bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly Selective, CRISPR/Cas9‐Mediated Isolation of Genes and Genomic Loci from Complex Genomes by TAR Cloning in Yeast
Authors: Kouprina Natalay , Kim Jung‐Hyun , Larionov Vladimir 
Published: August 2021

AbstractHere we describe an updated TAR cloning protocol for the selective and efficient isolation of any genomic fragment or gene of interest up to 280 kb in size from genomic DNA. The method exploits the special recombination machinery of the yeast Saccharomyces cerevisiae. TAR cloning is based on the high level of in vivo recombination that occurs between a specific genomic DNA fragment of interest and targeting sequences (hooks) in a TAR vector that are homologous to the 5′ and 3′ ends of the targeted region. Upon co‐transformation into yeast, this results in the isolation of the chromosomal region of interest as a circular YAC molecule, which then propagates and segregates in yeast cells and can be selected for. In the updated TAR cloning protocol described here, the fraction of region‐positive clones typically obtained is increased from 1% up to 35% by pre‐treatment of the genomic DNA with specifically designed CRISPR/Cas9 endonucleases that create double‐strand breaks (DSBs) bracketing the target genomic DNA sequence, thereby making the ends of the chromosomal region of interest highly recombinogenic. In addition, a new TAR vector was constructed that contains YAC and BAC cassettes, permitting direct transfer of a TAR‐cloned DNA from yeast to bacterial cells. Once the TAR vector with the hooks is constructed and genomic DNA is prepared, the entire procedure takes 3 weeks to complete. The updated TAR protocol does not require significant yeast experience or extensively time‐consuming yeast work because screening only about a dozen yeast transformants is typically enough to find a clone with the region of interest. TAR cloning of chromosomal fragments, individual genes, or gene families can be used for functional, structural, and population studies, for comparative genomics, and for long‐range haplotyping, and has potential for gene therapy. Published 2021. This article is a U.S. Government work and is in the public domain in the USA. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Preparation of CRISPR/Cas9‐treated genomic DNA for TAR cloningBasic Protocol 2: Isolation of a gene or genomic locus by TAR cloningBasic Protocol 3: Transfer of TAR/YAC/BAC isolates from yeast to E. coli
Theoretical Insights on Au‐based Bimetallic Alloy Electrocatalysts for Nitrogen Reduction Reaction with High Selectivity and Activity
Authors: Shi Jun‐Lin , Xiang Shi‐Qin , Su Dai‐Jian , Liu Xiaohong , Zhang Wei , Zhao Liu‐Bin 
Published: August 2021

AbstractElectrochemical reduction of nitrogen to produce ammonia at moderate conditions in aqueous solutions holds great prospect but also faces huge challenges. Considering the high selectivity of Au‐based materials to inhibit competitive hydrogen evolution reaction (HER) and high activity of transition metals such as Fe and Mo toward the nitrogen reduction reaction (NRR), it was proposed that Au‐based alloy materials could act as efficient catalysts for N2 fixation based on density functional theory simulations. Only on Mo3Au(111) surface the adsorption of N2 is stronger than H atom. Thermodynamics combined with kinetics studies were performed to investigate the influence of composition and ratio of Au‐based alloys on NRR and HER. The binding energy and reorganization energy affected performance for the initial N2 activation and hydrogenation process. By considering the free‐energy diagram, the computed potential‐determining step was either the first or the fifth hydrogenation step on metal catalysts. The optimum catalytic activity could be achieved by adjusting atomic proportion in alloys to make all intermediate species exhibit moderate adsorption. Free‐energy diagrams of N2 hydrogenation via Langmuir‐Hinshelwood mechanism and hydrogen evolution via Tafel mechanism were compared to reveal that the Mo3Au surface showed satisfactory catalytic performance by simultaneously promoting NRR and suppressing HER. Theoretical simulations demonstrated that Au‐Mo alloy materials could be applied as high‐performance electrocatalysts for NRR.
Multiobjective fuzzy knowledge‐based bacterial foraging optimization for congestion control in clustered wireless sensor networks
Authors: Moharamkhani Elaheh , Zadmehr Behrouz , Memarian Saeideh , Saber Mohammad Javad , Shokouhifar Mohammad 
Published: August 2021

