Miracle-dz/UniFAR-FTUs huggingface dataset:
A Course-Based Undergraduate Research Experience for High-Throughput Reverse Genetic Studies in Arabidopsis Thaliana with CRISPR-Cas9

Gene editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a five-week period. In the remote-learning version, students perform homology searches, design guide RNAs and primers, and learn the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as closures that have occurred in response to the Covid-19 pandemic. In the in-person version, students design guide RNAs, clone CRISPR-Cas9 constructs, and perform genetic transformation of the model plant Arabidopsis thaliana. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of course sections available. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be readily adapted to other organisms or projects that employ gene editing.
Gravitational Waves Carry Information about the Infalling Matter out of Black Holes: a Resolution of the Black Hole Information Paradox

9 The black hole information paradox is one of the most puzzling paradoxes in physics. 10 Black holes trap everything that falls into them, while their mass may leak away through 11 purely thermal Hawking radiation. When a black hole vanishes, all the information 12 locked inside, if any, is just lost, thus challenging the principles of quantum mechanics. 13 However, some information does have a way to escape from inside the black hole, that 14 is, through gravitational waves. Here, a concise extension of this notion is introduced. 15 When a black hole swallows something, whether it is a smaller black hole or an atom, 16 the system emits gravitational waves carrying the information about the “food”. 17 Although most of the signals are too weak to be detected, the information encoded within 18 them will persist in the universe. This speculation provides an explanation for a large 19 part, if not all, of the supposed “information loss” in black holes, and thus reconciles the 20 predictions of general relativity and quantum mechanics. 21
Insights into Nanoscale Wettability Effects of Low Salinity and Nanofluid Enhanced Oil Recovery Techniques

In this study, enhanced oil recovery (EOR) techniques—namely low salinity and nanofluid EOR—are probed at the nanometer-scale using an atomic force microscope (AFM). Mica substrates were used as model clay-rich rocks while AFM tips were coated to present alkyl (-CH3), aromatic (-C6H5) and carboxylic acid (-COOH) functional groups, to simulate oil media. We prepared brine formulations to test brine dilution and cation bridging effects while selected concentrations (0 to 1 wt%) of hydrophilic SiO2 nanoparticles dispersed in 1 wt% NaCl were used as nanofluids. Samples were immersed in fluid cells and chemical force mapping was used to measure the adhesion force between polar/non-polar moieties to substrates. Adhesion work was evaluated based on force-displacement curves and compared with theories. Results from AFM studies indicate that low salinity waters and nanoparticle dispersions promote nanoscale wettability alteration by significantly reducing three-phase adhesion force and the reversible thermodynamic work of adhesion, also known as adhesion energy. The maximum reduction in adhesion energy obtained in experiments was in excellent agreement with existing theories. Electrostatic repulsion and reduced non-electrostatic adhesion are prominent surface forces common to both low salinity and nanofluid EOR. Structural forces are complex in nature and may not always decrease total adhesion force and energy at high nanoparticle concentration. Wettability effects also depend on surface chemical groups and the presence of divalent Mg2+ and Ca2+ cations. This study provides fresh insights and fundamental information about low salinity and nanofluid EOR while demonstrating the application of force-distance spectroscopy in investigating EOR techniques.
Study of LCNF and CNF from pine and eucalyptus pulps

Abstract Nanocelluloses produced from wood pulp are widely studied for various economic applications. Most studies of cellulose nanofibrils (CNF) use lignin-free fibres obtained from bleached pulps; however, unbleached fibres with residual lignin may also be used to obtain lignocelluloses nanofibrils (LCNF). Research on lignocellulose nanofibrils is a recent subject in the field; thus, the aim of the present study was to determine the ultrastructure of lignocellulose nanofibrils compared to cellulose nanofibrils produced from the same raw material. Understanding of nanoparticle properties is of great relevance for their various applications; therefore, complete characterisation of the chemical, physical, and morphological structures of LCNF and CNF produced from pine and eucalyptus woods was performed. Unbleached cellulosic fibres are a viable alternative for LCNF production, which has properties comparable to that of traditional CNF production that uses lignin-free fibres. LCNF from pine and eucalyptus were obtained with 4.0 % and 1.8 % residual lignin, respectively. The nanofibrils had high thermal stability because LCNF had a higher maximum degradation temperature. Due to the low interaction of lignin with water, LCNF had a lower water retention value than CNF.
Sequential Auctions with Synergy and Affiliation across Auctions

This paper performs a structural analysis of sequential auctions with both synergy and affiliation across auctions. I propose a flexible yet tractable sequential auction model under the private value paradigm and establish its nonparametric identification, demonstrating an intuitive and general method for disentangling synergy from affiliation. After developing an estimation procedure closely tied to the identification steps, I apply it to data on adjacent oil and gas leases that are auctioned sequentially. I assess the role played by affiliation versus synergy in the observed allocation patterns and evaluate the counterfactual policy of bundled auctions.
Epidermis and re-epithelialization in Schmidtea mediterranea

