Miracle-dz/UniFAR-FTUs huggingface dataset:
sgRNA Design for Editing rs of a Gene Family Using tem on Lahav

The development of the CRISPR–Cas9 system in recent years has made eukaryotic genome editing, and specifically gene knockout for reverse genetics, a simple and effective task. The system is directed to a genomic target site by a programmed single-guide RNA (sgRNA) that base-pairs with it, subsequently leading to site-specific modifications. However, many gene families in eukaryotic genomes exhibit partially overlapping functions, and thus, the knockout of one gene might be concealed by the function of the other. In such cases, the reduced specificity of the CRISPR–Cas9 system, which may lead to the modification of genomic sites that are not identical to the sgRNA, can be harnessed for the simultaneous knockout of multiple homologous genes. We introduce CRISPys, an algorithm for the optimal design of sgRNAs that would potentially target multiple members of a given gene family. CRISPys first clusters all the potential targets in the input sequences into a hierarchical tree structure that specifies the similarity among them. Then, sgRNAs are proposed in the internal nodes of the tree by embedding mismatches where needed, such that the efficiency to edit the induced targets is maximized. We suggest several approaches for designing the optimal individual sgRNA and an approach to compute the optimal set of sgRNAs for cases when the experimental platform allows for more than one. The latter may optionally account for the homologous relationships among genefamily members. We further show that CRISPys outperforms simpler alignment-based techniques by in silico examination over all gene families in the Solanum lycopersicum genome. © 2018 Elsevier Ltd. All rights reserved.
Fabrication and Characterization of Iron Oxide Filled Polyvinyl Pyrrolidone Nanocomposites

The present work describes the synthesis and properties of nanomagnetic polymer composites (MPCs) com- prising iron oxide nanoparticles as a filler and polyvinyl pyrrolidone (PVP) as polymer shell. The iron oxide nanoparticles were synthesized under alkaline medium using iron (II) salt. The nanocomposites were synthesized through free radical polymerization under microwave (MW) irradiation. X-ray diffraction reveals the uniform dispersion of iron oxide nanopar- ticles into polymer matrix. Furthermore, scanning electron microscopy images ensure the development of polymer shell around the nanomagnetic core. The magnetic behaviour of MPCs was studied through vibration sample magnetometry. The thermal durability of MPCs was assessed through simultaneous thermogravimetric-differential thermal analysis-differential thermogravimetry. With MW power ranging 25 to 100 W, the polymerization reactions were progressed resulting in MPCs with improved yield over neat PVP.
Cost and learning efficiency drivers in Australian schools: a two-stage network DEA approach

ABSTRACT This article explore performance issues in Australian public schools, using a two-stage DEA network model, which accounts simultaneously for both cost and learning efficiency levels. In the cost efficiency stage, different types of expenses and investments are employed to support a given number of students, teachers and administrative staff. In the learning efficiency stage, these groups of individuals help to produce important outputs related to performance in student tests and school rankings. Results indicate that Australian public schools are heterogeneous. Policy implications are also discussed.
The specific energy of mixing of segments of polymer chains with molecules of solvent is adopted in the

A simplified model is developed for the elastic response of thermo-responsive gels subjected to swelling under an arbitrary deformation with finite strains. The constitutive equations involve five adjustable parameters that are determined by fitting observations in equilibrium water uptake tests and T -jump transient tests on thin gel disks. Two scenarios for water release under heating are revealed by means of numerical simulation. When the final temperature in a T -jump test is below the volume-phase transition temperature, deswelling is characterized by smooth distribution of water molecules and small tensile stresses. When the final temperature exceeds the critical temperature, a gel disk is split into three regions (central part with a high concentration of water molecules and two domains near the boundaries with low water content) separated by sharp interfaces, whose propagation is accompanied by development of large (comparable with the elastic modulus) tensile stresses. Key-words: Thermo-responsive gel; Volume phase transition; Transient swelling; Modeling
The Association and Formation Constants for CuCl 2 Stoichiometric Complexes with (E)-3-(2-Benzylidene Hydrazinyl)-3-oxo-N-(thiazol-2-yl)Propanamide in Absolute Ethanol Solution at 294.15 K

The association constants and Gibbs free energies for CuCl2 with (E)-3-(2-benzylidene hy- drazinyl)-3-oxo-N-(thiazol-2-yl)propanamide (H2BH) had been calculated by using the conductometric titration curves in absolute ethanol at 294.15 K. New equation was applied to determine the association constant for 1:2 asymmetric salts. Different stoichiometric complexes were obtained on drawing the relation between (/\m) and (M:L). The association free energies that were evaluated for CuCl2-ligand complexes were small and spontaneous indicating electrostatic attraction force. The formation constants and Gibbs free energies of different complexes follow that order: Kf (2:1) › Kf (1:1) › Kf (1:2) for (M:L), and ΔGf (2:1) › ΔGf (1:1) › ΔGf (1:2) for (M:L).
Approaches to Measuring Creativity: A Systematic Literature Review

