bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spotter’s guide to SNPtic exons: The common splice variants underlying some SNP–phenotype correlations
Authors: Keegan Niall Patrick , Fletcher Sue 
Published: October 2021

AbstractBackgroundCryptic exons are typically characterised as deleterious splicing aberrations caused by deep intronic mutations. However, low‐level splicing of cryptic exons is sometimes observed in the absence of any pathogenic mutation. Five recent reports have described how low‐level splicing of cryptic exons can be modulated by common single‐nucleotide polymorphisms (SNPs), resulting in phenotypic differences amongst different genotypes.MethodsWe sought to investigate whether additional ‘SNPtic’ exons may exist, and whether these could provide an explanatory mechanism for some of the genotype–phenotype correlations revealed by genome‐wide association studies.We thoroughly searched the literature for reported cryptic exons, cross‐referenced their genomic coordinates against the dbSNP database of common SNPs, then screened out SNPs with no reported phenotype associations.ResultsThis method discovered five probable SNPtic exons in the genes APC, FGB, GHRL, MYPBC3 and OTC. For four of these five exons, we observed that the phenotype associated with the SNP was compatible with the predicted splicing effect of the nucleotide change, whilst the fifth (in GHRL) likely had a more complex splice‐switching effect.ConclusionApplication of our search methods could augment the knowledge value of future cryptic exon reports and aid in generating better hypotheses for genome‐wide association studies.
Experimental comparison of photon versus particle computed tomography to predict tissue relative stopping powers
Authors: Bär Esther , Volz Lennart , Collins‐Fekete Charles‐Antoine , Brons Stephan , Runz Armin , Schulte Reinhard Wilhelm , Seco Joao 
Published: October 2021

AbstractPurpose: Measurements comparing relative stopping power (RSP) accuracy of state‐of‐the‐art systems representing single‐energy and dual‐energy computed tomography (SECT/DECT) with proton CT (pCT) and helium CT (HeCT) in biological tissue samples.Methods: We used 16 porcine and bovine samples of various tissue types and water, covering an RSP range from 0.900.06 to 1.78 0.05. Samples were packed and sealed into 3D‐printed cylinders ( cm, cm) and inserted into an in‐house designed cylindrical polymethyl methacrylate (PMMA) phantom ( cm, cm). We scanned the phantom in a commercial SECT and DECT (120 kV; 100 and 140 kV/Sn (tin‐filtered)); and acquired pCT and HeCT ( MeV/u, 2 steps, (p)/ (He) particles/projection) with a particle imaging prototype. RSP maps were calculated from SECT/DECT using stoichiometric methods and from pCT/HeCT using the DROP‐TVS algorithm. We estimated the average RSP of each tissue per modality in cylindrical volumes of interest and compared it to ground truth RSP taken from peak‐detection measurements.Results: Throughout all samples, we observe the following root‐mean‐squared RSP prediction errors combined uncertainty from reference measurement and imaging: SECT 3.102.88%, DECT 0.752.80%, pCT 1.19 2.81%, and HeCT 0.782.81%. The largest mean errors combined uncertainty per modality are SECT 8.22 2.79% in cortical bone, DECT 1.742.00% in back fat, pCT 1.80 4.27% in bone marrow, and HeCT 1.374.25% in bone marrow. Ring artifacts were observed in both pCT and HeCT reconstructions, imposing a systematic shift to predicted RSPs.Conclusion: Comparing state‐of‐the‐art SECT/DECT technology and a pCT/HeCT prototype, DECT provided the most accurate RSP prediction, closely followed by particle imaging. The novel modalities pCT and HeCT have the potential to further improve on RSP accuracies with work focusing on the origin and correction of ring artifacts. Future work will study accuracy of proton treatment plans using RSP maps from investigated imaging modalities.
Extraction of a vascular function for a fully automated dynamic contrast‐enhanced magnetic resonance brain image processing pipeline
Authors: Loos Wallace S. , Souza Roberto , Andersen Linda B. , Lebel R. Marc , Frayne Richard 
Published: October 2021

