syedzayyan/paper_mill_benchmark huggingface dataset:
A highly sensitive fluorescent sensor for ammonia detection based on aggregation-induced emission luminogen-doped liquid crystals.

As a toxic substance, ammonia can cause serious irritation to the human respiratory system and lungs.Although many detection techniques have been reported, most of them have drawbacks, such as expensive devices and complex and time-consuming fabrication processes.Thus, it is important to develop a simple method for ammonia detection.In this paper, we demonstrate a highly sensitive fluorescent sensor for ammonia detection based on aggregation-induced emission luminogen-doped liquid crystals without the use of polarizers.The homeotropic orientation of the liquid crystals on a modified substrate can be disturbed by ammonia, resulting in the fluorescence intensity change of an aggregation-induced emission luminogen.This aggregation-induced emission luminogen-doped liquid crystal-based fluorescent sensor for ammonia detection exhibited a low detection limit of 5.4 ppm, which is 3 times lower than previously reported liquid crystal-based optical sensors.The detection range is also broad from 0 ppm to 1600 ppm.Meanwhile, this sensor can be applied to detect aqueous ammonia with a low limit of detection of 1.8 ppm.The proposed fluorescent sensor for ammonia detection based on an aggregation-induced emission luminogen-doped liquid crystal is highly sensitive, highly selective, simple, and low cost with wide potential applications in chemical and biological fields.This strategy of designing a liquid crystal fluorescent sensor provides an inspiring stage for other toxic chemical substrates by changing specific decorated molecules.

Journal: Soft matter (2022)
Publication types: Journal Article
Comprehensive review of the recent advances in devices for endovascular treatment of complex brain aneurysms.

The international subarachnoid aneurysm trial (isat) showed superiority for endovascular treatment of ruptured aneurysms and technology has since moved on rapidly.Many approaches and technology now exist for the endovascular management of ruptured and unruptured intracranial aneurysms, which reflects their varied nature - there is no one-size-fits-all technique.We aim to provide an overview of the various classes of device and the major developments over the past decade.Coiling is the oldest of the technology and continues to demonstrate high levels of occlusion and acceptable risks, making it the default treatment choice, particularly in the acutely ruptured aneurysm setting.Advances on coiling include the use of adjuncts such as balloons, stents and fully retrievable temporary neck-bridging devices, which have facilitated the treatment of more complex aneurysms.Flow divertors have also revolutionised complex aneurysm treatment with small added risk in acute aneurysm treatment and seek to remodel the aneurysm-vessel interface without accessing the aneurysm sac.The latest development and most promising avenue appears to be intrasaccular flow disrupting devices like web, contour and neqstent that provide excellent opportunities to treat wide neck complex aneurysm with minimal mortality and morbidity and good occlusion rates and may in future replace a significant number of stent-assisted coiling too.

Journal: The British journal of radiology (2022)
Publication types: Journal Article;Review
Remote spectral detection of biodiversity effects on forest biomass.

Quantifying how biodiversity affects ecosystem functions through time over large spatial extents is needed for meeting global biodiversity goals yet is infeasible with field-based approaches alone.Imaging spectroscopy is a tool with potential to help address this challenge.Here, we demonstrate a spectral approach to assess biodiversity effects in young forests that provides insight into its underlying drivers.Using airborne imaging of a tree-diversity experiment, spectral differences among stands enabled us to quantify net biodiversity effects on stem biomass and canopy nitrogen.By subsequently partitioning these effects, we reveal how distinct processes contribute to diversity-induced differences in stand-level spectra, chemistry and biomass.Across stands, biomass overyielding was best explained by species with greater leaf nitrogen dominating upper canopies in mixtures, rather than intraspecific shifts in canopy structure or chemistry.Remote imaging spectroscopy may help to detect the form and drivers of biodiversity-ecosystem function relationships across space and time, advancing the capacity to monitor and manage earth's ecosystems.

