syedzayyan/paper_mill_benchmark huggingface dataset:
Upgrading cardoon biomass into Polyhydroxybutyrate based blends: A holistic approach for the synthesis of biopolymers and additives.

Cardoon, cynara cardunculus l.Represents a biorefinery crop with a great potential in the bioplastic field.This work investigates the valorization of different cardoon components into high added value products, finally recombined into novel upgraded bioplastics.Bioprocesses for polyhydroxybutyrate (phb) and medium-chain-length polyhydroxyalkanoates (mcl-pha) production were set up starting from root inulin and seed oil respectively, highlighting the effect of process conditions on polymer properties.The ternary blend, in which the phb polymer matrix was added with mcl-pha and epoxidized cardoon oil, evidenced a synergic effect of both additives in modulating phb structural and thermal properties, promoted by the physical interaction occurring among the components.This proof-of concept frames the paper in the holistic approach of circular economy applied to bioplastic production.

Journal: Bioresource technology (2022)
Publication types: Journal Article
Unravelling the full relaxation dynamics of superexcited helium nanodroplets.

The relaxation dynamics of superexcited superfluid he nanodroplets is thoroughly investigated by means of extreme-ultraviolet (xuv) femtosecond electron and ion spectroscopy complemented by time-dependent density functional theory (tddft).Three main paths leading to the emission of electrons and ions are identified: droplet autoionization, pump-probe photoionization, and autoionization induced by re-excitation of droplets relaxing into levels below the droplet ionization threshold.The most abundant product ions are he2+, generated by droplet autoionization and by photoionization of droplet-bound excited he atoms.He+ appear with some pump-probe delay as a result of the ejection he atoms in their lowest excited states from the droplets.The state-resolved time-dependent photoelectron spectra reveal that intermediate excited states of the droplets are populated in the course of the relaxation, terminating in the lowest-lying metastable singlet and triplet he atomic states.The slightly faster relaxation of the triplet state compared to the singlet state is in agreement with the simulation showing faster formation of a bubble around a he atom in the triplet state.

Journal: Physical chemistry chemical physics : PCCP (2021)
Publication types: Journal Article
Predictors of COVID-19 perceived susceptibility: insights from population-based self-reported survey during lockdown in the United States.

The covid-19 pandemic during lockdown has highlighted the importance of identifying individuals most at risk of infection with sars-co v-2, underscoring the need to assess factors contributing to susceptibility to disease.With the rapidly evolving nature of the pandemic and its new variants, there is an inadequate understanding on whether there are certain factors such as a specific symptom or collection of symptoms that combined with life-style behaviors may be useful to predict susceptibility.The study aims to explore such factors from pre-vaccination data to guide public health response to potential new waves.Methods an anonymous electronic survey was distributed through social media during the lockdown period in the united states from april to june 2020.Respondents were questioned regarding covid testing, presenting symptoms, demographic information, comorbidities, and confirmation of covid-19 test results.Stepwise logistic regression was used to identify predictors for covid-19 perceived susceptibility.Selected classifiers were assessed for prediction performance using area under receiver operating characteristic (auroc) curve analysis.Results a total of 130 participants deemed as susceptible because they self-reported their perception of having covid-19 (but without the evidence of positive test) were compared with 130 individuals with documented negative test results.Participants had a mean age of 45 years, and 165 (63%) were female.Final multivariable model showed significant associations with perceived susceptibility for the following variables: fever (or:33.5; 95%ci: 3.9,85.9), body ache (or:3.0; 95%ci:1.1,6.4), contact history (or:2.7; 95%ci:1.1,6.4), age> 50 (or:2.7; 95%ci:1.1, 6.6) and smoking (or:3.3; 95%ci: 1.2,9.1) after adjusting for other symptoms and presence of comorbid conditions.The auroc ranged from poor to fair (0.65-0.76) for cluster of symptoms but improved to a good model (auroc = 0.803) after inclusion of sociodemographic and lifestyle behaviors e.g., age and smoking tobacco.Conclusions fever and body aches suggest association with perceived covid-19 susceptibility in the presence of demographic and lifestyle behaviors.Using other constitutional and respiratory symptoms with fever and body aches, the parsimonious classifier correctly predicts 80.3% of covid-19 perceived susceptibility.A larger cohort of respondents will be needed to study and refine classifier performance in future lockdowns and with expected surge of new variants of covid-19 pandemic.