Epidermal layer is crucial for organism’s survival as its ability to close the wound is essential for tissue recovery. Planarian epidermis enables animal recovery and survival after virtually any body part amputation. Nevertheless, neither the epidermis nor the mechanisms endowing such a remarkable wound healing capacity is described in detail in planarians. Our work introduces live imaging methodology, which allows following epidermal cells and their response to tissue damage or tissue loss for extended time (hours) and in high resolution. Using our methods, we followed planarian cells live for the first time and in conjunction with electron microscopy analysis we described epidermal cell behaviors during tissue maintenance, response to tissue damage and tissue loss. Our data provides comprehensive description of cellular wound response, wound closure as well as preexisting tissue contribution to tissue restoration. In addition, we performed epidermal expression profile analysis to identify the candidate list of epidermally expressed genes to depict the machinery endowing these epidermal cell behaviors. In the pilot functional (RNAi) screen an array of transcription factors with a tissue maintenance phenotypes were identified. Our work established tools for subsequent functional studies of other epidermal expressed genes and paved the way to dissect the mechanisms of the epidermis’ maintenance and efficient wound healing in planarians.
Effect of different vase solutions on postharvest longevity of cut foliage Ophiopogon japonicus

Ophiopogon japonicus (L.f.) Ker-Gawl (family Liliaceae) is an export-oriented foliage plant with attractive white-green strips. The vase life of this cut foliage ends when the leaves loose turgidity and/ or bright green colour. Thus, to enhance the vase life of O. japonicus, effect of 0.25, 0.5, and 1.0 mM CuSO4.5H2O, 10, 20, and 30 g/L sucrose and combination of sucrose with 0.5 mM CuSO4.5H2O as holding treatments, 20 g/L and 30 g/L sucrose solutions as 24 h pulsing treatments and 6-Benzylaminopurine 5, 10, 20 mg/L BAP were tested. Relative fresh weight of leaves, solution uptake rate and vase life were assessed. Vase solution bacterial enumerations were carried out to evaluate the effectiveness of CuSO4.5H2O as a biocide. To investigate the function of BAP, amount of chlorophyll was quantified using leaf pigment extracts. The vase life of O. japonicus could be extended from 5.1 days to 12.5 days by giving BAP based vase solutions. Chlorophyll contents of leaves dipped in BAP solutions were significantly higher than the control (distilled water). CuSO4 solutions did not show any significant antibacterial effects compared to the control. According to vase life data, the most effective vase solutions were CuSO4.5H2O (0.5 mM), sucrose 20 g/L with CuSO4.5H2O (0.5 mM) as holding treatments, sucrose 20 g/L and 30 g/L as pulsing treatments and BAP treatments (5, 10, 20 mg/L).
Design prototyping for policymaking

: Design has an increasing role in the development of public services and policies. The implementation of policies is now considered a matter of design, especially in the field of public services. Moreover, design has been slowly entering the process of policymaking. Meanwhile, policy scientists’ promoters of Policy Design have started to analyse design discipline’s approaches on the design of policies. Among design activities, prototyping has been recognised as a valuable instrument for policy, also aligned with the new experimental approach in the public sector. However, it is still unclear how prototyping could intersect formal administrative and bureaucratic structures, including their traditional processes for policy analysis and experimentation. This research identifies frameworks for prototyping drawing on relevant authors in design-related disciplines in Europe. Then it characterises these diverse perspectives and suggests the benefits of design prototyping for policy analysis, to communicate, explore, evaluate and refine policy options before decision making.
Quantitative trait loci (QTL) mapping of resistance to coffee berry disease (Colletotrichum kahawae Waller Bridge) in Coffea arabica L. variety Rume Sudan

Coffee Berry Disease (CBD) is a major constraint that limits Coffea arabica production, whose resistance is governed by three genes, T, R that are dominant and recessive k in varieties Hibrido de Timor (HDT), Rume Sudan (RS) and K7 respectively. This study identified the genomic region occupied by R-gene using F2 genotypes from varieties RS and SL28; and Single Nucleotide Polymorphic (SNP) markers obtained through Genotyping by Sequencing. Redundant markers were removed and 699 markers obtained for linkage mapping and quantitative trait loci (QTL) analysis. The Linkage map spread over 5525.39 cM across eleven coffee chromosomes (Chr). The QTL was analyzed by both Interval Mapping (IM) and Inclusive Composite Interval Mapping (ICIM) using SNP markers and CBD resistance mean scores of the F2 genotypes and their parents. Three QTLs, qCBD 1-1 in Chr 1, qCBD 2-1 and qCBD 2-2 in Chr 2 were significantly associated with CBD resistance, detected by both IM and ICIM at LOD ≥ 2.5 (P≤0.05). Two flanking markers that were closer to the three QTLs; 100025973|F|0-59:T>C-59:T>C at a distance of 3 centi Morgans (cM) from qCBD 1-1 and 100034991|F|0-44:C>T-44:C>T, that was flanking in both qCBD 2-1 and qCBD 2-2 at 12.5 cM, whose SNPs were significant (P≤0.05), are recommended for validation and use in marker-assisted breeding. Key words: Coffee berry disease, linkage map, quantitative trait loci, genotyping by sequencing, single nucleotide polymorphism, SL 28, R-gene.
The Use of Portable EEG Devices in Development of Immersive Virtual Reality Environments for Converting Emotional States into Specific Commands

