bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyses of Homing Endonucleases and Mechanism of Action of CRISPR-Cas9 HNH Endonucleases
Authors: Palanivelu Peramachi 
Published: June 2020

Aim: To analyze different HNH endonucleases from various sources including the HNH endonuclease regions of CRISPR-Cas9 proteins for their conserved motifs, metal-binding sites and catalytic amino acids and propose a plausible mechanism of action for HNH endonucleases, using CRISPR-Cas9 as the model enzyme.
Study Design: Multiple sequence analysis (MSA) of homing endonucleases including the CRISPR-Cas9 using Clustal Omega was studied. Other biochemical, Site-directed mutagenesis (SDM) and X-ray crystallographic data were also analyzed.
Place and Duration of Study: School of Biotechnology, Madurai Kamaraj University, Madurai, India, between 2007 and 2013.
Methodology: Bioinformatics, Biochemical, SDM and X-ray crystallographic data of the HNH endonucleases from different organisms including CRISPR-Cas9 enzymes were analyzed. The advanced version of Clustal Omega was used for protein sequence analysis of different HNH endonucleases from various sources. The conserved motifs identified by the bioinformatics analysis were analyzed further with the data already available from biochemical and SDM and X-ray crystallographic analyses of this group of enzymes and to confirm the possible amino acids involved in the active sites and catalysis.
Results: Different types of homing endonucleases from various sources including the HNH endonuclease regions of CRISPR-Cas9 enzymes exhibit different catalytic regions and metal-binding sites. However, the catalytic amino acid, i.e., the proton acceptor histidine (His), is completely conserved in all homing endonucleases analyzed. From these data, a plausible mechanism of action for HNH endonucleases, using CRISPR-Cas9 from Streptococcus pyogenes, as the model enzyme is proposed. Furthermore, multiple sequence alignment (MSA) of various homing endonucleases from different organisms showed many highly conserved motifs also among them. However, some of the HNH endonucleases showed consensus only around the active site regions. Possible catalytic amino acids identified among them belong to either -DH---N or -HH--N types. There are at least two types of metal-binding sites and bind Mg2+ or Zn2+ or both. The CRISPR-Cas9 enzyme from S. pyogenes belongs to the -DH- based HNH endonucleases and possesses –DxD- type metal-binding site where it possibly binds to a Mg2+ ion. The other HNH enzymes possess one or two invariant Zn binding CxxC/ CxxxC motifs.
Conclusions: The CRISPR-Cas9 enzymes are found to be -DH- type where the first D is likely to involve in metal-binding and the second invariant H acts as the proton acceptor and the N in –HNH- Cas9 confers specificity by interacting with the nucleotide near the catalytic region. In this communication, a metal-bound water molecule is shown as the nucleophile initiating catalysis. Homing endonucleases may be used as novel DNA binding and cleaving reagents for a variety of genome editing applications and Zinc finger nucleases have already found applications in genome editing.
Hyperspectral Spectroscopic Study of Soil Properties- A Review
Authors: Goswami Chandan , Singh Naorem Janaki , Handique Bijoy Krishna 
Published: June 2020

Soil analysis is required for efficient use of inputs viz. seeds, fertilizers, irrigation water and other agricultural planning. However, there are several disadvantages of soil analysis such as they are time consuming, expensive and labour intensive. Many approaches are developed to overcome these difficulties. Hyperspectral spectroscopy is emerging as a promising tool for studying soil, water and vegetation. Therefore, an attempt has been made to review the scope of using hyperspectral reflectance spectroscopy for estimation of soil properties as an alternative to traditional laboratory soil analysis methods.
Spectral signature of soil can be used for fast and non destructive estimation of soil properties. Diffuse reflectance in 350-2500 nm range of electromagnetic spectra forms the basis of hyperspectral spectroscopy. An object is characterized by the characteristic absorptions and peaks in the electromagnetic spectra. A number of calibration techniques are applied for establishing relationship between reflectance spectra and soil properties. Multiple Linear Regression (MLR), Principal Component Regression (PCR) and Partial Least Square Regression (PLSR) are most commonly used techniques.
MLR, PCR and PLSR are also used for prediction of several soil properties such as pH, soil organic carbon content, nitrogen, phosphorus, potassium, calcium, magnesium, sodium, iron, manganese, zinc, copper, boron, molybdenum, sand silt, clay and soil moisture. Some commonly used spectral indices are also applied for prediction of soil properties. Some of the soil physical properties viz. sand, silt and clay as well as chemical properties viz. pH and organic carbon could be estimated with good to very good prediction using pure spectra of soil. However, contrasting results of prediction of soil properties using multivariate analysis techniques have also been reported. The content of this review article will be helpful for researchers who are working on alternate methods of estimation of soil properties.
Isolation and Characterization of Halophilic Bacteria from Salinity Soil of Shatkhira, Bangladesh
Authors: Mohanta Moni Krishno , Nasrin Samima , Haque Md. Fazlul , Hasi Alpona Sarker , Saha Ananda Kumar 
Published: June 2020