SummaryWireless sensor networks (WSNs) include a number of wireless sensor nodes distributed in a geographical area. Due to the intrinsic and functional nature of WSNs, these networks face many challenges such as limited energy resources of sensor nodes and the routing congestions. Clustering is the most common routing approach to control congestion and achieve energy efficiency in WSNs, which ultimately prolongs the network lifetime. In the cluster‐based routing protocols, optimal selection of cluster heads (CHs) is an NP‐hard problem, and consequently, heuristic and metaheuristic algorithms can be employed to obtain a near‐optimal solution. In this paper, a fuzzy knowledge‐based metaheuristic model based on multiobjective fuzzy inference system (moFIS) and bacterial foraging optimization (BFO), named moFIS‐BFO, is proposed as an efficient routing protocol for clustered WSNs. In the moFIS‐BFO model, the moFIS is utilized to calculate the chance of each node for becoming a CH based on different criteria including degree difference, residual energy, total distance to neighbors, and distance to the base station. Taking into account the calculated chances of nodes, the BFO is employed to select proper CHs at every round. To control the queue in cluster headings, a priority ranking method is used to control congestions and avoid packet wastages. Simulation results demonstrate the superiority of the moFIS‐BFO protocol against the existing techniques to control congestion and prolong the network lifetime.
Seasonal variation in sexual readiness in a facultatively sexual freshwater cnidarian with diapausing eggs
Authors: Tökölyi Jácint , Gergely Réka , Miklós Máté 
Published: August 2021

AbstractFacultative sexuality combines clonal propagation with sexual reproduction within a single life cycle. Clonal propagation enables quick population growth and the occupancy of favorable habitats. Sex, on the contrary, results in the production of offspring that are more likely to survive adverse conditions (such as the resting eggs of many freshwater invertebrates). In seasonal environments, the timing of sex is often triggered by environmental cues signaling the onset of winter (e.g., temperature drop or changes in photoperiod). Organisms switching to sex to produce resting eggs under these conditions face a trade‐off: Responding too early to an environmental cue increases the chances of missing out in clonal propagation, while having a delayed response to deteriorating conditions entails the risk of parental mortality before sexual reproduction could be completed. To mitigate these risks, increased sensitivity toward environmental cues with the onset of the winter might be an adaptive strategy. To test this hypothesis, we investigated sexual propensity and time to gonadogenesis in clonal strains derived from spring‐ and autumn‐collected polyps ofHydra oligactis, a facultatively sexual freshwater cnidarian where sex only occurs prior to the onset of winter. We show that autumn‐collected individuals and their asexual offspring have a higher propensity for sex and require less time for gonad development compared with strains established from spring‐collected individuals that were kept under similar conditions in the laboratory. To see whether the above results can be explained by phenotypic plasticity in sexual readiness, we exposed cold‐adapted laboratory strains to different lengths of warm periods. We found that sexual propensity increases with warm exposure. Our results suggest that reciprocal cold and warm periods are required for sex induction inH. oligactis, which would ensure proper timing of sex in this species. Increased sensitivity to environmental deterioration might help maximize fitness in environments that have both a predictable (seasonal) and an unpredictable component.
Clonotypic architecture of a Gag‐specific CD8+ T‐cell response in chronic human HIV‐2 infection
Authors: Moysi Eirini , Darko Samuel , Gea‐Mallorquí Ester , Petrovas Constantinos , Almeida Jorge R. , Wolinsky David , Peng Yanchun , Jaye Assan , Stewart‐Jones Guillaume , Douek Daniel C. , Koup Richard A. , Dong Tao , Rowland‐Jones Sarah 
Published: August 2021

AbstractThe dynamics of T‐cell receptor (TCR)selection in chronic HIV‐1 infection, and its association with clinical outcome, is well documented for an array of MHC‐peptide complexes and disease stages. However, the factors that may contribute to the selection and expansion of CD8+ T‐cells in chronic HIV‐2 infection, especially at the clonal level remain unclear. To address this question, we undertook a detailed molecular characterization of the clonotypic architecture of an HLA‐B*3501 restricted Gag‐specific CD8+ T‐cell response in donors chronically infected with HIV‐2 using a combination of flow cytometry, tetramer‐specific CD8+ TCR clonotyping, and in vitro assays. We show that the response to the NY9 epitope is hierarchical and narrow in terms of T‐cell receptor‐alpha (TCRA) and ‐beta (TCRB) gene usage yet clonotypically diverse. Furthermore, clonotypic dominance in shared origin CTL clones was associated with a greater magnitude of cytokine production and antigen sensitivity at limiting antigen dilution as well as enhanced cross‐reactivity for known HIV‐2 variants. Hence, our data suggest that effector mobilization and expansion in human chronic HIV‐2 infection may be linked to the qualitative features of specific CD8+ T‐cell clonotypes, which could have implications for viral control and disease outcome.
Assessment of cellular and molecular metrics for dose selection in an in vivo comet assay: A case study with MDI
Authors: Ji Zhiying , Koehler Matthew W. , Scott Andrew B. , LeBaron Matthew J. 
Published: August 2021

