syedzayyan/paper_mill_benchmark huggingface dataset:
Quantized Pulse Propagation in Josephson Junction Arrays.

We present time-domain electrical measurements and simulations of the quantized voltage pulses that are generated from series-connected josephson junction (jj) arrays.The transmission delay of the jj array can lead to a broadening of the net output pulse, depending on the direction of the output pulse propagation relative to the input bias pulse.To demonstrate this, we compare time-domain measurements of output pulses from radio-frequency josephson arbitrary waveform synthesizer (rf-jaws) circuits fabricated with two different output measurement configurations, so that the backward-propagating and forward-propagating pulses can be measured.Measurements were made on arrays with 1200 and 3600 jjs and show that the net backward-propagating output pulse is broadened by timing delays in the jj array while the net forward-propagating output pulse is insensitive to delay effects and can theoretically be further scaled to longer jj array lengths without significant output pulse broadening.These measurements match well with simulations and confirm the expectation that the net output pulses arise from the time-delayed superposition of individual jj output pulses from the series array of jjs.The measurements and analysis shown here have important implications for the realization of rf-jaws circuits to be used as quantum-based reference sources for communications metrology.

Journal: IEEE transactions on applied superconductivity : a publication of the IEEE Superconductivity Committee (2019)
Publication types: Journal Article
Accelerated magnetic resonance imaging tissue phase mapping of the rat myocardium using compressed sensing with iterative soft-thresholding.

Introduction tissue phase mapping (tpm) mri can accurately measure regional myocardial velocities and strain.The lengthy data acquisition, however, renders tpm prone to errors due to variations in physiological parameters, and reduces data yield and experimental throughput.The purpose of the present study is to examine the quality of functional measures (velocity and strain) obtained by highly undersampled tpm data using compressed sensing reconstruction in infarcted and non-infarcted rat hearts.Methods three fully sampled left-ventricular short-axis tpm slices were acquired from 5 non-infarcted rat hearts and 12 infarcted rat hearts in vivo.The datasets were used to generate retrospectively (simulated) undersampled tpm datasets, with undersampling factors of 2, 4, 8 and 16.Myocardial velocities and circumferential strain were calculated from all datasets.The error introduced from undersampling was then measured and compared to the fully sampled data in order to validate the method.Finally, prospectively undersampled data were acquired and compared to the fully sampled datasets.Results bland altman analysis of the retrospectively undersampled and fully sampled data revealed narrow limits of agreement and little bias (global radial velocity: median bias = -0.01 cm/s, 95% limits of agreement = [-0.16, 0.20] cm/s, global circumferential strain: median bias = -0.01%strain, 95% limits of agreement = [-0.43, 0.51] %strain, all for 4x undersampled data at the mid-ventricular level).The prospectively undersampled tpm datasets successfully demonstrated the feasibility of method implementation.Conclusion through compressed sensing reconstruction, highly undersampled tpm data can be used to accurately measure the velocity and strain of the infarcted and non-infarcted rat myocardium in vivo, thereby increasing experimental throughput and simultaneously reducing error introduced by physiological variations over time.

Journal: PloS one (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
CaMKIIβ knockdown decreases store-operated calcium entry in hippocampal dendritic spines.

Calcium/calmodulin-dependent protein kinase ii (ca mkii) and neuronal store-operated calcium entry (n soce) have been implicated in the development of alzheimer's disease (ad).N soce is involved in regulation of dendritic spine shape, particularly in stability of mushroom spines that play role in formation of strong synapses.Ca mkii is involved in regulation of induction of long-term potentiation, that is needed for shaping of memory.In the present study, we demonstrated that inhibition of kinase activity of ca mkii by kn-62 decreases n soce amplitude in soma of primary hippocampal neurons.We have shown that knockdown of ca mkiiβ leads to the downregulation of n soce in dendritic spines.In agreement with previously published data, we have also observed that ca mkiiβ knockdown causes mushroom spine loss in primary hippocampal culture.The effect of ca mkiiβ knockdown on the n soce may be associated with a decrease of dendritic spine head size.