Journal: Nature ecology & evolution (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Potential circRNA-Disease Association Prediction Using DeepWalk and Nonnegative Matrix Factorization.

Circular rnas (circ rnas) are a category of noncoding rnas that exist in great numbers in eukaryotes.They have recently been discovered to be crucial in the growth of tumors.Therefore, it is important to explore the association of circ rnas with disease.This paper proposes a new method based on deep walk and nonnegative matrix factorization (dwnmf) to predict circ rna-disease association.Based on the known circ rna-disease association, we calculate the topological similarity of circ rna and disease via the deep walk-based method to learn the node features on the association network.Next, the functional similarity of the circ rnas and the semantic similarity of the diseases are fused with their respective topological similarities at different scales.Then, we use the improved weighted k-nearest neighbor (iwknn) method to preprocess the circ rna-disease association network and correct nonnegative associations by setting different parameters k1and k2in the circ rna and disease matrices.Finally, the l2,1-norm, dual-graph regularization term and frobenius norm regularization term are introduced into the nonnegative matrix factorization model to predict the circ rna-disease correlation.We perform cross-validation on circ r2disease, circ rnadisease, and mndr.The numerical results show that dwnmf is an efficient tool for forecasting potential circ rna-disease relationships, outperforming other state-of-the-art approaches in terms of predictive performance.

Journal: IEEE/ACM transactions on computational biology and bioinformatics (2023)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Visual Thinking Strategies as a Tool for Reducing Burnout and Improving Skills in Healthcare Workers: Results of a Randomized Controlled Study.

The purpose of this study was to measure the effect that a learning method using art, such as visual thinking strategies, can have on nursing students and residents in hygiene and preventive medicine; we also aimed to improve skills of observation, communication, empathy and collaboration with the patient and other team members, and evaluate the impact on quality of life, burnout and positivity.methods: the experimentation was based on administering a form (written assessment) before and after the intervention, to measure the impact of the method on improving some useful skills for the nursing and medical professions by inserting one image of an artistic type and the other of a clinical type, and asking participants to answer basic questions on the vts method.Students participated in groups of eight in 90-min sessions for four meetings in the classroom and one at the museum, on a weekly basis.results: the experimental study concerned a randomized controlled sample involving undergraduate nursing students who voluntarily participated in the survey.84 students took part in the study, including 50 undergraduate nursing students (mean age 22.5, sd 2.7; 14 males and 34 females) and 34 residents in hygiene and preventive medicine (mean age 28.7, sd 2.6; 8 males and 26 females).For the artistic image, the median of the total score for all skills was -1.5 for the control group and 3 for the intervention group (p= 0.002), registering an increase for the delta identified items, which was -1.5 for the control group and 1 for the intervention group (p= 0.007).For the clinical image, the median of the total score for all skills was 0 for the control group and 2 for the intervention group (p= 0.025), recording an increase for delta observation skills, found to be 0 for the control group and 1 for the intervention group (p= 0.007).conclusions: most students who participated in the intervention reported considerable improvements in the skills the method promises to improve, and a reduction in personal and work burnout scores, suggesting that the use of the vts method in health professions curricula is viable.

Journal: Journal of clinical medicine (2022)
Publication types: Journal Article
Combining GRACE and satellite altimetry data to detect change in sediment load to the Bohai Sea.

