syedzayyan/paper_mill_benchmark huggingface dataset:
Synergistic effects of dual growth factor delivery from composite hydrogels incorporating 2-N,6-O-sulphated chitosan on bone regeneration.

A promising strategy to accelerate bone generation is to deliver a combination of certain growth factors to the integration site via a controlled spatial and temporal delivery mode.Here, a composite hydrogel incorporating poly(lactide-co-glycolide) (plga) microspheres was accordingly prepared to load and deliver the osteogenic rh bmp-2 and angiogenic rh vegf165in the required manner.In addition, 2-n,6-o-sulphated chitosan (26scs), which is a synergetic factor of growth factors, was incorporated in the composite hydrogel as well.The system showed a similar release behaviour of the two growth factors regardless of 26scs inclusion.Rh bmp-2 loaded in plga microspheres showed a sustained release over a period of 2 weeks, whereas rh vegf165loaded in hydrogel eluted almost completely from the hydrogel over the first 16 days.Both growth factors retained their efficacy, as quantified with relevant in vitro assays.Moreover, an enhanced cell response was achieved upon the delivery of dual growth factors, compared to that obtained with a single factor.Furthermore, in the presence of 26scs, the system revealed significantly upregulated alkaline phosphatase activity, human umbilical vein endothelial cell proliferation, sprouting, nitric oxide secretion, and angiogenic gene expression.This study highlighted that the composite hydrogel incorporated with 26scs appears to constitute a promising approach to deliver multiple growth factors.From our findings, we could also conclude that rh bmp-2 can promote angiogenesis and that the mechanism is worthy of further study in subsequent research.

Journal: Artificial cells, nanomedicine, and biotechnology (2018)
Publication types: Journal Article
Association between Vitamin D Supplementation and Cancer Mortality: A Systematic Review and Meta-Analysis.

Vitamin d deficiency is related to increased cancer risk and deaths.However, whether vitamin d supplementation reduces cancer mortality remains unclear, and several randomized controlled trials yield inconsistent results.Methods medline, embase, and the cochrane central register of controlled trials were searched from their inception until 28 june 2022, for randomized controlled trials investigating vitamin d supplementation.Pooled relative risks (rrs) and their 95% confidence intervals (cis) were estimated.Trials with vitamin d supplementation combined with calcium supplementation versus placebo alone and recruiting participants with cancer at baseline were excluded in the present study.Results this study included 12 trials with a total of 72,669 participants.Vitamin d supplementation did not reduce overall cancer mortality (rr 0.96, 95% ci 0.80-1.16).However, vitamin d supplementation was associated with a reduction in lung cancer mortality (rr 0.63, 95% ci 0.45-0.90).Conclusions vitamin d supplementation could not reduce cancer mortality in this highly purified meta-analysis.Further rcts that evaluate the association between vitamin d supplementation and total cancer mortality are still needed.

Journal: Cancers (2022)
Publication types: Journal Article;Review
The difference between arterial pCO2and etCO2after cardiac arrest - Outcome predictor or marker of unfavorable resuscitation circumstances?

Introduction in former studies, the arterio-alveolar carbon dioxide gradient (δco2) predicted in-hospital mortality after initially survived cardiac arrest.As early outcome predictors are urgently needed, we evaluated δco2as predictor for good neurological outcome in our cohort.Methods we retrospectively analyzed all patients ≥18 years of age after non-traumatic in- and out of hospital cardiac arrest in the year 2018 from our resuscitation database.Patients without advanced airway management, incomplete datasets or without return of spontaneous circulation were excluded.The first arterial p co2after admission and the et co2in mm hg at the time of blood sampling were recorded from patient's charts.We then calculated δco2(p co2- et co2).For baseline analyses, δco2was dichotomized into a low and high group with separation at the median.Good neurological outcome on day 30, expressed as cerebral performance category 1-2, defined our primary endpoint.Survival to 30 days was used as secondary endpoint.Results out of 302 screened patients, 128 remained eligible for analyses.Δco2was lower in 30-day survivors with good neurological outcome (12.2 mm hg vs.18.8 mm hg, p = 0.009) and in 30-day survivors (12.5 mm hg vs.20.0 mm hg, p = 0.001).In patients with high δco2, a cardiac etiology of arrest was found less often.They had a higher body mass index, longer duration of resuscitation, higher amounts of epinephrine, lower p o2levels but both higher p co2 and blood lactate levels, resulting in lower blood p h and hco3-levels at admission.In a crude binary logistic regression analysis, δco2was associated with 30-day neurological outcome (or = 1.041 per mm hg of δco2, 95% ci 1.008-1.074, p = 0.014).This association persisted after the adjustment for age, sex, witnessed arrest and shockable first rhythm.However, after addition of the duration of resuscitation or the cumulative epinephrine dosage to the model, δco2lost its association.Conclusion δco2at admission after a successfully resuscitated cardiac arrest is associated with 30 days survival with good neurological outcome.However, a higher δco2may rather be a surrogate for unfavorable resuscitation circumstances than an independent outcome predictor.