Abstract This paper presents a review of the literature on the measurement of creativity. Creativity definitions are discussed as a starting point for understanding the nature of this construct. The four major approaches to measuring creativity (process, person, product and press) are reviewed, pointing out commonly used instruments as well as the advantages and weaknesses of each approach. This review reveals that the measurement of creativity is an unsettled issue, and that the existing instruments purporting to measure creativity suffer from serious conceptual and psychometric shortcomings. Research gaps and suggestions for future research are discussed.
demethylase KDM 2 A regulation of methylated H 3 K 36 A molecular threading mechanism underlies Jumonji lysine Material

License Commons Creative . http://creativecommons.org/licenses/by-nc/4.0/ at Creative Commons License (Attribution-NonCommercial 4.0 International), as described ). After six months, it is available under a http://genesdev.cshlp. org/site/misc/terms.xhtml six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first
Steven Kelly maize homeolog gene evolution following whole genome duplication in The impact of widespread regulatory neofunctionalization on Material

Whole genome duplications are a widespread feature of plant genome evolution, having been detected in all flowering plant lineages. Despite the prevalence of these events, the extent to which duplicated genes (homeolog gene-pairs) functionally diverge (neofunctionalisation) is unclear. We present a genome-wide analysis of molecular evolution and regulatory neofunctionalisation in maize (Zea mays L.). We demonstrate that 13% of all homeolog gene-pairs in maize are regulatory neofunctionalised in leaves, and that regulatory neofunctionalised genes experience enhanced purifying selection. We show that significantly more genes have been regulatory neofunctionalised in foliar leaves than in husk leaves and that both leaf types have experienced selection for distinct functional roles. Furthermore, we demonstrate that biased subgenome expression dominance occurs only in the presence of regulatory neofunctionalisation and that in non-regulatory neofunctionalised genes sub-genome dominance is progressively acquired during development. Taken together, our study reveals several novel insights into the evolution of maize, genes and gene expression, and provides a general model for gene evolution following whole-genome duplication in plants. Cold Spring Harbor Laboratory Press on November 11, 2014 Published by genome.cshlp. org Downloaded from
The Research into the Training of the Meta-cognitive Strategy of College Students

the study on language learning strategies has become the focus of the second language acquisition research, and receives extensive attention from the linguists and educators. Besides, the meta-cognitive strategy is an important part of language learning strategies and it is also closely related to the English learning process. The article attempts to understand the condition of the meta-cognitive strategy use of college students, and explores whether the meta-cognitive strategy training can improve students' meta-cognitive strategy level and English learning achievements through investigating the students in the Chinese department and chemistry department of Jiangxi Institute of Education with the metacognitive strategy questionnaire investigation and a fifteenweek meta-cognitive strategy training. The study aims to improve the quality of the English teaching in colleges. Keywordsmeta-cognitive strategy; training; English achievement
a predictive regulatory sequence vocabulary in melanocytes Integration of ChIP-seq and machine learning reveals enhancers Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2012/09/13/gr.139360. 112.DC1. html P<P Published online September 27, 2012 in advance of the print journal. License Commons Creative . http://creativecommons.org/licenses/by-nc/3.0/ described at as a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), ). After six months, it is available under http://genome.cshlp. org/site/misc/terms.xhtml for the first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press
Characterization of a rare species of Neurospora isolated from a river water sample in China

A fungal isolate (ZZS4408) was obtained from a river water sample in Henan, China, and identified as a member of Neurospora brevispora, a rare species of Neurospora based on its morphological characteristics and ribosomal DNA internal transcribed spacer (rDNA-ITS) sequence. The temperatures suitable for growth of the isolate were 28-37°C with 31°C as the optimum. The growth rates of hyphal tips were 19.1-42.5 (av. 31.9) μm min-1 at 32°C. The pH suitable for vegetative growth ranged from 5 to 7, with pH 5.5 as the optimum. The heterodisaccharides (sucrose and lactose) and D-alanine were found to be most favorable for vegetative growth of the isolate, as carbon and nitrogen sources, respectively. The vegetative growth of the isolate was more significantly influenced by nitrogen sources compared to carbon sources. N. brevispora could be considered a desirable fungal species for morphodifferentiation studies due to its rapid growth rates under favorable conditions.
Identification of a Functional Polymorphism Affecting MicroRNA Binding in the Susceptibility Locus 1 q 25 . 3 for Colorectal Cancer † Abbreviated title : A Functional Polymorphism and Colorectal Cancer Risk

