bluuebunny/crossref_metadata_2025_split huggingface dataset:
ESCASA: Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance‐assisted protein structure modeling. I. Backbone and Hβ protons
Authors: Lubecka Emilia A. , Liwo Adam 
Published: May 2021

AbstractA method for the estimation of coordinates of atoms in proteins from coarse‐grained geometry by simple analytical formulas (ESCASA), for use in nuclear‐magnetic‐resonance (NMR) data‐assisted coarse‐grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side‐chain Hβ protons, given the Cα‐trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high‐resolution non‐homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR‐determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton–proton distances of the NMR‐determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all‐atom‐chain reconstruction algorithm and to the 0.12 Å standard deviation of the average‐structure proton–proton distance of NMR‐determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse‐grained molecular dynamics.
Characterization of orthogonal hydrogen and halogen bonds in thiobarbituric acid complexes with halogen molecules (X = I2, Br2, and Cl2): Structural and spectroscopic study
Authors: Alosaimi Abeer M. , Aljehani Abdulrahman S. , Ibrahim Mohamed M. , El‐Sheshtawy Hamdy S. , Altalhi Tariq 
Published: May 2021

AbstractThe molecular complexes between thiobarbituric acid (TBA) and halogen molecules (X2 = I2, Br2, and Cl2) in different solvents are explored. Density functional theory (DFT) calculations at rwb97xd/lanl2dz were used to corroborate the experimental electronic and optical properties of the molecular adducts. Experimental results (Fourier transform infrared spectroscopy) show the stability of the complexes by halogen bonding (XB) and competitive hydrogen bonding (HB), which was supported by the DFT calculations. The molecular electrostatic potential and the frontier orbital calculations supported engagement of the thione group in XB rather than the carbonyl group. Based on the Hirshfeld atomic population, noncovalent interaction, and natural bond orbital analysis, the stability of TBAX2 adducts increases in the order TBACl2 > TBABr2 > TBAI2, where the larger charge transfer and highest stabilization energy were calculated for TBACl2 adducts.
GPCR‐mediated YAP/TAZ inactivation in fibroblasts via EPAC1/2, RAP2C, and MAP4K7
Authors: Choi Kyoung Moo , Haak Andrew J. , Diaz Espinosa Ana M. , Cummins Katherine A. , Link Patrick A. , Aravamudhan Aja , Wood David K. , Tschumperlin Daniel J. 
Published: May 2021

AbstractYes‐associated protein (YAP) and PDZ‐binding motif (TAZ) have emerged as important regulators of pathologic fibroblast activation in fibrotic diseases. Agonism of Gαs‐coupled G protein coupled receptors (GPCRs) provides an attractive approach to inhibit the nuclear localization and function of YAP and TAZ in fibroblasts that inhibits or reverses their pathological activation. Agonism of the dopamine D1 GPCR has proven effective in preclinical models of lung and liver fibrosis. However, the molecular mechanisms coupling GPCR agonism to YAP and TAZ inactivation in fibroblasts remain incompletely understood. Here, using human lung fibroblasts, we identify critical roles for the cAMP effectors EPAC1/2, the small GTPase RAP2c, and the serine/threonine kinase MAP4K7 as the essential elements in the downstream signaling cascade linking GPCR agonism to LATS1/2‐mediated YAP and TAZ phosphorylation and nuclear exclusion in fibroblasts. We further show that this EPAC/RAP2c/MAP4K7 signaling cascade is essential to the effects of dopamine D1 receptor agonism on reducing fibroblast proliferation, contraction, and extracellular matrix production. Targeted modulation of this cascade in fibroblasts may prove a useful strategy to regulate YAP and TAZ signaling and fibroblast activities central to tissue repair and fibrosis.
Transmission electron microscopy of the liver mitochondria of N‐Nitrosodibutylamine‐treated mice
Authors: Dutta Sthiti Porna , Neog Kundal , Alam Anis 
Published: May 2021