Journal: IBRO neuroscience reports (2022)
Publication types: Journal Article
Hypoxia-Induced Cancer Cell Responses Driving Radioresistance of Hypoxic Tumors: Approaches to Targeting and Radiosensitizing.

Within aggressive malignancies, there usually are the "hypoxic zones"-poorly vascularized regions where tumor cells undergo oxygen deficiency through inadequate blood supply.Besides, hypoxia may arise in tumors as a result of antiangiogenic therapy or transarterial embolization.Adapting to hypoxia, tumor cells acquire a hypoxia-resistant phenotype with the characteristic alterations in signaling, gene expression and metabolism.Both the lack of oxygen by itself and the hypoxia-responsive phenotypic modulations render tumor cells more radioresistant, so that hypoxic tumors are a serious challenge for radiotherapy.An understanding of causes of the radioresistance of hypoxic tumors would help to develop novel ways for overcoming this challenge.Molecular targets for and various approaches to radiosensitizing hypoxic tumors are considered in the present review.It is here analyzed how the hypoxia-induced cellular responses involving hypoxia-inducible factor-1, heat shock transcription factor 1, heat shock proteins, glucose-regulated proteins, epigenetic regulators, autophagy, energy metabolism reprogramming, epithelial-mesenchymal transition and exosome generation contribute to the radioresistance of hypoxic tumors or may be inhibited for attenuating this radioresistance.The pretreatments with a multitarget inhibition of the cancer cell adaptation to hypoxia seem to be a promising approach to sensitizing hypoxic carcinomas, gliomas, lymphomas, sarcomas to radiotherapy and, also, liver tumors to radioembolization.

Journal: Cancers (2021)
Publication types: Journal Article;Review
Impact of disruptions to routine vaccination programs, quantifying burden of measles, and mapping targeted supplementary immunization activities.

Measles is a highly transmissible disease that requires high levels of vaccination coverage for control and elimination.Areas that are unable to achieve and maintain high coverage levels are at risk for measles outbreaks resulting in increased morbidity and mortality.Public health emergencies, such as the current covid-19 pandemic, pose a threat to the functioning of health systems by disrupting immunization services which can derail measles vaccination efforts.Efforts to bridge coverage gaps in immunization include the rapid return to fully functioning services as well as deploying supplementary immunization activities (sias), which are additional vaccination campaigns intended to catch-up children who have missed routine services.However, sias, which to date tend to be national efforts, can be difficult to mobilize quickly, resource-intensive, and even more challenging to deploy during a public health crisis.By mapping expected burden of measles, more effective sias that are setting-specific and resource-efficient can be planned and mobilized.Using a spatial transmission model of measles dynamics, we projected and estimated the expected burden of national and local measles outbreaks in zambia with the current covid-19 pandemic as a framework to inform disruptions to routine vaccination.We characterize the impact of disruptions to routine immunization services on measles incidence, map expected case burden, and explore sia strategies to mitigate measles outbreaks.We find that disruptions lasting six months or longer as well as having low mcv1 coverage prior to disruptions resulted in an observable increase of measles cases across provinces.Targeting provinces at higher risk of measles outbreaks for sias is an effective strategy to curb measles virus incidence following disruptions to routine immunization services.

Journal: Epidemics (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Molecular insights and therapeutic implications of nanoengineered dietary polyphenols for targeting lung cancer: part II.

Flavonoids represent a major group of polyphenolic compounds.Their capacity to inhibit tumor proliferation, cell cycle, angiogenesis, migration and invasion is substantially responsible for their chemotherapeutic activity against lung cancer.However, their clinical application is limited due to poor aqueous solubility, low permeability and quick blood clearance, which leads to their low bioavailability.Nanoengineered systems such as liposomes, nanoparticles, micelles, dendrimers and nanotubes can considerably enhance the targeted action of the flavonoids with improved efficacy and pharmacokinetic properties, and flavonoids can be successfully translated from bench to bedside through various nanoengineering approaches.This review addresses the therapeutic potential of various flavonoids and highlights the cutting-edge progress in the nanoengineered systems that incorporate flavonoids for treating lung cancer.

