syedzayyan/paper_mill_benchmark huggingface dataset:
Murine Mammary Carcinoma Induces Chronic Systemic Inflammation and Immunosuppression in BALB/c Mice.

The f3ii cell line is a highly invasive variant of mammary carcinoma.Although it is frequently used as a model to evaluate the efficacy of immunotherapy, its impact on the immune system remains poorly understood.The main objectives of this study were to evaluate the effects of f3ii tumors on the development of chronic inflammation and to characterize tumor-associated immunosuppression.Methods following the experimental implantation of f3ii tumors in balb/c mice, alterations in the liver and spleen anatomy and the numbers of circulating leukocytes, myeloid-derived suppressor cells (mdscs), and regulatory t cells were measured using hematological techniques, histopathological analysis, and flow cytometry.The capacity of the f3ii tumor-bearing mice to reject mb16f10 allogeneic tumor transplantation was also evaluated.In addition, the restoration of immune parameters in tumor-bearing mice was evaluated after standard breast cancer chemotherapy and surgical tumor excision.Results f3ii tumor implantation increased the levels of chronic inflammatory markers, such as the neutrophil-to-lymphocyte and platelet-to-lymphocyte ratios, and caused myeloid alterations, including extramedullary granulopoiesis and megakaryopoiesis, along with the recruitment of mdscs to the spleen.Chemotherapy or surgical f3ii tumor removal completely rescued the tumor-associated extramedullary granulopoiesis and megakaryopoiesis.Notably, the presence of f3ii tumors reduced the capacity of balb/c mice to reject mb16f10 allogeneic tumor transplantation.Conclusion these results support the occurrence of f3ii tumor-mediated immune cell dysfunction, which mimics the immune alterations characterized by chronic systemic inflammation and immunosuppression observed in breast cancer in clinical settings.Thus, the f3ii tumor model is relevant for evaluating novel breast cancer immunotherapies and combinations in preclinical studies.This model could also be useful for identifying appropriate therapeutic targets and developing proof-of-concept experiments in the future.

Journal: Journal of breast cancer (2022)
Publication types: Journal Article
X-linked dominant protoporphyria in a Chinese pedigree reveals a four-based deletion ofALAS2.

X-linked dominant protoporphyria (xldpp) is a rare, hereditary disorder that leads to hepatobiliary and hematologic abnormalities including increased erythrocyte protoporphyrin, cutaneous photosensitivity, and decreased iron stores that is caused by a pathogenic mutation of alas2gene.Methods this study aimed to confirm the existence of xldpp in a chinese pedigree.We observed and described the dermatoscopic findings of this disorder under dermoscopy, and assessed photo damage in xldpp patients using the fotofinder system and very high frequency (vhf) skin ultrasonic system.We performed next generation sequencing and sanger sequencing to detect and confirm genetic variants in dna samples from the xldpp family.Moreover, we monitored the hepatobiliary function as well as hematologic changes in related family members.Results as compared to unaffected control subjects, patients exhibited evidence of severe cutaneous photodamage, causing photoaging, an increase in the size of the gallbladder, increased levels of protoporphyrin in red blood cells, an increase in blood levels of uroporphyrin and hematoporphyrin, and iron deficiency.Conclusions xldpp was validated by the identification of a four-base-pair deletion (c.1706_1709del agtg, p.e569fs) in alas2(nm_000032.4) in the proband which segregated with the disease in an x-linked dominant pattern, with hemizygous males being more severely affected than heterozygous females.We also found a missense variant in gata binding protein 1 (gata1).

Journal: Annals of translational medicine (2020)
Publication types: Journal Article
COVID-19 vaccinology landscape in Africa.