PurposeTo develop a deep‐learning model that leverages the spatial and temporal information from dynamic contrast‐enhanced magnetic resonance (DCE MR) brain imaging in order to automatically estimate a vascular function (VF) for quantitative pharmacokinetic (PK) modeling.MethodsPatients with glioblastoma multiforme were scanned post‐resection approximately every 2 months using a high spatial and temporal resolution DCE MR imaging sequence ( s and cm3). A region over the transverse sinus was manually drawn in the dynamic T1‐weighted images to provide a ground truth VF. The manual regions and their resulting VF curves were used to train a deep‐learning model based on a 3D U‐net architecture. The model concurrently utilized the spatial and temporal information in DCE MR images to predict the VF. In order to analyze the contribution of the spatial and temporal terms, different weighted combinations were examined. The manual and deep‐learning predicted regions and VF curves were compared.ResultsForty‐three patients were enrolled in this study and 155 DCE MR scans were processed. The 3D U‐net was trained using a loss function that combined the spatial and temporal information with different weightings. The best VF curves were obtained when both spatial and temporal information were considered. The predicted VF curve was similar to the manual ground truth VF curves.ConclusionThe use of spatial and temporal information improved VF curve prediction relative to when only the spatial information is used. The method generalized well for unseen data and can be used to automatically estimate a VF curve suitable for quantitative PK modeling. This method allows for a more efficient clinical pipeline and may improve automation of permeability mapping.
Comparison of the sputtered TiO2 anatase and rutile thin films as electron transporting layers in perovskite solar cells
Authors: Shahvaranfard Fahimeh , Li Ning , Hosseinpour Saman , Hejazi Seyedsina , Zhang Kaicheng , Altomare Marco , Schmuki Patrik , Brabec Christoph J. 
Published: October 2021

AbstractWe examine comparatively the performance of sputtered TiO2 rutile and anatase thin films as an electron transport layer (ETL) in MAPbI3‐based perovskite solar cells. Both anatase and rutile TiO2 ETLs are deposited (on fluorine‐doped tin oxide [FTO] substrates) by magnetron sputtering in the form of nanocrystalline thin films. We systematically investigate the role of crystallographic phase composition of TiO2 ETLs on the photovoltaic performance of perovskite solar cells. The champion power conversion efficiencies (PCEs) of 18.4% and 17.7% under reverse scan mode are obtained for perovskite solar cells based on TiO2 anatase and TiO2 rutile ETL, respectively. The results show that the magnetron sputtering deposited ETLs differ from each other only in their phase composition while the overall performance of the devices is not greatly affected by the crystallographic phase of the TiO2 ETLs. Our results point to an important fact that for a proper and reliable comparison between the performance of TiO2 anatase and rutile ETLs, it is crucial to investigate films of similar morphology and structure that are synthesize under similar conditions.
An integrated feasibility study using passive geophysical methods for the investigation of the Gerolekas bauxite deposits site, Greece
Authors: Orfanos C. , Leontarakis K. , Polychronopoulou K. , Apostolopoulos G. , Athanasas K. , Martakis N. 
Published: October 2021

ABSTRACTThe scope of this research is to delineate an optimized strategy for the implementation of cost‐effective and environmentally friendly passive geophysical methods in a challenging environment, in this case the Gerolekas bauxite mines, Greece. In this region, bauxite deposits have been detected and are being exploited at the interfaces between limestone layers in the autochthonous zone of Parnassus–Giona. The area under investigation, Gerolekas, is an allochthonous overthrust zone that overlays a part of the autochthonous geological structure. Currently, there is no information about the possible continuation of the bauxite deposits under Gerolekas below a certain depth. In this study, an integrated multi‐parameter approach using gravity, magnetotelluric and passive seismic methodologies is evaluated through a feasibility study incorporating realistic synthetic data. The specific strategy involves building a lithological model of the area by exploiting more than 4000 boreholes and incorporating data from in situ geological observations and official geological mapping. The 3D lithological model is then converted to equivalent geophysical models, based on in situ measurements, both on the surface and inside the mining galleries, as well as on data from previous studies in the literature, which together serve as the basis for the inversion procedures. The feasibility study is applied, simulating two different extreme realistic scenarios, by adding synthetic boreholes to the real ones, setting the optimum parameterization to control any possible scenario to be resolved, and evaluating the contribution of a priori information, to create starting models. Finally, a multi‐parameter analysis is formulated and applied to all inverted models to create a litho‐constrained unified geophysical model, providing an unbiased, integrated, statistically driven model of the area and generating updated geophysical models that are significantly improved.
Weight loss in primary care: A pooled analysis of two pragmatic cluster‐randomized trials
Authors: Katzmarzyk Peter T. , Apolzan John W. , Gajewski Byron , Johnson William D. , Martin Corby K. , Newton Robert L. , Perri Michael G. , VanWormer Jeffrey J. , Befort Christie A. 
Published: October 2021

