syedzayyan/paper_mill_benchmark huggingface dataset:
Identifying risk of adverse outcomes in COVID-19 patients via artificial intelligence-powered analysis of 12-lead intake electrocardiogram.

Adverse events in covid-19 are difficult to predict.Risk stratification is encumbered by the need to protect healthcare workers.We hypothesize that artificial intelligence (ai) can help identify subtle signs of myocardial involvement in the 12-lead electrocardiogram (ecg), which could help predict complications.Objective use intake ecgs from covid-19 patients to train ai models to predict risk of mortality or major adverse cardiovascular events (mace).Methods we studied intake ecgs from 1448 covid-19 patients (60.5% male, aged 63.4 ± 16.9 years).Records were labeled by mortality (death vs discharge) or mace (no events vs arrhythmic, heart failure [hf], or thromboembolic [te] events), then used to train ai models; these were compared to conventional regression models developed using demographic and comorbidity data.Results a total of 245 (17.7%) patients died (67.3% male, aged 74.5 ± 14.4 years); 352 (24.4%) experienced at least 1 mace (119 arrhythmic, 107 hf, 130 te).Ai models predicted mortality and mace with area under the curve (auc) values of 0.60 ± 0.05 and 0.55 ± 0.07, respectively; these were comparable to auc values for conventional models (0.73 ± 0.07 and 0.65 ± 0.10).There were no prominent temporal trends in mortality rate or mace incidence in our cohort; holdout testing with data from after a cutoff date (june 9, 2020) did not degrade model performance.Conclusion using intake ecgs alone, our ai models had limited ability to predict hospitalized covid-19 patients' risk of mortality or mace.Our models' accuracy was comparable to that of conventional models built using more in-depth information, but translation to clinical use would require higher sensitivity and positive predictive value.In the future, we hope that mixed-input ai models utilizing both ecg and clinical data may be developed to enhance predictive accuracy.

Journal: Cardiovascular digital health journal (2022)
Publication types: Journal Article
Stable and Antibacterial Magnesium-Graphene Nanocomposite-Based Implants for Bone Repair.

Magnesium (mg)-based alloys are promising biodegradable materials for bone repair applications.However, due to their rapid degradation and high corrosion rate, mg-based alloys are typically associated within vivoinfections and implant failure.This study evaluated the synergistic stability and anti-inflammatory properties that could potentially be achieved by the modification of the mg alloy with graphene nanoparticles (gr).Incorporation of low dosages of gr (0.18 and 0.50 wt %) in a mg alloy with aluminum (al, 1 wt %) and copper (cu, 0.25 wt %) was successfully achieved by a spark plasma sintering (sps) method.Notably, the degradation rate of the mg-based alloys was reduced approximately 4-fold and the bactericidal activity was enhanced up to 5-fold with incorporation of only 0.18 wt % gr to the mg-1al-cu matrix.Moreover, the modified mg-based nanocomposites with 0.18 wt % gr demonstrated compressive properties within the range of native cancellous bone (modulus of approximately 6 gpa), whereasin vitrostudies with human mesenchymal stromal cells (h mscs) showed high cytocompatibility and superior osteogenic properties compared to non-gr-modified mg-1al-cu implants.Overall, this study provides foundations for the fabrication of stable, yet fully resorbable, mg-based bone implants that could reduce implant-associated infections.

Journal: ACS biomaterials science & engineering (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Outcome of primary ERCP versus primary PTC for biliary drainage in malignant hilar biliary strictures: a systematic review and meta-analysis.