The gravity recovery and climate experiment (grace) satellites provide a powerful tool for monitoring sediment mass change.However, signal leakage from nearby groundwater storage depletion in the north china plain limits the potential capacity of grace to estimate sediment input from the yellow river flows into the bohai sea.In the present work, we developed an improved approach based on forward modeling to reduce signal leakage from grace data and combined it with satellite altimetry to recover sediment load changes from 2003 to 2013 to the bohai sea.The total sediment input averaged 1.7 ± 0.8 gt/yr, which agrees well with the estimate based on in-situ sediment data measured from the sediment cores (1.1 gt/yr).Our method is also capable to describe sediment seasonal variations, with higher inputs in winter and spring, which confirm the output simulated by the sediment transportation model.We make presently tentative connections of seasonal variations to sediment resuspension driven by climatic monsoons contributed rough seas: although sediment load in rivers peaks in summer, low water discharge of the yellow river leads to most of the sediment being deposited in a narrow area near the river mouth and not transported into the bohai sea; in winter and spring, huge waves provide favorable conditions for resuspension resulting in large amounts of sediment near the estuary being transported to the ocean along with northward waves.Moreover, our results indicate coastal erosion is also a nonnegligible resource of the sediment in the bohai sea.Comparing to the traditional approach, our study provides a new technological way to derive sediment in the bohai sea, which is capable of providing continuous measurements with improved timeliness at a lower cost.

Journal: The Science of the total environment (2022)
Publication types: Journal Article
Immune Checkpoint Proteins, Metabolism and Adhesion Molecules: Overlooked Determinants of CAR T-Cell Migration?

Adoptive transfer of t cells genetically engineered to express chimeric antigen receptors (car) has demonstrated striking efficacy for the treatment of several hematological malignancies, including b-cell lymphoma, leukemia, and multiple myeloma.However, many patients still do not respond to this therapy or eventually relapse after an initial remission.In most solid tumors for which car t-cell therapy has been tested, efficacy has been very limited.In this context, it is of paramount importance to understand the mechanisms of tumor resistance to car t cells.Possible factors contributing to such resistance have been identified, including inherent car t-cell dysfunction, the presence of an immunosuppressive tumor microenvironment, and tumor-intrinsic factors.To control tumor growth, car t cells have to migrate actively enabling a productive conjugate with their targets.To date, many cells and factors contained within the tumor microenvironment have been reported to negatively control the migration of t cells and their ability to reach cancer cells.Recent evidence suggests that additional determinants, such as immune checkpoint proteins, cellular metabolism, and adhesion molecules, may modulate the motility of car t cells in tumors.Here, we review the potential impact of these determinants on car t-cell motility, and we discuss possible strategies to restore intratumoral t-cell migration with a special emphasis on approaches targeting these determinants.

Journal: Cells (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism.

The trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including t rubrum sensu stricto and t violaceum, as well as other less well-established or debatable taxa like t soudanense, t kuryangei and t megninii.Our previous study provided limited evidence in favour of the existence of two genetic lineages in the russian t rubrum sensu stricto population.Objectives we aimed to study the genetic structure of the russian population of t rubrum and to identify factors shaping this structure.Methods we analysed the polymorphism of 12 simple sequence repeat (ssr or microsatellite) markers and single nucleotide polymorphism in the terg_02941 protein-coding gene in 70 t rubrum isolates and performed a phylogenomic reconstruction.Results all three types of data provided conclusive evidence that the population consists of two genetic lineages.Clustering, performed by means of microsatellite length polymorphism analysis, was strongly dependent on the number of nucleotide repeats in the 5'-area of the fructose-1,6-bisphosphate aldolase gene.Analysis of molecular variance (amova) on the basis of ssr typing data indicated that 22%-48% of the variability was among groups within t rubrum.There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression or urease activity.Conclusion our results suggest that the russian population of t rubrum consists of two cosmopolitan genetic lineages.

Journal: Mycoses (2020)
Publication types: Journal Article
Improved Trimethylangelicin Analogs for Cystic Fibrosis: Design, Synthesis and Preliminary Screening.

A small library of new angelicin derivatives was designed and synthesized with the aim of bypassing the side effects of trimethylangelicin (tma), a promising agent for the treatment of cystic fibrosis.To prevent photoreactions with dna, hindered substituents were inserted at the 4 and/or 6 positions.Unlike the parent tma, none of the new derivatives exhibited significant cytotoxicity or mutagenic effects.Among the synthesized compounds, the 4-phenylderivative12and the 6-phenylderivative25exerted a promising f508del cftr rescue ability.On these compounds, preliminary in vivo pharmacokinetic (pk) studies were carried out, evidencing a favorable pk profileper seor after incorporation into lipid formulations.Therefore, the selected compounds are good candidates for future extensive investigation to evaluate and develop novel cftr correctors based on the angelicin structure.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Self-stigma formation process among younger and older Israeli Arabs diagnosed with depression.