AbstractObjectiveThe aim of this study was to report the results of five weight‐loss interventions in primary care settings in underserved patients and to compare the level of pragmatism across the interventions using the Pragmatic Explanatory Continuum Indicator Summary (PRECIS‐2) tool.MethodsData from 54 primary care clinics (2,210 patients) were pooled from the Promoting Successful Weight Loss in Primary Care in Louisiana (PROPEL) and Rural Engagement in Primary Care for Optimizing Weight Reduction (REPOWER) cluster‐randomized trials. Clinics were randomized to one of five comparators: PROPEL usual care, PROPEL combination of in‐clinic and telephone visits, REPOWER in‐clinic individual visits, REPOWER in‐clinic group visits, or REPOWER telephone group visits.ResultsAt 24 months, weight loss (kilograms) was −0.50 (95% CI: −1.77 to 0.76), −3.05 (−4.10 to −2.01), −4.30 (−5.35 to −3.26), −4.79 (−5.83 to −3.75), and −4.80 (−5.96 to −3.64) in the PROPEL usual care, REPOWER in‐clinic individual visits, REPOWER telephone group visits, REPOWER in‐clinic group visits, and PROPEL in‐clinic and telephone visits arms, respectively. At 24 months, percentage of weight loss was −0.360 (−1.60 to 0.88), −3.00 (−4.02 to −1.98), −4.23 (−5.25 to −3.20), −4.67 (−5.69 to −3.65), and −4.69 (−5.82 to −3.56), respectively, in the five arms. The REPOWER in‐clinic individual visits intervention was the most pragmatic and reflects the current Centers for Medicare and Medicaid Services funding model, although this intervention produced the least weight loss.ConclusionsClinically significant weight loss over 6 months in primary care settings is achievable using a variety of lifestyle‐based treatment approaches. Longer‐term weight‐loss maintenance is more difficult to achieve.
Functionalized PVA film with good adsorption capacity for anionic dye
Authors: Kandil Heba , Abdelhamid Ahmed E. , Moghazy Reda M. , Amin Amal 
Published: October 2021

AbstractThe dye‐water treatment by polyvinyl alcohol (PVA) is still a challenge as PVA is characterized by its strong affinity to water. Therefore, this study aims to fabricate a functional PVA film with good regeneration ability to remove anionic dyes from aqueous solution using polyamidoamine dendrimers (PAMAM) as a modifier and epichlorohydrin as a cross‐linker. Solution casting technique was applied to prepare the functionalized film. The adsorption efficiency of the film was evaluated by studying the effect of various parameters such as PAMAM loading (0, 12.5, 25, 50 wt%), initial dye concentration, film dose, solution pH, and adsorption time. The adsorption studies showed that with increasing PAMAM loading, the maximum adsorption capacity of the resulting film increased till it reached up to 73.8 mg/g by the PVA film with 50 wt% PAMAM. For understanding the nature of the adsorption process of the prepared film, the kinetics and isotherm analysis were studied. It was found that the mechanism of dye removal by the prepared film followed pseudo‐second‐order kinetic and Freundlich isotherm, respectively. The adsorption and regeneration studies indicated that this film has great potential to effectively remove anionic dye from wastewater.
Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles
Authors: Paul Anindita , Subhadarshini Seemadri , Srinivasan Narayanaswamy 
Published: October 2021

AbstractThe bilobal protein kinase‐like fold in pseudokinases lack one or more catalytic residues, conserved in canonical protein kinases, and are considered enzymatically deficient. Tertiary structures of pseudokinases reveal that their loops topologically equivalent to activation segments of kinases adopt contracted configurations, which is typically extended in active conformation of kinases. Herein, anisotropic network model based normal mode analysis (NMA) was conducted on 51 active conformation structures of protein kinases and 26 crystal structures of pseudokinases. Our observations indicate that although backbone fluctuation profiles are similar for individual kinase‐pseudokinase families, low intensity mean square fluctuations in pseudo‐activation segment and other sub‐structures impart rigidity to pseudokinases. Analyses of collective motions from functional modes reveal that pseudokinases, compared to active kinases, undergo distinct conformational transitions using the same structural fold. All‐atom NMA of protein kinase‐pseudokinase pairs from each family, sharing high amino acid sequence identities, yielded distinct community clusters, partitioned by residues exhibiting highly correlated fluctuations. It appears that atomic fluctuations from equivalent activation segments guide community membership and network topologies for respective kinase and pseudokinase. Our findings indicate that such adaptations in backbone and side‐chain fluctuations render pseudokinases competent for catalysis‐independent roles.
Chemical reactivity and binding interactions in ribonucleic acid‐peptide complexes
Authors: Srivastava Ruby 
Published: October 2021