Journal: Journal of infection and public health (2022)
Publication types: Journal Article
Arginine and Arginine-Rich Peptides as Modulators of Protein Aggregation and Cytotoxicity Associated With Alzheimer's Disease.

A substantial body of evidence indicates cationic, arginine-rich peptides (carps) are effective therapeutic compounds for a range of neurodegenerative pathologies, with beneficial effects including the reduction of excitotoxic cell death and mitochondrial dysfunction.Carps, therefore, represent an emergent class of promising neurotherapeutics with multimodal mechanisms of action.Arginine itself is a known chaotrope, able to prevent misfolding and aggregation of proteins.The putative role of proteopathies in chronic neurodegenerative diseases such as alzheimer's disease (ad) warrants investigation into whether carps could also prevent the aggregation and cytotoxicity of amyloidogenic proteins, particularly amyloid-beta and tau.While monomeric arginine is well-established as an inhibitor of protein aggregation in solution, no studies have comprehensively discussed the anti-aggregatory properties of arginine and carps on proteins associated with neurodegenerative disease.Here, we review the structural, physicochemical, and self-associative properties of arginine and the guanidinium moiety, to explore the mechanisms underlying the modulation of protein aggregation by monomeric and multimeric arginine molecules.Arginine-rich peptide-based inhibitors of amyloid-beta and tau aggregation are discussed, as well as further modulatory roles which could reduce proteopathic cytotoxicity, in the context of therapeutic development for ad.

Journal: Frontiers in molecular neuroscience (2021)
Publication types: Journal Article;Review
Anogenital Distance and Endometriosis: Results of a Case-Control Study.

Agd is the distance measured from the anus to the genital tubercle.Recent evidence suggests that a shorter agd, a sensitive biomarker of the prenatal hormonal environment, could be associated with higher endometriosis risk.However, studies investigating agd in affected women are scanty.We have set up a case-control study recruiting nulliparous women (aged 18-40 years) with endometriosis between 2017 and 2018.Cases were 90 women with a surgical or with a current nonsurgical diagnosis of endometriosis (n = 45 deep infiltrating endometriosis (die), and n = 45 ovarian endometrioma (oma)).Controls were 45 asymptomatic women referring for periodical gynaecological care and without a previous diagnosis of endometriosis.They were matched to cases for age and bmi.For each woman, two measures were obtained using a digital calliper: agdac, from the clitoral surface to the upper verge of the anus, and agdaf, from the posterior fourchette to the upper verge of the anus.Each distance was derived from the mean of six measurements acquired from two different gynaecologists.The mean ± sd agdacin women with die, oma and without a diagnosis of endometriosis was 76.0 ± 12.1, 76.1 ± 11.1 and 77.8 ± 11.4 mm, respectively (p = 0.55).The mean ± sd agdafin women with die, oma and without a diagnosis of endometriosis was 22.8 ± 5.0, 21.7 ± 9.0 and 23.7 ± 7.8 mm, respectively (p = 0.38).Our study failed to find an association between agd and the presence of endometriosis.Agd does not seem to represent a reliable indicator of the presence of endometriosis to be used in clinical practice.

Journal: Reproductive sciences (Thousand Oaks, Calif.) (2022)
Publication types: Journal Article
The Therapeutic Value of Bone Marrow-Derived Endothelial Progenitor Cell Transplantation after Intracerebral Hemorrhage in Rats.