Journal: The American journal of emergency medicine (2022)
Publication types: Journal Article
The potential contribution of the WRKY53 transcription factor, gamma-aminobutyric acid (GABA) transaminase, and histone deacetylase in regulating growth, organogenesis, photosynthesis, and transcriptional responses of tomato to different light-emitting diodes (LEDs).

Impressive progress in developing light-emitting diodes (leds) offers a new dimension for meeting agricultural and biological expectations.The present study addresses how tomato (solanum lycopersicum) seedlings respond to the different spectral qualities of leds (white, red, blue, and blue + red).The light treatments in a wavelength-dependent manner contributed to the variations in biomass accumulation, morphology, and organogenesis pattern.Light quality epigenetically contributed to the transcriptional regulation of the histone deacetylase (hda3) gene.The expression of wrky53 transcription factor and gamma-aminobutyric acid transaminase (gaba-tp1) genes displayed a similar upward trend in response to the blue wavelength.On the contrary, the sole red light downregulated the wrky53 and gaba-tp1 genes.The blue irradiation was associated with the upregulation in the glycolate oxidase (glo2) and ribulose-1,5-bisphosphate carboxylase‐oxygenase large subunit (rbc l) genes, while the red wavelength down-regulated the glo2 and rbc l genes.Moreover, rbc l statistically correlated with glo2, referring to the balanced regulation of photorespiration and the calvin cycle.The blue wavelengths were more capable of improving the concentrations of photosynthetic pigments and proline.The seedlings grown under the white leds displayed the maximum activity of the catalase enzyme.The cultivation of tomato seedlings under the blue lights enhanced the activities of the superoxide dismutase and ascorbate peroxidase enzymes.The light treatments were associated with the variation in the nutritional status of k+and ca2+in both leaves and roots.The presented findings and inferences support the potential contribution of wrky53, hda3, and gaba signaling in modulating plant responses to light quality.

Journal: Journal of photochemistry and photobiology. B, Biology (2022)
Publication types: Journal Article
Identification of a prognostic index system and tumor immune infiltration characterization for lung adenocarcinoma based on mRNA molecular of pyroptosis.

And purpose pyroptosis is a form of programmed cell death, which plays an important role in tumorigenesis, progression, and regulation of the tumor microenvironment.It can affect lung adenocarcinoma (luad) progression.This study aimed to construct a pyroptosis-related m rna prognostic index (prmpi) for luad and clarify the tumor microenvironment infiltration characterization of luad.Materials and methods we performed a univariate cox regression analysis for pyroptosis-related m rnas in the tcga cohort.Then, we used lasso cox regression to establish a prmpi.The quantitative real time polymerase chain reaction (q rt-pcr) was used to quantify the relative expression of pyroptosis-related m rnas.The cptac cohort was used to confirm the stability and wide applicability of the prmpi.The single-sample gene set enrichment analysis (ss gsea) was performed to assess the tumor microenvironment infiltration characterization.Results a total of 36 pyroptosis-related m rnas were identified.The prmpi was established based on five pyroptosis-related m rnas.The expression patterns of these m rnas were verified in luad samples from our medical center by q rt-pcr.High-prmpi patients had worse overall survival than low-prmpi patients.The result was validated in the cptac cohort.The comprehensive analysis indicated that the high-prmpi patients exhibited lower immune activity, more aggressive immunophenotype, lower expression of immune checkpoint molecule, higher tp53 mutation rate, and higher tumor stemness than low-prmpi patients.Low-prmpi patients may be more sensitive to immunotherapy, while high-prmpi patients may benefit more from chemotherapy and targeted therapy.Conclusions the prmpi may be a promising biomarker to predict the prognosis, tumor microenvironment infiltration characterization, and the response to adjuvant therapy in luad.