Patients with malignant hilar biliary strictures can suffer from obstructive jaundice.Controversy remains on the optimal approach to obtain preoperative or palliative biliary drainage in these patients.A systematic review and meta-analysis was conducted to compare the two modalities most commonly used in this scenario: endoscopic retrograde cholangiopancreatography (ercp) and percutaneous transhepatic cholangiography (ptc).Methods medline via pub med was searched for relevant articles published from 2005 to april 2019.Following outcome measures were used to compare ercp and ptc: therapeutic success rate, cholangitis, pancreatitis, bleeding, tube dislocation, reintervention rate, mortality such as 30d mortality and in-hospital death, median survival time, drainage patency, duration until decompression and hospital stay.Risk of bias assessment for the retrospective studies was conducted by nos.Ro b 2 was used for rct.A meta-analysis was performed by using review manager 5.3.The certainty of evidence was appraised using grade.Results eleven articles of which one rct and ten retrospective cohort studies fulfilled the inclusion criteria for data-analysis (1417 patients; 784 ercp, 633 ptc).The combined odds ratio (or) for therapeutic succes was 3.5 times higher in the ptc group (95% ci 2.05-5.97; high certainty).In terms of cholangitis, ercp carried a 1.7-fold risk as compared to ptc (95% ci 0.92-3.08; moderate certainty).Patients who underwent ercp were 11.50 times more likely to undergo a reintervention (95% ci 3.51-37.70; moderate certainty).Ercp was comparable to ptc in terms of pancreatitis (low certainty), bleeding (high certainty) and tube dislocation rate (moderate certainty).Mortality tended to be numerically higher in the ptc group but low patient numbers, selection bias and study heterogeneity did not allow uniform comparative analysis.Conclusions in patients with malignant hilar biliary strictures, ptc is associated with a better therapeutic success rate, less cholangitis and lower reintervention rate as compared to ercp.

Journal: Surgical endoscopy (2022)
Publication types: Journal Article;Meta-Analysis;Review;Systematic Review
High-Dimensional Unbalanced Binary Classification by Genetic Programming with Multi-Criterion Fitness Evaluation and Selection.

High-dimensional unbalanced classification is challenging because of the joint effects of high dimensionality and class imbalance.Genetic programming (gp) has the potential benefits for use in high-dimensional classification due to its built-in capability to select informative features.However, once data are not evenly distributed, gp tends to develop biased classifiers which achieve a high accuracy on the majority class but a low accuracy on the minority class.Unfortunately, the minority class is often at least as important as the majority class.It is of importance to investigate how gp can be effectively utilized for high-dimensional unbalanced classification.In this article, to address the performance bias issue of gp, a new two-criterion fitness function is developed, which considers two criteria, that is, the approximation of area under the curve (auc) and the classification clarity (i.e., how well a program can separate two classes).The obtained values on the two criteria are combined in pairs, instead of summing them together.Furthermore, this article designs a three-criterion tournament selection to effectively identify and select good programs to be used by genetic operators for generating offspring during the evolutionary learning process.The experimental results show that the proposed method achieves better classification performance than other compared methods.

Journal: Evolutionary computation (2022)
Publication types: Journal Article
Type and size effect of functional groups on the novel antifolate target recognition folate receptors α and β: Docking, molecular dynamics and MM/PBSA study.

A series of novel antifolates (32 compounds) were used to study the interactions with folate receptors α and β.The compounds had different sizes of methyl (-ch3), carboxyl (-cooh), hydroxyl (-oh), and amino groups (-nh2).The binding properties of the complexes were studied by molecular docking, molecular dynamic (md) simulations, and mm/pbsa free energy calculations.The docked binding energies and modes were analyzed to identify compounds with good recognition of frα from frβ.The stable conformers, root mean square displacement, root mean square fluctuation free binding energy, and contribution of residues to the binding energy of the complexes were further analyzed to illustrate the interactions between the novel compounds and folate receptors.The data show that introducing long functional groups in folate will increase the binding affinity with frα but will decrease the binding affinity with frβ.The results provide a strategy for the design of novel antifolates targeted to frα.

Journal: Journal of molecular graphics & modelling (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Tigecycline-induced life-threatening coagulopathy in a patient with a Mycobacterium abscess: a case report and step-by-step diagnostic approach.

Tigecycline is a broad-spectrum antibiotic that is indicated in the treatment of complicated intra-abdominal infections and complicated skin and skin and soft-tissue infections.We report the case of a 53-year old kidney transplant patient with a severe mycobacterium abscess who developed life-threatening coagulopathy after initiation of tigecycline therapy.Further analysis revealed a severe hypofibrinogenemia.A few case reports previously described an association between tigecycline and prolongation of clotting time.Our case confirms an uncommon yet possibly life-threatening side-effect of tigecycline.Medical practitioners should be aware of this potential coagulopathy and we recommend routine monitoring of coagulation parameters in patients receiving tigecycline.

