bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection
Authors: Miranda-Quintana Ramón Alain , Rácz Anita , Bajusz Dávid , Héberger Károly 
Published: April 2021

AbstractDespite being a central concept in cheminformatics, molecular similarity has so far been limited to the simultaneous comparison of only two molecules at a time and using one index, generally the Tanimoto coefficent. In a recent contribution we have not only introduced a complete mathematical framework for extended similarity calculations, (i.e. comparisons of more than two molecules at a time) but defined a series of novel idices. Part 1 is a detailed analysis of the effects of various parameters on the similarity values calculated by the extended formulas. Their features were revealed by sum of ranking differences and ANOVA. Here, in addition to characterizing several important aspects of the newly introduced similarity metrics, we will highlight their applicability and utility in real-life scenarios using datasets with popular molecular fingerprints. Remarkably, for large datasets, the use of extended similarity measures provides an unprecedented speed-up over “traditional” pairwise similarity matrix calculations. We also provide illustrative examples of a more direct algorithm based on the extended Tanimoto similarity to select diverse compound sets, resulting in much higher levels of diversity than traditional approaches. We discuss the inner and outer consistency of our indices, which are key in practical applications, showing whether then-ary and binary indices rank the data in the same way. We demonstrate the use of the newn-ary similarity metrics ont-distributed stochastic neighbor embedding (t-SNE) plots of datasets of varying diversity, or corresponding to ligands of different pharmaceutical targets, which show that our indices provide a better measure of set compactness than standard binary measures. We also present a conceptual example of the applicability of our indices in agglomerative hierarchical algorithms. The Python code for calculating the extended similarity metrics is freely available at:https://github.com/ramirandaq/MultipleComparisons
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics†
Authors: Miranda-Quintana Ramón Alain , Bajusz Dávid , Rácz Anita , Héberger Károly 
Published: April 2021

AbstractQuantification of the similarity of objects is a key concept in many areas of computational science. This includes cheminformatics, where molecular similarity is usually quantified based on binary fingerprints. While there is a wide selection of available molecular representations and similarity metrics, there were no previous efforts to extend the computational framework of similarity calculations to the simultaneous comparison of more than two objects (molecules) at the same time. The present study bridges this gap, by introducing a straightforward computational framework for comparing multiple objects at the same time and providing extended formulas for as many similarity metrics as possible. In the binary case (i.e. when comparing two molecules pairwise) these are naturally reduced to their well-known formulas. We provide a detailed analysis on the effects of various parameters on the similarity values calculated by the extended formulas. The extended similarity indices are entirely general and do not depend on the fingerprints used. Two types of variance analysis (ANOVA) help to understand the main features of the indices: (i) ANOVA of mean similarity indices; (ii) ANOVA of sum of ranking differences (SRD). Practical aspects and applications of the extended similarity indices are detailed in the accompanying paper: Miranda-Quintana et al. J Cheminform. 2021. 10.1186/s13321-021-00504-4. Python code for calculating the extended similarity metrics is freely available at: https://github.com/ramirandaq/MultipleComparisons.
Low bicarbonate replacement fluid normalizes metabolic alkalosis during continuous veno-venous hemofiltration with regional citrate anticoagulation
Authors: Köglberger Paul , Klein Sebastian J. , Lehner Georg Franz , Bellmann Romuald , Peer Andreas , Schwärzler Daniel , Joannidis Michael 
Published: April 2021

Abstract
Background
Metabolic alkalosis is a frequently occurring problem during continuous veno-venous hemofiltration (CVVH) with regional citrate anticoagulation (RCA). This study aimed to evaluate the effectiveness of switching from high to low bicarbonate (HCO3−) replacement fluid in alkalotic critically ill patients with acute kidney injury treated by CVVH and RCA.

Methods
A retrospective-comparative study design was applied. Patients who underwent CVVH with RCA in the ICU between 09/2016 and 11/2017 were evaluated. Data were available from the clinical routine. A switch of the replacement fluid Phoxilium® (30 mmol/l HCO3−) to Biphozyl® (22 mmol/l HCO3−) was performed as blood HCO3− concentration persisted ≥ 26 mmol/l despite adjustments of citrate dose and blood flow. Data were collected from 72 h before the switch of the replacement solutions until 72 h afterwards.