More than two years after the start of covid-19 pandemic, africa still lags behind in terms vaccine distribution.This highlights the predicament of africa in terms of vaccine development, deployment, and sustainability, not only for covid-19, but for other major infectious diseases that plague the continent.This opinion discusses the challenges africa faces in its race to vaccinate its people, and offers recommendations on the way forward.Specifically, to get out of the ongoing vaccine shortage trap, africa needs to diversify investment not only to covid-19 but also other diseases that burden the population.The continent needs to increase its capacity to acquire vaccines more equitably, improve access to technologies to enable local manufacture of vaccines, increase awareness on vaccines both in rural and urban areas to significantly reduce disease incidence of covid-19 and as well as other prevalent diseases on the african continent such as hiv and tb.Such efforts will go a long way to reduce the disease burden in africa.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
COVIDHunter: COVID-19 Pandemic Wave Prediction and Mitigation via Seasonality Aware Modeling.

Early detection and isolation of covid-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread.With a limited number of daily covid-19 tests performed in every country, simulating the covid-19 spread along with the potential effect of each mitigation strategy currently remains one of the most effective ways in managing the healthcare system and guiding policy-makers.We introduce covidhunter, a flexible and accurate covid-19 outbreak simulation model that evaluates the current mitigation measures that are applied to a region, predicts covid-19 statistics (the daily number of cases, hospitalizations, and deaths), and provides suggestions on what strength the upcoming mitigation measure should be.The key idea of covidhunter is to quantify the spread of covid-19 in a geographical region by simulating the average number of new infections caused by an infected person considering the effect of external factors, such as environmental conditions (e.g., climate, temperature, humidity), different variants of concern, vaccination rate, and mitigation measures.Using switzerland as a case study, covidhunter estimates that we are experiencing a deadly new wave that will peak on 26 january 2022, which is very similar in numbers to the wave we had in february 2020.The policy-makers have only one choice that is to increase the strength of the currently applied mitigation measures for 30 days.Unlike existing models, the covidhunter model accurately monitors and predicts the daily number of cases, hospitalizations, and deaths due to covid-19.Our model is flexible to configure and simple to modify for modeling different scenarios under different environmental conditions and mitigation measures.We release the source code of the covidhunter implementation at and show how to flexibly configure our model for any scenario and easily extend it for different measures and conditions than we account for.

Journal: Frontiers in public health (2022)
Publication types: Journal Article
Association between Apolipoprotein E Polymorphism and Clinical Outcome after Ischemic Stroke, Intracerebral Hemorrhage, and Subarachnoid Hemorrhage.

S previous studies reported inconsistent results regarding associations between apolipoprotein e (apoe) polymorphism and clinical outcomes after ischemic stroke (is), intracerebral hemorrhage (ich), or subarachnoid hemorrhage (sah).Thus, the study was designed to make a systematic review and meta-analysis regarding the association between apoe polymorphism and clinical outcome after is, ich, and sah.Methods to identify studies eligible for this meta-analysis, we searched for articles published before august 2021 in the databases (pub med, web of science, and google scholar).We used stata 12.0 software to compute hazard ratios (hrs) and their 95% confidence intervals (cis) regarding apoe polymorphism and clinical outcome after is, ich, and sah.Results meta-analysis showed no significant association between apoe polymorphism and functional outcome after is with fixed effects models (ε4 carrier vs.Non-ε4 carrier: hr, 1.00; 95% ci: 0.83-1.21, i2 = 29.4%, p = 0.183; ε2 carrier vs.Non-ε2 carrier: hr, 0.92; 95% ci: 0.72-1.16, i2 = 15.6%, p = 0.307).Meta-analysis showed that ich patients carrying ε4 allele have increased risk of poor outcome in caucasian population with fixed effects models (ε4 carrier vs.Non-ε4 carrier: hr, 1.75; 95% ci: 1.19-2.57, i2 = 0.0%, p = 0.543).Meta-analysis showed no significant association between apoe polymorphism and functional outcomes after sah with random effects models (ε4 carrier vs.Non-ε4 carrier: hr, 1.51; 95% ci: 0.80-2.84, i2 = 57.1%, p = 0.022).Conclusions in conclusion, the present study demonstrated apoe ε4 carriers show worse functional outcomes after ich, but not after is or sah.More large-scale studies were critical to explore the association between apoe polymorphism and clinical outcome after is, ich, and sah.

Journal: Cerebrovascular diseases (Basel, Switzerland) (2022)
Publication types: Meta-Analysis;Systematic Review;Journal Article
On the limitations of partial Fourier acquisition in phase-contrast MRI of turbulent kinetic energy.