Aim: The aim of this study was undertaken for the isolation and molecular characterization of the halophilic bacteria from salt affected soils.
Place and Duration of Study: This study was conducted on the salinity affected area in Ramzan Nagor under Shamnagor Upazilla of Shatkhira District, Bangladesh. The collection of soil sample, isolation of halophilic bacteria and subsequent experiments were done from May to December 2018.
Methodology: Salt affected soil could be good source of halophilic bacteria as it contain high amount of salt. Hence, one gram of salt affected soil sample which was containing high amount of salt was suspended to 100 ml sterile distilled water and one ml of sample from the top of the suspension were taken in to 250 ml Erlenmeyer flaks containing 100 ml of mineral salts (MS) medium. The primary enrichment was incubated for several days at 37°C with shaking at 120 rpm (revolution per minute) on an orbital shaker. Cultures which were found to be turbid after a period of up to 4 days were used as inocula in subsequent experiments.
Results: Four halophilic bacterial strains viz. Bacillus sp. strain 8-15, Enterobacter sp. strain LCR75, Acinetobacter sp. strain 407 and Acinetobacter junii strain F27 were isolated from the saline soil and screened for their growth at a range of salt (NaCl) concentrations viz., 0%, 2%, 2.5%, 3%, 3.5%, 4%, 4.5% and 5%. Out of four isolates, Bacillus sp. showed the highest capacity to tolerate 5% salt concentration whereas Enterobacter sp. and other two isolates (Acinetobacter sp. and Acinetobacter junii) showed the capacity to tolerate 4% and 2.5% salt concentration respectively. Based on their morphological and biochemical characteristics the isolates were found to be Gram-positive and Gram-negative, rod shaped, motile bacteria which were later identified on the basis of 16S rRNA gene sequencing. The optimum culture conditions of the isolates were pH 7.0 and temperature 37°C. Results on the antibiogram profiles of the isolates revealed that the strains were sensitive to most of the antibiotics used in this study except Kenamycin, Ceftazidime and Ampicillin.
Conclusion: The isolated halophilic bacteria may play an important role to optimize the salt affected soil; hence they could be important candidates for further research on slat bioremediation.
Qualitative & Quantitative Analysis of Adult Arboreal Individuals from the Afforestation in the Municipality of Várzea, Paraíba, Brazil
Authors: Rocha Iara Cristina Araujo , Medeiros Jaqueline Rocha de , Silva Geovanio Alves da , Ferreira Vinícius Staynne Gomes , Lima Joedla Rodrigues de , Junior Marcelo Pereira Dutra , Ferreira Maria Beatriz , Sousa Geovana Gomes de , Azevedo Sebastiana Renata Vilela , Oliveira Elisabeth de 
Published: June 2020

