syedzayyan/paper_mill_benchmark huggingface dataset:
Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling.

Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins.The nematode caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry.Using the highly active biotin ligase turbo id, we optimize here a proximity labeling protocol for c.Elegans.An advantage of turbo id is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions.By combining extensive sonication with aggressive denaturation using sds and urea, we achieved near-complete solubilization of worm proteins.We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system.Neurons are among the smallest c.Elegans cells.To probe the method's sensitivity, we expressed turbo id exclusively in the two afd neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in afd.The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify.To test if our protocol could solubilize active zone proteins, we knocked turbo id into the endogenous elks-1 gene, which encodes a presynaptic active zone protein.We identified many known elks-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins.Versatile vectors and the inherent advantages of using c.Elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.

Journal: The Journal of biological chemistry (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Molecular engineering for construction of a novel ONOO-- activated multicolor fluorescent nanoprobe for early diagnosis and assessing treatment of arthritis in vivo.

Early diagnosis and assessment of the therapeutic effect of arthritis requires a reliable bioanalytical method to quantitatively and selectively detect the biomarkers peroxynitrite (onoo-) in inflammatory diseases.Compared with previously reported probes for the specific detection of onoo-, molecular engineering based on onoo--activated multicolor fluorescence nanoprobes will have the advantages of providing multi-channel information and be more suitable for bioimaging in multicomponent complex environments.Herein, for the first time, a fluorescent nanoprobe (csu-ft) based on fluorescence resonance energy transfer (fret), which can be activated by onoo-, was constructed for multicolor fluorescence imaging, diagnosis and treatment of arthritis in inflammatory mice.Specifically, an energy transfer scaffold was constructed by conjugation of a near-infrared (nir) xanthane fluorophore with a rhodamine b fluorophore and multicolor by onoo--modulated, which was then grafted onto sodium chondroitin sulfate (csna) to form csu-ft through self-assembly.This nanoprobe shows a fast response time (<20s), outstanding selectivity and excellent detection limits as low as 11.7 n m.Interestingly, csu-ft has been successfully used for intracellular multichannel imaging of endogenous onoo-production as well as for diagnosis and treatment in a mice model of arthritis with impressive results, revealing practical application in physiological and pathological connection between onoo-and arthritis.

Journal: Biosensors & bioelectronics (2022)
Publication types: Journal Article
Impacts of the COVID-19 pandemic restrictions on solid waste pollution in the worldwide iconic Copacabana Beach (Rio de Janeiro, Brazil).

Total and partial restrictions to beach access during covid-19 pandemic created an opportunity to evaluate its effect on coastal pollution.We aimed to determine the impact of access restrictions on solid waste pollution at copacabana beach, brazil.Solid waste amount was analyzed considering beach access restrictions: unrestricted, total closure, partial restriction, new normal.Relationships of atmospheric temperature and precipitation with access restrictions were assessed and confounding effects controlled for further analyses.Beach access restrictions significantly reduced solid waste pollution at copacabana beach, beach closure reduced waste amount in 72 %.Partial restrictions and new normal periods have significantly reduced solid wastes amount on the beach in 60 % and 36.88 %, respectively.Qualitative data revealed that most of solid wastes were single-use plastics recently disposed at copacabana beach, reflecting beachgoer's effects on waste left on the beach.A positive impact of covid-19 pandemic restrictions was detected on solid waste pollution at copacabana beach.

Journal: Marine pollution bulletin (2022)
Publication types: Journal Article
"Bi-Bi" technique for lip augmentation: A retrospective study on 30 cases.

Introduction lip augmentation is achieved mainly by using hyaluronic acid (ha) fillers.The injection procedures are performed either superficially or deeply with a needle or a cannula, and only one type of hyaluronic acid is used.The authors' objective was to evaluate the feasibility, safety, and satisfaction level of a procedure combining two anatomical injection plans, two injection modes (i.e., cannula and needle), and two types of hyaluronic acid fillers.Method the retrospective study included 30 patients who underwent the following procedure: intramuscular retro-trace injections of stylage m (vivacy® laboratories) were conducted through a 27-gauge cannula at the level of the upper and lower hemi-lip.Then, intradermal injections of stylage lips (vivacy® laboratories) using a 33-gauge needle were carried out on the entire lip border as well as the cupid's bow.During a post-injection follow-up, subjects were asked to evaluate satisfaction level and the effect of fillers over time.Elastic (g') and viscosity (g′′) moduli of ha fillers were measured with a rheometer (ar2000, ta instruments) prior to and after extrusion through a 33-gauge needle.Results rheological assessment showed that passage through a 33-gauge needle did not alter the viscoelastic properties of ha fillers.After the clinical procedure, no side effects were observed except for standard post-treatment bruises and edema.No vascular incident occurred.Moreover, overall patient satisfaction was high (2.6/3) and there was a long-lasting perception of the effect of the filler.Conclusion the current study demonstrated that dissociating the anatomical zones of the lip during the injection procedure by means of different hyaluronic acids in the muscular and dermal planes would efficiently and safely provide both lip projection and fullness for a natural and lasting effect.

