bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implications of differential peroxyl radical-induced inactivation of glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase for the pentose phosphate pathway
Authors: Reyes Juan Sebastián , Fuentes-Lemus Eduardo , Figueroa Juan David , Rojas Javier , Fierro Angélica , Arenas Felipe , Hägglund Per M. , Davies Michael J. , López-Alarcón Camilo 
Published: December 2022

AbstractEscherichia coli glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) are key enzymes of the pentose phosphate pathway, responsible for the NADPH production in cells. We investigated modification of both enzymes mediated by peroxyl radicals (ROO·) to determine their respective susceptibilities to and mechanisms of oxidation. G6PDH and 6PGDH were incubated with AAPH (2,2′-azobis(2-methylpropionamidine)dihydrochloride), which was employed as ROO· source. The enzymatic activities of both enzymes were determined by NADPH release, with oxidative modifications examined by electrophoresis and liquid chromatography (LC) with fluorescence and mass (MS) detection. The activity of G6PDH decreased up to 62.0 ± 15.0% after 180 min incubation with 100 mM AAPH, whilst almost total inactivation of 6PGDH was determined under the same conditions. Although both proteins contain abundant Tyr (particularly 6PGDH), these residues were minimally affected by ROO·, with Trp and Met being major targets. LC–MS and in silico analysis showed that the modification sites of G6PDH are distant to the active site, consistent with a dispersed distribution of modifications, and inactivation resulting from oxidation of multiple Trp and Met residues. In contrast, the sites of oxidation detected on 6PGDH are located close to its catalytic site indicating a more localized oxidation, and a consequent high susceptibility to ROO·-mediated inactivation.
Geographical classification of malaria parasites through applying machine learning to whole genome sequence data
Authors: Deelder Wouter , Manko Emilia , Phelan Jody E. , Campino Susana , Palla Luigi , Clark Taane G. 
Published: December 2022

AbstractMalaria, caused by Plasmodium parasites, is a major global health challenge. Whole genome sequencing (WGS) ofPlasmodium falciparumandPlasmodium vivaxgenomes is providing insights into parasite genetic diversity, transmission patterns, and can inform decision making for clinical and surveillance purposes. Advances in sequencing technologies are helping to generate timely and big genomic datasets, with the prospect of applying Artificial Intelligence analytical techniques (e.g., machine learning) to support programmatic malaria control and elimination. Here, we assess the potential of applying deep learning convolutional neural network approaches to predict the geographic origin of infections (continents, countries, GPS locations) using WGS data ofP. falciparum(n = 5957; 27 countries) andP. vivax(n = 659; 13 countries) isolates. Using identified high-quality genome-wide single nucleotide polymorphisms (SNPs) (P. falciparum: 750 k,P. vivax: 588 k), an analysis of population structure and ancestry revealed clustering at the country-level. When predicting locations for both species, classification (compared to regression) methods had the lowest distance errors, and > 90% accuracy at a country level. Our work demonstrates the utility of machine learning approaches for geo-classification of malaria parasites. With timelier WGS data generation across more malaria-affected regions, the performance of machine learning approaches for geo-classification will improve, thereby supporting disease control activities.
A novel virulent Litunavirus phage possesses therapeutic value against multidrug resistant Pseudomonas aeruginosa
Authors: Lerdsittikul Varintip , Thongdee Metawee , Chaiwattanarungruengpaisan Somjit , Atithep Thassanant , Apiratwarrasakul Sukanya , Withatanung Patoo , Clokie Martha R. J. , Korbsrisate Sunee 
Published: December 2022