Results
Of 153 patients treated with CVVH during that period, 45 patients were switched from Phoxilium® to Biphozyl®. Forty-two patients (42 circuits) were available for statistical analysis. After switching the replacement fluid from Phoxilium® to Biphozyl® the serum HCO3− concentration decreased significantly from 27.7 mmol/l (IQR 26.9–28.9) to 25.8 mmol/l (IQR 24.6–27.7) within 24 h (p < 0.001). Base excess (BE) decreased significantly from 4.0 mmol/l (IQR 3.1–5.1) to 1.8 mmol/l (IQR 0.2–3.4) within 24 h (p < 0.001). HCO3− and BE concentration remained stable from 24 h till the end of observation at 72 h after the replacement fluid change (p = 0.225). pH and PaCO2 did not change significantly after the switch of the replacement fluid until 72 h.

Conclusions
This retrospective analysis suggests that for patients developing refractory metabolic alkalosis during CVVH with RCA the use of Biphozyl® reduces external HCO3− load and sustainably corrects intracorporeal HCO3− and BE concentrations. Future studies have to prove whether correcting metabolic alkalosis during CVVH with RCA in critically ill patients is of relevance in terms of clinical outcome.
Enhanced detection of expanded repeat mRNA foci with hybridization chain reaction
Authors: Glineburg M. Rebecca , Zhang Yuan , Krans Amy , Tank Elizabeth M. , Barmada Sami J. , Todd Peter K. 
Published: April 2021

AbstractTranscribed nucleotide repeat expansions form detectable RNA foci in patient cells that contribute to disease pathogenesis. The most widely used method for detecting RNA foci, fluorescence in situ hybridization (FISH), is powerful but can suffer from issues related to signal above background. Here we developed a repeat-specific form of hybridization chain reaction (R-HCR) as an alternative method for detection of repeat RNA foci in two neurodegenerative disorders:C9orf72associated ALS and frontotemporal dementia (C9 ALS/FTD) and Fragile X-associated tremor/ataxia syndrome. R-HCR to both G4C2and CGG repeats exhibited comparable specificity but > 40 × sensitivity compared to FISH, with better detection of both nuclear and cytoplasmic foci in human C9 ALS/FTD fibroblasts, patient iPSC derived neurons, and patient brain samples. Using R-HCR, we observed that integrated stress response (ISR) activation significantly increased the number of endogenous G4C2repeat RNA foci and triggered their selective nuclear accumulation without evidence of stress granule co-localization in patient fibroblasts and patient derived neurons. These data suggest that R-HCR can be a useful tool for tracking the behavior of repeat expansion mRNA in C9 ALS/FTD and other repeat expansion disorders.
The influence of Antarctic ice loss on polar motion: an assessment based on GRACE and multi-mission satellite altimetry
Authors: Göttl Franziska , Groh Andreas , Schmidt Michael , Schröder Ludwig , Seitz Florian 
Published: April 2021

AbstractIncreasing ice loss of the Antarctic Ice Sheet (AIS) due to global climate change affects the orientation of the Earth’s spin axis with respect to an Earth-fixed reference system (polar motion). Here the contribution of the decreasing AIS to the excitation of polar motion is quantified from precise time variable gravity field observations of the Gravity Recovery and Climate Experiment (GRACE) and from measurements of the changing ice sheet elevation from altimeter satellites. While the GRACE gravity field models need to be reduced by noise and leakage effects from neighboring subsystems, the ice volume changes observed by satellite altimetry have to be converted into ice mass changes. In this study we investigate how much individual gravimetry and altimetry solutions differ from each other. We show that due to combination of individual solutions systematic and random errors of the data processing can be reduced and the robustness of the geodetic derived AIS polar motion excitations can be increased. We investigate the interannual variability of the Antarctic polar motion excitation functions by means of piecewise linear trends. We find that the long-term behavior of the three ice sheet subregions: EAIS (East Antarctic Ice Sheet), WAIS (West Antarctic Ice Sheet) and APIS (Antarctic Peninsula Ice Sheet) is quite different. While APIS polar motion excitations show no significant interannual variations during the study period$$2003-2015$$2003-2015, the trend of the WAIS and EAIS polar motion excitations increased in 2006 and again in 2009 while it started slightly to decline in 2013. AIS mass changes explain about$$45\%$$45%of the observed magnitude of the polar motion vector (excluding glacial isosatic adjustment). They cause the pole position vector to drift along$$59^{\circ }$$59∘East longitude with an amplitude of 2.7 mas/yr. Thus the contribution of the AIS has to be considered to close the budget of the geophysical excitation functions of polar motion.
Application of response surface methodology for color removing from dyeing effluent using de-oiled activated algal biomass
Authors: El-Mekkawi Samar A. , Abdelghaffar Rehab A. , Abdelghaffar Fatma , El-Enin S. A. Abo 
Published: April 2021