AbstractThe in vivo comet assay can evaluate the genotoxic potential of a chemical in theoretically any tissue that can be processed to a single cell suspension. This flexibility enables evaluation of point‐of‐contact tissues using a relevant route of test material administration; however, assessing cytotoxicity is essential for the interpretation of comet results. Histopathological evaluation is routinely utilized to assess cytotoxicity, but temporal‐ and cell‐specific considerations may compromise applicability to the comet assay. In the present study, 1,1′‐methylenebis(4‐isocyanatobenzene) (4,4'‐MDI) was administered to rats for 6 h by nose‐only inhalation, and the comet assay was conducted to evaluate genotoxicity in the site‐of‐contact tissue (bronchoalveolar lavage cells) and distal tissues (liver and glandular stomach). Given the reactive nature of MDI, cellular and molecular metrics at the site‐of‐contact‐ including inflammation, macrophage activation, apoptosis/necrosis, and oxidative stress‐ were used to set appropriate exposure concentrations, in addition to the standard systemic measures of toxicity. In the range‐finding study, a concentration of 4 mg/m3 was considered the maximum noninflammatory concentration; hence target concentrations of 2, 5, and 11 mg/m3 were selected for the comet study. In the lung lavage, MDI exposure substantially increased total protein and β‐glucuronidase, along with cellular apoptosis. Although MDI did not increase the comet assay response (% tail DNA) in any of the tissues examined, the positive control (ethyl methanesulfonate, EMS) significantly increased % tail DNA in all tissues. In total, these data indicate that appropriate cellular and molecular measurements may facilitate dose selection to discern cellular status in the comet assay.
Aneurysmal bone cyst with an unusual clinical presentation and a novel VDR‐USP6 fusion
Authors: Papke David J. , Bredella Miriam A. , Lozano‐Calderon Santiago , Oliveira Andre M. , Lennerz Jochen , Nielsen G. Petur 
Published: August 2021

AbstractAneurysmal bone cyst is a benign bone neoplasm that most commonly arises from the metaphyses of long bones in the first and second decades of life. Here, we describe a case of an aneurysmal bone cyst that occurred in the distal tibial diaphysis of a 72‐year‐old female that was concerning for malignancy on imaging, demonstrating cortical breakthrough and soft tissue extension. Histologically, the tumor showed the characteristic morphologic features of aneurysmal bone cyst. Fluorescence in situ hybridization was positive for USP6 rearrangement, and RNA sequencing revealed a USP6 gene fusion with VDR, a novel partner that encodes the vitamin D receptor and that has not been implicated previously in human neoplasia. This case highlights the diagnostic challenges presented by aneurysmal bone cyst in elderly adults, and it expands the genetic spectrum of USP6 rearrangements.
TV exposure and food consumption patterns–evidence from Indonesia
Authors: Oberlander Lisa 
Published: August 2021

AbstractUsing cross‐sectional survey data from Indonesia from 2007 and 2014, this study estimates the effect of the number of available television channels during childhood on food consumption later in life with a focus on unhealthy food items. To address endogeneity of television signal strength, I exploit exogenous variations in television signal quality due to random diffractions caused by topography within a small area. Using an instrumental variables approach the results suggest that exposure to television during youth of the household head has a positive effect on household‐level snack and soft drink expenditures. At the individual level I document more frequent consumption of soft drinks. Additional analysis suggests that households shift their consumption basket at the expense of vegetables and staples. Finally, heterogeneous effects analysis imply that results are driven by young individuals who are younger than 24 years old.
Diastolic hypertension is associated with proteinuria in pediatric patients
Authors: Myette Robert L. , Burger Dylan , Geier Pavel , Feber Janusz 
Published: August 2021