AbstractPseudomonas aeruginosa is a notable nosocomial pathogen that can cause severe infections in humans and animals. The emergence of multidrug resistant (MDR) P. aeruginosa has motivated the development of phages to treat the infections. In this study, a novel Pseudomonas phage, vB_PaeS_VL1 (VL1), was isolated from urban sewage. Phylogenetic analyses revealed that VL1 is a novel species in the genus Litunavirus of subfamily Migulavirinae. The VL1 is a virulent phage as no genes encoding lysogeny, toxins or antibiotic resistance were identified. The therapeutic potential of phage VL1 was investigated and revealed that approximately 56% (34/60 strains) of MDR P. aeruginosa strains, isolated from companion animal diseases, could be lysed by VL1. In contrast, VL1 did not lyse other Gram-negative and Gram-positive bacteria suggesting its specificity of infection. Phage VL1 demonstrated high efficiency to reduce bacterial load (~ 6 log cell number reduction) and ~ 75% reduction of biofilm in pre-formed biofilms of MDR P. aeruginosa. The result of two of the three MDR P. aeruginosa infected Galleria mellonella larvae showed that VL1 could significantly increase the survival rate of infected larvae. Taken together, phage VL1 has genetic and biological properties that make it a potential candidate for phage therapy against P. aeruginosa infections.
Molecular dynamics simulations reveal membrane lipid interactions of the full-length lymphocyte specific kinase (Lck)
Authors: Prakaash Dheeraj , Fagnen Charline , Cook Graham P. , Acuto Oreste , Kalli Antreas C. 
Published: December 2022

AbstractThe membrane-bound lymphocyte-specific protein-tyrosine kinase (Lck) triggers T cell antigen receptor signalling to initiate adaptive immune responses. Despite many structure–function studies, the mode of action of Lck and the potential role of plasma membrane lipids in regulating Lck’s activity remains elusive. Advances in molecular dynamics simulations of membrane proteins in complex lipid bilayers have opened a new perspective in gathering such information. Here, we have modelled the full-length Lck open and closed conformations using data available from different crystalographic studies and simulated its interaction with the inner leaflet of the T cell plasma membrane. In both conformations, we found that the unstructured unique domain and the structured domains including the kinase interacted with the membrane with a preference for PIP lipids. Interestingly, our simulations suggest that the Lck-SH2 domain interacts with lipids differently in the open and closed Lck conformations, demonstrating that lipid interaction can potentially regulate Lck’s conformation and in turn modulate T cell signalling. Additionally, the Lck-SH2 and kinase domain residues that significantly contacted PIP lipids are found to be conserved among the Src family of kinases, thereby potentially representing similar PIP interactions within the family.
Diagnostic value of “hyperdense consolidation sign” as a characteristic new computed tomography sign of diffuse alveolar hemorrhage
Authors: Kumasaka Soma , Kumasaka Yuka , Jingu Akiko , Tsushima Yoshito 
Published: December 2022

AbstractDiffuse alveolar hemorrhage (DAH) is an uncommon but life-threatening condition. Although DAH must be distinguished from other lung diseases, no specific computed tomography (CT) signs of DAH have been reported. This study aimed to evaluate the diagnostic value of “hyperdense consolidation” CT sign. We retrospectively evaluated non-contrast CT findings of 25 DAH patients and age- (≤ 2 years) and sex-matched controls with symptoms of dyspnea and hypoxemia. Two radiologists compared the two groups for the presence of hyperdense consolidation signs in lung parenchyma, defined as consolidation that visually contains areas with higher density than the aorta in the specific narrow window setting (window level = 35 Hounsfield units [HU], width = 80 HU) with a mediastinal filter. The sensitivity, specificity, positive- and negative-predictive values of the hyperdense consolidation sign for detection of DAH were 32.0%, 100%, 100%, and 59.5% with perfect interobserver agreement (к = 1.00). The hyperdense consolidation sign was found to be a highly specific sign for DAH.
Role of the elastography strain ratio using transrectal ultrasonography in the diagnosis of prostate cancer and clinically significant prostate cancer
Authors: Yoo Jeong Woo , Koo Kyo Chul , Chung Byung Ha , Lee Kwang Suk 
Published: December 2022

AbstractThis study investigated the efficacy of the elastography strain ratio (ESR) as a predictor of prostate cancer (PCa) in targeted prostate biopsy. In total, 257 patients who underwent magnetic resonance imaging-targeted biopsy were enrolled. Before biopsy, we placed regions of interest (zone A and B) in the lesion and levator ani. The ESR was measured as zone A/zone B. Multivariate analyses were performed to predict PCa and clinically significant PCa. There were 206 (71.5%) positive cancer lesions. No difference in digit rectal examination findings was found between patients with and without PCa. For predicting clinically significant PCa, an ESR ≥ 6.8 was significantly higher in the PCa (+) group than in the PCa (−) group (p < 0.001). The area under the receiver operating characteristic curve (AUC) for the conventional variables (model 1) plus the ESR was 0.845, which was significantly higher than that for model 1 (p = 0.001). In prostate imaging reporting and data system score 3 lesions, an ESR ≥ 4.6 was a significant predictor of PCa (p = 0.002). The AUC in model 1 plus the ESR was 0.856, which was significantly higher than that in model 1 alone (p = 0.017). The ESR is useful for predicting clinically significant PCa.
A retrospective observational cohort study evaluating the postoperative outcomes of intracapsular coblation tonsillectomy in children
Authors: Bitar Mohamad A. , Nazir Tanvir , Abd-Ul-Salam Hani 
Published: December 2022