To investigate limitations of partial fourier acquisition in phase-contrast mri of turbulent kinetic energy (tke).Methods to assess the validity of partial fourier reconstruction of tke and phase images, computational fluid dynamics data of mean and turbulent velocities in a stenotic u-bend phantom was used.Partial fourier acquisition with 75% k-space coverage was simulated and tke data were reconstructed using zero-filling, homodyne reconstruction, and the method of projections onto convex sets (pocs).Results were compared to data from fully sampled k-space and 75% symmetric sampling.In addition, compressed sensing (cs) reconstruction was compared for a standard variable density sampling pattern and a variable density sampling pattern combined with 75% partial fourier.For illustration purposes, in vivo examples of velocity magnitude and tke maps of aortic flow reconstructed with the different methods are provided.Results in accordance with theory, partial fourier reconstruction of tke maps from phase-contrast data results in artifacts relative to fully sampled data.It is demonstrated that neither homodyne reconstruction nor pocs can improve reconstruction of tke data with respect to zero-filling reconstruction when compared to ground-truth (rms error: 4.70%, 4.34%, and 2.45% for homodyne, pocs, and zero-filling reconstruction of in vivo data, respectively).Cs reconstruction from data acquired with partial fourier did not recover the resolution loss incurred by partial fourier sampling.Conclusion partial fourier reconstruction of tke maps from phase-contrast data does not yield a benefit over zero-filling reconstruction.In consequence, symmetric sampling is preferred over partial fourier acquisition for a given number of phase-encodes in phase-contrast mri.

Journal: Magnetic resonance in medicine (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Quality-of-Life and Surgical Outcomes for Breast Cancer Patients Treated with Therapeutic Reduction Mammoplasty Versus Mastectomy with Immediate Reconstruction.

Therapeutic reduction mammoplasty (trm) is a safe and effective surgical technique that has oncologic outcomes comparable with those achieved by mastectomy.This study aimed to compare surgical and patient-reported outcomes between breast cancer patients treated with trm and those who had mastectomy with immediate reconstruction (mir).Methods a 4-year, single-institution, retrospective cohort study analyzed breast cancer patients undergoing trm and mir.Patient characteristics and perioperative data were collected from electronic records.Patient-reported outcome data were collected via breast-q questionnaires preoperatively, then 3 months and 12 months postoperatively.A subgroup analysis was performed on locally advanced breast cancer (labc) patients for trm and mir.Results the study included 249 breast reconstructions, of which 77 (31%) were trm and 172 (69%) were mir.The mean follow-up time was 2.4 ± 1.2 years.Compared with mir, trm had significantly lower major complication rates (9% vs 21%; p = 0.02) and fewer revisionary surgeries (5% vs 37%; p < 0.0001).At 1 year postoperatively, trm had a significantly greater change in satisfaction with breasts, (+ 27.7 vs + 4.6; p < 0.01) and sexual well-being (+ 20.0 vs - 5.5; p = 0.02) than mir.Conclusion for select breast cancer patients, trm continues to be a safe and effective alternative to mastectomy.The current study demonstrated that trm patients had fewer major complications and revisionary surgeries, as well as better patient-reported outcomes than mir.

Journal: Annals of surgical oncology (2020)
Publication types: Journal Article
Usefulness of Tp-Te interval and Tp-Te/QT ratio in the prediction of ventricular arrhythmias and mortality in acute STEMI patients undergoing fibrinolytic therapy.