Abstract
Background
Conservation of the ecosystem is a prime concern of human communities. Industrial development should adopt this concern. Unfortunately, various related activities release lots of noxious materials concurrently with significant leakage of renewable resources. This work presents a new biosorbent activated de-oiled microalgae, Chlorella vulgaris, (AC) for biosorption of Acid Red 1 (AR1) from aqueous solution simulated to textile dyeing effluent. The biosorption characteristics of AC were explored as a function of the process parameters, namely pH, time, and initial dye concentration using response surface methodology (RSM).

Results
Optimization is carried out using the desirability approach of the process parameters for maximum dye removal%. The ANOVA analysis of the predicted quadratic model elucidated significant model terms with a regression coefficient value of 0.97, F value of 109.66, and adequate precision of 34.32 that emphasizes the applicability of the model to navigate the design space. The optimization depends on the priority of minimizing the time of the process to save energy and treating high concentrated effluent resulted in removal % up to 83.5%. The chemical structure and surface morphology of AC, and the dye-loaded biomass (AB) were characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDX), and transmission electron microscope (TEM). The activation process transforms the biomass surface into a regular and small homogeneous size that increases the surface area and ultimately enhances its adsorption capacity

Conclusion
The optimization of the process parameters simultaneously using RSM performs a high-accurate model which describes the relationship between the parameters and the response through minimum number of experiments. This study performed a step towards an integrated sustainable solution applicable for treating industrial effluents through a zero-waste process. Using the overloaded biomass is going into further studies as micronutrients for agricultural soil.
Prescribed fire alters structure and composition of a mid-Atlantic oak forest up to eight years after burning
Authors: Dems Cody L. , Taylor Alan H. , Smithwick Erica A. H. , Kreye Jesse K. , Kaye Margot W. 
Published: April 2021

Abstract
Background
Prescribed fire in Eastern deciduous forests has been understudied relative to other regions in the United States. In Pennsylvania, USA, prescribed fire use has increased more than five-fold since 2009, yet forest response has not been extensively studied. Due to variations in forest composition and the feedback between vegetation and fire, Pennsylvania deciduous forests may burn and respond differently than forests across the eastern US. We measured changes in forest structure and composition up to eight years after prescribed fire in a hardwood forest of the Ridge and Valley region of the Appalachian Mountains in central Pennsylvania.

Results
Within five years post fire, tree seedling density increased more than 72% while sapling density decreased by 90%, midstory density decreased by 46%, and overstory response varied. Following one burn in the mixed-oak unit, overstory tree density decreased by 12%. In the aspen–oak unit, where pre-fire harvesting and two burns occurred, overstory tree density increased by 25%. Not all tree species responded similarly and post-fire shifts in species relative abundance occurred in sapling and seedling size classes. Abundance of red maple and cherry species decreased, whereas abundance of sassafras, quaking aspen, black oak, and hickory species increased.

Conclusions
Forest composition plays a key role in the vegetation–fire relationship and localized studies are necessary to measure forest response to prescribed fire. Compositional shifts in tree species were most pronounced in the aspen–oak unit where pre-fire overstory thinning and two prescribed fires were applied and significant structural changes occurred in all stands after just one burn. Increases in fire-tolerant tree species combined with reductions in fire-intolerant species highlight the role of prescribed fire in meeting management objectives such as altering forest structure and composition to improve game habitat in mid-Atlantic hardwood forests.
The effect of rolling resistance on people’s willingness to cycle during wintertime
Authors: Fenre Mathis Dahl , Klein-Paste Alex 
Published: April 2021