Journal: Nanomedicine (London, England) (2022)
Publication types: Journal Article;Review
Mfn2 Overexpression Attenuates MPTP Neurotoxicity In Vivo.

Mitochondrial dysfunction represents a critical event in the pathogenesis of parkinson's disease (pd).Increasing evidence demonstrates that disturbed mitochondrial dynamics and quality control play an important role in mitochondrial dysfunction in pd.Our previous study demonstrated that mpp+induces mitochondrial fragmentation in vitro.In this study, we aimed to assess whether blocking mptp-induced mitochondrial fragmentation by overexpressing mfn2 affords neuroprotection in vivo.We found that the significant loss of dopaminergic neurons in the substantia nigra (sn) induced by mptp treatment, as seen in wild-type littermate control mice, was almost completely blocked in mice overexpressing mfn2 (h mfn2 mice).The dramatic reduction in dopamine neuronal fibers and dopamine levels in the striatum caused by mptp administration was also partially inhibited in h mfn2 mice.Mptp-induced oxidative stress and inflammatory response in the sn and striatum were significantly alleviated in h mfn2 mice.The impairment of motor function caused by mptp was also blocked in h mfn2 mice.Overall, our work demonstrates that restoration of mitochondrial dynamics by mfn2 overexpression protects against neuronal toxicity in an mptp-based pd mouse model, which supports the modulation of mitochondrial dynamics as a potential therapeutic target for pd treatment.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article
RNA expression and disease tolerance are associated with a "keystone mutation" in the ochre sea starPisaster ochraceus.

An overdominant mutation in an intron of the elongation factor 1-α(ef1a) gene in the sea star pisaster ochraceushas shown itself to mediate tolerance to "sea star wasting disease", a pandemic that has significantly reduced sea star populations on the pacific coast of north america.Here we use rna sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype.Our results show that individuals carrying this mutation have lower expression at a large contingent of gene regions.Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease.Given the ecological significance of p.Ochraceus, these results may be useful in predicting the evolutionary and demographic future for pacific intertidal communities.

Journal: PeerJ (2017)
Publication types: Journal Article
Susac syndrome and pregnancy: a relationship to clarify. About two cases and review of the literature.

Susac syndrome is a vasculopathy that affects the central nervous system, mainly the brain parenchyma, retina and inner ear.It affects mainly young women and.Management is based on expert consensus and in pregnant women the treatment is not well established.It is necessary to start treatment early because of its potential severity and sequelae.Method we present two cases of susac syndrome related to pregnancy/puerperium and performed a review of the literature.Conclusions susac syndrome is a disease that requires a high clinical suspicion, especially in pregnant women.Treatment in pregnancy or puerperium is not well established.Précis susac syndrome is a disease that requires a high clinical suspicion, especially in pregnant women.Treatment in pregnancy or puerperium is not well established.

Journal: The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians (2022)
Publication types: Journal Article;Review
Recessive Dystrophic Epidermolysis bullosa due to Hemizygous 40 kb Deletion of COL7A1 and the Proximate PFKFB4 Gene Focusing on the Mutation c.425A>G Mimicking Homozygous Status