And aim acute st-elevation myocardial infarction (stemi) is associated with fatal and non-fatal ventricular arrhythmic events (vae).Although primary percutaneous intervention (pci) is first-line treatment in stemi, fibrinolytic therapy (ft) is still widely used in many countries.Tp-te interval; tp-te/qt ratio and qt dispersion (qtd) are novel markers of ventricular repolarization (vr) and associate with vae and mortality.Hereby, we assessed tp-te, qtd and tp-te/qt in acute stemi patients undergoing ft and analyzed their relationship with post-ft vae, and arrhythmic and overall deaths.Methods a total of 207 consecutive stemi patients treated with ft were retrospectively evaluated.Patients were divided in group 1 (non-vae group) and group 2 (vae group).Ecg, clinical and demographic data were noted.Relationship between the pre-ft electrocardiographic parameters of vr and post-ft vae, arrhythmic and overall death was evaluated.Results tp-te, tp-te/qt and qtd were significantly higher in group 2 compared to group 1 (p 0.305 with 87.5% sensitivity and 60.1% specificity (auc: 0.90; 95% ci: 0.85-0.95; p 0.315 with 83.3% sensitivity and 62% specificity (auc: 0.70; 95% ci: 0.60-0.81; p = 0.018).Conclusion tp-te, tp-te/qt, qtc, qtd and lvef are independent predictors of post-ft vae in acute stemi.Tp-te/qt ratio is associated with va-related deaths.

Journal: Journal of electrocardiology (2019)
Publication types: Journal Article
A mathematical model of potassium homeostasis: Effect of feedforward and feedback controls.

Maintaining normal potassium (k+) concentrations in the extra- and intracellular fluid is critical for cell function.K+ homeostasis is achieved by ensuring proper distribution between extra- and intracellular fluid compartments and by matching k+ excretion with intake.The na+-k+-atpase pump facilitates k+ uptake into the skeletal muscle, where most k+ is stored.Na+-k+-atpase activity is stimulated by insulin and aldosterone.The kidneys regulate long term k+ homeostasis by controlling the amount of k+ excreted through urine.Renal handling of k+ is mediated by a number of regulatory mechanisms, including an aldosterone-mediated feedback control, in which high extracellular k+ concentration stimulates aldosterone secretion, which enhances urine k+ excretion, and a gastrointestinal feedforward control mechanism, in which dietary k+ intake increases k+ excretion.Recently, a muscle-kidney cross talk signal has been hypothesized, where the k+ concentration in skeletal muscle cells directly affects urine k+ excretion without changes in extracellular k+ concentration.To understand how these mechanisms coordinate under different k+ challenges, we have developed a compartmental model of whole-body k+ regulation.The model represents the intra- and extracellular fluid compartments in a human (male) as well as a detailed kidney compartment.We included (i) the gastrointestinal feedforward control mechanism, (ii) the effect of insulin and (iii) aldosterone on na+-k+-atpase k+ uptake, and (iv) aldosterone stimulation of renal k+ secretion.We used this model to investigate the impact of regulatory mechanisms on k+ homeostasis.Model predictions showed how the regulatory mechanisms synthesize to ensure that the extra- and intracelluller fluid k+ concentrations remain in normal range in times of k+ loading and fasting.Additionally, we predict that without the hypothesized muscle-kidney cross talk signal, the model was unable to predict a return to normal extracellular k+ concentration after a period of high k+ loading or depletion.

Journal: PLoS computational biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A rapidly expanding nodule on the lower leg.

We present a case of a 34-year-old man who developed a lesion over his posterior calf.We discuss the clinical and histopathological features, as well as relevant immunohistochemical markers.Click here for the corresponding questions to this cme article.

Journal: Clinical and experimental dermatology (2022)
Publication types: Case Reports;Journal Article
The value of MALDI-TOF failure to provide an identification ofStaphylococcalspecies direct from blood cultures and rule outStaphylococcus aureusbacteraemia: a post-hoc analysis of the RAPIDO trial.

