syedzayyan/paper_mill_benchmark huggingface dataset:
Non-invasive biomonitoring of infant exposure to environmental organic pollutants in north-western Spain based on hair analysis. Identification of potential sources.

Recent years have seen growing interest in hair sample analysis to detect organic pollutants (ops).This biological matrix can be analysed non-invasively for biomonitoring of ops over a wide exposure window.Obtaining hair sample amounts that meet the needs of the analytical methodology required for the determination of the pos of interest can be challenging, especially in infants.As a result, studies assessing organic pollutants in infant hair have been very scarce.We quantified levels of about 60 ops, including persistent organic pollutants (pops), in 110 hair samples from a patient cohort (60 mothers and 50 infants) from santiago de compostela (north-western spain).For each participant we examined relationship between op levels and corresponding epidemiological parameters using correlations, principal component analysis (pca), hierarchical cluster analysis, and multivariate analysis of variance (manova).For many ops we observed significant correlations with place of residence, parity, and maternal age, as well as pet ownership.Evaluation of dietary habits showed significant associations between levels some ops and the consumption of fish, molluscs, and cereal.There were significant associations between chlorpyrifos and deltamethrin levels and infant birth characteristics such as birthweight and head circumference.Relations between op levels in the hair of mothers and their infants were also examined, revealing common sources of exposure for dioxin-like polychlorinated biphenyls (dlpcbs), non-dioxin-like polychlorinated biphenyls (ndlpcbs), polybrominated diphenyl ethers (pbdes), and polycyclic aromatic hydrocarbons (pahs).Levels of fluoranthene (f), pyrene (p), endrin, and some pbdes in maternal hair were significantly correlated with those in infant hair.Our findings identified common sources of exposure to ops of distinct chemical classes.

Journal: Environmental pollution (Barking, Essex : 1987) (2023)
Publication types: Journal Article
The UnProcessed Pantry Project (UP3): A Community-Based Intervention Aimed to Reduce Ultra-Processed Food Intake Among Food Pantry Clients.

Low-income populations are more likely to experience food and nutrition insecurity and suffer a greater burden of noncommunicable disease than the general population.The un processed pantry project (up3) is an intervention aimed to reduce ultra-processed food availability and consumption of food pantry clients accessing the emergency food system.The pilot study included nutrition education, food boxes, and social support for 16 weeks at 2 food pantries.Data collection included the asa24 dietary recall to calculate healthy eating index-2015 (hei-2015) scores, biomarkers (hemoglobin a1c, total cholesterol, blood pressure, waist circumference, body mass index [bmi]), and a demographic and psychosocial survey.Dietary quality among 43 participants significantly (p < .05) improved as measured by the hei-2015 for total hei-2015, whole grains, total protein foods, and added sugars scores.Bmi, total cholesterol, and waist circumference also significantly improved across study participants.Findings indicate that the emergency food system may be an effective access point to apply frameworks including up3 to address ultra-processed food consumption, dietary quality, and noncommunicable chronic disease risk among food-insecure populations.Programs and policies that limit the amount of ultra-processed food in the emergency food system should be further tested and could be efficacious in addressing inequities among vulnerable populations.

Journal: Family & community health (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Multicomponent Reaction for Diastereoselective Synthesis of Spiro[carbazole-3,4'-pyrazoles] and Spiro[carbazole-3,4'-thiazoles].

In the presence of copper sulfate, the three-component reaction of aromatic aldehydes, ethylindole-3-acetate and 4-arylidene-5-methyl-2-phenylpyrazol-3-ones, in refluxing toluene afforded spiro[carbazole-3,4'-pyrazoles] in good yields with high diastereoselectivity.More importantly, the similar cu so4promoted the four-component reaction of two molecular aromatic aldehydes with ethylindole-3-acetate and 5-methyl-2-phenyl-pyrazol-3-one resulted in 2,4-diarylspiro[carbazole-3,4'-pyrazoles] in satisfactory yields.Additionally, cu so4promoted the four-component reaction of two molecular aromatic aldehydes, ethylindole-3-acetate and 2-phenylthiazol-4-one, in refluxing toluene gave 2,4-diarylspiro[carbazole-3,4'-thiazoles] with diastereomeric ratios in the range of 3:1 to 20:1.

Journal: The Journal of organic chemistry (2021)
Publication types: Journal Article
Exploration for Countering the Episodic Memory.