Journal: Acta clinica Belgica (2021)
Publication types: Case Reports;Journal Article
Nonlinear Probability Weighting in Depression and Anxiety: Insights From Healthy Young Adults.

Both depressive and anxiety disorders have been associated with excessive risk avoidant behaviors, which are considered an important contributor to the maintenance and recurrence of these disorders.However, given the high comorbidity between the two disorders, their independent association with risk preference remains unclear.Furthermore, due to the involvement of multiple cognitive computational factors in the decision-making tasks employed so far, the precise underlying mechanisms of risk preference are unknown.In the present study, we set out to investigate the common versus unique cognitive computational mechanisms of risk preference in depression and anxiety using a reward-based decision-making task and computational modeling based on economic theories.Specifically, in model-based analysis, we decomposed risk preference into utility sensitivity (a power function) and probability weighting (the one-parameter prelec weighting function).Multiple linear regression incorporating depression (bdi-ii) and anxiety (stai state anxiety) simultaneously indicated that only depression was associated with one such risk preference parameter, probability weighting.As the symptoms of depression increased, subjects' tendency to overweight small probabilities and underweight large probabilities decreased.Neither depression nor anxiety was associated with utility sensitivity.These associations remained even after controlling covariates or excluding anxiety-relevant items from the depression scale.To our knowledge, this is the first study to assess risk preference due to a concave utility function and nonlinear probability weighting separately for depression and anxiety using computational modeling.Our results provide a mechanistic account of risk avoidance and may improve our understanding of decision-making deficits in depression and anxiety.

Journal: Frontiers in psychiatry (2022)
Publication types: Journal Article
Recent progress in the microbial production of xylonic acid.

Interest in the production of renewable chemicals from biomass has increased in the past years.Among these chemicals, carboxylic acids represent a significant part of the most desirable bio-based products.Xylonic acid is a five-carbon sugar-acid obtained from xylose oxidation that can be used in several industrial applications, including food, pharmaceutical, and construction industries.So far, the production of xylonic acid has not yet been available at an industrial scale; however, several microbial bio-based production processes are under development.This review summarizes the recent advances in pathway characterization, genetic engineering, and fermentative strategies to improve xylonic acid production by microorganisms from xylose or lignocellulosic hydrolysates.In addition, the strengths of the available microbial strains and processes and the major requirements for achieving biotechnological production of xylonic acid at a commercial scale are discussed.Efficient native and engineered microbial strains have been reported.Xylonic acid titers as high as 586 and 171 g l-1were obtained from bacterial and yeast strains, respectively, in a laboratory medium.Furthermore, relevant academic and industrial players associated with xylonic acid production will be presented.

Journal: World journal of microbiology & biotechnology (2022)
Publication types: Journal Article;Review
A Prospective Comparative Observational Study of Clinical Efficacy of Isobaric Ropivacaine 0.75% with of Isobaric Bupivacaine 0.5% Intrathecally in Elective Inguinal Hernia Repair Surgeries.