S self-stigma is common among persons with depression.Still, studies that examined the process of self-stigma concentrated mostly on younger adults (ages 18-65) with mental illness in general, with a limited number of studies examining older adults with depression.This study was aimed to examine and compare the self-stigma formation process and its relation to self-esteem among younger (ages 18-64) and older israeli arabs (age 65+) diagnosed with depression.The study was based on a self-stigma model which defines the self-stigma formation process as composed of three stages: stereotypes awareness, stereotype agreement, and self-concurrence.Method a total of 160 younger and older israeli arabs with depression completed measures of self-stigma formation process, self-esteem, and socio-demographic and health characteristics.Results the self-stigma formation process was found as a multi-level and progressive model for both younger and older adults, despite that older adults reported significantly higher levels of self-stigma in all stages of the process.Low self-esteem was significantly associated with higher levels of stereotype agreement and self-concurrence in both age groups.Conclusion the self-stigma formation process provides an adequate model for understanding depression self-stigma in both younger and older adults.Appropriate intervention programs aiming to reduce self-stigma should be developed, focusing on reducing the three stages of self-stigma.

Journal: Aging & mental health (2021)
Publication types: Journal Article
Neoadjuvant camrelizumab and chemotherapy in patients with resectable stage IIIA squamous non-small-cell lung cancer: Clinical experience of three cases.

Neoadjuvant immunochemotherapy has attracted much attention as a treatment for locally advanced non-small-cell lung cancer.However, there is scarce evidence of the safety and efficacy of camrelizumab as neoadjuvant in lung cancer.Here, we present three patients who were diagnosed with iiia squamous non-small-cell lung cancer from september to december in 2020 and received two cycles of neoadjuvant camrelizumab plus nab-paclitaxel and nedaplatin, followed by surgical resection.All three patients had a reduction in the tumor size on ct image and not delayed planned surgery.We did not observe grade 3 or 4 adverse events.Two of the three patients achieved a major pathological response (mpr), including one complete tumor regression of the primary lung tumor.Multiplex fluorescent immunohistochemistry revealed that cd8+ t cells, fox p3+ regulatory t cells, and pd-l1 expression on immune cells in the surgical specimen were much higher than in the pretreatment biopsy sample in patients with mpr.This was not observed in the patient without mpr.Camrelizumab plus chemotherapy could potentially be a neoadjuvant regimen for resectable iiia squamous non-small-cell lung cancer, with a high mpr proportion, and did not compromise surgical procedure.Our findings should be validated in a future randomized clinical trial.

Journal: Frontiers in oncology (2022)
Publication types: Journal Article
Assessing physical activity and health-related quality of life in individuals with spinal cord injury: a national survey in Thailand.