Reinforcement learning is a prominent computational approach for goal-directed learning and decision making, and exploration plays an important role in improving the agent's performance in reinforcement learning.In low-dimensional markov decision processes, table reinforcement learning incorporated within count-based exploration works well for states of the markov decision processes that can be easily exhausted.It is generally accepted that count-based exploration strategies turn inefficient when applied to high-dimensional markov decision processes (generally high-dimensional state spaces, continuous action spaces, or both) since most states occur only once in deep reinforcement learning.Exploration methods widely applied in deep reinforcement learning rely on heuristic intrinsic motivation to explore unseen states or unreached parts of one state.The episodic memory module simulates the performance of hippocampus in human brain.This is exactly the memory of past experience.It seems logical to use episodic memory to count the situations encountered.Therefore, we use the contextual memory module to remember the states that the agent has encountered, as a count of states, and the purpose of exploration is to reduce the probability of encountering these states again.The purpose of exploration is to counter the episodic memory.In this article, we try to take advantage of the episodic memory module to estimate the number of states experienced, so as to counter the episodic memory.We conducted experiments on the open ai platform and found that counting accuracy of state is higher than that of the cts model.At the same time, this method is used in high-dimensional object detection and tracking, also achieving good results.

Journal: Computational intelligence and neuroscience (2022)
Publication types: Journal Article
Construction of a Highly Diverse mRNA Library forin vitroSelection of Monobodies.

Recently, we developed transcription/translation coupled with the association of puromycin linker (trap) display as a quickin vitroselection method to obtain antibody-like proteins.For thein vitroselection, it is important to prepare m rna libraries among which the diversity is high.Here, we describe a method for the preparation of monobody m rna libraries with greater than 1013theoretical diversity.First, we synthesized two long single-stranded dnas that corresponded to fragments of monobody dna, with random codons in the bc and fg loops.These oligonucleotides were ligated by t4 dna ligase with the support of guide oligonucleotides containing 3' ends that were protected by a modification.After amplifying the product dnas by pcr, one end of each dna fragment was digested with the type ii restriction enzyme bsa i, and the resulting dna fragments were ligated using t4 dna ligase.After amplification of the dna product, m rnas were synthesized by t7 rna polymerase.This method is simple and could be used for the preparation of m rna libraries for various antibody-like proteins.Graphic abstract: construction of a highly diverse m rna library.

Journal: Bio-protocol (2021)
Publication types: Journal Article
MR spectroscopy and imaging-derived measurements in the supplementary motor area for biomarkers of amyotrophic lateral sclerosis.

The diagnosis of amyotrophic lateral sclerosis (als) requires both upper and lower motor neuron signs.However, quite a few patients with als lack the upper motor neuron sign during the disease.This study sought to investigate whether metabolites, including glutamate (glu), n-acetyl aspartate (naa), and gamma aminobutyric acid (gaba), in the supplementary motor area (sma) measured by magnetic resonance spectroscopy (mrs), could be a surrogate biomarker for als.Twenty-five patients with als and 12 controls underwent 3.0-t mr scanning, which measured glu, naa, and gaba.Finally, receiver operating characteristic (roc) curves were created and the area under curve (auc) was calculated to assess the diagnostic power.Logistic regression analysis revealed the usefulness of both glu and naa for the differentiation of als from controls (glu, p = 0.009; naa, p = 0.033).The ratio of glu to naa or gaba was significantly increased in patients with als (glu/naa, p = 0.027; glu/gaba, p = 0.003).Both the aucs were more than 0.7, with high specificity but low sensitivity.The present findings might indicate that both the glu/naa and the glu/gaba ratios in the sma could be potential biomarkers for the diagnosis of als.

Journal: Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology (2021)
Publication types: Journal Article
Hsa-microRNA-370-3p targeting Snail and Twist1 suppresses IL-8/STAT3-driven hepatocellular carcinoma metastasis.

The pro-inflammatory factor interleukin-8 (il-8) is related to poor prognosis in hepatocellular carcinoma (hcc) patients.Interleukin-8 enhanced hcc invasion by upregulating snail and twist1, whether this modulation relies on micro rnas (mi r) is unclear.In this study, hsa-mi r-370-3p was screened as candidate mi rna targeting snail and twist1, and its expression was downregulated by il-8.Luciferase assays and rna electrophoretic mobility shift assays were used to evaluate the interaction between mi r-370-3p and targeted m rnas.Coimmunoprecipitation, luciferase, and ch ip assays were undertaken to investigate the mechanisms underlying il-8-mediated modification of mi r-370-3p.Gain- and loss-of-function studies, transwell assays, and a xenograft nude mouse model were used to investigate pro- and antitumor activities.Interleukin-8 and mi r-370-3p levels were analyzed for clinical relevance in hcc patients.Our results showed that hcc patients with high levels of il-8 experienced more metastasis and shorter survival.Interleukin-8 induced epithelial-mesenchymal transition and promoted liver cancer cell migration, invasion, and metastasis both in vitro and in vivo.Micro rna-370-3p interacted with its cognate m rna within the 3'-utr regions of twist1 and snail m rna directly and specifically and attenuated il-8 protumoral effects on liver cancer cells.Interleukin-8 negatively modulated mi r-370-3p through signal transducer and activator of transcription 3 (stat3) activation by recruiting histone deacetylase 1 (hdac1) to mi r-370-3p promoter.The stat3 and hdac antagonists inhibited liver cancer cell migration and invasion.Patients with high mi r-370-3p and low il-8 levels had longer overall survival.In conclusion, our study elucidated a novel axis il-8/stat3/mi r-370-3p/twist1 and snail relying on hdac1 recruitment, which showed both diagnostic and therapeutic potentials of mi r-370-3p in hcc metastasis.