S to evaluate the efficacy of intrathecal isobaric ropivacaine and its comparison with intrathecal isobaric bupivacaine in elective inguinal hernia repair surgeries.Settings and design a prospective, randomized study was conducted in a tertiary care hospital with 80 patients of asa grade i-iii undergoing elective inguinal hernia repair surgery under spinal anaesthesia.Ethical committee clearance and written consent taken.The patients were randomly divided into two equal groups to the ropivicaine group (group r) and to the bupivicaine group (group b).Parameters observed were onset and duration of sensory and motor block, maximum sensory level achieved degree of motor blockade, two segment regression, and haemodynamic changes.Results the development of sensory block was faster with isobaric ropivicaine (12.1 ± 4.9 minutes) as than isobaric bupivicaine (13.94 ± 4.52 minutes) but the difference was not statistically significant.Onset of grade iii motor block was longer with isobaric ropivicaine (8.51 ± 3.39 minutes) as compared to isobaric bupivicaine (8.51 ± 3.39 minutes), but the difference was not statistically significant.Time of complete sensory regression was significantly shorter with isobaric ropivicaine (212.69 ± 27.31 minutes) with statistical significance.Time to complete motor recovery was significantly shorter in ropivacaine group (253.38 ± 27.13 minutes)as compared to bupivacaine group (258.55 ± 35.81min), with statistical significance.Time to achieve discharge criteria was relatively shorter with isobaric ropivicaine.Haemodynamic parameters did not differ significantly in both the groups during the entire study period.Conclusion intrathecal administration of isobaric ropivacaine (0.75%) 15 mg provides similar quality of spinal anaesthesia but of significantly shorter duration, maintaining similar hemodynamic stability and discharge criteria without significant adverse effects when compared to isobaric bupivicaine (0.5%) 10 mg.

Journal: Anesthesia, essays and researches (2017)
Publication types: Journal Article
Comparison of plasma total solids concentration as measured by refractometry and plasma total protein concentration as measured by biuret assay in pet rabbits and ferrets.

To determine the agreement between plasma total solids (ts) concentration as measured by refractometry and plasma total protein (tp) concentration as measured by biuret assay in pet rabbits and ferrets.Sample 253 and 146 blood samples from 146 and 121 ferrets and rabbits, respectively, with results of cbc and plasma biochemical analyses.Procedures data were collected from medical records regarding plasma ts and tp concentrations, pcv, plasma biochemical values, plasma appearance, and patient signalment.Agreement was determined between refractometer and biuret assay (reference method) values for plasma ts and tp concentration.Other variables were examined for an impact on this agreement.Results mean ± sd plasma tp and ts concentrations were 6.4 ± 0.8 mg/d l and 6.6 ± 0.8 mg/d l, respectively, for rabbits and 6.3 ± 1.2 mg/d l and 6.4 ± 1.1 mg/d l for ferrets.On average, refractometer values overestimated plasma tp concentrations as measured by biuret assay.Plasma cholesterol, glucose, and bun concentrations and hemolysis and lipemia had significant effects on this bias for ferrets; only bun concentration had an effect on bias for rabbits given the available data.Other variables had no influence on bias.The limits of agreement were wider than the total allowable analytic error, and > 5% of the data points were outside acceptance limits, indicating that the 2 methods were not in clinical agreement.Conclusions and clinical relevance refractometer measurements of plasma ts concentration failed to provide a good estimation of biuret assay measurements of plasma tp concentration in rabbits and ferrets, suggesting that these 2 analytic methods and the results they yield cannot be used interchangeably in these species.

Journal: Journal of the American Veterinary Medical Association (2021)
Publication types: Journal Article
Monitoring the elimination of gambiense human African trypanosomiasis in the historical focus of Batié, South-West Burkina Faso.

The world health organisation has targeted the elimination of human african trypanosomiasis (hat) as zero transmission by 2030.Continued surveillance needs to be in place for early detection of re-emergent cases.In this context, the performance of diagnostic tests and testing algorithms for detection of the re-emergence of trypanosoma brucei gambiense hat remains to be assessed.We carried out a door-to-door active medical survey for hat in the historical focus of batié, south-west burkina faso.Screening was done using three rapid diagnostic tests (rdts).Two laboratory tests (elisa/t.B.Gambiense and immune trypanolysis) and parasitological examination were performed on rdt positives only.In total, 5883 participants were screened, among which 842 (14%) tested positive in at least one rdt.Blood from 519 rdt positives was examined microscopically but no trypanosomes were observed.The hat sero-k-set test showed the lowest specificity of 89%, while the specificities of sd bioline hat and r hat sero-strip were 92% and 99%, respectively.The specificity of elisa/t.B.Gambiense and trypanolysis was 99% (98-99%) and 100% (99-100%), respectively.Our results suggest that t.B.Gambiense is no longer circulating in the study area and that zero transmission has probably been attained.While a least cost analysis is still required, our study showed that rdt preselection followed by trypanolysis may be a useful strategy for post-elimination surveillance in burkina faso.