AbstractN‐Nitrosodibutylamine (DBN) has been found in a wide variety of products because of the nitrosation of amines present in these products. An extensive series of synthesis and carcinogenicity studies of various compounds related to DBN and its metabolites have revealed that they have markedly different carcinogenic effects. The role of mitochondria in disease has been found to be expanded beyond the respiratory chain, as defects in additional mitochondrial functions and behaviors have been linked to cancer, metabolic disorders, and many neurodegenerative diseases, such as Alzheimer's, Parkinson's, and Huntington's disease (Nunnari & Suomalainen (2012) Cell, 148, 1145–1159). The sample preparation was performed using the protocol standardized by Sophisticated Analytical Instrumentation Facility (SAIF) laboratory in NEHU. The prepared sample was then mounted and observed under the transmission electron microscope model JEM‐100 CC II. The micrographs obtained from transmission electron microscopy (TEM) at various magnifications 2,000, 5,000, and 12,000× from DBN‐treated mice showed significant changes. Mitochondria showed variability in number, size, and shape. This significant alteration in the morphology and population of liver mitochondria observed in DBN‐treated animals in comparison to that of the age‐matched normal control mice provide a unique potential for the use of mitochondria as markers for the early detection for the treatment of liver cancer.
Quantitative MRI T2 Mapping is Able to Assess Tissue Quality After Reparative and Regenerative Treatments of Osteochondral Lesions of the Talus
Authors: Rizzo Giulio , Cristoforetti Alessandro , Marinetti Alessandro , Rigoni Marta , Puddu Leonardo , Cortese Fabrizio , Nollo Giandomenico , Della Sala Sabino W. , Tessarolo Francesco 
Published: May 2021

BackgroundQuantitative MRI has potential for tissue characterization after reparative and regenerative surgical treatment of osteochondral lesions of the talus (OCLTs). However available data is inconclusive and quantitative sequences can be difficult to implement in real‐time clinical application.PurposeTo assess the potential of T2 mapping in discriminating articular tissue characteristics after reparative and regenerative surgery of OCLTs in real‐world clinical settings.Study TypeObservational and prospective cohort study.Population15 OCLT patients who had received either reparative treatment with arthroscopic microfracture surgery (MFS) for a grade I lesion or regenerative treatment with bone marrow derived cell transplantation (BMDCT) for a grade II lesion.Field Strength/Sequence1.5 T, proton density weighted TSE, T2‐weighted true fast imaging with steady‐state‐free precession and multi‐echo T2 mapping sequences.AssessmentPatients were evaluated at a minimum postoperative follow‐up of 24 months. T2 maps of the ankle were generated and the distribution of T2 values was analyzed in manually identified volumes of interest (VOIs) for both treated lesions (TX) and healthy cartilage (CTRL). The amount of fibrocartilage, hyaline‐like and remodeling tissue in TX VOIs was obtained, based on T2 thresholds from CTRL VOIs.Statistical TestsFisher's exact test for categorical data, nonparametric Mann–Whitney U test for continuous data. The statistical significance level was P < 0.05.ResultsFrom CTRL VOI analysis, T2 < 25 msec, 25 msec ≤ T2 ≤ 45 msec, and T2 > 45 msec were considered as representative for fibrocartilage, hyaline‐like and remodeling tissue, respectively. Tissue composition of the two treatment groups was different, with significantly more fibrocartilage (+28%) and less hyaline‐like tissue (−15%) in MFS than in BMDCT treated lesions. No difference in healthy tissue composition was found between the two groups (P = 0.75).Data ConclusionsT2 mapping of surgically treated OCLTs can provide quantitative information about the type and amount of newly formed tissue at the lesion site, thereby facilitating surgical follow‐up in a real‐word clinical setting.Level of Evidence2Technical EfficacyStage 3
Recent advances in the extraction of triazine herbicides from water samples
Authors: Manousi Natalia , Kabir Abuzar , Zachariadis George A. 
Published: May 2021

AbstractPesticides are excessively used in agriculture to improve the quality of crops by eliminating the negative effects of pests. Among the different groups of pesticides, triazine pesticides are a group of compounds that contain a substituted C3H3N3 heterocyclic ring, and they are widely used. Triazine pesticides can be dangerous for humans as well as for the aquatic environment because of their high toxicity and endocrine disrupting effect. However, the concentration of these chemical compounds in water samples is low. Moreover, other compounds that may exist in the water samples can interfere with the determination of triazine pesticides. As a result, it is important to develop sample preparation methods that provide preconcentration of the target analyte and sufficient clean‐up of the samples. Recently, a wide variety of novel microextraction and miniaturized extraction techniques (e.g., solid‐phase microextraction and liquid‐phase microextraction, stir bar sorptive extraction, fabric phase sorptive extraction, dispersive solid‐phase extraction, and magnetic solid‐phase extraction) have been developed. In this review, we aim to discuss the recent advances regarding the extraction of triazine pesticides from environmental water samples. Emphasis will be given to novel sample preparation methods and novel sorbents developed for sorbent‐based extraction techniques.
Optical Implementation of 2 × 2 Universal Unitary Matrix Transformations
Authors: Macho‐Ortiz Andrés , Pérez‐López Daniel , Capmany José 
Published: May 2021