AbstractCoblation intracapsular tonsillectomy (ICT) is becoming popular due to its decreased postoperative complications. However, a concern exists about the need for revision surgery. We conducted a retrospective observational cohort study, with a null hypothesis that Coblation ICT is not associated with recurrence of the preoperative symptoms, obstructive tonsillar regrowth, or the need for revision tonsillar surgery. We reviewed 345 patients (median age of 4.5 years; IQR 3.2–6.3), operated by the senior author between Feb 2017 and Sep 2020, for a median follow-up of 395.0 days (IQR 221.5–654.5). Most patients had snoring (94.2%), mouth breathing (92.8%), restless sleep (62.6%), and sleep disorder breathing (52.8%); 12.5% had recurrent tonsillitis. The mean initial total symptoms score (TSS) was 5.2 (SD 1.4, range 1–8); 87.5% had three or more symptoms; 86.7% underwent ICT; TSS decreased postoperatively to a mean of 0.2, SD 0.8, range 0–7. The mean hospital stay was 0.96 day (SD 0.36, range 0–3). Secondary bleeding occurred in 0.7% of ICT patients. No patient required admission or intervention. There was no documented tonsillar regrowth resulting in upper airway obstruction. No one needed tonsillar revision surgery. Intracapsular tonsillectomy was shown to be an effective procedure with long-lasting results.
DNMT1/PKR double knockdowned HepG2 (HepG2-DP) cells have high hepatic function and differentiation ability
Authors: Tanaka-yachi Rieko , Aizawa Kazuko , Shimizu Kie , Akutsu Hidenori , Nakamura Kazuaki 
Published: December 2022

AbstractHepG2 cells are widely used as a human hepatocytes model, but their functions, including drug metabolism, are inferior to primary hepatocytes. We previously reported that the hepatic gene expressions in HepG2 cells were upregulated by treatment with zebularine, which is an inhibitor of DNA methylation, through the inhibition of both DNA methyltransferase 1 (DNMT1) and double-stranded RNA-dependent protein kinase (PKR). In this study, we established a new HepG2 cell subline, HepG2-DP cells, by stable double knockdown of DNMT1 and PKR and evaluated its function. Albumin production, expression of CYP1A2 genes, and accumulation of lipid droplets were increased in HepG2-DP cells compared with the original HepG2 cells. Comprehensive gene expression analysis of transcription factors revealed that the expression of important genes for hepatic function, such as HNF1β, HNF4α, ONECUT1, FOXA1, FOXA2, FOXA3, and various nuclear receptors, was upregulated in HepG2-DP cells. These results indicate that the newly established HepG2-DP cells are a highly functional hepatocyte cell line. In addition, we investigated whether HepG2-DP cells are able to mature by differentiation induction, since HepG2 cells are derived from hepatoblastoma. The gene expression of major CYPs and Phase II, III drug-metabolizing enzyme genes was significantly increased in HepG2-DP cells cultured in differentiation induction medium. These results suggest that HepG2-DP cells can be further matured by the induction of differentiation and could therefore be applied to studies of drug metabolism and pharmacokinetics.
Exact multistability and dissipative time crystals in interacting fermionic lattices
Authors: Alaeian Hadiseh , Buča Berislav 
Published: December 2022