AbstractBackground and AimsBlood pressure lability has been observed in certain cohorts of pediatric patients with variable degrees of proteinuria; however, the impact of proteinuria on blood pressure is not fully elucidated. The objective of our study was to analyze blood pressure and heart rate in pediatric patients with proteinuria.MethodsWe performed a retrospective chart review of patients (age 1‐18) diagnosed with idiopathic nephrotic syndrome, with varying degrees of proteinuria. Blood pressure and heart rate data were analyzed in relation to anthropometric and biochemical parameters. A total of 72 urine sample analyses, along with associated blood pressure measurements, were obtained from the charts of 33 children (males = 25).ResultsDiastolic blood pressure Z‐scores were significantly higher in proteinuric patients (urine protein/creatinine >0.02 g/mmol) compared to non‐proteinuric patients (P = .006; Cohen‐d 0.97 [0.41; 1.53]). Systolic blood pressure was also significantly higher in proteinuric patients (P = .04), but with a less significant effect size (Cohen‐d 0.54 [−0.002; 1.08]). Proteinuria (>0.02 g/mmol) was the most significant predictor of diastolic (β = .79, P = .04), but not systolic blood pressure elevation on multivariate analysis.ConclusionsWe observed a disproportionate increase in diastolic blood pressure vs systolic blood pressure in patients with proteinuria.
Significance of thermal radiation and thermo‐physical properties on the modeling of sodium droplet explosion with different reaction rates
Authors: Kolawole Sunday Adegbie , Boluwaji Dennis Obideyi 
Published: August 2021

AbstractThe temperature of explosive substances (i.e., coolants) in the nuclear industries are necessary to ensure safety. The present study is focused on the analysis of the significance of thermal radiation and variable thermo‐physical properties on thermal stability characteristics of sodium droplet use as a coolant in the design of nuclear facilities. It is pertinent to note that the inclusion of heat loss by convection and heat generated by the reaction is based on Newton's law of cooling and Arrhenius kinetic equation, respectively, with the P‐1 approximation radiative heat loss model. The emerging mathematical model is a highly nonlinear ordinary differential equation. The model is solved using the classical fourth‐order Runge‐Kutta scheme. Consequently, the analysis of the results of the present study reveals the quantitative impacts of the thermal radiative model and variable thermo‐physical properties on the temperature of the sodium droplet. The results reveal that the combined inclusion of variable thermophysical properties and thermal radiation significantly reduces the droplet temperature. The temperature of the coolant increases with an increase in the reactants' numerical exponent and thermal radiation reduces the temperature of the sodium droplet at the initial temperature with the reverse effect at free stream temperature.
Asymmetric Autocatalysis as a Link Between Crystal Chirality and Highly Enantioenriched Organic Compounds
Authors: Soai Kenso , Matsumoto Arimasa , Kawasaki Tsuneomi 
Published: August 2021

AbstractThe origin of biological homochirality has attracted much attention. Pyrimidyl alkanols exhibit asymmetric autocatalysis with significant amplification of enantiomeric excess in the reaction between pyrimidine‐5‐carbaldehyde and diisopropyl zinc (the Soai reaction). Chiral inorganic crystals such as quartz, cinnabar and sodium chlorate act as chiral triggers of asymmetric autocatalysis to afford highly enantioenriched pyrimidyl alkanol, with the absolute configurations corresponding to those of the chiral crystals. Chiral organic crystals composed of achiral organic compounds such as cytosine, adenine dinitrate, and γ‐glycine act as the chiral triggers of the Soai reaction to afford pyrimidyl alkanol with high ee that corresponds to the absolute configuration of the chiral trigger. This review describes that chiral minerals and chiral organic crystals act as the chiral triggers of the Soai reaction and that these chiral crystals are correlated to near‐enantiopure chiral organic compounds.
Classification ofelectroencephalogramrecords related to cursor movements with a hybrid method based on deep learning
Authors: Türk Ömer 
Published: August 2021