AbstractUnitary operations are a specific class of linear transformations that have become an essential ingredient for the realization of classical and quantum information processing. The ability of implementing any n‐dimensional unitary signal transformation by using a reconfigurable optical hardware has recently led to the pioneering concept of programmable linear optical processor, whose basic building block (BB) must be correctly designed to guarantee that the whole system is able to perform universal (i.e., arbitrary) unitary matrix transformations. Here, it is demonstrated that the present architectures of the BB do not fulfil the universal unitary property (at least) in optical processors, limiting the number of unitary matrix transformations that may be generated. Aiming to solve this fundamental constraint, the theoretical tools required to analyze and design universal unitary optical circuits and their corresponding BBs are presented. The consequences of this mathematical framework are explored, obtaining a simple route to implement different BB architectures, all of them guaranteeing a true universal unitary functionality in the resulting optical processors. These findings may pave the way to revisit the design of high‐dimensional unitary optical processors, unleashing the potential of programmable integrated photonics technology.
The ASH‐ASPHO Choosing Wisely Campaign: 5 hematologic tests and treatments to question
Authors: O'Brien Sarah H. , Badawy Sherif M. , Rotz Seth J. , Shah Mona D. , Makarski Julie , Bercovitz Rachel S. , Hogan Mary‐Jane S. , Luchtman‐Jones Lori , Panepinto Julie A. , Priola Ginna M. , Witmer Char M. , Wolfson Julie A. , Yee Marianne , Hicks Lisa K. 
Published: May 2021

AbstractChoosing Wisely is a medical stewardship and quality‐improvement initiative led by the American Board of Internal Medicine Foundation in collaboration with leading medical societies in the United States. The American Society of Hematology (ASH) has been an active participant in the Choosing Wisely project. In 2019, ASH and the American Society of Pediatric Hematology/Oncology (ASPHO) formed a joint task force to solicit, evaluate, and select items for a pediatric‐focused Choosing Wisely list. By using an iterative process and an evidence‐based method, the ASH‐ASPHO Task Force identified 5 hematologic tests and treatments that health care providers and patients should question because they are not supported by evidence, and/or they involve risks of medical and financial costs with low likelihood of benefit. The ASH‐ASPHO Choosing Wisely recommendations are as follows: (1) avoid routine preoperative hemostatic testing in an otherwise healthy child with no previous personal or family history of bleeding, (2) avoid platelet transfusion in asymptomatic children with a platelet count 10 × 103/μL unless an invasive procedure is planned, (3) avoid thrombophilia testing in children with venous access‐associated thrombosis and no positive family history, (4) avoid packed red blood cells transfusion for asymptomatic children with iron deficiency anemia and no active bleeding, and (5) avoid routine administration of granulocyte colony‐stimulating factor for prophylaxis of children with asymptomatic autoimmune neutropenia and no history of recurrent or severe infections. We recommend that health care providers carefully consider the anticipated risks and benefits of these identified tests and treatments before performing them.
Clinical survey and predictors for the development of tracheobronchomalacia in preterm infants
Authors: Chiu Chun‐Che , Lai Shen‐Hao , Lin Jainn‐Jim , Chan Oi‐Wa , Chiu Chih‐Yung , Tseng Pei‐Ling , Hsia Shao‐Hsuan , Lee En‐Pei 
Published: May 2021