AbstractHarsh winters reduce utilitarian cycling in many cities. Using an online survey, we examined how increasing rolling resistance due to snow and ice affect people’s cycling willingness. The respondents (N = 1318) reported their willingness to cycle on various winter cycling conditions presented in photos. The answers were compared to the rolling resistance levels on the presented conditions, measured in a previous study. Respondents’ cycling willingness dropped from 91.2% at very low to 18.3% at very high rolling resistances. The cyclist’s age, gender, local climate, winter cycling experience and studded tire use affected the cycling willingness significantly. Electric bike usage did not affect cycling willingness. “Summer-only” cyclists did not cycle during the winter due to low temperatures (29%), lacked feeling of safety (27%), bicycle wear (17%), increased travel time (17%) and increased physical effort (10%). Hence, lower rolling resistance and increased use of studded tires can increase the cycling frequency of existing winter cyclists. To recruit new winter cyclists, the surface conditions should not only offer a low rolling resistance but should also be perceived as safe and comfortable.
Non-Western interventions for stress reduction and resilience
Authors: Gerbarg Patricia L. , Brown Richard P. 
Published: April 2021

SUMMARYComplementary and integrative medicine provides safe, low-cost, effective treatments for conditions ranging from everyday stress to post-traumatic stress disorder. The evidence for herbs, nutrients and mind–body practices is growing, despite disproportionately small amounts of financial support compared with funding for expensive pharmaceuticals. The unsustainable cost of conventional treatments, the moral imperative to care for millions of uninsured and the impact of COVID-19 compel us to fully explore known and potential benefits of treatments being used by complementary and integrative practitioners.
Assessment of Brain Metastasis at Diagnosis in Non–Small-Cell Lung Cancer: A Prospective Observational Study From North India
Authors: Naresh Gundu , Malik Prabhat Singh , Khurana Sachin , Pushpam Deepam , Sharma Vinod , Yadav Mukesh , Jain Deepali , Pathy Sushmita 
Published: April 2021

PURPOSE The incidence of symptomatic brain metastasis at diagnosis in non–small-cell lung cancer (NSCLC) is 5%-10%, and up to 40% develop during the disease course. There is a paucity of data supporting the role of brain imaging at diagnosis in asymptomatic cases particularly from resource-constraint settings. Here, we present our experience of mandatory baseline brain imaging with contrast-enhanced computed tomography (CECT) scans of all patients with NSCLC. MATERIALS AND METHODS This was a prospective observation study of patients with NSCLC with mandatory baseline brain CECT and a CNS examination. All histology proven patients with NSCLC diagnosed between January 2018 and October 2019 were included irrespective of stage. RESULTS A total of 496 patients were enrolled. The median age was 57 years (range, 23-84) with majority being males (75%) and smokers (66%). The prevalence of epidermal growth factor receptor mutations and anaplastic lymphoma kinase fusions was 33.4% and 12%, respectively. Brain imaging leads to upstaging in 7% cases. The prevalence of brain metastases was 21% (n = 104), with half being asymptomatic (51%). Factors associated with higher proportion of brain metastasis were young age (≤ 40 years), adenocarcinoma histology, poor Eastern Cooperative Oncology Group performance status (3 and 4), and high neutrophil-lymphocyte ratio (NLR) (> 2.5). After a median follow-up of 10.8 months (95% CI, 7.33 to 12.73), the median overall survival was 7.46 versus 12.76 months (hazard ratio 0.67; 95% CI, 0.46 to 0.96; P = .03) in patients with and without brain metastases, respectively. On multivariate analyses, high NLR and molecular graded prognostic assessment affected the overall survival significantly. CONCLUSION In our study, 21% of patients had brain metastasis at diagnosis detected with a mandatory baseline brain imaging with CECT. NLR and molecular graded prognostic assessment are significant predictors of survival in patients with brain metastasis.
Patient-Reported Complications, Symptoms, and Experiences of Living With X-Linked Hypophosphatemia Across the Life-Course
Authors: Cheung Moira , Rylands Angela J , Williams Angela , Bailey Karen , Bubbear Judith 
Published: April 2021

Abstract

Context
X-linked hypophosphatemia (XLH) is a rare, genetic phosphate-wasting disease resulting in bone, muscular, and dental problems, beginning in childhood and increasing in adulthood.

Objective
This qualitative analysis aimed to explore patient-reported symptoms, complications, and experiences of XLH over the life-course, using data from a large multinational online survey.