Journal: Frontiers in medicine (2022)
Publication types: Journal Article
Postpartum Psychosis after Traumatic Cesarean Delivery.

An emergency cesarean delivery can be a traumatic childbirth experience for a woman and a risk factor for postpartum psychosis, especially in a patient with a history of bipolar disorder.This article describes the case of a pregnant woman with an unknown history of bipolar disorder who developed an acute psychotic reaction during the procedure of an emergency caesarian section and switched to mania.The purpose of this case study is for perinatal health care professionals to identify suspicious symptoms and promptly refer to psychiatric services so as to ensure the mother's and the newborn's safety.This case study highlights the importance of assessing women with bipolar disorder or a previous psychotic episode for the risk of psychiatric complications in pregnancy and after childbirth.Midwifery education on perinatal mental health is crucial for the detection of suspicious symptoms and early referral to a specialist.

Journal: Healthcare (Basel, Switzerland) (2021)
Publication types: Case Reports;Journal Article
Acupuncture for acute musculoskeletal pain management in the emergency department and continuity clinic: a protocol for an adaptive pragmatic randomised controlled trial.

Introduction chronic musculoskeletal pain causes a significant burden on health and quality of life and may result from inadequate treatment of acute musculoskeletal pain.The emergency department (ed) represents a novel setting in which to test non-pharmacological interventions early in the pain trajectory to prevent the transition from acute to chronic pain.Acupuncture is increasingly recognised as a safe, affordable and effective treatment for pain and anxiety in the clinic setting, but it has yet to be established as a primary treatment option in the ed.Methods and analysis this pragmatic clinical trial uses a two-stage adaptive randomised design to determine the feasibility, acceptability and effectiveness of acupuncture initiated in the ed and continued in outpatient clinic for treating acute musculoskeletal pain.The objective of the first (treatment selection) stage is to determine the more effective style of ed-based acupuncture, auricular acupuncture or peripheral acupuncture, as compared with no acupuncture.All arms will receive usual care at the discretion of the ed provider blinded to treatment arm.The objective of the second (effectiveness confirmation) stage is to confirm the impact of the selected acupuncture arm on pain reduction.An interim analysis is planned at the end of stage 1 based on probability of being the best treatment, after which adaptations will be considered including dropping the less effective arm, sample size re-estimation and unequal treatment allocation ratio (eg, 1:2) for stage 2.Acupuncture treatments will be delivered by licensed acupuncturists in the ed and twice weekly for 1 month afterward in an outpatient clinic.Ethics and dissemination this study has been reviewed and approved by the duke university health system institutional review board.Informed consent will be obtained from all participants.Results will be disseminated through peer-review publications and public and conference presentations.Trial registration number nct04290741.

Journal: BMJ open (2022)
Publication types: Clinical Trial Protocol;Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
A multiphysics modeling approach for in-stent restenosis: Theoretical aspects and finite element implementation.

Development of in silico models that capture progression of diseases in soft biological tissues are intrinsic in the validation of the hypothesized cellular and molecular mechanisms involved in the respective pathologies.In addition, they also aid in patient-specific adaptation of interventional procedures.In this regard, a fully-coupled high-fidelity lagrangian finite element framework is proposed within this work which replicates the pathology of in-stent restenosis observed post stent implantation in a coronary artery.Advection-reaction-diffusion equations are set up to track the concentrations of the platelet-derived growth factor, the transforming growth factor-β, the extracellular matrix, and the density of the smooth muscle cells.A continuum mechanical description of volumetric growth involved in the restenotic process, coupled to the evolution of the previously defined vessel wall constituents, is presented.Further, the finite element implementation of the model is discussed, and the behavior of the computational model is investigated via suitable numerical examples.Qualitative validation of the computational model is presented by emulating a stented artery.Patient-specific data are intended to be integrated into the model to predict the risk of in-stent restenosis, and thereby assist in the tuning of stent implantation parameters to mitigate the risk.