AbstractBackgroundTracheobronchomalacia (TBM) contributes to the increased morbidity and mortality observed in preterm infants. Effective strategies for the prevention of TBM are necessary to achieve better outcomes. We sought to identify risk factors associated with the development of TBM in preterm infants. Optimal cut‐off values for each risk factor were also determined.MethodsA total of 80 infants who were born at 36 week's gestation or earlier and underwent flexible bronchoscopy were included in our study sample. A comparison of demographic and clinical risk factors between those with TBM (n = 35, 44%) and those without TBM (n = 45, 56%) was conducted using multivariate logistic regression analysis. Receiver operating characteristic curve analysis was performed to determine the appropriate cut‐off values for predicting the development of TBM.ResultsIn the multivariate analysis, only peak inspiratory pressure (PIP) and the number of intubation days remained significantly different between infants with and without TBM. Preterm infants with TBM received higher PIP (odds ratio: [OR], 1.067; 95% confidence interval [CI], 1.010–1.128; p = .020) and were intubated for longer (odds ratio [OR], 1.019; 95% CI, 1.003–1.035; p = .016) than those without TBM. Infants who received PIP > 19.5 cmH2O or were intubated for >79.5 days were associated with a significantly higher risk of presence of TBM.ConclusionHigh PIP and prolonged intubation were major risk factors for the development of TBM in premature infants. Those who require PIP > 19.5 cmH2O or intubation >79.5 days warrant bronchoscopy examination for early diagnosis and management of TBM.
Persistent pulmonary air leak in the pediatric intensive care unit: Characteristics and outcomes
Authors: Kagan Shelly , Nahum Elhanan , Kaplan Eytan , Kadmon Gili , Gendler Yulia , Weissbach Avichai 
Published: May 2021

AbstractBackgroundPersistent air leak (PAL) complicates various lung pathologies in children. The clinical characteristics and outcomes of children hospitalized in the pediatric intensive care unit (PICU) with PAL are not well described. We aimed to elucidate the course of disease among PICU hospitalized children with PAL.MethodsA retrospective cohort study of all PICU‐admitted children aged 0–18 years diagnosed with pneumothorax complicated by PAL, between January 2005 and February 2020 was conducted at a tertiary center. PAL was defined as a continuous air leak of more than 48 h.ResultsPAL complicated the course of 4.8% (38/788) of children hospitalized in the PICU with pneumothorax. Two were excluded due to missing data. Of 36 children included, PAL was secondary to bacterial pneumonia in 56%, acute respiratory distress syndrome (ARDS) in 31%, lung surgery in 11%, and spontaneous pneumothorax in 3%. Compared to non‐ARDS causes, children with ARDS required more drains (median, range: 4, 3–11 vs. 2, 1–7; p < .001) and mechanical ventilation (100% vs. 12%; p < .001), and had a higher mortality (64% vs. 0%; p < .001). All children with bacterial pneumonia survived to discharge, with a median air leak duration of 14 days (range 3–72 days). Most of which (90%) were managed conservatively, by continuous chest drainage.ConclusionBacterial pneumonia was the leading cause of PAL in this cohort. PAL secondary to ARDS was associated with a worse outcome. In contrast, non‐ARDS PAL was successfully managed conservatively, in most cases.
C4N8O6: A Promising Ternary CNO‐Compound With Good Detonation Performance And Low Sensitivity
Authors: Li Xin , Wang Qian , Zhang Shujia , Lin Qiuhan , Lu Ming 
Published: May 2021

AbstractAmong energetic materials, there is a significant challenge facing researchers: to seek an optimal balance between detonation performance and molecular stability. By introducing an azo1,2,4‐oxadiazole backbone and low‐sensitivity C‐NO2 moieties, a promising energetic molecule, 1,2‐bis(3‐nitro‐1,2,4‐oxadiazol‐5‐yl)diazene (4) was prepared through three‐step reaction and well‐characterized by IR and multinuclear NMR spectroscopy, DSC measurement, elemental analysis, and single‐crystal X‐ray diffraction. It shows high thermal stability (Td=260 °C), good mechanical sensitivity (IS: 21 J, FS: 220 N), and superior detonation performance (D: 9336 m s−1, P: 37.7 GPa). The combination of advanced performance and desirable safety as well as the simple reaction process make it highly competitive in the field of energetic materials.
Phytopathogenic infection alters rice–pest–parasitoid tri‐trophic interactions
Authors: Sun Ze , Shi Jin‐Hua , Liu Hao , Yin Le‐Tong , Abdelnabby Hazem , Wang Man‐Qun 
Published: May 2021

