syedzayyan/paper_mill_benchmark huggingface dataset:
The color of skin: blue diseases of the skin, nails, and mucosa.

Diseases of the skin, hair, nails and mucosa can appear as flesh-colored lesions or may present as any of the colors of the visual spectrum.Diseases associated with blue (or shades of blue) discoloration represent a unique group of conditions that occur de novo or as a reaction to either a topical or a systemic agent to which the individual has been exposed.Blue diseases can affect the skin, the nails or the mucosal membranes of the mouth (buccal mucosa, gingiva, lips, palate or tongue) or eyes (sclera).In addition to appearing blue, they can also appear as blue-black, blue-brown, blue-gray, blue-green, blue-purple, blue-red, and blue-silver.The conditions range from those secondary to exogenous agents (systemic or tattoo or topical) to syndromes to systemic diseases to tumors (adnexal, melanocytic, vascular, or miscellaneous).A comprehensive attempt to include all conditions that have been described as blue (or a shade of blue) has been performed by evaluating the following terms using the medical search engine pub med: blue and either gingiva, lips, lunula, mucosa, nails, oral, palate, sclera, skin, or tongue.Subsequently, the conditions were organized by color (blue and shades of blue) and within each color by location (skin, nails, oral mucosa and sclera).The results are presented in organized tables; in addition, there is discussion of some of the conditions that are unique to one or more specific locations.In conclusion, 'preserve and cherish the pale blue dot' and remember that a big red rock eater with chrysiasis is the answer to the riddle, "what is big and blue and eats rocks?"

Journal: Clinics in dermatology (2019)
Publication types: Journal Article;Review
A Predictive Biophysical Model of the Combined Action of Radiation Therapy and Immunotherapy of Cancer.

Immunotherapy with checkpoint inhibitors has an enormous potential in therapy of metastatic cancers.Immunotherapy is generally combined with local treatments, such as radiation therapy.The time schedule of drug-radiation combination is largely based on empirical observations, and a comprehensive predictive model would be needed to optimize treatments.We present a biophysical model predicting the combined interaction and apply it to describe preclinical experimental data.Methods and materials the model considers the dependences of primary and distal tumor masses, immune cell kinetics targeting tumor cells, and signals causing immune cell replenishment after radiation mechanistic interpretation of the low frequency of abscopal responses.It is benchmarked against 16 experiments with synthetic tumors in murine models.Results the model predicts that immune response is stronger for checkpoint inhibitor administration at the time of irradiation or shortly after.The model discriminates correctly between tumor remission and continued growth in all considered experimental cases, including radiation and checkpoint delivery alone or in combination.It identifies a radiation dose window maximizing immune response and avoiding on one side the understimulation of the immune system and radiation-induced depletion of the immune cell pool on the other.Consequently, abscopal effects can be established in certain circumstances only.Conclusions the model allows a quantitative mechanistic interpretation of the interaction of radiation with checkpoint blockers and will be helpful for optimizing clinical trials.

Journal: International journal of radiation oncology, biology, physics (2022)
Publication types: Journal Article
Impact of policy-based and institutional interventions on postoperative opioid prescribing practices.

We assessed the impact of policy-based and institutional interventions to limit postoperative opioid prescribing.Methods retrospective cohort study of patients who underwent laparoscopic/open appendectomies, laparoscopic/open cholecystectomies, and laparoscopic/open inguinal hernia repair during a 6-month interval in 2018 (control), 2019 (post-policy intervention), and 2020 (post-institutional intervention) to assess changes in postoperative opioid prescribing patterns.A survey was collected for the 2020 cohort.Results comparing the 762 patients identified in 2018, 2019, and 2020 cohorts there was a significant decrease in mean opioid tabs prescribed (23.5 ± 8.9 vs.16.2 ± 7.0 vs.12.8 ± 4.9, p < 0.01) and mean ome dosage (148.0 ± 68.0 vs.108.6 ± 51.8 vs.95.4 ± 38.0, p < 0.01), without a difference in refill requests.Patient survey (response rate 63%) indicated 91.4% of patients reported sufficient pain control.Conclusion formalized opioid-prescribing guidelines and statewide regulations can significantly decrease postoperative opioid prescribing with good patient satisfaction.Surgeon education may facilitate efforts to minimize narcotic over-prescription without compromising pain management.