Journal: Computers in biology and medicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Evaluating the Impact of Language Concordance on Coronavirus Disease 2019 Contact Tracing Outcomes Among Spanish-Speaking Adults in San Francisco Between June and November 2020.

We evaluated the impact of language concordance-clinician or public health worker fluency in a patient's primary language-on coronavirus disease 2019 (covid-19) contact tracing outcomes among 2668 spanish-speaking adults in san francisco.Language concordance was associated with 20% greater odds of covid-19 testing and 53% greater odds of support service referrals.

Journal: Open forum infectious diseases (2022)
Publication types: Journal Article
Synthesis and structure-activity relationship studies of 1,5-isomers of triazole-pyrrolopyrimidine as selective Janus kinase 1 (JAK1) inhibitors.

Jak inhibitors have been considered as useful targets for the treatment of related diseases.However, first-generation jak inhibitors have side effects such as anemia, thrombocytopenia, neutropenia and headaches which have been suggested to result from high jak2 inhibition.Second-generation jak inhibitors with more specific jak isozyme inhibition have been studied to eliminate these adverse effects.In this study, novel 4-(1,5- or 2,5-triazole)-pyrrolopyrimidine derivatives with aromatic moieties were synthesized as jak1 inhibitors, and an in vitro enzyme assay was used to evaluate the jak inhibitory effects.Among these jak1 inhibitors, the compound 23a showed an ic50level of 72 n m, as well as being selective against other jaks by 12 times or more: the results of molecular docking studies suggested that the high jak1 selectivity resulted from a key interaction between the iodine atom of compound 23a and his-885 of h jak1.

Journal: Bioorganic & medicinal chemistry letters (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Genome-wide identification, evolution analysis of cytochrome P450 monooxygenase multigene family and their expression patterns during the early somatic embryogenesis in Dimocarpus longan Lour.

Cytochrome p450 (cyp), a multi-gene superfamily, is involved in a broad range of physiological processes, including hormone responses and secondary metabolism throughout the plant life cycle.Longan (dimocarpus longan), a subtropical and tropical evergreen fruit tree, its embryonic development is closely related to the yield and quality of fruits.And a large number of secondary metabolites, such as flavonoids and carotenoids, are also produced during the longan somatic embryogenesis (se).It is important, therefore, to study potential functions of cyps in longan.However, the knowledge of longan cyps is still very limited.Here, a total of 327 dl cyps were identified using the genome-search method, which could be classified into nine clans.The expansion of the dl cyp family was mainly caused by tandem duplication (td) events.Promoter cis-acting elements analysis elucidated that dl cyps played important roles in hormonal responses.A total of 246 dl cyps exhibited six different expression patterns during the early se based on longan transcriptomic data.Eight dl cyps underwent alternative splicing (as) events, and they might produce one to six isoforms.And the as transcript of dl cyp97c1 might act as an alternative to the full-length transcript in icp ec and ge stages.Finally, protein-protein interaction (ppi) networks and mi rna target prediction elucidated that dl cyps might be involved in the phenylpropanoid metabolic pathway and primarily regulated and targeted by mi r413.In summary, our results provided valuable inventory for understanding the classification and biological functions of dl cyps and provided insight into further functional verification of dl cyps during the longan early se.

Journal: Gene (2022)
Publication types: Journal Article
Gene module analysis of juvenile myelomonocytic leukemia and screening of anticancer drugs.