S to study the effect of endothelial progenitor cell (epc) treatment on intracerebral hemorrhage (ich) in rats and elucidate possible mechanisms.Methods the rats were randomly divided into three groups: (1) epc group: ich + epc, (2) phosphate-buffered saline group: ich + pbs, and (3) sham group.Epcs were transplanted intravenously 6 h after ich.Modified neurological severity score was used to evaluate neurological function.Blood-brain barrier (bbb) integrity was evaluated.Dead cells, inflammatory cytokines, and neuroprotective cytokines were assessed to investigate possible mechanisms.Results the animals in the epc group showed significant improvement in neurological function at 48 h, 72 h, and 7 days after ich, compared with those in the pbs group.Epc transplantation significantly reduced brain edema and the number of dead cells in the hematoma boundary areas.The intensity of evans blue was decreased, and expression levels of zonula occluden-1 and claudin-5 were increased in the epc group.Proinflammatory cytokines, including interferon-γ, il-6, and tnf-α, were decreased, whereas anti-inflammatory cytokines, including transforming growth factor-β1 and il-10, were increased in the epc group.In addition, expression levels of brain-derived neurotrophic factor, vascular endothelial growth factor, and neurotrophic growth factor were increased following transplantation of epcs.Conclusion epc transplantation could improve neurological function of ich rats.The protective effect may be mediated by promotion of neuroprotective cytokine secretion, restoration of the bbb, reduction of cell death, and the decrease in inflammation.

Journal: Frontiers in neurology (2017)
Publication types: Journal Article
Prevalence of hypertension in older people in Africa: a systematic review and meta-analysis.

The prevalence of hypertension in older people living on the african continent has not been comprehensively assessed.We aimed to provide accurate estimates of hypertension prevalence and variations by major predictive characteristics in this population to assist prevention and monitoring efforts.Methods for this systematic review and meta-analysis, we searched major electronic databases for population-based studies on hypertension prevalence reported from 1 january 2000 to 5 march 2016.Two independent reviewers undertook quality assessment and data extraction.We stabilized the variance of study-specific prevalence with the freeman-tukey single arcsine transformation before pooling the data with random-effects models.Results from the 2864 citations identified via searches, 91 studies providing 156 separate data contributions involving 54 198 individuals met the inclusion criteria.The overall prevalence of hypertension was 55.2% (95% confidence interval 53.1-57.4).Prevalence was higher in urban compared with rural settings [59.0% (55.3-62.6) vs.48.0% (43.8-52.3), p 94%, p < 0.001) and no evidence of publication bias.Conclusion our findings highlight the need to implement timely and aggressive strategies for prevention, detection, and control of hypertension among older people in africa.registration: prospero id crd42016034003.

Journal: Journal of hypertension (2017)
Publication types: Journal Article;Meta-Analysis;Review;Systematic Review
Geochemical stability of acid-generating pyrrhotite tailings 4 to 5 years after addition of oxygen-consuming organic covers.

Oxygen-consuming organic covers can serve as a reactive barrier to minimize sulfide oxidation in acid-generating tailings but may lead to metal mobilization in surface oxidized layers.We evaluated changes in the bio-geochemical stability of acid-generating, cu-ni pyrrhotite tailings 4 to 5 years after addition of a 50 cm-thick or a 1 m-thick biosolid cover planted with energy crops.The original tailings (p h 2.5) were oxidized in the first 10 to 40 cm, and goethite was the dominant sink for cu and ni, the main metal contaminants in these tailings.Both covers increased p h, nutrient availability, microbial activity and diversity in the oxidized tailings, and led to a reduction of water-soluble cu, ni, fe and al after 4 to 5 years of application.Changes in p h, humidity, organic c content, and redox conditions resulted in partial dissolution of jarosite and gypsum below the cover but goethite apparently remained stable.Under both covers, total ni decreased in the oxidized layer, indicating remobilization, but cu was retained.Significant accumulation of cu as cu sulfide at the oxidized/unoxidized tailings interface was detected only under the 1 m-thick cover, suggesting that the thinner cover may not sufficiently decrease the oxidizing conditions to mitigate acid mine drainage.Migration of nitrate and p down to the unoxidized tailings was observed under both covers and raises the concern of continued sulfide oxidation in unoxidized tailings.Although the implementation of thinner covers is economically more sustainable than thick covers, our results indicate that further research is required to establish their long-term suitability and performance to prevent acid mine drainage.

Journal: The Science of the total environment (2018)
Publication types: Journal Article
The Impact of Primary Versus Secondary Muscle-invasive Bladder Cancer at Diagnosis on the Response to Neoadjuvant Chemotherapy.