Journal: Cancer science (2022)
Publication types: Journal Article
Effect of High-Dose Glucocorticoids on Markers of Inflammation and Bone Metabolism in Patients with Primary Glomerular Disease.

Glucocorticoids are one of the most commonly used drugs for treatment of inflammatory and autoimmune diseases.Sirtuin-1 (sirt-1) belongs to the family of proteins involved in protection against inflammation and oxidative stress.A role of sirt-1 in regulation of bone metabolism during high-dose steroid therapy is unknown.Objectives the study assessed influence of high doses of intravenous corticosteroids on plasma inflammation and bone markers in patients with primary glomerular disease.Methods the study included 40 patients (25 m, 15 f; mean age 53.1 ± 14 years) with chronic kidney disease (mean estimated glomerular filtration rate, 58.9 ± 31.3 m l/min).The main inclusion criterion was clinical and histopathological diagnosis of primary glomerular disease and urine protein excretion >2.0 g/24 h.The patients received intravenous pulses of methylprednisolone 20-30 mg/kg/day for three consecutive days followed by oral prednisone 0.8-1.0 mg/kg/day.The blood was taken before administration of methylprednisolone to assess plasma sirt-1, sclerostin, calcium, phosphate, and parathormone; and first-morning urine sample was taken for measurement of calcium, phosphate, and albumin to creatinine ratio.The same laboratory tests were repeated after 4, 7, and 30 days during steroid therapy.Results plasma sirt-1 increased significantly during steroid administration.Plasma sclerostin did not change significantly.There was a significant linear negative correlation between changes in sirt-1 levels and sclerostin throughout the study.In a multiple regression model, changes of plasma sclerostin induced by steroid therapy explained the largest part of variance of respective changes of plasma sirt-1.Conclusions plasma sirt-1 increase during high-dose corticosteroid therapy is negatively related to the change of plasma sclerostin that may suggest a protective role of sirt-1 against the negative effects of steroid therapy on bone.

Journal: Kidney & blood pressure research (2022)
Publication types: Journal Article
Coordination of services for people with serious mental illness and general medical conditions: Perspectives from rural northeastern United States.

The objective of the study was to investigate providers' perspectives on how medical, mental health, and social services are coordinated for people with serious mental illnesses and general medical conditions in 2 predominantly rural states.Method to achieve multiple perspectives on service coordination, this study includes perspectives from providers employed in community mental health centers, social service agencies, and primary care settings in 2 northern rural new england states with contrasting approaches to financing and organizing services.We conducted 29 individual semistructured interviews and 1 focus group, which included administrative leaders, team leaders, primary care providers, social workers, and case managers who provide services for people with serious mental illness.Data were analyzed using qualitative thematic content analysis.Results we identified key themes at 3 levels: (a) provider-level coordination: bridging across services; managing interprofessional communications; and contrasting perspectives on the locus of responsibility for coordination; (b) individual-level coordination: support for self-management and care navigation; trusting and continuous relationships; and the right to individual choice and autonomy; (c) system-level coordination: linking appropriate residential and care provision services, funding, recruiting and retaining staff, policy enablers, and integration solutions.Conclusions three levels of provider-reported coordination themes are described for the 2 states, reflecting efforts to coordinate and integrate service delivery across medical, mental health, and social services.Implications improvements in patient outcomes will need additional actions that target key social determinants of health.(psyc info database record (c) 2020 apa, all rights reserved).

Journal: Psychiatric rehabilitation journal (2020)
Publication types: Journal Article
Change in the neurochemical signature and morphological development of the parvocellular isthmic projection to the avian tectum.