Dystrophic epidermolysis bullosa (deb) is a rare inherited mechanobullous disease characterised by the hyperfragility of the skin and mucous membranes.It is (typically) caused by (loss-of-function) mutations in the col7a1 gene that impair the formation of collagen type vii, which represents the major constituent of anchoring fibrils within the basement membrane zone of epithelialised tissues.In a 4-year-old patient diagnosed with the clinical features of recessive deb, genotyping via next-generation eb panel sequencing initially revealed the homozygosity of the maternal c.425a>g mutation, while the paternal heterozygosity in exon 3 was lacking.This genetic profile suggested incongruent gene transmission due to uniparental isodisomy (upd) or the occurrence of a hemizygous deletion of unknown size.Methods: thus, the eb panel sequencing of genomic dna, followed by a paternity test and analysis of microsatellite markers, as well as multiplex ligation-dependent probe amplification (mlpa) copy number analysis using patient and parental dna, were performed.Results: this approach revealed a paternally derived hemizygous deletion spanning from exon 3 to exon 118.Linear amplification-mediated pcr (lam-pcr) determined the breaking points within intron 2 of the col7a1 gene, comprising a 40kb segment within intron 1 of the adjacent pfkfb4 gene.Conclusion: this report highlights the relevance of advanced molecular profiling to determine new/exceptional/unusual genotypes and the accurate mode of genetic transmission in deb.

Journal: Diagnostics (Basel, Switzerland) (2022)
Publication types: Journal Article
Does weight management research for adults with severe obesity represent them? Analysis of systematic review data.

Our objective was to determine the extent to which current evidence from long-term randomised controlled trials (rcts) of weight management is generalisable and applicable to underserved adult groups with obesity (body mass index (bmi) ≥35 kg/m2).Methods descriptive analysis of 131 rcts, published after 1990-may 2017 with ≥1 year of follow-up, included in a systematic review of long-term weight management interventions for adults with bmi ≥35 kg/m2(the rebalance project).Studies were identified from medline, embase, psych info, sci, central and from hand searching.Reporting of trial inclusion and exclusion criteria, trial recruitment strategies, baseline characteristics and outcomes were analysed using a predefined list of characteristics informed by the progress (place of residence, race/ethnicity/culture/language, occupation, gender/sex, religion, education, socioeconomic status, social capital)-plus framework and the uk equality act 2010.Results few (6.1%) trials reported adapting recruitment to appeal to underserved groups.10.0% reported culturally adapting their trial materials.Only 6.1% of trials gave any justification for their exclusion criteria, yet over half excluded participation for age or mental health reasons.Just over half (58%) of the trials reported participants' race or ethnicity, and one-fifth reported socioeconomic status.Where outcomes were reported for underserved groups, the most common analysis was by sex (47.3%), followed by race or ethnicity (16.8%).3.1% of trials reported outcomes according to socioeconomic status.Discussion although we were limited by poor trial reporting, our results indicate inadequate representation of people most at risk of obesity.Guidance for considering underserved groups may improve the appropriateness of research and inform greater engagement with health and social care services.Funding national institute for health research health technology assessment programme (project number: 15/09/04).Prospero registration number crd42016040190.

Journal: BMJ open (2022)
Publication types: Journal Article;Systematic Review;Research Support, Non-U.S. Gov't
Preoperative Hemoglobin Level, Oxygen Saturation and Postoperative Outcomes in Children With Cyanotic Congenital Heart Disease: A Propensity-Score Matching Analysis.

The optimal preoperative hemoglobin (hb) level is difficult to define in children with cyanotic congenital heart disease (chd) due to hypoxemia-induced secondary erythrocytosis.This retrospective study integrated preoperative hb and pulse oxygen saturation (sp o2) using the product of hb × sp o2to predict postoperative outcomes in children with cyanotic chd.Patients and methods children aged <18 years undergoing cardiac surgery with cyanotic chd were included.The cutoff value of hb × sp o2was the age-adjusted lower limit of normal hb (aa hb) in healthy children.The main outcomes were in-hospital death and the composite outcome of severe postoperative events.Multivariate logistic regression analysis and propensity score matching analysis were used to adjust for important confounders.Results the presence of preoperative hb × sp o2< aa hb was observed in 21.6% of cyanotic children (n= 777).Children with hb × sp o2< aa hb had higher in-hospital mortality (12.5% vs.4.6%,p< 0.001) and composite outcome incidence (69.6% vs.32.3%,p< 0.001) than those with hb × sp o2≥ aa hb.After propensity score matching, 141 pairs of children were successfully matched.Multivariate analysis showed that preoperative hb × sp o2< aa hb was significantly associated with the composite outcome in the entire population (odds ratio = 4.092, 95% confidence interval = 2.748-6.095,p< 0.001) and the matched cohorts (odds ratio = 2.277, 95% confidence interval = 1.366-3.795,p= 0.002).Conclusion our results suggest that a preoperative hb × sp o2value below the lower limit of normal hemoglobin is a prognostic factor in cyanotic children undergoing cardiac surgery and is a potential criterion to evaluate preoperative anemia in this population.