AbstractThe covalent and noncovalent backbone binding interactions in RNA‐peptide complexes were studied by DFT methods. Four RNA structures R1(GGCUAGCC), R2(AAUCGAUU), R3(GGGAUCCC), and R4(AAAGCUUU) has been selected for eight protonated peptides (DR, ER, GR, KR, NGR, RR, tmeGnd (tme), and VR) interactions based on an experimental study (Anal Chem. 2019; 91:1659‐1664). Chemical reactivity theory is used to study the reactivity of eight peptides with global descriptors. Lower hardness values reflected low stability and high reactivity for the protonated peptides. DR, ER, GR, KR, NGR, RR, and VR show lower value of ω, μ while tme has high value of ω, μ. Larger highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap for ER, GR, and KR showed greater structural stability for peptides. AutoDock and PatchDock results indicated that R1, R2, and R4 retain hairpin structures while interacting with peptide complexes. The calculated binding energies of (R1–R4)‐peptide complexes from AutoDock tools are (1.49–11.12) kcal/mol. Results showed that the noncovalent interactions are stronger than the covalent interactions for R1‐peptide complexes. The reason might be the transfer of proton from protonated ligand to deprotonated RNA, which has initiated the loss of the ligand. Also it has been observed that proton transfer has become energetically unfavorable in presence of additional hydrogen bonds which is predicted in the experimental results.
Donepezil improves vascular function in a mouse model of Alzheimer’s disease
Authors: Pellegrini Carolina , D’Antongiovanni Vanessa , Fornai Matteo , Duranti Emiliano , Baldacci Filippo , Bernardini Nunzia , Taddei Stefano , Virdis Agostino , Blandizzi Corrado , Masi Stefano , Antonioli Luca 
Published: October 2021

AbstractCardiovascular complications in Alzheimer's disease (AD) patients can occur years to decades prior to the onset of clinical symptoms of the disease. Donepezil represents the most effective drug in the treatment of AD. However, the potential effect of donepezil on vascular function and structure remains largely unexplored. Here, we assessed the impact of donepezil on the vascular phenotype of an established model of accelerated senescence that develops spontaneously AD, the SAMP8 mouse. Three groups of animals were included: SAMR1 (control strain), SAMP8, and SAMP8 treated with donepezil. Treatment with donepezil was administered from the 4th to the 6th month of life. At 6 months, after cognitive tests by Morris Water Maze, animals were euthanized, and their mesenteric arteries were processed for functional experiments. Untreated SAMP8 developed cognitive impairment compared to SAMR1, while donepezil treatment significantly attenuated cognitive dysfunction. SAMP8 exhibited a higher media‐to‐lumen ratio than SAMR1 and donepezil‐treated animals. Endothelial function was impaired in SAMP8 animals compared to SAMR1. The addition of vitamin C improved the vasodilatory response to acetylcholine in SAMP8. Treatment with donepezil improved endothelial function in SAMP8 animals and reduced the additional vasodilation induced by vitamin C. In conclusion, in the SAMP8 AD model, cognitive impairment is associated with endothelial dysfunction and vascular remodeling which could contribute to cardiovascular events in AD since the prodromal phases of the disease. Treatment with donepezil alleviates vascular dysfunction associated with AD through an increase in NO availability likely by counteracting inflammation and oxidative stress.
Beneficial rhizobacteria inoculation on Ocimum basilicum reduces the growth performance and nutritional value of Spodoptera frugiperda
Authors: Palermo Tamara Belén , Cappellari Lorena del Rosario , Chiappero Julieta , Giordano Walter , Banchio Erika 
Published: October 2021