AbstractBACKGROUNDPlant pathogens and pests often occur together, causing damage while interfering with plant growth. The effects of phytopathogenic infections on plant–herbivore–natural enemy tri‐trophic interactions (TTIs) have been extensively investigated, but little is known about how the interval of infection influences such relationships. Here, the effect of rice plants infected by the phytopathogen Rhizoctonia solani on the herbivorous rice brown planthopper (BPH) and associated egg parasitoid Anagrus nilaparvatae over a temporal scale was examined.RESULTSOur results showed that rice plants infected by R. solani showed increased volatile profiles and significantly attracted BPH and A. nilaparvatae at 5–15 days post infection (DPI) and 5–10 DPI, respectively, when compared with healthy plants. Jasmonic acid and salicylic acid content decreased significantly in BPH‐damaged plants after 15 DPI, whereas oxalic acid accumulated soon after 5 DPI when compared with healthy plants. To adapt to adverse environment, BPH laid more eggs and developed into macropterous adults. Under field conditions, R. solani infection had no substantial effect on the arthropod community when compared with healthy plants.CONCLUSIONTaken together, R. solani infection altered rice–pest–parasitoid TTIs over a temporal scale. This result will shed more light on our understanding of plant pathogen–insect cross‐talk essential for developing novel pest management strategies. © 2021 Society of Chemical Industry.
Paraffin oil induces resistance against powdery mildew in grapevine through salicylic acid signaling
Authors: Pálfi Xénia , Lovas Miklós , Zsófi Zsolt , Kátai János , Karácsony Zoltán , Váczy Kálmán Z 
Published: May 2021

AbstractBACKGROUNDMineral oils have been widely used in the pest control of several crops. However, their mode of action is poorly understood, especially in the case of their antifungal properties. The possible direct fungicidal activity and the stress‐inducing capability of paraffin oil on grapevine were examined using Vitis vinifera L. cv ‘Kékfrankos’ cuttings and the fungus Erysiphe necator, the causal agent of powdery mildew.RESULTSOur experiments demonstrated that paraffin oil does not have fungicide activity on E. necator, but induces significant stress‐related changes in grapevine physiology. Elevated H2O2 production and the accumulation of the phytohormone salicylic acid were measured. Secondary thickening of the cell wall by lignin deposition and the accumulation of phenolic compounds were also observed. Some enzyme activities related to the detoxification of reactive oxygen species, disease response, and the synthesis of lignin were changed in accordance with the determined changes in cell wall composition and H2O2 levels.CONCLUSIONThe results suggest that paraffin oil induces stress responses on grapevine leaves through oxidative burst, and this response is systemized by salicylic acid. The accumulation of lignin and water‐soluble phenolics may be directly responsible for the paraffin oil‐induced resistance of grapevine against powdery mildew. © 2021 Society of Chemical Industry.
Measuring epistemologies in science learning and teaching: A systematic review of the literature
Authors: Lee Silvia Wen‐Yu , Luan Hui , Lee Min‐Hsien , Chang Hsin‐Yi , Liang Jyh‐Chong , Lee Yuan‐Hsuan , Lin Tzung‐Jin , Wu An‐Hsuan , Chiu Ying‐Ju , Tsai Chin‐Chung 
Published: May 2021

AbstractPromoting understanding of the epistemologies of science has long been the primary objective in science education, and can be viewed as a form of science learning outcome. Many studies have attempted to understand learners' conceptions of epistemology in science from various perspectives and methods; however, no recent reviews have focused on the measurement of various constructs and variables of epistemologies of science. The main purpose of this review study is to understand how these epistemologies in science teaching and learning were measured, and to provide an overview of recent developments with respect to the measurement issue in the epistemology of science. We searched for articles that were published between 2010 and 2019 and retained 225 eligible studies passing all review criteria for inclusion in this review. Major constructs of epistemologies of science emerging from the studies include epistemic beliefs and views, nature of science, epistemic emotions, epistemic metacognition, epistemic practices, and epistemic resources. These constructs were further categorized into personal, productive, and practical epistemologies. Among these studies, most of the quantitative studies used questionnaires for measuring personal epistemologies, while only a few utilized close‐ended items. The majority of the studies adopting qualitative methods investigated personal epistemologies as well. Nevertheless, among studies of practical epistemologies, more studies adopted qualitative methods than quantitative methods. We summarize the characteristics and psychometric properties of the most frequently used quantitative research instruments. Examples of qualitative data collection and data analyses are provided. Relationships between epistemologies and science learning outcomes are discussed, and suggestions are made for future directions.