Neurons can change their classical neurotransmitters during ontogeny, sometimes going through stages of dual release.Here, we explored the development of the neurotransmitter identity of neurons of the avian nucleus isthmi parvocellularis (ipc), whose axon terminals are retinotopically arranged in the optic tectum (te o) and exert a focal gating effect upon the ascending transmission of retinal inputs.Although cholinergic and glutamatergic markers are both found in ipc neurons and terminals of adult pigeons and chicks, the m rna expression of the vesicular acetylcholine transporter, vach t, is weak or absent.To explore how the ipc neurotransmitter identity is established during ontogeny, we analyzed the expression of m rnas coding for cholinergic (ch at, vach t, and cht) and glutamatergic (vglu t2 and vglu t3) markers in chick embryos at different developmental stages.We found that between e12 and e18, ipc neurons expressed all cholinergic m rnas and also vglu t2 m rna; however, from e16 through posthatch stages, vach t m rna expression was specifically diminished.Our ex vivo deposits of tracer crystals and intracellular filling experiments revealed that ipc axons exhibit a mature paintbrush morphology late in development, experiencing marked morphological transformations during the period of presumptive dual vesicular transmitter release.Additionally, although ch at protein immunoassays increasingly label the growing ipc axon, this labeling was consistently restricted to sparse portions of the terminal branches.Combined, these results suggest that the synthesis of glutamate and acetylcholine, and their vesicular release, is complexly linked to the developmental processes of branching, growing and remodeling of these unique axons.

Journal: The Journal of comparative neurology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Damage Characterization of Carbon Fiber Composite Pressure Vessels Based on Modal Acoustic Emission.

This study characterized the damage characteristics of carbon fiber composite pressure vessels by the modal acoustic emission (mae) method.The study showed how to use the extracted damage modal features and established mae parameters to determine the damage mode of composite pressure vessels.First, the a0and s0lamb modes of the ae signal were split through mode separation, and the time window was selected to establish the mae characteristic parameters.Subsequently, based on the mae parameters and the damage mode characteristics established from single damage experiments, a damage mode discrimination method was established.A bending test of carbon fiber composite laminates proved that the modal separation method and the mae parameters establishment are reasonable and effective.The results from the hydraulic test of the graded loading performed on 20 mpa carbon fiber composite pressure vessels showed the accuracy of the damage mode discrimination method, and the damage state of the pressure vessel could be analyzed using the fiber fracture damage threshold according to the mae parameters.

Journal: Materials (Basel, Switzerland) (2022)
Publication types: Journal Article
Spin-defect qubits in two-dimensional transition metal dichalcogenides operating at telecom wavelengths.

Solid state quantum defects are promising candidates for scalable quantum information systems which can be seamlessly integrated with the conventional semiconductor electronic devices within the 3d monolithically integrated hybrid classical-quantum devices.Diamond nitrogen-vacancy (nv) center defects are the representative examples, but the controlled positioning of an nv center within bulk diamond is an outstanding challenge.Furthermore, quantum defect properties may not be easily tuned for bulk crystalline quantum defects.In comparison, 2d semiconductors, such as transition metal dichalcogenides (tmds), are promising solid platform to host a quantum defect with tunable properties and a possibility of position control.Here, we computationally discover a promising defect family for spin qubit realization in 2d tmds.The defects consist of transition metal atoms substituted at chalcogen sites with desirable spin-triplet ground state, zero-field splitting in the tens of ghz, and strong zero-phonon coupling to optical transitions in the highly desirable telecom band.

Journal: Nature communications (2022)
Publication types: Journal Article
Assessment of panfungal PCR performance with formalin-fixed paraffin-embedded tissue specimens†.

We reviewed the performance of a panfungal its-2 pcr and sanger sequencing assay performed on 88 ffpe specimens at the hospital for sick children (toronto, canada) in 2019.A potential fungal pathogen was identified by its pcr in 62.7 and 2.9% of positive and negative direct slide examination of tissue specimens, respectively.Its amplicons were detected in 87/88 specimens, with 53/88 (60.2%) considered as 'positive-contaminants' and 34/88 (38.6%) as 'positive-potential pathogen' upon sequencing.Potential pathogens included blastomyces dermatitidis (17.1%), cryptococcus neoformans (17.1%), histoplasma capsulatum (14.3%) and mucormycetes (11.4%).Laboratories should only perform its pcr on ffpe tissues if fungal elements have been confirmed on histopathology slides.Lay summary in this study, we examined how well a dna-based test could detect dna from fungi in archived human biopsy tissues.The best performance was achieved if fungi were seen in the tissue under a microscope before being tested.Our results indicate that we should only use this test if these conditions are met.

Journal: Medical mycology (2022)
Publication types: Journal Article;Review
Insights into the modular design of kinase inhibitors and application to Abl and Axl.

Scaffold hopping is a common strategy for generating kinase inhibitors that bind to the dfg-out inactive conformation.Small structural differences in inhibitor scaffolds can have significant effects on potency and selectivity across the kinome, however, these effects are often not studied in detail.Herein, we outline a design strategy to generate an array of dfg-out conformation inhibitors with three different hinge-binders and two dfg-pocket groups.We studied inhibitor selectivity across a large segment of the kinome and elucidated binding preferences that can be used in scaffold hopping campaigns.Using these analyses, we identified two selective inhibitors that display low nanomolar potency against axl or wild-type and clinically relevant mutants of abl.

Journal: RSC medicinal chemistry (2022)
Publication types: Journal Article