AbstractThe existence of multistability in quantum systems beyond the mean-field approximation remains an intensely debated open question. Quantum fluctuations are finite-size corrections to the mean-field as the full exact solution is unobtainable and they usually destroy the multistability present on the mean-field level. Here, by identifying and using exact modulated dynamical symmetries in a driven-dissipative fermionic chain we exactly prove multistability in the presence of quantum fluctuations. Further, unlike common cases in our model, rather than destroying multistability, the quantum fluctuations themselves exhibit multistability, which is absent on the mean-field level for our systems. Moreover, the studied model acquires additional thermodynamic dynamical symmetries that imply persistent periodic oscillations, constituting the first case of a boundary time crystal,to the best of our knowledge, a genuine extended many-body quantum system with the previous cases being only in emergent single- or few-body models. The model can be made into a dissipative time crystal in the limit of large dissipation (i.e. the persistent oscillations are stabilized by the dissipation) making it both a boundary and dissipative time crystal.
Low-dimensional electronic state at the surface of a transparent conductive oxide
Authors: Naamneh Muntaser , Guedes Eduardo B. , Prakash Abhinav , Cardoso Henrique M. , Shi Ming , Plumb Nicholas C. , Brito Walber H. , Jalan Bharat , Radović Milan 
Published: December 2022

AbstractMaterials that blend physical properties that are usually mutually exclusive could facilitate devices with novel functionalities. For example, the doped perovskite alkaline earth stannates BaSnO3 and SrSnO3 show the intriguing combination of high light transparency and high electrical conductivity. Understanding such emergent physics requires deep insight into the materials’ electronic structures. Moreover, the band structure at the surfaces of those materials can deviate significantly from their bulk counterparts, thereby unlocking novel physical phenomena. Employing angle-resolved photoemission spectroscopy and ab initio calculations, we reveal the existence of a 2-dimensional metallic state at the SnO2-terminated surface of 1% La-doped BaSnO3 thin films. The observed surface state is characterized by a distinct carrier density and a lower effective mass compared to the bulk conduction band, of about 0.12me. These particular surface state properties place BaSnO3 among the materials suitable for engineering highly conductive transition metal oxide heterostructures.
Regioselective O-alkylation of 2-pyridones by TfOH-catalyzed carbenoid insertion
Authors: Yan Zhewei , He Hangli , Yuan Dabiao , Yan Qiongjiao , Wang Wei , Jiang Haipeng , Wang Haifeng , Chen Fener 
Published: December 2022

We have developed a novel TfOH-catalyzed regioselective O-alkylation of 2-pyridones with diazo compounds in high regioselectivity. This protocol is characterized by mild reaction conditions, metal-free, and simplicity.
Speaking Rate, Immediate Memory, and Grammatical Processing in Prelingual Cochlear Implant Recipients
Authors: Shin Sujin , Warner-Czyz Andrea , Geers Ann , Katz William F. 
Published: December 2022

Purpose:This study examined the extent to which prelingual cochlear implant (CI) users show a slowed speaking rate compared with typical-hearing (TH) talkers when repeating various speech stimuli and whether the slowed speech of CI users relates to their immediate verbal memory.Method:Participants included 10 prelingually deaf teenagers who received CIs before the age of 5 years and 10 age-matched TH teenagers. Participants repeated nonword syllable strings, word strings, and center-embedded sentences, with conditions balanced for syllable length and metrical structure. Participants' digit span forward and backward scores were collected to measure immediate verbal memory. Speaking rate data were analyzed using a mixed-design, repeated-measures analysis of variance, and the relationships between speaking rate and digit spans were evaluated by Pearson correlation.Results:Participants with CIs spoke more slowly than their TH peers during the sentence repetition task but not in the nonword string and word string repetition tasks. For the CI group, significant correlations emerged between speaking rate and digit span scores (both forward and backward) for the sentence repetition task but not for the nonword string or word string repetition task. For the TH group, no significant correlations were found.Conclusions:The findings indicate a relation between slowed speech production, reduced immediate verbal memory, and diminished language capabilities of prelingual CI users, particularly for syntactic processing. These results support theories claiming that immediate memory, including components of a central executive, influences the speaking rate of these talkers. Implications for therapies designed to increase speech fluency in CI recipients are discussed.Supplemental Material:https://doi.org/10.23641/asha.21644795
Superconvergence and postprocessing of the continuous Galerkin method for nonlinear Volterra integro-differential equations
Authors: Zhang Mingzhu , Mao Xinyu , Yi Lijun 
Published: December 2022