There might be differential sensitivity to neoadjuvant chemotherapy (nac) in patients with primary muscle-invasive bladder cancer (mibc) in comparison to patients with secondary mibc after a history of non-muscle-invasive disease.Objective to investigate pathologic response rates and survival associated with primary versus secondary mibc among patients treated with cisplatin-based nac for c t2-4n0m0 mibc.Design setting and participants oncologic outcomes were compared for 350 patients with primary mibc and 64 with secondary mibc treated with nac and radical cystectomy between 1992 and 2021 at 11 academic centers.Genomic analyses were performed for 476 patients from the memorial sloan kettering/the cancer genome atlas cohort.Outcome measurements and statistical analysis the outcome measures were pathologic objective response (p or; ≤yp t1 n0), pathologic complete response (p cr; yp t0 n0), overall mortality, and cancer-specific mortality.Results and limitations the primary mibc group had higher p or (51% vs 34%;p= 0.02) and p cr (33% vs 17%;p= 0.01) rates in comparison to the secondary mibc group.On multivariable logistic regression analysis, primary mibc was independently associated with both p or (odds ratio [or] 0.49, 95% confidence interval [ci] 0.26-0.87;p= 0.02) and p cr (or 0.41, 95% ci 0.19-0.82;p= 0.02).However, on multivariable cox regression analysis, primary mibc was not associated with overall mortality (hazard ratio 1.70, 95% ci 0.84-3.44;p= 0.14) or cancer-specific mortality (hazard ratio 1.50, 95% ci 0.66-3.40;p= 0.3).Genomic analyses revealed a significantly higher ercc2mutation rate in primary mibc than in secondary mibc (12.4% vs 1.3%;p< 0.001).Conclusions patients with primary mibc have better pathologic response rates to nac in comparison to patients with secondary mibc.Chemoresistance might be related to the different genomic profile of primary versus secondary mibc.Patient summary we investigated the treatment response to neoadjuvant chemotherapy (nac; chemotherapy received before the primary course of treatment) and survival for patients with a primary diagnosis of muscle-invasive bladder cancer (mibc) in comparison to patients with a history of non-muscle-invasive bladder cancer that progressed to mibc.Patients with primary mibc had a better response to nac but this did not translate to better survival after accounting for other tumor characteristics.

Journal: European urology open science (2022)
Publication types: Journal Article
Research protocol for delivering on the front line: a qualitative exploration of paramedics' experiences of providing pre-hospital maternity care in the United Kingdom.

And aim maternity patients form a small but significant portion of paramedical workload and this research aims to pragmatically explore east of england ambulance service paramedics' experiences of providing pre-hospital maternity care.Methods through semi-structured individual interviews, participants' thoughts and feelings regarding obstetric confidence and competence will be explored.It will be investigated whether they think their training and equipment is adequate and what they would change about maternity patient management.Data will be thematically analysed and the findings used to improve paramedic training, with a view to improving their confidence and competence.In turn, this should improve patient experiences and outcomes.

Journal: British paramedic journal (2022)
Publication types: Journal Article
NicotinamideN-Methyltransferase as Promising Tool for Management of Gastrointestinal Neoplasms.

Gastrointestinal (gi) neoplasms include esophageal, gastric, colorectal, hepatic, and pancreatic cancers.They are characterized by asymptomatic behavior, being responsible for diagnostic delay.Substantial refractoriness to chemo- and radiotherapy, exhibited by late-stage tumors, contribute to determine poor patient outcome.Therefore, it is of outmost importance to identify new molecular targets for the development of effective therapeutic strategies.In this study, we focused on the enzyme nicotinamide n-methyltransferase (nnmt), which catalyzes the n-methylation reaction of nicotinamide and whose overexpression has been reported in numerous neoplasms, including gi cancers.The aim of this review was to report data illustrating nnmt involvement in these tumors, highlighting its contribution to tumor cell phenotype.Cited works clearly demonstrate the interesting potential use of enzyme level determination for both diagnostic and prognostic purposes.Nnmt was also found to positively affect cell viability, proliferation, migration, and invasiveness, contributing to sustain in vitro and in vivo tumor growth and metastatic spread.Moreover, enzyme upregulation featuring tumor cells was significantly associated with enhancement of resistance to treatment with chemotherapeutic drugs.Taken together, these results strongly suggest the possibility to target nnmt for setup of molecular-based strategies to effectively treat gi cancers.