Journal: American journal of surgery (2021)
Publication types: Journal Article
The necessity of a loading dose when prescribing intravenous colistin in critically ill patients with CRGNB-associated pneumonia: a multi-center observational study.

The importance or necessity of a loading dose when prescribing intravenous colistin has not been well established in clinical practice, and approximate one-third to half of patients with carbapenem-resistant gram-negative bacteria (crgnb) infection did not receive the administration of a loading dose.The aim of this study is to investigate the efficacy and risk of acute kidney injury when prescribing intravenous colistin for critically ill patients with nosocomial pneumonia caused by crgnb.Methods this was a multicenter, retrospective study that recruited icu-admitted patients who had crgnb-associated nosocomial pneumonia and were treated with intravenous colistin.Then, we classified the patients into colistin loading dose (n = 85) and nonloading dose groups (n = 127).After propensity-score matching for important covariates, we compared the mortality rate, clinical outcome and microbiological eradication rates between the groups (n = 67).Results the loading group had higher percentages of patients with favorable clinical outcomes (55.2% and 35.8%, p = 0.037) and microbiological eradication rates (50% and 27.3%, p = 0.042) at day 14 than the nonloading group.The mortality rates at days 7, 14 and 28 and overall in-hospital mortality were not different between the two groups, but the kaplan-meier analysis showed that the loading group had a longer survival time than the nonloading group.Furthermore, the loading group had a shorter length of hospital stay than the nonloading group (52 and 60, p = 0.037).Regarding nephrotoxicity, there was no significant difference in the risk of developing acute kidney injury between the groups.Conclusions the administration of a loading dose is recommended when prescribing intravenous colistin for critically ill patients with nosocomial pneumonia caused by crgnb.

Journal: Critical care (London, England) (2022)
Publication types: Journal Article;Multicenter Study;Observational Study
Healthcare Expenditures Associated With Comorbid Anxiety and Depression Among Adults With Migraine.

Introduction:depression and anxiety are common among patients with migraine and usually associated with a humanistic and financial burden.This study aims to examine the direct healthcare expenditures among adults with migraine alone or with comorbid anxiety and/or depression.methods:this was a retrospective cross-sectional study using 2012, 2014, and 2016 medical expenditure panel survey data.Adult patients aged ≥22 years with migraine headache were included in the study.The direct healthcare expenditures of four migraine groups (migraine alone, migraine and anxiety, migraine and depression, and migraine and both conditions) were compared.results:there were 1,556 patients who met the inclusion criteria and eventually enrolled in the study.Approximately 42% of the study sample had migraine with comorbid depression and/or anxiety (16.1% have depression, 12.3% have anxiety disorder, and 13.9% have both).The mean total healthcare expenditures of adults with migraine alone ($6,461) were significantly lower than those with comorbid depression and anxiety ($11,102), comorbid anxiety ($10,817), and comorbid depression ($14,577).Migraine with comorbid anxiety and depression was significantly associated with incremental costs of $1,027 in outpatient and $662 emergency room healthcare expenditures and prescription drug compared to the migraine alone group.conclusions:the healthcare expenditures associated with migraine with comorbid depression and/or anxiety are significantly higher than those without mental health comorbidities.Therefore, regular depression and anxiety screening for patients with migraine may help reduce the healthcare expenditures associated with depression and/or anxiety comorbidities and improve the quality of care.

Journal: Frontiers in neurology (2021)
Publication types: Journal Article
Attention-Deficit/Hyperactivity Disorder as a Risk Factor for COVID-19 Infection.