Journal: Frontiers in pediatrics (2021)
Publication types: Journal Article
Impact of the COVID-19 Pandemic on Liver Cancer Staging at a Multidisciplinary Liver Cancer Clinic.

To compare liver cancer resectability rates before and during the covid-19 pandemic.Background liver cancers usually present with nonspecific symptoms or are diagnosed through screening programs for at-risk patients, and early detection can improve patient outcomes.In 2020, the covid-19 pandemic upended medical care across all specialties, but whether the pandemic was associated with delays in liver cancer diagnosis is not known.Methods we performed a retrospective review of all patients evaluated at the johns hopkins multidisciplinary liver cancer clinic from january 2019 to june 2021 with a new diagnosis of suspected or confirmed hepatocellular carcinoma (hcc) or biliary tract cancer (btc).Results there were 456 liver cancer patients (258 hcc and 198 btc).From january 2019 to march 2020 (pre-pandemic), the surgical resectability rate was 20%.The subsequent 6 months (early pandemic), the resectability rate decreased to 11%.Afterward from october 2020 to june 2021 (late pandemic), the resectability rate increased to 27%.The resectability rate early pandemic was significantly lower than that for pre-pandemic and later pandemic combined (11% lower; 95% confidence interval [ci], 2%-20%).There was no significant difference in resectability rates pre-pandemic and later pandemic (7% difference; 95% ci, -3% to 16%).In subgroup analyses, the early pandemic was associated with a larger impact in btc resectability rates than hcc resectability rates.Time from btc symptom onset until multidisciplinary liver clinic evaluation increased by over 6 weeks early pandemic versus pre-pandemic (hazard ratio, 0.63; 95% ci, 0.44-0.91).Conclusions during the early covid-19 pandemic, we observed a drop in the percentage of patients presenting with curable liver cancers.This may reflect delays in liver cancer diagnosis and contribute to excess mortality related to the covid-19 pandemic.

Journal: Annals of surgery open : perspectives of surgical history, education, and clinical approaches (2022)
Publication types: Journal Article
Antimicrobial Peptide BCp12 InhibitsStaphylococcus aureusGrowth by Altering Lysine Malonylation Levels in the Arginine Synthesis Pathway.

To adapt to external stimuli, bacteria fine-tune important protein activities using post-translational modifications.The present study provides novel insights into the molecular mechanism of the antimicrobial peptide bcp12.We demonstrate that bcp12 significantly suppressed bacterial growth, induced cell apoptosis, and modulated overall malonylation levels in staphylococcus aureuscells.Malonylateomic analysis was performed to identify the proteins malonylated by the bcp12 treatment of s.Aureus.In total, 53 malonylated proteins (17 up-regulated, 36 down-regulated) were identified as differentially expressed malonylated proteins (dmps; > 1.5-fold or 1,p< 0.05) in the arginine and proline metabolome.Bioinformatic analysis revealed that the dmps and dms were especially enriched in the arginine synthesis pathway.By integrating our lysine malonylational and metabolomic data, we provide new insights into the mechanism by which bcp12 inhibits s.Aureus.

Journal: Journal of agricultural and food chemistry (2022)
Publication types: Journal Article