AbstractIn brain computer interface (BCI), many transformation methods are used when processing electroencephalogram (EEG) signals. Thus, the EEG can be represented in different domains. However, designing an EEG‐based BCI system without any transformation technique is a challenge. For this purpose, in this study, a BCI model is proposed without any transformation. The classification of cursor down and cursor up movements using the EEG signals received from the brain is aimed at in the proposed model. The EEG patterns were classified using two methods. Firstly, EEG signals were classified by classic convolutional neural network (CNN). Secondly, proposed hybrid structure obtained the EEG features, which were classified by k‐NN and SVM, using CNN. Classification with CNN architecture gave a result of 68.15% while the hybrid method using k‐NN and SVM classifiers yielded 97.55% and 97.61% respectively. The hybrid proposed method were more successful than the studies in the literature.
Influence of foot traffic, irrigation, nitrogen fertilization, and weather factors on tissue N content in creeping bentgrass ‘Focus’
Authors: Zhou Qiyu , Soldat Douglas J. 
Published: August 2021

AbstractTissue nitrogen content is an important indicator of N removal in clippings from putting greens. To help managers determine the average tissue N content, a better understanding of factors controlling turfgrass tissue N content is needed. This study aimed to quantify how different N application rates, foot traffic intensities, soil volumetric water content (VWC), and weather factors influence the tissue N content of creeping bentgrass ‘Focus’ (Agrostis stolonifera L.). Field experiments on combined effects of foot traffic and nitrogen fertilizer on tissue N content were performed on two greens with 0.6 and 0.9% soil organic matter (SOM) in 2018, where N fertilizer was applied at 0, 10, or 20 kg N ha−1 every 2 wk, and foot traffic intensity was maintained at three rates: 0, 1,800, and 3,600 rounds wk−1 from 16 May to 28 August. A field experiment on the combined effects of VWC and traffic on tissue N content was conducted on the 0.9% SOM green in 2019, with the VWCs maintained at low (12–15%), medium (17–22%), and high (25–29%) levels by hand‐watering, with the assistance of time domain reflectometry; foot traffic intensities were 0, 700, and 1,400 rounds wk−1 from 31 May to 4 October. The tissue N content ranged from 2.5 to 5.0% (average: 3.9%). The N fertilizer rate was the main factor controlling the tissue N content, but foot traffic and VWC had no impact. Temperature, relative humidity, and evapotranspiration on the tissue N content also had minimal or nonexistent impacts.
Clinical review and role of clinical pharmacists in obesity management: An opinion of the endocrine and metabolism practice and research network of the American College of Clinical Pharmacy
Authors: Clements Jennifer N. , Albanese Nicole P. , D'Souza Jennifer J. , Misher Anne , Reece Sara (Mandy) , Trujillo Jennifer , Whitley Heather P. 
Published: August 2021

AbstractThe objective of this practice and research network opinion paper was to identify literature for pharmacist‐led services with obesity management, summarize clinical evidence for this disease state, and describe the role of a clinical pharmacist among patients who are overweight or have obesity. Clinical pharmacists play a critical role in the safe and effective management of obesity in both the inpatient and outpatient settings. In an outpatient setting, the role of the clinical pharmacist includes a comprehensive patient interview to design an individualized therapeutic plan involving nonpharmacological interventions with or without pharmacological interventions or surgical options. A clinical pharmacist conducts a risk‐benefit analysis for pharmacological interventions. Furthermore, the potential of medications to contribute to weight gain or prevent weight loss can be reviewed by a clinical pharmacist when managing comorbid conditions. In an inpatient setting, a clinical pharmacist conducts medication reconciliation, determines appropriate supplements for nutritional deficiencies, and provides medication management for people with obesity who may or may not be undergoing bariatric surgery. In addition, a clinical pharmacist can provide thorough patient education with monitoring for transitions from hospital to the outpatient setting and subsequent follow‐up visits.
Individual consumption in collective households: Identification using repeated observations with an application to PROGRESA
Authors: Sokullu Senay , Valente Christine 
Published: August 2021

SummaryIndividual consumption is typically not observed for individuals living with others. Identification of individual resource shares from household expenditure data requires assumptions on preferences that are often difficult to justify. We show that individual resource shares can be identified from repeated observations under the intuitive assumption that individual preferences over a subset of goods are stable over time. Using this method to estimate the effect of PROGRESA on the intrahousehold distribution of household expenditure, and hence on individual consumption, we find unequal gains, with children's individual consumption increasing by 27.8%, fathers' consumption by 17.8%, and mothers' consumption by 5.8%.