To postulate that adhd is a potential risk factor for covid-19 infection; to evaluate the covid-19 risk factor on drug-treated adhd subjects.Methods a retrospective chart review was performed on adhd subjects aged 6 to 18 years in israel, who had undergone at least one covid-19 test during the study period.Results of the 64,409 subjects included in the study, 6,207 (9.64%) had at least one positive covid-19 test result, 13,300 (20.65%) were diagnosed with adhd, and of whom 1,751 (13%) had purchased at least two adhd medications 3 months prior to covid-19 testing and were defined as being medically treated.Medically-treated adhd subjects had a significantly lower likelihood to be infected with covid-19 than untreated subjects.Conclusion untreated adhd patients seem to constitute a risk group for covid-19 infection.Drug treatment ameliorates risk of spreading covid-19 infection within the pediatric population and secondary spread in the general population.

Journal: Journal of attention disorders (2022)
Publication types: Journal Article
Single high-dose peroral caffeine intake inhibits ultraviolet radiation-induced apoptosis in human lens epithelial cells in vitro.

The aim of the present study was to determine whether caffeine concentrations in human lens epithelial cells (lecs) achieved from acute peroral caffeine intake inhibit ultraviolet radiation-induced apoptosis in vitro.Methods patients were planned for cataract surgery of both eyes with a caffeine abstinence of 2 weeks in total, starting 1 week before surgery of the first eye.The second eye was scheduled 1 week after the first eye.At the day of the second eye surgery, patients were given coffee containing 180 mg caffeine shortly before surgery.Lens capsules including lec, harvested after capsulorhexis, were transferred to a cell culture dish and immediately exposed to close to threshold ultraviolet radiation (uvr).At 24 hr after uvr exposure, apoptotic lecs were analysed by td t-mediated d utp-biotin nick end labeling (tunel) staining.Results tunel-positive cells were detected in uvr-exposed lens capsules both after caffeine intake and in controls.The mean difference in tunel-positive cells between caffeine intake and contralateral controls (no caffeine) resulted in a 95% ci 15.3 ± 10.4% (degrees of freedom: 16).Conclusion peroral caffeine consumption significantly decreased uvr-induced apoptosis in lec supporting epidemiological findings that caffeine delays the onset of cataract.

Journal: Acta ophthalmologica (2021)
Publication types: Journal Article;Randomized Controlled Trial
Bile components affect the functions and transcriptome of the rainbow trout intestinal epithelial cell line RTgutGC.

The concomitant increase in cultivation of fish and decrease in supply of marine ingredients, have greatly increased the demand for new nutrient sources.This also regards so-called functional ingredients which may benefit health and welfare of the fish.In vitro cell line-based intestinal epithelial barrier models may serve as tools for narrowing down the broad range of ingredient options, to identify the most promising candidates before in vivo feeding trials are run.In vivo, differentiation of the various epithelial cells in the fish intestine, from the multipotent stem cells, takes place in the presence of a variety of substances from dietary and endogenous origin.Among these, bile salts have recently received attention as regulators of epithelial function in health and disease but have not, until now, been included in the medium when culturing fish gut epithelial cells in vitro.As bile salts are present at high levels in the chyme of the fish intestine, in particular in salmon and rainbow trout, mostly as taurocholate (>90%), their role for effects of diet ingredients on the in vitro gut cell model should be understood.With this study, we wanted to investigate whether inclusion of bile from rainbow trout or pure taurocholate in the culture media would modulate functions of the rtgut gc epithelial cells.Here, we demonstrated that the rainbow trout intestinal epithelial cell line rtgut gc responded significantly to the presence of bile components.Treatment with rainbow trout bile taken from the gall bladder (rtbile) or pure taurocholate (tc) at taurocholate concentrations of ≤0.5 mg/m l retained normal cell morphology, cell viability as in cell oxidation-reduction metabolic activity and membrane integrity, and barrier features, while high concentrations of bile salts (≥1 mg/m l) were cytotoxic to the cells.After long-term (4 days) bile treatment, transcriptome responses showed how bile salts play important roles in intestinal epithelial cell metabolism.Q pcr data demonstrated that barrier function genes, brush border enzyme genes and immune genes were significantly affected.Although similar trends were seen, treatment with bile salt as a component of rainbow trout bile or pure taurocholate, induced somewhat different effects.In conclusion, this study clearly indicates that bile salts should be included in the cell medium when running in vitro studies of gut cell functions, not at least immune functions, preferably at the level of ∼0.5 mg/m l supplemented as pure taurocholate to ensure reproducibility.