This study sought to; (i) investigate the proportion of thai individuals with spinal cord injury (thai-sci) who met sci-specific physical activity (pa) guidelines, (ii) describe pa and health-related quality of life (hrqol) of thai-sci across different sociodemographic strata, and, (iii) measure the variance in hrqol associated with the intensity and volume of leisure-time physical activities (ltpa).Methods two surveys, measuring pa and hrqol, were used in this study.Descriptive analysis, parametric and non-parametric tests for comparing two or more groups were used to analyse the data.The relationship between pa levels and hrqol scores was investigated using spearman's correlation coefficients.All statistical significance level in this study were set to alpha < 0.05.Results from the 200 participants, 14.5% met aerobic, 20.5% met strength training and 13.5% met both aerobic and strength training sci-specific pa guidelines.Sedentary thai-sci accounted for 49% of the study sample.Thai-sci spent 132.0 ± 254.3 (mean ± sd) minutes per week on moderate-to-heavy intensity ltpa.Average physical and mental component summary (pcs and mcs scores) of thai-sci were 42.3 ± 7.6 and 49.3 ± 8.4 (mean ± sd), respectively.Increases in average ltpa of moderate-to-heavy intensities were weakly correlated with increases in pcs scores and its sub-domains (r= 0.1-0.3,n= 200, allp< 0.05).Conclusion the average time spent on moderate-to-heavy intensity adls and ltpa were below sci-specific pa guidelines and the who global recommendations for pa.The proportion of thai-sci who were sedentary was high, suggesting immediate action and implementation of strategies to promote pa for thai-sci.implications for rehabilitationthe proportion of thai people with spinal cord injury with a sedentary lifestyle was high.healthcare providers in thailand must engage to a greater degree in health-related physical activity promotion to effectively deliver physical activity and exercise knowledge to their clients with spinal cord injury.likely, structured programs of physical activity and exercise deployed by healthcare professionals with the appropriate knowledge and skills might reverse the current trend to sedentary lifestyle in this population.interventions to improve participation in physical activity and health-related quality of life should be tailored to the individual needs of thai individuals with a spinal cord injury and might be better delivered seperately.

Journal: Disability and rehabilitation (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
CRISPRi enables fast growth followed by stable aerobic pyruvate formation inEscherichia coliwithout auxotrophy.

Crispr interference (crispri) was applied to enable the aerobic production of pyruvate in escherichia coli mg1655 under glucose excess conditions by targeting the promoter regions oface eorpdh r.Knockdown strains were cultivated in aerobic shaking flasks and the influence of inducer concentration and different sg rna binding sites on the production of pyruvate was measured.Targeting the promoter regions oface eorpdh rtriggered pyruvate production during the exponential phase and reduced expression oface e.In lab-scale bioreactor fermentations, anace esilenced strain successfully produced pyruvate under fully aerobic conditions during the exponential phase, but loss of productivity occurred during a subsequent nitrogen-limited phase.Targeting the promoter region ofpdh renabled pyruvate production during the growth phase of cultivations, and a continued low-level accumulation during the nitrogen-limited production phase.Combinatorial targeting of the promoter regions of bothace eandpdh rin e.Coli mg1655 pd cas9 psg rna_ace e_234_pdh r_329 resulted in the stable aerobic production of pyruvate with non-growing cells at yp/s= 0.36 ± 0.029 g pyruvate/g glucosein lab-scale bioreactors throughout an extended nitrogen-limited production phase.

Journal: Engineering in life sciences (2022)
Publication types: Journal Article
CCG•CGG interruptions in high-penetrance SCA8 families increase RAN translation and protein toxicity.

Spinocerebellar ataxia type 8 (sca8), a dominantly inherited neurodegenerative disorder caused by a ctg•cag expansion, is unusual because most individuals that carry the mutation do not develop ataxia.To understand the variable penetrance of sca8, we studied the molecular differences between highly penetrant families and more common sporadic cases (82%) using a large cohort of sca8 families (n = 77).We show that repeat expansion mutations from individuals with multiple affected family members have ccg•cgg interruptions at a higher frequency than sporadic sca8 cases and that the number of ccg•cgg interruptions correlates with age at onset.At the molecular level, ccg•cgg interruptions increase rna hairpin stability, and in cell culture experiments, increase p-e if2α and poly ala and poly ser ran protein levels.Additionally, ccg•cgg interruptions, which encode arginine interruptions in the poly gln frame, increase toxicity of the resulting proteins.In summary, sca8 ccg•cgg interruptions increase poly ala and poly ser ran protein levels, poly gln protein toxicity, and disease penetrance and provide novel insight into the molecular differences between sca8 families with high vs.Low disease penetrance.

Journal: EMBO molecular medicine (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't