syedzayyan/paper_mill_benchmark huggingface dataset:
Metabolic Interventions to Prevent Hypertrophy-Induced Alterations in Contractile Properties In Vitro.

(1) background: the exact mechanism(s) underlying pathological changes in a heart in transition to hypertrophy and failure are not yet fully understood.However, alterations in cardiac energy metabolism seem to be an important contributor.We characterized an in vitro model of adrenergic stimulation-induced cardiac hypertrophy for studying metabolic, structural, and functional changes over time.Accordingly, we investigated whether metabolic interventions prevent cardiac structural and functional changes; (2) methods: primary rat cardiomyocytes were treated with phenylephrine (pe) for 16 h, 24 h, or 48 h, whereafter hypertrophic marker expression, protein synthesis rate, glucose uptake, and contractile function were assessed; (3) results: 24 h pe treatment increased expression of hypertrophic markers, phosphorylation of hypertrophy-related signaling kinases, protein synthesis, and glucose uptake.Importantly, the increased glucose uptake preceded structural and functional changes, suggesting a causal role for metabolism in the onset of pe-induced hypertrophy.Indeed, pe treatment in the presence of a pan-akt inhibitor or of a glut4 inhibitor dipyridamole prevented pe-induced increases in cellular glucose uptake and ameliorated pe-induced contractile alterations; (4) conclusions: pharmacological interventions, forcing substrate metabolism away from glucose utilization, improved contractile properties in pe-treated cardiomyocytes, suggesting that targeting glucose uptake, independent from protein synthesis, forms a promising strategy to prevent hypertrophy and hypertrophy-induced cardiac dysfunction.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article
Enhancer grammar in development, evolution, and disease: dependencies and interplay.

Each language has standard books describing that language's grammatical rules.Biologists have searched for similar, albeit more complex, principles relating enhancer sequence to gene expression.Here, we review the literature on enhancer grammar.We introduce dependency grammar, a model where enhancers encode information based on dependencies between enhancer features shaped by mechanistic, evolutionary, and biological constraints.Classifying enhancers based on the types of dependencies may identify unifying principles relating enhancer sequence to gene expression.Such rules would allow us to read the instructions for development within genomes and pinpoint causal enhancer variants underlying disease and evolutionary changes.

Journal: Developmental cell (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't;Review
The full spectrum of human naive T cells.

Naive t cells have long been regarded as a developmentally synchronized and fairly homogeneous and quiescent cell population, the size of which depends on age, thymic output and prior infections.However, there is increasing evidence that naive t cells are heterogeneous in phenotype, function, dynamics and differentiation status.Current strategies to identify naive t cells should be adjusted to take this heterogeneity into account.Here, we provide an integrated, revised view of the naive t cell compartment and discuss its implications for healthy ageing, neonatal immunity and t cell reconstitution following haematopoietic stem cell transplantation.

Journal: Nature reviews. Immunology (2018)
Publication types: Journal Article;Review
Hypofractionated radiotherapy with temozolomide in diffuse intrinsic pontine gliomas: a randomized controlled trial.

Introduction diffuse intrinsic pontine glioma (dipg) is the most common form of brainstem glioma.The present study was performed to assess if hypofractionated radiotherapy completed in < 3 weeks with temozolomide improves survival in dipg.Material and methods the present study is a phase ii open label randomized trial.The study included newly diagnosed patients with dipg.Patients in arm a received conventional fractionated rt of 60 gy in 30 fractions over 6 weeks while patients in arm b received hypo-fractionated radiotherapy of 39 gy in 13 fractions over 2.6 weeks along with concurrent temozolomide (tmz) 75 mg/m2from day 1 to day 17 followed by adjuvant tmz for six cycles.The survival analysis was performed with modified intention to treat analysis.Results a total of 35 patients were randomized.33 patients were evaluable.93% (n = 14) of patients in the conventional arm completed treatment while only 17% (n = 3) of the children could complete planned course of treatment in the experimental arm.The median overall survival (os) was 11 months (95% ci - 7.5 to 14.5 months) in the conventional arm and 12 months (95% ci - 10.5 to 13.5 months) in the experimental arm (p = 0.208).28% (n = 5) patients in the experimental arm developed grade 3 or 4 hematological toxicity.Conclusion the above study shows that hypofractionated radiotherapy with concurrent and adjuvant temozolomide does not improve os and has higher hematological toxicity.Conventional radiotherapy remains the standard of care.

Journal: Journal of neuro-oncology (2020)
Publication types: Clinical Trial, Phase II;Journal Article;Randomized Controlled Trial
Simultaneous determination of paclitaxel and lansoprazole in rat plasma by LC-MS/MS method and its application to a preclinical pharmacokinetic study of investigational PTX-LAN-PLGA nanoformulation.

