes, and may, therefore, impair terrestrial foraging ability, predator avoidance, or dispersal across the terrestrial environment.Remarkably, older fish voluntarily left water to a similar degree as younger fish despite the age-related deterioration of traits important for terrestrial life.

Journal: Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Antibacterial, Anticandidal, and Antibiofilm Potential of Fenchone: In Vitro, Molecular Docking and In Silico/ADMET Study.

The aim of the present study is to investigate the effective antimicrobial and antibiofilm properties of fenchone, a biologically active bicyclic monoterpene, against infections caused by bacteria and candida spp.The interactions between fenchone and three distinct proteins from escherichia coli (β-ketoacyl acyl carrier protein synthase), candida albicans (1, 3-β−d-glucan synthase), and pseudomonas aeruginosa (anthranilate-co a ligase) were predicted using molecular docking and in silico/admet methods.Further, to validate the in-silico prediction, the antibacterial and antifungal potential of fenchone was evaluated against e.Coli, p.Aeruginosa, and c.Albicans by determining minimum inhibitory concentration (mic), minimum bacterial concentration (mbc), and minimum fungicidal concentration (mfc).The lowest mic/mbc values of fenchone against e.Coli and p.Aeruginosa obtained was 8.3 ± 3.6/25 ± 0.0 and 266.6 ± 115.4/533.3 ± 230.9 mg/m l, respectively, whereas the mic/mfc value for c.Albicans was found to be 41.6 ± 14.4/83.3 ± 28.8 mg/m l.It was observed that fenchone has a significant effect on antimicrobial activity (p < 0.05).Our findings demonstrated that fenchone at 1 mg/m l significantly reduced the production of biofilm (p < 0.001) in e.Coli, p.Aeruginosa, and c.Albicans by 70.03, 64.72, and 61.71%, respectively, in a dose-dependent manner when compared to control.Based on these results, it has been suggested that the essential oil from plants can be a great source of pharmaceutical ingredients for developing new antimicrobial drugs.

Journal: Plants (Basel, Switzerland) (2022)
Publication types: Journal Article
Green and stable lignin-based nanofillers reinforced poly(l-lactide) with supertough and strong performance.

Lignin nanoparticles (lnps), as a new type of green nanomaterial, initiate many promising applications in polymer composites.However, their heterogeneity, dissolution in organic solvents, and poor compatibility in the polymer matrix greatly limited the applications of lnps fillers.Herein, we proposed an antisolvent precipitation of the fractionations by combining a hydrothermal treatment-assisted synthesis to fabricate self-crosslinked lnps (sc lnps), which have good stability in the organic solvent and controllable sizes.After surface grafting modification with d-lactide, sc lnps-graft-poly(d-lactide) (sc lnps-g-pdla) exhibited excellent dispersion and compatibility in plla matrix.Using the rational design and addition of sc lnps-g-pdla fillers, the strength and toughness of the generated plla composite reached 31.6 mpa and 396 % (the highest value among the plla materials), respectively.Furthermore, the mechanical performance can also be well-tuned by the sizes and amounts of lnps fillers.This strategy involving only green and recyclable materials provides an effective route to producing sustainable polymeric plastics with integrated strength and super-toughness.

Journal: International journal of biological macromolecules (2022)
Publication types: Journal Article
Explainable machine learning approach to predict extubation in critically ill ventilated patients: a retrospective study in central Taiwan.

Weaning from mechanical ventilation (mv) is an essential issue in critically ill patients, and we used an explainable machine learning (ml) approach to establish an extubation prediction model.Methods we enrolled patients who were admitted to intensive care units during 2015-2019 at taichung veterans general hospital, a referral hospital in central taiwan.We used five ml models, including extreme gradient boosting (xgboost), categorical boosting (cat boost), light gradient boosting machine (light gbm), random forest (rf) and logistic regression (lr), to establish the extubation prediction model, and the feature window as well as prediction window was 48 h and 24 h, respectively.We further employed feature importance, shapley additive explanations (shap) plot, partial dependence plot (pdp) and local interpretable model-agnostic explanations (lime) for interpretation of the model at the domain, feature, and individual levels.Results we enrolled 5,940 patients and found the accuracy was comparable among xgboost, light gbm, cat boost and rf, with the area under the receiver operating characteristic curve using xgboost to predict extubation was 0.921.The calibration and decision curve analysis showed well applicability of models.We also used the shap summary plot and pdp plot to demonstrate discriminative points of six key features in predicting extubation.Moreover, we employed lime and shap force plots to show predicted probabilities of extubation and the rationale of the prediction at the individual level.Conclusions we developed an extubation prediction model with high accuracy and visualised explanations aligned with clinical workflow, and the model may serve as an autonomous screen tool for timely weaning.