Aims: Perform a qualiquantitative analysis of adult arboreal individuals in urban roads in the municipality of Várzea, Paraíba, Brazil.
Study Design: Census inventory.
Place and Duration of Study: Várzea Municipality, Paraíba, Brazil from March to April 2018.
Methodology: The qualitative and quantitative census inventory of adult shrubs-tree individuals was carried out in the urban roads of the municipality, the level of inclusion of the individuals was circumference at breast height (CBH) of (1.30 m) was ≥ 6 cm. Common name of the species was recorded, CBH measurements, height of the first bifurcation and total and physical conditions that were classified as good, regular, bad and dead. The data were tabulated, processed and presented in tables and graphs.
Results: A total of 429 individuals were recorded on public roads distributed in 20 species. Azadirachta indica A. Juss and Ficus benjamina L. had the highest number of individuals.
85% of the species were exotic and 15% were native. 12 species offered direct nutritional benefit to man and local fauna as they were fruit trees. The physical conditions of the individuals were 55.94% good, 40.33% regular, 3.73% poor, however, 47.50% of individuals had some type of conflict. 41.72% of individuals were concentrated in the diametric class of 15-21 cm. 54.78% of individuals had height of the first bifurcation greater than 200 cm and 62% of the individuals medium size.
Conclusion: The afforestation of the municipality was satisfactory in relation to plant health. Attention needs to be paid to the diversity of native species and the injuries caused to vegetation. The height of the first fork was adequate. The trees were medium sized. It is suggested that studies of perception of afforestation be carried out in the municipality.
Effects of Mentoring Enhanced Strategy on Self-regulation in Physics among Secondary School Students in Benue State, Nigeria
Authors: Ankeli Gabriel Odeh 
Published: June 2020

The study determined the effects of mentoring enhanced strategy on secondary school students’ self-regulation (SR) in physics in education zone ‘C’ of Benue State, Nigeria. The study was guided by two research questions while two hypotheses were formulated and tested at 0.05 level of significance. The design of the study was the quasi-experimental, non-randomized, pre-test and post-test control groups. The population of the study consisted of 4,064 SS Two physics students in the 94 schools in Education Zone C. The sample comprised 406 SS Two physics students drawn from 10 schools using multi-stage sampling technique. The research instrument adapted and used for data collection was Students’ Self-Regulation Scale (SSRS). The research instruments was subjected to a reliability analysis using Cronbach’s Alpha Formula which yielded a reliability co-efficient of 0.85. Data collected were analyzed using descriptive statistics of mean and standard deviation to answer the research questions while inferential statistics of Analysis of Covariance (ANCOVA) was used to test the hypotheses. The findings revealed that students who were exposed to mentoring exhibited higher self-regulation levels (P = 0.007 ˂ 0.05) than those students who were not exposed to mentoring. There was no significant difference between male and female students’ self-regulation level (P = 0.036 ˃ 0.05). Based on these findings, it was recommended among others that the use of mentoring enhanced strategy should be encouraged and used in physics instruction in secondary schools.
Using failure mode and effects analysis (FMEA) to generate an initial plan check checklist for improved safety in radiation treatment
Authors: Rassiah Prema , Su Fan‐Chi Frances , Huang Y. Jessica , Spitznagel Dan , Sarkar Vikren , Szegedi Martin W. , Zhao Hui , Paxton Adam B. , Nelson Geoff , Salter Bill J. 
Published: June 2020

AbstractPurposeTo apply failure mode and effect analysis (FMEA) to generate an effective and efficient initial physics plan checklist.MethodsA team of physicists, dosimetrists, and therapists was setup to reconstruct the workflow processes involved in the generation of a treatment plan beginning from simulation. The team then identified possible failure modes in each of the processes. For each failure mode, the severity (S), frequency of occurrence (O), and the probability of detection (D) was assigned a value and the risk priority number (RPN) was calculated. The values assigned were based on TG 100. Prior to assigning a value, the team discussed the values in the scoring system to minimize randomness in scoring. A local database of errors was used to help guide the scoring of frequency.ResultsTwenty‐seven process steps and 50 possible failure modes were identified starting from simulation to the final approved plan ready for treatment at the machine. Any failure mode that scored an average RPN value of 20 or greater was deemed “eligible” to be placed on the second checklist. In addition, any failure mode with a severity score value of 4 or greater was also considered for inclusion in the checklist. As a by‐product of this procedure, safety improvement methods such as automation and standardization of certain processes (e.g., dose constraint checking, check tools), removal of manual transcription of treatment‐related information as well as staff education were implemented, although this was not the team's original objective. Prior to the implementation of the new FMEA‐based checklist, an in‐service for all the second checkers was organized to ensure further standardization of the process.ConclusionThe FMEA proved to be a valuable tool for identifying vulnerabilities in our workflow and processes in generating a treatment plan and subsequently a new, more effective initial plan checklist was created.
Soluble Flt‐1, Placental Growth Factor, and Vascular Endothelial Growth Factor Serum Levels to Differentiate Between Active Lupus Nephritis During Pregnancy and Preeclampsia
Authors: de Jesús Guilherme R. , Lacerda Marcela I. , Rodrigues Bruna C. , dos Santos Flávia C. , do Nascimento Adriana P. , Cristóvão Porto Luís , de Jesús Nilson R. , Levy Roger A. , Klumb Evandro M. 
Published: June 2020