Journal: Fish & shellfish immunology (2022)
Publication types: Journal Article
DeepBarcoding: Deep Learning for Species Classification Using DNA Barcoding.

Dna barcodes with short sequence fragments are used for species identification.Because of advances in sequencing technologies, dna barcodes have gradually been emphasized.Dna sequences from different organisms are easily and rapidly acquired.Therefore, dna sequence analysis tools play an increasingly crucial role in species identification.This study proposed deep barcoding, a deep learning framework for species classification by using dna barcodes.Deep barcoding uses raw sequence data as the input to represent one-hot encoding as a one-dimensional image and uses a deep convolutional neural network with a fully connected deep neural network for sequence analysis.It can achieve an average accuracy of >90 percent for both simulation and real datasets.Although deep learning yields outstanding performance for species classification with dna sequences, its application remains a challenge.The deep barcoding model can be a potential tool for species classification and can elucidate dna barcode-based species identification.

Journal: IEEE/ACM transactions on computational biology and bioinformatics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Mortality and complication rates in nonagenarians and octogenarians undergoing total hip and knee arthroplasty: a systematic review and meta-analysis.

Advancing age is a significant risk factor for the development of perioperative complications and mortality in patients undergoing total hip or knee arthroplasty (tha or tka) due to their compromised health status and the associated medical comorbidities.The purpose of this review is to identify if nonagenarians having a tha or tka are associated with a higher incidence of mortality and morbidity compared to octogenarians.Methods medline, scopus, and the cochrane library were searched for relevant studies.The primary outcome of the review was the incidence of mortality.The secondary outcomes were the 30-day readmission, the perioperative complications, and the length of hospital stay (los).Results six studies with 479,630 patients were included in the review.No difference between nonagenarians and octogenarians was detected regarding the in-hospital mortality, the 30-day readmission rate, and the los.However, nonagenarians were associated with a greater 1-year mortality rate (or: 2.4; 95% ci 1.91-3.01, p < 0.001; i2= 0%) and increased odds of perioperative complications (or: 1.6; 95% ci 1.48-1.72, p < 0.001; i2= 0%).This finding was unchanged after adjusting for baseline characteristics (oradj: 1.68; 95% ci 1.53-1.84, p < 0.001; i2= 0%).Conclusion although nonagenarians undergoing tka or tha can achieve the same clinical benefit as octogenarians, they have a higher risk of perioperative complications and 1-year mortality.Therefore, meticulous preoperative screening, proper patient selection and optimization of comorbidities are essential to minimize any postoperative side effects in patients over 90 years of age.

Journal: European geriatric medicine (2022)
Publication types: Journal Article;Meta-Analysis;Systematic Review
Sex differences in response to emotion recognition training after traumatic brain injury.

To examine sex differences in the effectiveness of a stories intervention for teaching affect recognition in people with a traumatic brain injury (tbi).Setting post-acute rehabilitation facilities.Participants 203 participants (53 women and 150 men) with moderate to severe tbi were screened.71 were eligible and randomized to one of three treatment conditions: two affect recognition conditions and an active control (cognition).This paper examines sex differences between the stories intervention (n = 23, 5 women and 18 men) and the cognitive treatment control (n = 24, 8 women and 16 men).Design randomized controlled trial with immediate, 3- and 6-month follow-up post-tests.Interventions were 9 hours of computer-based training with a therapist.Measures facial affect recognition (danva2-af); emotional inference from stories test (eist).Results a significant treatment effect was observed for the stories intervention for women, who demonstrated and maintained improved facial affect recognition.In contrast, males in our sample did not benefit from the stories intervention.Conclusion this positive finding for the stories intervention for females contrasts with our conclusions in a previous paper, where an analysis collapsed across sex did not reveal an overall effectiveness of the stories intervention.This intervention warrants further research and development.