Abbreviated title: A Functional Polymorphism and Colorectal Cancer Risk Juntao Ke; Jianbo Tian; Jiaoyuan Li; Yajie Gong; Yang Yang; Ying Zhu; Yi Zhang; Rong Zhong; Jiang Chang; Jing Gong 1 State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. 2 Key Laboratory for Environment and Health (Ministry of Education), School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.
PNS1200072 599..609

Over the last three decades, dietary pattern analysis has come to the forefront of nutritional epidemiology, where the combined effects of total diet on health can be examined. Two analytical approaches are commonly used: a priori and a posteriori. Cluster analysis is a commonly used a posteriori approach, where dietary patterns are derived based on differences in mean dietary intake separating individuals into mutually exclusive, non-overlapping groups. This review examines the literature on dietary patterns derived by cluster analysis in adult population groups, focusing, in particular, on methodological considerations, reproducibility, validity and the effect of energy mis-reporting. There is a wealth of research suggesting that the human diet can be described in terms of a limited number of eating patterns in healthy population groups using cluster analysis, where studies have accounted for differences in sex, age, socio-economic status, geographical area and weight status. Furthermore, patterns have been used to explore relationships with health and chronic diseases and more recently with nutritional biomarkers, suggesting that these patterns are biologically meaningful. Overall, it is apparent that consistent trends emerge when using cluster analysis to derive dietary patterns; however, future studies should focus on the inconsistencies in methodology and the effect of energy mis-reporting.
The Bridge Program: A Model for Delivering Mental Health Services to Asian Americans through Primary Care

Compared to all other racial and ethnic groups, Asian Americans have the lowest utilization of mental health services. Contributing factors include extremely low community awareness about mental health, a lack of culturally competent Asian American mental health professionals, and severe stigma associated with mental illness. This manuscript describes an innovative program that bridges the gap between primary care and mental health services. The Bridge Program, cited in the supplement to the Surgeon General's Report on Mental Health: Culture, Race and Ethnicity as a model for delivery of mental health services through primary care, has three goals: (1) to improve access by providing mental health services in primary care; (2) to improve capacity by enhancing the skills of primary care providers to identify and treat mental disorders commonly seen in primary care; and (3) to raise community awareness by providing health education on mental health and illness. Results are presented and the potential for rep.
CRISPR / Cas 9 Technology e Based Xenograft Tumors as Candidate Reference Materials for

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 jmd.amjpathol. org 63 64 65 66 67 68 69 70 71 72 73 74 75 76 CRISPR/Cas9 TechnologyeBased Xenograft Tumors as Candidate Reference Materials for 77 78 79 80 81 82 Multiple EML4-ALK Rearrangements Testing Rongxue Peng,*yz Rui Zhang,*z Guigao Lin,*z Xin Yang,*yz Ziyang Li,*yz Kuo Zhang,*z Jiawei Zhang,*yz and Jinming Li*yz
The Saale-Project -A multidisciplinary approach towards sustainable integrative catchment management -

In the joint research project “Development of an integrated methodology for the sustainable management of river basins – The Saale River Basin example”, coordinated by the Centre of Environmental Research (UFZ), concepts and tools for an integrated management of large river basins are developed and applied for the Saale river basin. The ultimate objective of the project is to contribute to the holistic assessment and benchmarking approaches in water resource planning, as required by the European Water Framework Directive. The study presented here deals (1) with the development of a river basin information and modelling system, (2) with the refinement of a regionalisation approach adapted for integrated basin modelling. The approach combines a user friendly basin disaggregation method preserving the catchment’s physiographic heterogeneity with a process oriented hydrological basin assessment for scale bridging integrated modelling. The well tested regional distribution concept of Response Units (RUs) will be enhanced by landscape metrics and decision support tools for objective, scale independent and problem oriented RU delineation to provide the spatial modelling entities for process oriented and distributed simulation of vertical and lateral hydrological transport processes. On basis of this RUs suitable hydrological modelling approaches will be further developed with strong respect to a more detailed simulation of the lateral surface and subsurface flows as well as the channel flow. This methodical enhancement will be applied to the river basin of the Saale (Ac: 23 179 km2) and validated by a nested catchment approach, which allows multi-response-validation and estimation of uncertainties of the modelling results. Integrated modelling of such a complex basin strongly influenced by manifold human activities (reservoirs, agriculture, urban areas and industry) can only be achieved by coupling the various modelling approaches within a well defined model framework system. The latter is interactively linked with a sophisticated geo-relational database (DB) serving all research teams involved in the project. This interactive linkage is a core element comprising an object-oriented, internet-based modelling framework system (MFS) for building interdisciplinary modelling applications and offering different analysis and visualisation tools.
the transcriptome diversity of cerebellar development Alternative transcription exceeds alternative splicing in generating Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2011/05/25/gr.120535. 111.DC1. html References http://genome.cshlp. org/content/21/8/1260.full. html#ref-list-1 This article cites 54 articles, 15 of which can be accessed free at: License Commons Creative http://creativecommons.org/licenses/by-nc/3.0/. described at a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as ). After six months, it is available under http://genome.cshlp. org/site/misc/terms.xhtml first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the
Effects of Immediate versus Delayed Feedback on Error Detection Accuracy in a Quality Control Simulation