ObjectiveTo evaluate mean serum levels of vascular endothelial growth factor (VEGF), placental growth factor (PlGF), and soluble Flt‐1 (sFlt‐1) in pregnant patients with systemic lupus erythematosus (SLE) with inactive disease, active lupus nephritis, and preeclampsia for differential diagnosis between these conditions.MethodsPregnant women with SLE, with singleton pregnancies and no other autoimmune diseases, were classified according to disease activity (inactive SLE and active lupus nephritis) and the presence of preeclampsia. Serum samples were collected within 3 weeks of delivery and frozen for subsequent blinded analysis through the enzyme‐linked immunosorbent assay method.ResultsA total of 71 women were included, with 41 classified as having inactive SLE (group 1; Systemic Lupus Erythematosus Pregnancy Disease Activity Index [SLEPDAI] score <4), 15 with a diagnosis of active lupus nephritis (group 2, SLEPDAI score ≥4, including renal criteria), and 15 with a diagnosis of preeclampsia (group 3). Patients in group 3 had higher mean levels of sFlt‐1 and lower mean levels of PlGF compared to groups 1 and 2, both findings with statistical significance. The sFlt‐1:PlGF ratio was also significantly higher in patients with preeclampsia, while mean VEGF levels were higher in pregnant woman with active lupus nephritis compared to patients with preeclampsia or inactive SLE.ConclusionEvaluation of serum VEGF, PlGF, and sFlt‐1 levels can differentiate between preeclampsia, inactive SLE, and active lupus nephritis during pregnancy.
Racial Disparities in Medication Adherence between African American and Caucasian Patients With Systemic Lupus Erythematosus and Their Associated Factors
Authors: Sun Kai , Eudy Amanda M. , Criscione‐Schreiber Lisa G. , Sadun Rebecca E. , Rogers Jennifer L. , Doss Jayanth , Corneli Amy L. , Bosworth Hayden B. , Clowse Megan E. B. 
Published: June 2020

ObjectiveMedication nonadherence is more common in African Americans compared with Caucasians. We examined the racial adherence gaps among patients with systemic lupus erythematosus (SLE) and explored factors associated with nonadherence.MethodsCross‐sectional data were obtained from consecutive patients prescribed SLE medications seen at an academic lupus clinic between August 2018 and February 2019. Adherence was measured using both self‐report and pharmacy refill data. High composite adherence was defined as having both high self‐reported adherence and high refill rates. Covariates were patient‐provider interaction, patient‐reported health status, and clinical factors. We compared adherence rates by race and used race‐stratified analyses to identify factors associated with low composite adherence.ResultsAmong 121 patients (37% Caucasian, 63% African American), the median age was 44 years (range 22‐72), 95% were female, 51% had a college education or more, 46% had private insurance, and 38% had high composite adherence. Those with low composite adherence had higher damage scores, patient‐reported disease activity scores, and more acute care visits. High composite adherence rate was lower among African Americans compared with Caucasians (30% vs 51%, P = 0.02), and the gap was largest for those taking mycophenolate (26% vs 75%, P = 0.01). Among African Americans, low composite adherence was associated with perceiving fewer “Compassionate respectful” interactions with providers and worse anxiety and negative affect. In contrast, among Caucasians, low composite adherence was only associated with higher SLE medication regimen burden and fibromyalgia pain score.ConclusionSignificant racial disparities exist in SLE medication adherence, which likely contributes to racial disparities in SLE outcomes. Interventions may be more effective if tailored by race, such as improving patient‐provider interaction and mental health among African Americans.
Unveiling the Essential Nature of Lewis Basicity in Thermodynamically and Dynamically Promoted Nitrogen Fixation
Authors: Wang Mengfan , Liu Sisi , Ji Haoqing , Liu Jie , Yan Chenglin , Qian Tao 
Published: June 2020