Journal: Journal of cosmetic dermatology (2022)
Publication types: Journal Article
Clinical outcomes among out-of-hospital cardiac arrest patients treated by extracorporeal cardiopulmonary resuscitation: The CRITICAL study in Osaka.

Extracorporeal cardiopulmonary resuscitation (ecpr) is performed in refractory out-of-hospital cardiac arrest (ohca) patients, and the eligibility has been conventionally determined based on three criteria (initial cardiac rhythm, time to hospital arrival within 45 minutes, and age <75 years) in japan.Owing to limited information, this study descriptively determined neurological outcomes after applying the three criteria among ohca patients who underwent ecpr.Methods this study conducted a post-hoc analysis of data from the comprehensive registry of intensive care for ohca survival (critical) study.This was a multi-institutional prospective observational study of ohca patients in osaka prefecture, japan.All adult (aged ≥18 years) ohca patients with internal medical causes treated with ecpr between 1 july 2012 and 31 december 2019 were evaluated.We described one-month neurological favourable outcomes based on the three criteria (initial shockable, time to hospital arrival within 45 minutes, and age <75 years), and we compared them using the chi-square test.Results among 18,379 patients screened from the critical study database, we included 517 ohca patients treated by ecpr; 311 (60.2%) patients met all three criteria.Favourable neurological outcomes were as follows: patients meeting no or one criterion: 2.3% (1/43), those meeting two criteria: 8% (13/163), and those meeting all criteria: 16.1% (50/311) (p-value = 0.004).Conclusions in this study, approximately 60% of patients treated by ecpr met the three criteria (initial shockable, time to hospital arrival within 45 minutes, and age <75 years), and the greater the number of criteria met, the better were the neurological outcomes achieved.

Journal: Resuscitation (2022)
Publication types: Journal Article;Observational Study;Research Support, Non-U.S. Gov't
Carbonylation of atrial myosin prolongs its interaction with actin.

Carbonylation induced by hyperthyroidism suppresses force generation of skeletal myosin and sliding velocity of actin filaments in an in vitro motility assay.However, its effects on cardiac myosin at the molecular level have not been studied.Hyperthyroidism induces a change in expression of myosin heavy chains in ventricles, which may mask the effect of oxidation.In contrast to ventricular myosin, expression of myosin heavy chains in the atrium does not change upon hyperthyroidism and enables investigation of the effect of oxidation on cardiac myosin.We studied the influence of carbonylation, a type of protein oxidation, on the motor function of atrial myosin and ca2+regulation of actin-myosin interaction at the level of isolated proteins and single molecules using an in vitro motility assay and an optical trap.Carbonylation of atrial myosin prolonged its attached state on actin and decreased maximal sliding velocity of thin filaments over this myosin but did not affect the calcium sensitivity of the velocity.The results indicate that carbonylation of atrial myosin induced by hyperthyroidism can be a rate-limiting factor of atrium contractility and so participates in the genesis of heart failure in hyperthyroidism.

Journal: European biophysics journal : EBJ (2018)
Publication types: Journal Article
The molecular, immune features, and risk score construction of intraductal papillary mucinous neoplasm patients.