AbstractBACKGROUNDPlant growth‐promoting rhizobacteria (PGPR) has a significant role in plant–insect interaction. However, the extent of their impact on insects is still not well understood. This investigation was designed to evaluate the role of inoculation with Bacillus amyloliquefaciens GB03 on sweet basil (Ocimum basilucum L.) in the development and nutritional parameters of Spodoptera frugiperda. In addition, the feeding preferences on inoculated and non‐inoculated plants were assessed.RESULTSSpodoptera frugiperda larvae reared with inoculated sweet basil leaves had a strong negative effect on the development of the insect, resulting in lower larval and pupal weights, and a longer period for larval–adult development. Moreover, adult emergence was reduced, but the relative consumption rate (RCR) value was unaffected, thereby revealing no alteration of the palatability. Growth rate and nutritional indicators, such as the efficiency of conversion of ingested food (ECI) and the efficiency of conversion of digested food (ECD), were reduced in larvae reared from treated plants. In the choice test, larvae avoided feeding on inoculated leaves.CONCLUSIONThe higher occurrence of secondary metabolites in inoculated plants could have been the reason for the reduction of the plant nutritional rate and also for the food selection, since it has been previously reported that GB03 inoculated sweet basil increased the essential oil yield. Therefore, PGPR inoculation could be used as a growth promoter, making it a promising candidate for plant protection programs against insects in aromatic plant production. © 2021 Society of Chemical Industry.
Effects of curcumin on menstrual pattern, premenstrual syndrome, and dysmenorrhea: A triple‐blind, placebo‐controlled clinical trial
Authors: Bahrami Afsane , Zarban Asghar , Rezapour Hadis , Agha Amini Fashami Akram , Ferns Gordon A. 
Published: October 2021

Premenstrual syndrome (PMS) and primary dysmenorrhea are common complaints among young women. This study evaluated the effects of curcumin supplements on symptoms of pain in young women with PMS and dysmenorrhea. A randomized, triple‐blinded, placebo‐controlled clinical trial was undertaken. Women who suffered from both PMS and dysmenorrhea were enrolled, and were randomly allocated to the curcumin (n = 62), or placebo (n = 62) groups. Each subject received one capsule (500 mg of curcuminoid, or placebo) daily, from 7 days pre‐ until 3 days post‐menstruation for three successive menstrual cycles. Participants recorded the severity of PMS, or dysmenorrhea using a Premenstrual Syndrome Screening Tool (PSST) and the visual analog scale, respectively. Baseline characteristics of participants did not differ between the curcumin and placebo groups. At the end of the trial, the PSST scores were significantly lower in both the curcumin (32.5 ± 9.8 vs. 21.6 ± 9.8); and placebo groups (31.7 ± 9.4 vs. 23.4 ± 12.8). There was a significant reduction of dysmenorrhea pain in both the curcumin and placebo groups (by 64% and 53.3%, respectively). Hence, curcumin had comparable effects as placebo, regarding the amelioration of symptoms of PMS and dysmenorrhea. Further studies are required with larger samples, using higher doses curcumin for longer durations, and perhaps in combination therapy.
Dipole transition‐matrix elements and oscillator strengths for the C4+doubly excited states with Coulomb and screened Coulomb (Debye–Hückel) potentials
Authors: Wang Yang , Wei Baisi , Kar Sabyasachi , Ho Yew Kam 
Published: October 2021

AbstractThe dipole transition‐matrix elements (DTMEs) and oscillator strengths (OSs) for the doubly excited states (DESs) in heliumlike carbon are investigated using the correlated exponential wavefunctions (CEW). The interactions between the charged particles are taken care of by using both Coulomb and screened Coulomb (Debye–Hückel) potentials. The singly excited 1s3p1P state and doubly excited 2p2 1Destate are also calculated using CEW. The singly excited states of C4+in terms of Debye length (DL) are calculated using the Ritz variational principle. The DESs for different DLs are determined using the stabilization method. The DTMEs and OSs for the transitions between the 2p2 1Destate and the 1s2p1P, 1s3p1P, 2s2p+1Po, 2s3p−1Po, 2s3p+1Po, 2p3d1Postates, along with the 2p2 1Deresonance parameters are reported for various DLs. The benchmark data for DTMEs and OSs for the DESs in the C4+ion in pure Coulomb and screened Coulomb environments, obtained by employing highly CEW functions and utilizing the stabilization method, are reported for the first time.