Journal: Biomolecules (2022)
Publication types: Journal Article;Review
Automatic quality control of brain T1-weighted magnetic resonance images for a clinical data warehouse.

Many studies on machine learning (ml) for computer-aided diagnosis have so far been mostly restricted to high-quality research data.Clinical data warehouses, gathering routine examinations from hospitals, offer great promises for training and validation of ml models in a realistic setting.However, the use of such clinical data warehouses requires quality control (qc) tools.Visual qc by experts is time-consuming and does not scale to large datasets.In this paper, we propose a convolutional neural network (cnn) for the automatic qc of 3d t1-weighted brain mri for a large heterogeneous clinical data warehouse.To that purpose, we used the data warehouse of the hospitals of the greater paris area (assistance publique-hôpitaux de paris [ap-hp]).Specifically, the objectives were: 1) to identify images which are not proper t1-weighted brain mris; 2) to identify acquisitions for which gadolinium was injected; 3) to rate the overall image quality.We used 5000 images for training and validation and a separate set of 500 images for testing.In order to train/validate the cnn, the data were annotated by two trained raters according to a visual qc protocol that we specifically designed for application in the setting of a data warehouse.For objectives 1 and 2, our approach achieved excellent accuracy (balanced accuracy and f1-score >90%), similar to the human raters.For objective 3, the performance was good but substantially lower than that of human raters.Nevertheless, the automatic approach accurately identified (balanced accuracy and f1-score >80%) low quality images, which would typically need to be excluded.Overall, our approach shall be useful for exploiting hospital data warehouses in medical image computing.

Journal: Medical image analysis (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Prevalence and Severity of Diabetic Retinopathy in Patients with Macular Telangiectasia Type 2.

To study the prevalence and severity of diabetic retinopathy (dr) in patients with macular telangiectasia type 2 (mac tel 2).Design retrospective case series.Participants patients with a diagnosis of mac tel 2 treated at the rotterdam eye hospital or erasmus medical center between 2014 and 2018 were included.Methods the following information was retrieved from patient files: demographics, history of diabetes mellitus and hypertension, presence of dr, and severity of dr, that is, mild, moderate, severe, or proliferative.Presence of diabetic macular edema (dme) was assessed using oct.Main outcome measures presence and severity of dr.Results two hundred six eyes of 103 patients were included.At the onset of mac tel 2, the mean age was 61 years (standard deviation [sd], 9.8 years) and 64 (62%) were women.Mean follow-up was 71 months (sd, 60 months).Diabetes mellitus type 2 was present in 50 patients (49%) and hypertension was present in 47 patients (46%).Mild dr was present in 22 eyes (11%), of which 14 eyes (7%) showed signs at baseline and 8 eyes (4%) showed signs at a later time during follow-up.Ten eyes (5%) demonstrated remission of mild dr during follow-up.Both eyes (1%) in 1 patient progressed to moderate dr.Severe dr, proliferative dr, and dme did not occur.Conclusions although diabetes mellitus was highly prevalent among mac tel 2 patients, no patients showed severe or proliferative dr or dme.These findings suggest that mac tel 2 could have a protective effect on the progression of dr.We hypothesize that our results may be explained by the role of müller cells in the development of mac tel 2 and dr, and therefore a link between both diseases warrants additional studies.

Journal: Ophthalmology. Retina (2021)
Publication types: Journal Article
Christchurch shallow groundwater quality survey dataset.

Shallow groundwater quality and level across the low-lying coastal city of christchurch, new zealand were surveyed at a high spatial resolution (1.3 piezometers/km2) in the spring of 2020.The groundwater quality parameters recorded across 99 piezometers include specific conductance, temperature, p h, and dissolved oxygen, following the pumping of approximately three bore volumes.Additionally, 27 out of 99 piezometers were analysed for chloride concentration and alkalinity as calcium carbonate.This dataset is useful to explore shallow groundwater conditions and how these might impact co-existing subsurface infrastructure and ecosystems.Furthermore, this dataset provides a valuable point of comparison against future changes, for example due to increased seawater intrusion, pollution events, or groundwater level rise.

Journal: Data in brief (2022)
Publication types: Journal Article