Journal: BMC anesthesiology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Visible-Light-Driven Photocatalytic CO2Reduction to CO/CH4Using a Metal-Organic "Soft" Coordination Polymer Gel.

The self-assembly of a well-defined and astutely designed, low-molecular weight gelator (lmwg) based linker with a suitable metal ion is a promising method for preparing photocatalytically active coordination polymer gels.Here, we report the design, synthesis, and gelation behaviour of a tetrapodal lmwg based on a porphyrin core connected to four terpyridine units (tpy-por) through amide linkages.The self-assembly of tpy-por lmwg with ru iiions results in a ru-tpy-por coordination polymer gel (cpg), with a nanoscroll morphology.Ru-tpy-por cpg exhibits efficient co2photoreduction to co (3.5 mmol g-1h-1) with >99 % selectivity in the presence of triethylamine (tea) as a sacrificial electron donor.Interestingly, in the presence of 1-benzyl-1,4-dihydronicotinamide (bnah) with tea as the sacrificial electron donor, the 8e-/8h+photoreduction of co2to ch4is realized with >95 % selectivity (6.7 mmol g-1h-1).In cpg, porphyrin acts as a photosensitizer and covalently attached [ru(tpy)2]2+acts as a catalytic center as demonstrated by femtosecond transient absorption (ta) spectroscopy.Further, combining information from the in situ drift spectroscopy and dft calculation, a possible reaction mechanism for co2reduction to co and ch4was outlined.

Journal: Angewandte Chemie (International ed. in English) (2022)
Publication types: Journal Article
Bioaccessibility, gut microbial metabolism and intestinal transport of phenolics from 100% Concord grape juice and whole grapes are similar in a simulated digestion and fecal fermentation model.

Phenolic rich 100% grape juice has been associated with many health benefits, but its place in dietary guidance is controversial relative to whole fruit.Direct comparisons of phenolic profiles and bioavailability between these food forms are needed.Phenolic bioaccessibility and metabolism from concord (cg) and niagara (ng) grapes and corresponding 100% juices were investigated using anin vitrodigestion coupled with anaerobic gut fermentation model.Intestinal transport of resulting bioaccessible phenolics and microbial metabolites was estimated using a caco-2 cell model.Total bioaccessible phenolics from both upper and lower digestion were similar (p> 0.05) between ng (400.9 ± 26.3 μmol per 100 g) and ngj (349.5 ± 8.3 μmol per 100 g) and significantly different (p 0.05) between whole grapes (89.4 ± 5.3 μmol per 100 g for cg, and 71.8 ± 2.4 μmol per 100 g for ng) and 100% juices (88.0 ± 5.6 μmol per 100 g for cgj, and 85.3 ± 9.4 μmol per 100 g for ngj).Differences were observed between the location of phenolic metabolism, bioaccessibility and subsequent cellular transport of individual phenolics between grapes and juice matrices.Specifically, greater amounts of phenolics were transported from grape juices than whole grapes from the upper tract.However, cumulative bioaccessibility and transport from upper and lower gi digestion/fermentation together indicates that the absorbable phenolics from 100% grape juice is similar to that of whole grapes, suggesting that phenolic-mediated health benefits from consumption of whole fruit and juice may be similar.

Journal: Food & function (2022)
Publication types: Journal Article
SARS-CoV-2 is not found in the sweat of COVID-19 positive patients.

As the sars-co v-2 virus made a pandemic all over the world, its transmission routes became significant.Transmission from human to human is known, but other possible routes are not determined well.Aims this study aimed to reveal the presence of sars-co v-2 virus in sweat.Methods this prospective study was conducted in a tertiary care education and training hospital.Fifty patients were included in this study.Skin disinfection was done with an alcohol-based solution.Swabs for rt-pcr (real-time reverse transcriptase polymerase chain reaction) were taken from forehead and axilla skin after sweating patients for 30 min.After collection of sweat, swabs were placed into 2 ml of sterile viral transport medium, then transported quickly to the microbiology laboratory.Results no sars-co v-2 virus was detected in rt-pcr of forehead and axilla swabs.Conclusion this study showed that there is no transmission of sars-co v-2 virus via sweat.However, general precautions must be taken while doing interventional procedures.