Intraductal papillary mucinous neoplasm (ipmn) is a common pancreatic precancerous lesion, with increasing incidence in recent years.However, the mechanisms of ipmn progression into invasive cancer remain unclear.The m rna expression data of ipmn/paad patients were extracted from the tcga and geo databases.First, based on gse19650, we analyzed the molecular alterations, tumor stemness, immune landscape, and transcriptional regulation of ipmn progression.The results indicated that gene expression changed dramatically, specifically at the intraductal papillary-mucinous adenoma (ipma) stage.Gene ontology (go), kyoto encyclopedia of genes and genomes (kegg), and kyoto encyclopedia of genes and genomes (gsea) pathway analyses showed that glycoprotein-related, cell cycle, and p53 pathways displayed the most significant changes during progression.With ipmn progression, tumor stemness increased continuously, and kras, erbb3, runx1, and elf3 are essential driver genes affecting tumor stemness.Motif analysis suggested that klf4 may be a specific transcription factor that regulates gene expression in the ipma stage, while myb and mybl1 control gene expression in the ipmc and invasive stages, respectively.Then, gse19650 and gse71729 transcriptome data were combined to perform the least absolute shrinkage and selection operator (lasso) method and cox regression analysis to develop an 11-gene prediction model (kcnk1, fhl2, lamc2, cdca7, gpx3, c7, vip, hba1, btg2, mt1e, and lyve1) to predict the prognosis of pancreatic cancer patients.The reliability of the model was validated in the gse71729 and tcga databases.Finally, 11 additional ipmn patients treated in our hospital were included, and the immune microenvironment changes during ipmn progression were analyzed by immunohistochemistry (ihc).Ihc results suggest that myeloid-derived suppressor cells (mdscs) and macrophages may be key in the formation of immunosuppressive microenvironment of ipmn progression.Our study deepens our understanding of ipmn progression, especially the changes in the immune microenvironment.The findings of this work may contribute to the development of new therapeutic strategies for ipmn.

Journal: Frontiers in molecular biosciences (2022)
Publication types: Journal Article
Exosomes and alpha-synuclein within retina from autophagy to protein spreading in neurodegeneration.

In the course of age-related macular degeneration (amd) as well as in multiple retinal disorders protein aggregates are described at various levels in the retina.In amd this fills the space between retinal pigment epithelium (rpe) in the form of drusen, which contains amyloid and other protein aggregates along with lipids.Nonetheless, in very advanced stages of amd, as well as in other retinal pathologies and early on in retinitis pigmentosa, a number of neuronal inclusions, which stain for α-synuclein spreads all over the retinal layers.Thus, an early or later defect in the clearance of α-synuclein may represent a final common pathway to these phenomena.The physiological clearance of α-synuclein is provided by the autophagy machinery starting at the level of the rpe and occurring throughout the retina.Such a process is also involved in the clearance of melanin-dependent toxic metabolites under the effects of different wavelengths and the stimulatory activity of the sympathetic nervous system.In search for the occurrence of these culprits, here we report the presence of α-synuclein in the retina combined with exosomal detection to document the presence of a α-synuclein spreading apparatus.This was correlated with the occurrence of autophagy markers throughout retinal layers, along with sympathetic innervation, which in turn was related to melanin content.

Journal: Archives italiennes de biologie (2021)
Publication types: Journal Article
Linking scientific instruments and computation: Patterns, technologies, and experiences.

Powerful detectors at modern experimental facilities routinely collect data at multiple gb/s.Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space.Thus, methods are required for configuring and running distributed computing pipelines-what we call flows-that link instruments, computers (e.g., for analysis, simulation, artificial intelligence [ai] model training), edge computing (e.g., for analysis), data stores, metadata catalogs, and high-speed networks.We review common patterns associated with such flows and describe methods for instantiating these patterns.We present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages powerful computers for data inversion,model training, or other purposes.We also discuss implications of such methods for operators and users of scientific facilities.

Journal: Patterns (New York, N.Y.) (2022)
Publication types: Journal Article
Research note: The resistome of commensal Escherichia coli isolated from broiler carcasses "produced without the use of antibiotics"a.

Several strategies have been in place in food animal production to reduce the unnecessary use of antimicrobial agents.Beyond the monitoring of their use, the evaluation of the effect of these strategies on the occurrence and types of antimicrobial resistance (amr) associated genes is crucial to untangle the potential emergence and spread of amr to humans through the food chain.In the present study, the occurrence of these genes was evaluated in commensal escherichia coli isolated from broiler carcasses "produced without the use of antibiotics" in 3 antibiotic-free (ab-free) farms in italy in 2019.Sequenced data were analyzed along with publicly available genomes of e.Coli collected in italy from the broiler food chain from previous years (2017-2018).The genetic relationships among all 93 genomes were assessed on de novo assemblies by in silico mlst and snp calling.Moreover, the resistomes of all genomes were investigated.According to snp calling, genomes were gathered in three clades.Clade a encompassed, among others, st117, st8070, and st1011 genomes.St10 belonged to clade b, whereas clade c included st58, st297, st1101, and st23 among others.Regarding the occurrence of amr genes, a statistically significant lower occurrence of these genes in the genomes of this study in comparison to the public genomes was observed considering the whole group of genes as well as genes specifically conferring resistance to aminoglycosides, β-lactams, phenicols, trimethoprim, and lincosamides.Moreover, significant reductions were observed by comparing the whole group of amr associated mutations, as well as those specifically for fluoroquinolones and fosfomycin resistance.Although the identification of 3° generation cephalosporin resistance associated genes in ab-free e.Coli is a concern, this study provides a first indication of the impact of a more prudent use of antimicrobial agents on the occurrence of amr genes in italian broiler production chain.More studies are needed in next years on a higher number of genomes to confirm this preliminary observation.