Methods
Responses to 2 open-ended questions from 209 adults and 86 children/adolescents (proxy report) with self-reported XLH were analyzed in 8 age groups. Two researchers independently coded and analyzed the responses, using thematic analysis, with differences settled among a multidisciplinary group. Six themes were identified, with age subgroup analysis conducted on the 3 most common, according to coding frequency.

Results
Within theme 1, “Clinical Signs and Symptoms of XLH,” “Pain” was a dominant subtheme across the life-course, but “Skeletal Pathology” dominated the responses of children/adolescents. Within theme 2, “Impacts of Clinical Signs and Symptoms,” interference with “Physical Exertion” and “Emotional Wellbeing” (comprising depression/anxiety in adults and lack of self-esteem in children/adolescents) was reported across all ages. For theme 3, “Negative Treatment Experiences,” “Medication” was problematic for children, with adults reporting lack of “Access to Appropriate Treatment.” Three further themes were identified: “Resilience,” “Positive Treatment Experiences,” and “Information Needs.”

Conclusion
The multiple burdens imposed on people with XLH throughout their lifetime encompassed the physical, emotional, and social, although the most challenging symptoms or complications differed between ages. Burden was further exacerbated by adults’ lack of access to appropriate treatment, illustrating the need for age-appropriate multidisciplinary care.
Comparative Efficacy of 6 Topical Pharmacological Agents for Preventive Interventions of Postoperative Sore Throat After Tracheal Intubation: A Systematic Review and Network Meta-analysis
Authors: Wang Ge , Qi Yang , Wu LiNa , Jiang GuiChun 
Published: April 2021

BACKGROUND:
Topical pharmacological agents typically used to treat postoperative sore throat (POST) after tracheal intubation include nonsteroidal anti-inflammatory drugs (NSAIDs), corticosteroids, lidocaine, Glycyrrhiza (licorice), and N-methyl-d-aspartate (NMDA) receptor antagonists (including ketamine and magnesium). However, the optimal prophylactic drug remains elusive.

METHODS:
The literature published before September 8, 2019 was searched on the PubMed, the Embase, the Web of Science, and the Cochrane Library. Randomized controlled trials (RCTs) covering topical prophylactic medications for patients with POST were included. Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system was used to assess the quality of evidence. The primary outcome is the risk of POST. Combining both direct and indirect evidence, a network meta-analysis was performed to assess odds ratios (ORs) between the topical pharmacological agents and surface under the cumulative ranking (SUCRA) curve for the treatment-based outcomes. This study is registered with PROSPERO, number CRD42020158985.

RESULTS:
Sixty-two RCTs (at least 73% of which were double blinded) that included a total of 6708 subjects and compared 6 categories of drugs and/or placebos were ultimately enrolled. All preventive interventions except lidocaine were more effective than placebo at the 4 time intervals. Lidocaine (OR: 0.35, 95% credible interval [CrI], 0.16-0.79) has a greater POST preventative intervention effect than the placebo at a time interval of only 2 to 3 hours after surgery. Relative to lidocaine, the risk of POST except 2 to 3 hours was lower for the following treatments: corticosteroids, ketamine, magnesium, NSAIDs, and Glycyrrhiza. The NMDA receptor antagonists studied here included ketamine and magnesium. Magnesium generally demonstrated greater benefit than ketamine at 24 hours postsurgery/extubation (OR: 0.41, 95% CrI, 0.18-0.92). Compared with ketamine, corticosteroids were associated with a reduced risk of POST during the 4 to 6 hours (OR: 0.40, 95% CrI, 0.19-0.83) and 24 hours (OR: 0.34, 95% CrI, 0.16-0.72) time intervals. During the 2 to 3 hours time interval, Glycyrrhiza (OR: 0.38, 95% CrI, 0.15-0.97) was more efficacious than magnesium.

CONCLUSIONS:
Our analysis shows that, among the 6 topical medications studied, lidocaine is not optimal for topical use to prevent POST. Glycyrrhizin, corticosteroids, NSAIDs, and NMDA receptor antagonists (ketamine and magnesium) are associated with a reduced postoperative pharyngeal pain across the 4 postsurgical time intervals studied, all of which can be chosen according to the clinical experience of the anesthesiologists and the patient preferences and are recommended for the reduction of postoperative throat pain.