Introduction rapid differentiation between staphylococcus aureus(sa) and coagulase-negative staphylococci (co ns) is critical in clinical infection.Direct matrix-assisted laser desorption/ionization time-of-flight (maldi-tof) identification from blood culture is highly accurate, but is associated with a significant failure rate, delaying identification.However, maldi-tof failure may itself be indicative of co ns infection.Aim we sought to examine whether failure of maldi-tof direct id was indicative of co ns infection and could be used as a diagnostic tool to promote antimicrobial stewardship.Methodology results of gram stains, maldi-tof identification and formal identification were extracted from the large, multi-centre rapido trial.All blood cultures with presumed staphylococci were included.Maldi-tof performance (correct identification, incorrect identification, failed identification) was calculated for each sample and across sites.Risk of sa disease was calculated for each group (correct, incorrect, failed) and across sites.Logistic regression was used to identify if clinical features are associated with maldi-tof performance.Results in the rapido trial, 4312 patients were allocated to the maldi-tof arm.After exclusions, 880 patients were eligible and had a blood culture with a gram stain consistent with presumed staphylococci.In total, 204 of these (23.2 %) were ultimately identified as sa.Maldi-id was successful 83.9 % of the time, and was 100 % accurate when successful.Failure was more common in co ns isolates (124/641, 19.3 %) than in sa (13/191, 6.4 %).When maldi-tof failed, the risk of sa disease was 9.2 % across the whole cohort, although failure rates and risk of sa disease varied significantly between centres.Maldi-tof failure was independent of clinical characteristics.Conclusion presumed staphylococci that fail direct maldi-tof identification from blood culture are significantly more likely to be co ns isolates than sa.In low-risk or low-prevalence settings, sa therapy can be withheld if maldi-tof is unsuccessful.

Journal: Access microbiology (2021)
Publication types: Journal Article
Is Adolescent E-Cigarette Use Associated With Subsequent Smoking? A New Look.

Introduction prospective studies have consistently reported a strong association between e-cigarette use and subsequent cigarette smoking, but many failed to adjust for important risk factors.Methods using longitudinal data from the population assessment of tobacco and health (path) study, we employed multivariable logistic regressions to assess the adolescent vaping-to-smoking relationship, with four regressions (models 1-4) sequentially adding more risk factors.our sample included all waves (waves 1-5) of the path study.Results the association between ever e-cigarette use and subsequent cigarette smoking decreased substantially in magnitude when adding more control variables, including respondents' sociodemographic characteristics, exposure to tobacco users, cigarette susceptibility, and behavioral risk factors.Using the most recent data (waves 4-4.5 and waves 4.5-5), this association was not significant in the most complete model (model 4).Using wave 4.5-5 data, the adjusted odds ratio (a or) for ever e-cigarette use at initial wave and subsequent past 12-month smoking declined from 4.07 (95% confidence interval [ci, 2.86-5.81) in model 1, adjusting only for sociodemographic characteristics, to 1.35 (95% ci, 0.84-2.16) in model 4, adjusting for all potential risk factors.Similarly, the a or of ever e-cigarette use and past 30-day smoking at wave 5 decreased from 3.26 (95% ci, 1.81-5.86) in model 1 to 1.21 (95% ci, 0.59-2.48) with all covariates (model 4).Conclusions among adolescent never cigarette smokers, those who had ever used e-cigarettes at baseline, compared with never e-cigarette users, exhibited modest or non-significant increases in subsequent past 12-month or past 30-day smoking when adjusting for behavioral risk factors.

Journal: Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco (2022)
Publication types: Journal Article
A single healthcare experience with Impella RP.

S to understand the predictors of survival and indications for impella rp in a single healthcare experience.Background the impella rp can be used to temporarily support patients with right ventricular (rv) dysfunction after left ventricular assist device (lvad) placement or myocardial infarction (mi).However, recent postmarket approval data have raised concerns of higher than expected mortality with this device.Methods a retrospective chart review and analysis of all patients that underwent impella rp placement in the emory healthcare system between january 2016 and december 2018 were performed.Patients were classified according to the indication.Results a total of 39 patients underwent impella rp placement.Six patients were post-lvad, 9 were implanted for massive pulmonary embolism with persistent shock, 8 for postcardiac surgery rv failure (non-lvad), 11 for rv failure post-mi, and 5 for new or worsening nonischemic cardiomyopathy.The worst survival was noted in mi-related cardiogenic shock group and in patients who presented with cardiac arrest (3/12).All observed deaths were due to persistent refractory shock.There was no device related death.Survival improved during the last year of experience compared to the first 2 years.Conclusion this study supports the selective use of the impella rp, with a higher than national reported survival rate (49% vs.28.6%).Indication appears to be an important factor determining survival.

Journal: Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions (2021)
Publication types: Journal Article