Juvenile myelomonocytic leukemia (jmml) is a rare but severe primary hemopoietic system tumor of childhood, most frequent in children 4 years and younger.There are currently no specific anticancer therapies targeting jmml, and the underlying gene expression changes have not been revealed.To define molecular targets and possible biomarkers for early diagnosis, optimal treatment, and prognosis, we conducted microarray data analysis using the gene expression omnibus, and constructed protein‐protein interaction networks of all differentially expressed genes.Modular bioinformatics analysis revealed four core functional modules for jmml.We analyzed the gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) pathway functions associated with these modules.Using the cmap database, nine potential anticancer drugs were identified that modulate expression levels of many jmml‐associated genes.In addition, we identified possible mi rnas and transcription factors regulating these differentially expressed genes.This study defines a new research strategy for developing jmml‐targeted chemotherapies.

Journal: Oncology reports (2018)
Publication types: Journal Article
Using Blood Transcriptome Analysis to Determine the Changes in Immunity and Metabolism of Giant Pandas with Age.

A low reproductive rate coupled with human activities has endangered the giant panda, a species endemic to southwest china.Although giant pandas feed almost exclusively on bamboo, they retain carnivorous traits and suffer from carnivorous diseases.Additionally, their immune system is susceptible to aging, resulting in a reduced ability to respond to diseases.This study aimed to determine the genes and pathways expressed differentially with age in blood tissues.The differentially expressed genes in different age groups of giant pandas were identified by rna-seq.The elderly giant pandas had many differentially expressed genes compared with the young group (3 years old), including 548 upregulated genes and 401 downregulated genes.Further, functional enrichment revealed that innate immune upregulation and adaptive immune downregulation were observed in the elderly giant pandas compared with the young giant pandas.Meanwhile, the immune genes in the elderly giant pandas changed considerably, including genes involved in innate immunity and adaptive immunity such as plscr1, clec7a, ccl5, ccr9, and epas1.Time series analysis found that giant pandas store glycogen by prioritizing fat metabolism at age 11, verifying changes in the immune system.The results reported in this study will provide a foundation for further research on disease prevention and the energy metabolism of giant pandas.

Journal: Veterinary sciences (2022)
Publication types: Journal Article
Identification of candidate genes and pathways in dexmedetomidine-induced neuroprotection in rats using RNA sequencing and bioinformatics analysis.

Traumatic brain injury (tbi) is a major cause of disability worldwide, without definitive and effective intervention.Dexmedetomidine (dex) has a neuroprotective effect against tbi; however, the detailed mechanism underlying this effect remains unclear.Methods ten male sprague dawley rats were used to establish a tbi model.The rats were randomly divided into two groups: the tbi group (tbi, control group) and the dex treatment group (dex).The next day, the neurological function of the rats were evaluated by the modified neurological severity score (m nss).Then, the rats were sacrificed, and rna sequencing was performed to identify differentially expressed messenger rnas (m rnas) and micro rnas (mi rnas) in brain tissue samples.Additionally, we performed a bioinformatics analysis to explore the candidate genes and pathways that might play important roles in dex-induced neuroprotection.The most significantly differentially expressed mi rnas and possible hub genes were validated by quantitate reverse transcription-polymerase chain reaction (q rt-pcr) using more samples.Results in the dex group, 517 m rnas (352 up-regulated and 165 down-regulated) and 35 mi rnas (18 up-regulated and 17 down-regulated) were differentially expressed compared to the tbi group.Gene ontology analysis revealed the up-regulated m rnas to be significantly enriched in microtubule-based movement or processes, microtubule and tubulin binding.Kyoto encyclopedia of genes and genomes analysis showed that these up-regulated m rnas were significantly enriched in the b-cell receptor signaling pathway as well as the cell cycle pathway.Also, lyn and cdk1 were found to be associated with the b-cell receptor signaling and cell cycle pathways, respectively.Furthermore, the down-regulated mi rnas were significantly enriched in cellular components, although no significant gene ontology terms or kegg pathways were found for the down-regulated m rnas or up-regulated mi rnas.Conclusions differentially expressed m rnas and mi rnas were identified after the administration of dex in a tbi rat model.The b-cell receptor signaling pathway and the cell cycle pathway might be involved in the neuroprotective effect of dex against tbi, lyn and cdk1 might be hub genes.

Journal: Annals of palliative medicine (2021)
Publication types: Journal Article