We propose a novel postprocessing technique for improving the global accuracy of the continuous Galerkin (CG) method for nonlinear Volterra integro-differential equations. The key idea behind the postprocessing technique is to add a higher order Lobatto polynomial of degree k + 1 to the CG approximation of degree k. We first show that the CG method superconverges at the nodal points of the time partition. We further prove that the postprocessed CG approximation converges one order faster than the unprocessed CG approximation in the L2-, H1- and L∞-norms. As a by-product of the postprocessed superconvergence results, we construct several a posteriori error estimators and prove that they are asymptotically exact. Numerical examples are presented to highlight the superconvergence properties of the postprocessed CG approximations and the robustness of the a posteriori error estimators.
Outpatient Foley Catheter for Induction of Labor in Obese Nulliparous Patients: A Secondary Analysis of OFFSITE II Randomized Controlled Trial
Authors: Seasely Angela R. , Xue Yumo , Ausbeck Elizabeth B. , Jauk Victoria C. , Blanchard Christina T. , Files Pamela , Kuper Spencer C. , Casey Brian M. , Szychowski Jeff M. , Harper Lorie M. , Tita Alan T. , Subramaniam Akila 
Published: December 2022

Objective In the OFFSITE II randomized controlled trial, outpatient cervical ripening with a Foley catheter (CF) in nulliparous patients undergoing elective induction of labor (eIOL) shortened the time from admission to delivery. Given that patients with obesity have protracted labor and higher rates of failed IOL, we sought to determine if outpatient ripening with a CF may be even more beneficial for this high-risk group.
Study Design We performed a secondary analysis of the OFFSITE II randomized controlled trial. For this analysis, all patients from the primary trial were classified by their intervention assignment (inpatient vs. outpatient) and also by their admission body mass index (BMI) class (BMI ≥ 30 and BMI < 30 kg/m2). The primary outcome was time from labor and delivery (L&D) admission to delivery. Secondary outcomes included cesarean delivery, time from admission to hospital discharge, and rates of clinically diagnosed chorioamnionitis and endometritis.
Results In patients with BMI ≥ 30, the primary outcome, time from admission to delivery, (18.0 [13.5–20.9] vs. 20.4 [16.6–31.3] hours, p = 0.01), as well as total hospitalization length (3.2 [2.5–3.3] vs. 3.4 [3.1–4.3] days, p = 0.02) were shorter in the outpatient group. There were no differences in rates of chorioamnionitis or endometritis in outpatient compared with inpatient CF. Furthermore, in those with a BMI ≥ 30, the cesarean rate was significantly lower with outpatient CF (19.4% vs. 44.7%, p = 0.03); it was not statistically different in patients with BMI < 30.
Conclusion In this exploratory retrospective secondary analysis of the OFFSITE II randomized control trial, we found that in patients with BMI ≥ 30 undergoing eIOL, outpatient CF was associated with a lower time from L&D admission until delivery. This was also associated with a shorter time of total hospital duration and decreased the rate of cesarean, a benefit not detected in the overall analysis presented in the primary study. In nulliparas undergoing induction of labor, ripening with outpatient cervical Foley may even more significantly reduce labor duration, total hospital duration, and the rate of cesarean in patients with obesity.
Key Points
Eigenvalues of a periodic Schrödinger operator perturbed by a fast decaying potential
Authors: Safronov Oleg 
Published: December 2022

Let [λ, μ] be an interval contained in a spectral gap of a periodic Schrödinger operator H. Consider H(α) = H − αV, where V is a fast decaying positive function. We study the asymptotic behavior of the number of eigenvalues of H(α) in [λ, μ] as α → ∞.
Overcritical electron acceleration and betatron radiation in the bubble-like structure formed by re-injected electrons in a tailored transverse plasma
Authors: Zhao Yuan , Lu Haiyang , Zhou Cangtao , Zhu Jungao 
Published: December 2022

We present a novel scheme for dense electron acceleration driven by the laser irradiation of a near-critical-density plasma. The electron reflux effect in a transversely tailored plasma is particularly enhanced in the area of peak density. We observe a bubble-like distribution of re-injected electrons, which forms a strong quasistatic electromagnetic field that can accelerate electrons longitudinally while also preserving the electron transverse emittance. Simulation results demonstrate that over-dense electrons could be trapped in such an artificial bubble and accelerated to an energy of ∼500MeV. The obtained relativistic electron beam can reach a total charge of up to 0.26 nC and is well collimated with a small divergence of 17 mrad. Moreover, the wavelength of electron oscillation is noticeably reduced due to the shaking of the bubble structure in the laser field. As a result, the energy of the produced photons is substantially increased to the γ range. This new regime provides a path to generating high-charge electron beams and high-energy γ-ray sources.