Journal: Irish journal of medical science (2022)
Publication types: Journal Article
Human Mitochondrial RNA Processing and Modifications: Overview.

Mitochondria, often referred to as the powerhouses of cells, are vital organelles that are present in almost all eukaryotic organisms, including humans.They are the key energy suppliers as the site of adenosine triphosphate production, and are involved in apoptosis, calcium homeostasis, and regulation of the innate immune response.Abnormalities occurring in mitochondria, such as mitochondrial dna (mt dna) mutations and disturbances at any stage of mitochondrial rna (mt rna) processing and translation, usually lead to severe mitochondrial diseases.A fundamental line of investigation is to understand the processes that occur in these organelles and their physiological consequences.Despite substantial progress that has been made in the field of mt rna processing and its regulation, many unknowns and controversies remain.The present review discusses the current state of knowledge of rna processing in human mitochondria and sheds some light on the unresolved issues.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article;Review
Educational needs assessment identifying opportunities to improve sepsis care.

Introduction in 2015, the centers for medicare and medicaid services developed a national quality bundle for the management of patients with severe sepsis and septic shock (sep-1).Despite performance improvement measures, compliance remains low.This needs assessment is the first stage of a quality improvement initiative to improve sep-1 compliance.Using a conceptual outcomes framework, this needs assessment analyses sep-1 compliance data, knowledge, and competence to identify gaps in care and educational opportunities.Methods the needs assessment began with a review of national and statewide sep-1 compliance data to identify a need for improvement.The needs assessment proceeded with a retrospective chart review to evaluate process measures and identify which providers would most likely benefit from educational interventions.A focus group provided perspective on the chart review findings.Results during the period of 1 april 2017-31 march 2018, national sep-1 compliance was 51% and compliance at the studied institution was 19%.The chart review included 51 patients (66.7% severe sepsis, 33.3% septic shock).Frequently missed sep-1 measures included administration of intravenous fluids (0% severe sepsis, 58.8% septic shock), repeat lactate levels (52.6% severe sepsis, 60% septic shock), documentation of volume and tissue perfusion assessment (58.8%), vasopressor administration (73.3%) and administration of broad-spectrum antibiotics (76.5%, severe sepsis).Focus group perceptions identified themes related to gaps in declarative and dispositional knowledge.Conclusions this educational needs assessment highlights gaps in sep-1 clinician performance, competence and knowledge.A multifaceted education programme is the next step for this performance improvement project.Education should include a series of meetings, activities, and workshops that include declarative knowledge, procedural knowledge and dispositional knowledge.Simulation activities can provide an opportunity for providers to demonstrate competence.Point-of-care prompts and performance measurement and feedback of patient care data can support clinician performance.This needs assessment underscores the need for a multifaceted approach to clinician education and performance to improve sep-1 compliance.

Journal: BMJ open quality (2022)
Publication types: Review;Journal Article
Decreased DNA Repair Ability: A Mechanism for Low Early Embryonic Development Potential of Oocytes From Overweight Patients After Fertilization in IVF Cycles.

Whether female bmi impacts the dna repair ability in the oocytes after fertilization has not been investigated.The aim of this study is to assess the early embryo quality and reproductive outcomes of oocytes from overweight women when fertilized with sperm with varying degrees of dna fragmentation.Methods a total number of 1,612 patients undergoing fresh autologousin vitrofertilization (ivf) cycles was included.These patients were divided into two groups according to maternal body mass index (bmi): normal weight group (18.5-24.9 kg/m2; n=1187; 73.64%) and overweight group (≥25 kg/m2; n=425; 26.36%).Each group was then subdivided into two groups by sperm dna fragmentation index (dfi): low fragmentation group (<20% dfi, lf) and high fragmentation group (≥20% dfi, hf).Laboratory and clinical outcomes were compared between subgroups.Results for the normal-weight group, there was no statistical significance in embryo quality and reproductive outcomes between the lf and hf groups.But in the overweight group, significantly lower fertilization rate (lf: 64%; hf: 59%; p=0.011), blastocyst development rate (lf: 57%; hf: 44%; p=0.001), as well as high-quality blastocyst rate (lf: 32%; hf: 22%; p=0.034) were found in the hf group, despite the similar pregnancy rates (lf: 56%; hf: 60%; p=0.630).Conclusions decreased dna repair activity in oocytes may be a possible mechanism for the low early development potential of embryos from overweight patients inin vitrofertilization cycles.

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