In spite of having a remarkable anti tumor activity against a wide variety of cancers, the clinical effectiveness of the major chemotherapeutic drug paclitaxel is often limited by the issues of drug resistance that hampers the therapeutic effectiveness of the drug.The combination of proton pump inhibitor with paclitaxel is an effective approach to overcome therapeutic resistance caused by the acidic microenvironment (warburg effect) in tumor.In the present study a new simple, precise and selective liquid chromatography tandem mass spectrometry method was developed for quantification of paclitaxel and lansoprazole using esomeprazole as an internal standard and applied for the pharmacokinetic study of investigational paclitaxel - lansoprazole loaded plga nanoparticles.The developed method quantifies both the drugs simultaneously irrespective of their dissimilar stability concerns.The detection was exercised with multiple reaction-monitoring mode in positive ionization that yielded highly intense response of parent-product (m/z) transition pair 854.4 → 286.1, 370.1 → 251.9 and 346 → 198 for paclitaxel, lansoprazole and esomeprazole respectively.The chromatographic separation was achieved using phenomenex kinetex 5 μ c18 100a 50 × 3.0 mm column and a gradient mobile phase combination of ammonium acetate in deionized water (p h 6.8, 2 m m, w/v) and acetonitrile spiked with formic acid (1:1000, v/v ).This method showed good linearity over a concentration range of 10-320 ng/m l and 100-3200 ng/m l with correlation coefficient (r2) 0.98 and 0.94 for paclitaxel and lansoprazole respectively.Using liquid liquid extraction process both the drugs were extracted from rat plasma.The intra- and inter-day precision and accuracy values were within the variability limits and both the analytes were found to be stable throughout the freeze-thaw, auto-sampler, bench top and long term stability studies.The liquid chromatography tandem mass spectrometry method was successfully validated in accordance with united states food and drug administration guidelines and the results were within the acceptable limits.The liquid chromatography tandem mass spectrometry method was successfully utilized for the pharmacokinetic investigation of experimental paclitaxel - lansoprazole loaded plga nanoparticles in rat plasma.

Journal: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences (2019)
Publication types: Evaluation Study;Journal Article
Mollification of Doxorubicin (DOX)-Mediated Cardiotoxicity Using Conjugated Chitosan Nanoparticles with Supplementation of Propionic Acid.

Doxorubicin is an extensively prescribed antineoplastic agent.It is also known for adverse effects, among which cardiotoxicity tops the list.The possible mechanism underlying doxorubicin (dox)-mediated cardiotoxicity has been investigated in this study.Further, to reduce the dox-mediated cardiotoxicity, dox was conjugated with chitosan nanoparticles (dcnps) and supplemented with propionic acid.Initially, the drug loading efficacy and conjugation of dox with chitosan was confirmed by uv-visible spectroscopy (uv) and fourier transform infrared spectroscopy (ftir).The average sizes of the synthesized chitosan nanoparticles (cnps) and dcnps were measured by dynamic light scattering (dls) analysis as 187.9 ± 1.05 nm and 277.3 ± 8.15 nm, respectively, and the zeta potential values were recorded as 55.2 ± 0.7 m v and 51.9 ± 1.0 m v, respectively.The size and shape of cnps and dcnps were recorded using a high-resolution electron microscopy (hrtem).The particles measured <30 nm and 33-84 nm, respectively.The toxic effects of dcnps and propionic acid were evaluated in rat model.The data from the electrocardiogram (ecg), cardiac biomarkers, peroxisome proliferator-activated receptor gamma (pparγ) and histological observations indicated evidence of dox-mediated cardiotoxicity, whereas the administration of dcnps, as well as propionic acid (pa), brought about a restoration to normalcy and offered protection in the context of dox-induced cardiotoxicity.

Journal: Nanomaterials (Basel, Switzerland) (2022)
Publication types: Journal Article
Open-Design for a Smart Cover of a Night-Time Telescope for Day-Time Use.

Robotic observatories are ideal infrastructures that can be remotely accessed by scientists, amateurs, and general public for research and education in astronomy.Its robotization is a complex process for ensuring autonomy, safety, and coordination among all subsystems.Some observatories, such as francisco sanchez's, are equipped with two types of telescopes: one for the night and one for the day.The night-time telescope must be protected from exposure to sunlight in order to use them in an automated way.For this purpose, this article proposes the design and construction of a smart cover that opens and closes according to the time of day.The mechatronic design covers the electronic, mechanical, and software programming, and it has been devised taking while taking the principles of open design, ease of reproduction, low-cost, and smart behaviour into account.The design has been parameterized, so that it can be adapted to telescopes of any size.The final prototype is lightweight, cost-effective, and can be built while using common 3d printing and pcb milling machines.The complete design is licensed under the gnu general public license v3.0 and all the documentation, schematics, and software are available in public repositories, like zenodo, git hub, and instructables.