A computer simulation was developed to examine the effects of immediate versus delayed visual feedback on the accuracy of identifying errors (signals) in sample stimuli. In a self-paced computer tutorial, subjects learned to identify particular aberrations in a schematic diagram of a hard disk drive. During experimental sessions, subjects were exposed to a series of 200 samples presented four at a time sequentially on a computer screen, and were required to indicate with a computer mouse whether or not each sample drive contained a signal. Accuracy of signal detection was assessed under four experimental conditions: (1) self-paced, immediate feedback, in which the pace of stimulus presentations was controlled by the subject and the cumulative percentage of correct responses was displayed on the computer screen immediately following each quality control response, (2) self-paced, delayed feedback, in which feedback was displayed only at the end of the session (following completion of the 200th quality contr.
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Background: We hypothesized that tonsillectomy modifies the risk of PD. Objectives: To test the hypothesis in a nationwide population-based cohort study. Methods: We used Danish medical registries to construct a cohort of all patients in Denmark with an operation code of tonsillectomy 1980-2010 (n 5 195,169) and a matched age and sex general population comparison cohort (n 5 975,845). Patients were followed until PD diagnosis, death, censoring, or end of followup 30 November 2013. Using Cox regression, we computed hazard ratios for PD and corresponding 95% confidence intervals, adjusting for age and sex by study design, and potential confounders. Results: We identified 100 and 568 patients diagnosed with PD among the tonsillectomy and general population comparison cohort, respectively, finding similar risks of PD (adjusted hazard ratio 5 0.95 [95% confidence interval: 0.76-1.19]; for > 20 years’ follow-up (adjusted hazard ratio 5 0.96 [95% confidence interval: 0.64-1.41]). Conclusion: Tonsillectomy is not associated with risk of PD, especially early-onset PD. VC 2017 International Parkinson and Movement Disorder Society
Title : Bundle sheath lignification mediates the linkage of leaf hydraulics and venation Short running title : Lignification of bundle sheath cells in minor veins

The lignification of the leaf vein bundle sheath (BS) has been observed in many species, and would reduce conductance from xylem to mesophyll. We hypothesized that lignification of the BS in lower-order veins would provide benefits for water delivery through the vein hierarchy but that the lignification of higher-order veins would limit transport capacity from xylem to mesophyll and leaf hydraulic conductance (Kleaf). We further hypothesized that BS lignification would mediate the relationship of Kleaf to vein length per area (VLA). We analyzed the dependence of Kleaf, and its light response, on the lignification of the BS across vein orders for 11 angiosperm tree species. Eight of 11 species had lignin deposits in the BS of the midrib, and two species additionally only in their secondary veins, and for six species up to their minor veins. Species with lignification of minor veins had a lower hydraulic conductance of xylem and outside-xylem pathways and lower Kleaf. Kleaf could be strongly predicted by VLA and highest lignified vein order (R = 0.69). The light-response of Kleaf was
Leaf economic and hydraulic divergences underpin ecological differentiation in the Bromeliaceae Running title : Ecological differentiation in the Bromeliaceae

Leaf economic and hydraulic theory have rarely been applied to the ecological differentiation of speciose herbaceous plant radiations. The role of character trait divergences and network reorganisation in the differentiation of the functional types in the megadiverse Neotropical Bromeliaceae was explored by quantifying a range of leaf economic and hydraulic traits in 50 diverse species. Functional types, which are defined by combinations of C3 or CAM photosynthesis, terrestrial or epiphytic habits, and non-specialised, tank-forming or atmospheric morphologies, segregated clearly in trait space. Most classical leaf economic relationships were supported, but they were weakened by the presence of succulence. Functional types differed in trait-network architecture, suggesting that rewiring of trait-networks caused by innovations in habit and photosynthetic pathway is an important aspect of ecological differentiation. The hydraulic data supported the coupling of leaf hydraulics and gas exchange, but not the hydraulic safety vs. efficiency hypothesis, and hinted at an important role for the extra-xylary compartment in the control of bromeliad leaf hydraulics. Overall, our findings highlight the fundamental importance of structure-function relationships in the generation and maintenance of ecological diversity.