AbstractElectrochemical N2 reduction provides a promising alternative to the Haber–Bosch process for sustainable ammonia production but enhancing its selectivity and activity remains a significant challenge. Here, this issue is tackled by triggering strong Lewis basicity within the catalyst, which boosts ambient ammonia synthesis from both thermodynamic and dynamic viewpoints. The enhanced π back donation induced by the Lewis base as the electron donor is first confirmed by first‐principle calculations, which greatly activates the NN bond and promotes its dissociation. Moreover, as suggested by molecular dynamics simulations, such abundant Lewis base would contribute to more surface heterogeneity and thus enhanced van der Waals interactions between nitrogen and the catalyst. Localized high concentration of N2 molecules can be realized at the catalyst surface, enabling efficient N2 delivery with a high flux and benefiting the following reaction process. As expected, the proof‐of‐concept metal‐free catalyst achieves a Faradaic efficiency of 62.9% and ammonia yield rate of 41.1 µg h−1 mg−1 at −0.2 V versus reversible hydrogen electrode. With this Lewis base‐assisted strategy, the superior efficiency would greatly reduce the energy loss of the system and cut down the fundamental cost, thus contributing to future practical applications.
Boosting Ultrafast Lithium Storage Capability of Hierarchical Core/Shell Constructed Carbon Nanofiber/3D Interconnected Hybrid Network with Nanocarbon and FTO Nanoparticle Heterostructures
Authors: Koo Bon‐Ryul , Sung Ki‐Wook , Ahn Hyo‐Jin 
Published: June 2020

AbstractThe aim of the study involves accelerating ultrafast electrochemical behavior of lithium‐ion batteries (LIBs) by proposing hierarchical core/shell heterostructure of carbon nanofiber (CNF)/3D interconnected hybrid network with nanocarbon and fluorine‐doped tin oxide (FTO) nanoparticles (NPs) via a one‐pot process of horizontal ultrasonic spray pyrolysis deposition. This is constructed via a pyrolysis reaction of ketjen black forming 3D interconnected FTO NPs covered with nanocarbon network on CNF. It offers fast electrical conductivity to the overall electrode with improved Li ion diffusion due to decreased size effect and relaxed structural variation of FTO NPs via nanocarbon network, leading to high discharge capacity (868.7 mAh g−1 after 100 cycles) at 100 mA g−1 and superior rate capability. Nevertheless, at extremely high current density (2000 mA g−1), significant ultrafast electrochemical performances with reversible discharge capacity (444.4 mAh g−1) and long‐term cycling retention (89.9% after 500 cycles) are noted. This is attributed to the novel effects of 3D interconnected hybrid network accelerating receptive capacity of Li ions into the FTO NPs via nanocarbon network, delivery of formed Li ions and electrons by hybrid network with FTO NP and nanocarbon, and prevention of FTO NP pulverization from CNFs via nanocarbon network. Therefore, the proposed heterostructure holds significant promise for effective development of ultrafast anode material for enhancing the practical applications of LIBs.
Hybrid FeNiOOH/α‐Fe2O3/Graphene Photoelectrodes with Advanced Water Oxidation Performance
Authors: Kormányos Attila , Kecsenovity Egon , Honarfar Alireza , Pullerits Tönu , Janáky Csaba 
Published: June 2020

AbstractIn this study, the photoelectrochemical behavior of electrodeposited FeNiOOH/Fe2O3/graphene nanohybrid electrodes is investigated, which has precisely controlled structure and composition. The photoelectrode assembly is designed in a bioinspired manner where each component has its own function: Fe2O3 is responsible for the absorption of light, the graphene framework for proper charge carrier transport, while the FeNiOOH overlayer for facile water oxidation. The effect of each component on the photoelectrochemical behavior is studied by linear sweep photovoltammetry, incident photon‐to‐charge carrier conversion efficiency measurements, and long‐term photoelectrolysis. 2.6 times higher photocurrents are obtained for the best‐performing FeNiOOH/Fe2O3/graphene system compared to its pristine Fe2O3 counterpart. Transient absorption spectroscopy measurements reveal an increased hole‐lifetime in the case of the Fe2O3/graphene samples. Long‐term photoelectrolysis measurements in combination with Raman spectroscopy, however, prove that the underlying nanocarbon framework is corroded by the photogenerated holes. This issue is tackled by the electrodeposition of a thin FeNiOOH overlayer, which rapidly accepts the photogenerated holes from Fe2O3, thus eliminating the pathway leading to the corrosion of graphene.