Journal: Poultry science (2022)
Publication types: Journal Article
Ocrelizumab: A Review in Multiple Sclerosis.

Ocrelizumab (ocrevus®) is an intravenously administered, humanized anti-cd20 monoclonal antibody approved for the treatment of adults with relapsing forms of multiple sclerosis (rms) or primary progressive multiple sclerosis (ppms).The efficacy of ocrelizumab in reducing relapse rates and disease activity in patients with rms was demonstrated in pivotal trials (versus interferon β-1a) and supporting single-arm studies in specific subpopulations.In patients with ppms, ocrelizumab reduced measures of clinical and mri progression relative to placebo.Clinical benefits were maintained over ≥ 7.5 study years of treatment.Ocrelizumab was generally well tolerated and no new safety signals have emerged with long-term use.Extensive (albeit short-term) real-world data pertaining to ocrelizumab is consistent with that from clinical trials.Ocrelizumab provides the convenience of short, half-yearly infusions.Ocrelizumab continues to represent a generally well-tolerated, high-efficacy disease-modifying therapy (dmt) for rms and is a valuable treatment for delaying disease progression in patients with ppms (for whom there are currently no other approved dmts).

Journal: Drugs (2022)
Publication types: Journal Article;Review
Association Between Diet-Related Inflammation and COPD: Findings From NHANES III.

And aims:little is known about diet-related inflammation in chronic obstructive pulmonary disease (copd).In this study, we aimed to explore the association between copd and dietary inflammatory index (dii) scores in adults over 40 years old.methods:data were obtained from the 2013 to 2018 national health and nutrition examination survey (nhanes).In the present study, 9,929 participants were included and analyzed.The dii score was calculated and divided into tertiles.Logistic regression analysis was performed to determine the odds ratios of dii tertiles.results:participants were categorized into copd (565, 5.69%) and non-copd groups (9,364, 94.31%) according to interview information.Copd individuals had higher dii scores than non-copd individuals (0.429 ± 1.809 vs.-0.191 ± 1.791,p< 0.001).The highest dii score tertile included 46.55% of copd individuals was associated with lower family incomes and education and a higher smoking rate (p< 0.01).The odds ratios (95% cis) of copd according to logistic regression were 0.709 (0.512-0.982) for t1 and 0.645 (0.475-0.877) for t2 of the dii score (p= 0.011).conclusion:higher dii scores were positively correlated with copd in participants over 40 years old.These results further support that diet can be used as an intervention strategy for copd management.

Journal: Frontiers in nutrition (2021)
Publication types: Journal Article
Israeli social workers' recommendations on guardianship and supported decision-making: Examination of client and social worker factors.

We examined social workers' recommendations regarding the possible appointment of a guardian, a supported decision maker (sdm), or neither for persons with disabilities.Social workers (n = 328) were presented with four vignettes that contained factors potentially relevant to guardianship and sdm judgments.They expressed higher support of sdm and maintaining the status quo (without a guardian or sdm) and lower support for guardianship.Social workers were more likely to recommend guardianship when the person depicted in the vignette was labeled as having an intellectual disability, needed support in decision-making, lacked familial support, and agreed to guardianship.They were more inclined to support the status quo for individuals with mental illness, when there was little need for decision-making support, when the family was supportive, and when the individual refused guardianship.Social workers who had not heard of the sdm reform, and those with positive attitudes toward guardianship, supported guardianship.Findings are discussed in light of the status and functional approaches to guardianship and the relational notion of autonomy.As part of the sdm reform, decision-making capacity should not be assessed based on diagnosis or on independent decision-making, but rather on the ability to make decisions when receiving appropriate support.(psyc info database record (c) 2022 apa, all rights reserved).

Journal: The American journal of orthopsychiatry (2022)
Publication types: Journal Article
Early Lyme disease-associated Guillain Barre Syndrome: A case report.

Lyme disease is the most common tick-borne disease in the united states.Left untreated, it can lead to neuroborreliosis.Here we describe a case of early disseminated lyme disease-associated guillain barre syndrome in a previously healthy adult that early clinical suspicion and accurate testing led to proper diagnosis and case management.It is important to be aware of guillain barre syndrome as an early consequence of lyme disease especially during tick activity season.This case report is meant to raise awareness among clinicians and calls for protective measures especially where there is significant outdoor activity.

Journal: IDCases (2022)
Publication types: Case Reports;Journal Article