Journal: Parasite (Paris, France) (2022)
Publication types: Journal Article
The Prevalence of Mesangial Electron-Dense Deposits in PLA2R-Positive Membranous Nephropathy.

Introduction membranous nephropathy (mn) is a common cause of nephrotic syndrome in adults and can be primary or secondary.The antigenic target of antibodies in 70% of primary cases is phospholipase a2 receptor (pla2r).The presence or absence of mesangial electron-dense deposits has been used to distinguish between primary and secondary mn.Mesangial deposits suggest mn due to lupus, infection, or other causes, though they are reported to occur in approximately 10% of primary mn.Staining for pla2r is now frequently used for confirming a diagnosis of primary mn.If mesangial deposits predict a secondary cause, they should be more frequent in pla2r-negative biopsies.Methods a review of institutional kidney biopsies between march 2017 and june 2020 identified all cases of mn.Cases with a diagnosis of lupus or near "full-house" staining by immunofluorescence microscopy (if) were excluded.Light microscopy, if, and electron microscopy (em) were performed.Pla2r staining was performed by if.Em for all cases was reviewed and electron-dense deposit location, distribution, and size were determined.Results ninety-three cases of mn were identified, of which 86 had both pla2r staining and em performed.Of these, 51 cases (59%) were positive for pla2r and 35 (41%) were negative.Mesangial electron-dense deposits were present in 22 (25.6%) of the 86 cases, including 27.5% (14/51) of pla2r-positive cases and 22.8% (8/35) of pla2r-negative cases.No difference was seen in size or distribution of deposits, or other features considered suggestive of secondary mn.Conclusion pla2r-negative cases were not more likely to have mesangial deposits than pla2r-positive cases.Mesangial deposits should not be used as an indicator of secondary mn.

Journal: Nephron (2022)
Publication types: Journal Article;Review
Evaluation of an Expedited Trauma Transfer Protocol: Right Place, Right Time.

Trauma patients may initially be evaluated at non-trauma centers.This may cause a delay in treatment, which could affect their outcome.Additionally, advanced imaging may be performed which may be suboptimal or unnecessary, increase time to transfer, or unable to be viewed when the patient reaches a trauma center increasing the delays to treatment or need for repeat imaging.Rapid identification and transfer to definitive trauma care, minimizing unnecessary delays should be the priority.Methods the trauma registry at a regional level 1 adult/pediatric trauma center was queried for transferred trauma patients over a 3-y period.A retrospective review was performed.Transferred trauma patients were compared prior to an expedited transfer protocol to after implementation.Demographics, mechanism of injury, injury severity score, computerized tomography scans performed prior to transfer, mortality, hospital and intensive care unit length of stay were compared using bivariate and multivariable regression statistics where appropriate.Results transferred trauma patients were identified, 683 in the pre-protocol group and 821 in the post-protocol group, an increase of 16.8%.There were no differences in age, sex, injury severity score, mechanism of injury, mortality, hospital, or intensive care unit length of stay (los) throughout the study period.There was a significant decrease in time to transfer (263 min ± 222 versus 227 ± 189, p < 0.001) and computerized tomography scans performed prior to transfer (head 47% versus 32%, c-spine 36% versus 23%, thorax 22% versus 16%, abdomen/pelvis 24% versus 14%, all p values <0.001 except ct thorax).Interestingly, the rate of underinsured patients did not increase (21% versus 25%, p = 0.05).Risk-adjusted mortality and hospital los also did not change during the study period.Conclusions after implementation of an expedited trauma transfer protocol to a regional level 1 trauma center there was an associated reduced time of arrival to definitive care and decreased advanced imaging done prior to transfer.However, there was no associated decrease in mortality or los among transferred patients.Further studies examining prehospital transport or hospital choice decisions and subsequent care provided at non-trauma facilities regarding imaging obtained, care rendered, and transfer decisions can be explored.

Journal: The Journal of surgical research (2022)
Publication types: Journal Article