Journal: Sensors (Basel, Switzerland) (2021)
Publication types: Journal Article
Predicting the behavioral intentions of hospice and palliative care providers from real-world data using supervised learning: A cross-sectional survey study.

Hospice and palliative care (hpc) aims to improve end-of-life quality and has received much more attention through the lens of an aging population in the midst of the coronavirus disease pandemic.However, several barriers remain in china due to a lack of professional hpc providers with positive behavioral intentions.Therefore, we conducted an original study introducing machine learning to explore individual behavioral intentions and detect factors of enablers of, and barriers to, excavating potential human resources and improving hpc accessibility.Methods a cross-sectional study was designed to investigate healthcare providers' behavioral intentions, knowledge, attitudes, and practices in hospice care (kaphc) with an indigenized kaphc scale.Binary logistic regression and random forest classifier (rfc) were performed to model impacting and predict individual behavioral intentions.Results the rfc showed high sensitivity (accuracy = 0.75; f1 score = 0.84; recall = 0.94).Attitude could directly or indirectly improve work enthusiasm and is the most efficient approach to reveal behavioral intentions.Continuous practice could also improve individual confidence and willingness to provide hpc.In addition, scientific knowledge and related skills were the foundation of implementing hpc.Conclusion individual behavioral intention is crucial for improving hpc accessibility, particularly at the initial stage.A well-trained rfc can help estimate individual behavioral intentions to organize a productive team and promote additional policies.

Journal: Frontiers in public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Chemical effects of different types of rubber-based products on early life stages of Pacific oyster, Crassostrea gigas.

Rubber products and debris with specific chemical signatures can release their constitutive compounds into the surrounding environment.We investigated the chemical toxicity of different types of new and used rubber products (tires, crumb rubber granulates, aquaculture rubber bands) on early life stages of a model marine organism, pacific oyster crassostrea gigas.Leachates obtained from used products were generally less toxic than those from new ones.Leachates from new products induced embryotoxicity at different concentrations: oyster-farming rubber bands (lowest observed effect concentration, loec = 1 g l-1) and crumb rubber granulates (loec = 1 g l-1) > tires (loec = 10 g l-1).Moreover, new oyster-farming rubber bands induced spermiotoxicity at 10 g l-1(-29% survival) resulting in decreased oyster reproductive output (-17% fertilization yield).Targeted chemical analyses revealed some compounds (2 mineral contaminants, 15 pahs, 2 pcbs) in leachates, which may have played a role.Rubber used in marine aquaculture (rubber bands) or present at sea as waste (tire, crumb rubber granulates) therefore release hazardous chemical molecules under realistic conditions, which may affect oyster development.Aquaculture development work is necessary to improve practices for eco-safety, as efforts to limit the contamination of marine environments by terrestrial rubber debris.

Journal: Journal of hazardous materials (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Does specialized psychological treatment for offending reduce recidivism? A meta-analysis examining staff and program variables as predictors of treatment effectiveness.

A meta-analysis was conducted to examine whether specialized psychological offense treatments were associated with reductions in offense specific and non-offense specific recidivism.Staff and treatment program moderators were also explored.The review examined 70 studies and 55,604 individuals who had offended.Three specialized treatments were examined: sexual offense, domestic violence, and general violence programs.Across all programs, offense specific recidivism was 13.4% for treated individuals and 19.4% for untreated comparisons over an average follow up of 66.1 months.Relative reductions in offense specific recidivism were 32.6% for sexual offense programs, 36.0% for domestic violence programs, and 24.3% for general violence programs.All programs were also associated with significant reductions in non-offense specific recidivism.Overall, treatment effectiveness appeared improved when programs received consistent hands-on input from a qualified registered psychologist and facilitating staff were provided with clinical supervision.Numerous program variables appeared important for optimizing the effectiveness of specialized psychological offense programs (e.g., arousal reconditioning for sexual offense programs, treatment approach for domestic violence programs).The findings show that such treatments are associated with robust reductions in offense specific and non-offense specific recidivism.We urge treatment providers to pay particular attention to staffing and program implementation variables for optimal recidivism reductions.

Journal: Clinical psychology review (2019)
Publication types: Journal Article;Meta-Analysis;Review
The gut microbiome: implications for neurogenesis and neurological diseases.

There is an increasing recognition of the strong links between the gut microbiome and the brain, and there is persuasive evidence that the gut microbiome plays a role in a variety of physiological processes in the central nervous system.This review summarizes findings that gut microbial composition alterations are linked to hippocampal neurogenesis, as well as the possible mechanisms of action; the existing literature suggests that microbiota influence neurogenic processes, which can result in neurological disorders.We consider this evidence from the perspectives of neuroinflammation, microbial-derived metabolites, neurotrophins, and neurotransmitters.Based on the existing research, we propose that the administration of probiotics can normalize the gut microbiome.This could therefore also represent a promising treatment strategy to counteract neurological impairment.