Journal: Brain injury (2018)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, U.S. Gov't, Non-P.H.S.
Hydrotropic function of ATP in the crystalline lens.

The hypothesis proposed herein is presented to explain the unexpectedly high concentration of atp and provide evidence to support its hydrotropic function in the crystalline lens determined using31p nmr.The lens, historically considered to be a metabolically quiescent organ, has the requisite machinery to synthesize atp, such that the homeostatic level is maintained at about 3 m m.This relatively high concentration of atp has been found to be consistent among multiple mammalian species including humans.This millimolar quantity is many times greater than the micromolar amounts required for the other known functions of atp.The recent postulation that atp at millimolar concentrations functions as a hydrotrope in various cell/tissue homogenates preventing protein aggregation coupled with observations presented herein, provide support for extending the hypothesis that atp functions as a hydrotrope not only in homogenates but in an intact functioning organ, the crystalline lens.Concentrations of atp of this magnitude are hypothesized to be required to maintain protein solubility and effectively prevent protein aggregation.This concept is important considering protein aggregation is the etiology for age-related cataractogenesis.Atp is a common ubiquitous intracellular molecule possessing the requisite hydrotropic properties for maintaining intracellular proteins in a fluid, non-aggregated state.It is proposed that the amphiphilic atp molecule shields the hydrophobic regions on intralenticular fiber cell protein molecules and provides a hydrophilic interfacial surface comprised of the atp negatively charged triphosphate side chain.Evidence is presented that this side chain is exposed to and has been reported to organize intracellular interstitial water to form an interfacial rheologically dynamic water layer.Such organization of water is substantiated with the effect of deuterium oxide (heavy water) on atp line widths of the side chain phosphates measured ex vivo by31p nmr.A novel model is presented to propose how this water layer separates adjacent lens fiber cell proteins, keeping them from aggregating.This hypothesis proposes that atp can prevent protein aggregation in normal intact lenses, and with declining concentrations can be related to the disease process in age-related cataractogenesis, an affliction that affects every older human being.

Journal: Experimental eye research (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Management of neurosarcoidosis.

This is a brief and purposefully practical approach to the therapeutic and rehabilitative management of patients affected by neurological complications of systemic sarcoidosis.The review notes the drugs used and their monitoring, and their role in the series of clinical subgroups identified to form the condition.Treatment guidelines for individual clinical subtypes of the disorder are provided, and the importance of rehabilitative measures and lifestyle changes are emphasised.

Journal: Journal of neuroimmunology (2022)
Publication types: Journal Article
Inhibition of CL-11 reduces pulmonary inflammation in a mouse model of Klebsiella pneumoniae lung infection.

Infection caused by k.Pneumoniae is associated with severe inflammation due to stimulation of the innate immune components including the complement system, which is the main player of the innate immune response.Excessive complement-mediated inflammation may cause severe lung injury.Here we clearly show that k.Pneumoniae binds to different lectin pathway carbohydrate recognition molecules and activates the complement cascade via the lp.Administration of anti-cl-11 antibodies 6 h before the infection impairs lp functional activity but it shows no effect on the survival time of mice infected with k.Pneumoniae.Similarly, no significant difference in bacterial load in blood and lung tissues was observed between mice that received anti-cl-11 and control group treated with an isotype antibody.Interestingly, treatment of mice with anti-cl-11 prior to infection significantly improved histopathological changes and lung injury score induced by k.Pneumoniae.Moreover, administration of anti-cl-11 reduced leukocytes infiltration into lung tissues and decreased the levels of the inflammatory mediators tnf-α, il-6, and il-1β in the infected mice.These findings indicate that inhibition of the lp could secure a significant level of protection against lung injury during the infection caused by k.Pneumoniae.

Journal: Microbial pathogenesis (2022)
Publication types: Journal Article