Journal: Neural regeneration research (2022)
Publication types: Journal Article
Survival of pediatric Hodgkin lymphoma patients treated with doxorubicin, bleomycin, vincristine, etoposide, prednisone, and cyclophosphamide (ABVE-PC) versus doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) at a single institution.

Adriamycin, bleomycin, vinblastine, dacarbazine (abvd), the de facto standard of care in adult-onset hodgkin lymphoma (hl), has not been directly compared to doxorubicin, bleomycin, vincristine, etoposide, prednisone, and cyclophosphamide (abve-pc), a pediatric-aimed regimen designed to reduce late effects.We aimed to describe the single-institution experience of using both regimens in patients with pediatric hl.Methods this retrospective cohort study evaluated a total of 224 patients diagnosed with hl between 1999 and 2018 at children's hospital los angeles (chla), of which 93 patients were eligible having received abvd (n = 46) or abve-pc (n = 47) chemotherapy as their initial treatment.Descriptive analyses were performed using the student's t-test or fisher's exact test.Survival analysis used the kaplan-meier method.Events included death, relapse, and secondary malignancy.We also describe the use of radiation therapy, pulmonary toxicity, and cardiomyopathy determined by shortening fraction <29%.Analyses followed an intention-to-treat principle.Results there was no difference in baseline characteristics between the patients receiving abve-pc or abvd in regard for stage, risk group, or prognostic variables, such as the presence or absence of "b" symptoms, bulky disease, and extra-nodal involvement.A greater proportion of patients treated with abve-pc received consolidating external beam radiation treatment (xrt) either by randomization or by response compared to abvd (59.6% vs.32.6%, respectively, p = .01).While not statistically significant, response to therapy, assessed by positron emission tomography/computerized tomography (pet/ct) where available, mirrored the use for radiation (rapid response 58.3% vs.90.0%, n = 34, p = .11).The median dose of anthracycline (doxorubicin) was the same in patients receiving abve-pc versus abvd (200 vs.200 mg/m2, interquartile range 200-250 vs.200-300 mg/m2, p = .002).There was no difference in event-free survival (p = .63) or overall survival (p = .37) with a median follow-up length of 3.9 years.Conclusions abvd and abve-pc achieved similar survival outcomes in our single-institution cohort.

Journal: Pediatric blood & cancer (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
The Role of the Nephrologist in Management of Poisoning and Intoxication: Core Curriculum 2022.

Poisoning is a common problem in the united states.Acid-base disturbances, electrolyte derangements, or acute kidney injury result from severe poisoning from toxic alcohols, salicylates, metformin, and acetaminophen.Lithium is highly sensitive to small changes in kidney function.These poisonings and drug overdoses often require the nephrologist's expertise in diagnosis and treatment, which may require correction of acidosis, administration of selective enzyme inhibitors, or timely hemodialysis.The clinical and laboratory abnormalities associated with the poisonings and drug overdoses can develop rapidly and lead to severe cellular dysfunction and death.Understanding the pathophysiology of the disturbances and their clinical and laboratory findings is essential for the nephrologist to rapidly recognize the poisonings and establish an effective treatment plan.This installment of ajkd's core curriculum in nephrology presents illustrative cases of individual poisonings and drug overdoses and summarizes up to date information on their prevalence, clinical and laboratory findings, pathophysiology, diagnosis, and treatment.

Journal: American journal of kidney diseases : the official journal of the National Kidney Foundation (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
The Phylosymbiosis Pattern Between the Fig Wasps of the Same Genus and Their Associated Microbiota.

Microbial communities can be critical for many metazoans, which can lead to the observation of phylosymbiosis with phylogenetically related species sharing similar microbial communities.Most of the previous studies on phylosymbiosis were conducted across the host families or genera.However, it is unclear whether the phylosymbiosis signal is still prevalent at lower taxonomic levels.In this study, 54 individuals from six species of the fig wasp genus ceratosolen(hymenoptera: agaonidae) collected from nine natural populations and their associated microbiota were investigated.The fig wasp species were morphologically identified and further determined by mitochondrial co1 gene fragments and nuclear its2 sequences, and the v4 region of 16s r rna gene was sequenced to analyze the bacterial communities.The results suggest a significant positive correlation between host genetic characteristics and microbial diversity characteristics, indicating the phylosymbiosis signal between the phylogeny of insect hosts and the associated microbiota in the lower classification level within a genus.Moreover, we found that the endosymbiotic wolbachiacarried by fig wasps led to a decrease in bacterial diversity of host-associated microbial communities.This study contributes to our understanding of the role of host phylogeny, as well as the role of endosymbionts in shaping the host-associated microbial community.

Journal: Frontiers in microbiology (2021)
Publication types: Journal Article