The application of electroencephalography electrodes in Virtual Reality (VR) glasses allows users to relate cognitive, emotional, and social functions with the exposure to certain stimuli. The development of non-invasive portable devices, coupled with VR, allows for the collection of electroencephalographic data. One of the devices that embraced this new trend is Looxid LinkTM, a system that adds electroencephalography to HTC VIVETM, VIVE ProTM, VIVE Pro EyeTM, or Oculus Rift STM glasses to create interactive environments using brain signals. This work analyzes the possibility of using the Looxid LinkTM device to perceive, evaluate and monitor the emotions of users exposed to VR.
Determination of ruminal dry matter and crude protein degradability and degradation kinetics of several concentrate feed ingredients in cashmere goat

ABSTRACT The objective of this study was to determine the dry matter (DM) and crude protein (CP) degradation parameters of several commercially available concentrate feed ingredients used in Shaanbei White Cashmere Goat (SWCG). Three 4-year-old female SWCGs fitted with permanent rumen fistula were fed with corn straw and concentrate feed. Tested energy and protein feed ingredients were corn, wheat bran (WB), corn germ meal, soybean meal (SBM), rape seed meal (RSM), and distillers dried grains. The feed samples were placed in a nylon bag and incubated in the rumen for 0, 2, 6, 12, 24, 36, and 48 h to measure the ruminal disappearance of DM and CP. The exponential model was used to calculate the degradation kinetics. There were significant differences between sources in terms of DM and CP disappearance and degradability. In terms of energy feed ingredients, the potential degradability of DM and CP of corn was significantly higher than those of the other energy feed ingredients, whereas the effective degradability (ED) of CP of WB at three outflow rates was significantly higher than those of the others. In protein feed ingredients, SBM had the highest potential degradability of DM and CP. Furthermore, the ED of DM of SBM at three outflow rates was significantly higher than those of the other protein feed ingredients, whereas the ED of CP of RSM at three outflow rates was significantly higher than those of others. Those feed ingredients with low degradability can increase the bypass nutrients, which will be digested in the small intestine. The degradation parameters obtained in this experiment using SWCG would be useful in improving the accuracy of formulation of cashmere goat diet in Northwest of China.
Study of Nuclear Structure for 36Si Isotope by Using Shell Model with Several Interactions

In this study, the nuclear shell model was applied to calculate the energy levels and reduced electric quadruple transition probability B(E2) for 36Si isotope using the OXBASH code within (1d3/2, 2s1/2, 2p3/2, 1f7/2) model space and using (HASN, ZBM2 and VPTH) interactions, As this isotope contains eight neutrons outside 28Si core in the region and when comparing the results of this study with the values. Available process compatibility was acceptable. There was good agreement at level 2+1, and angular momentum and parity were confirmed for levels 4+, 6+, and for all interactions, and the value of B(E2) corresponds well with the only practical value available for the transition .
Effect of grassland harvesting frequency and N-fertilization on stocks and dynamics of soil organic matter in the temperate climate

ABSTRACT Management of grassland may affect the dynamics of soil organic carbon (SOC). Objectives were to analyze the effect of different harvesting frequencies and nitrogen fertilization regimes on SOC and total N stocks in a field trial on a sandy loam to loamy sand soil of a grassland site near Kiel (Germany). Additionally, effects on microbial biomass C (Cmic) and ergosterol (as proxy for fungi) contents, water-stable aggregate size-classes and density fractions were studied. In the surface soil (0–10 cm), SOC and total N stocks, amounts of large water-stable macroaggregates (> 2000 µm) and contents of Cmic and ergosterol were significantly higher under a five cut regime. Cmic (rSpearman = 0.61) and ergosterol contents (rSpearman = 0.67) were correlated with amounts of large water-stable macroaggregates suggesting that fungi and microbial biomass play an important role in binding of small macroaggregates into large macroaggregates. The free light fraction of SOM showed significantly higher C concentrations under three cut compared to five cut at 30–60 cm, presumably related to the C/N ratio and the decomposability of root litter. This study indicates the importance of cutting frequency on SOC and total N stocks, amounts of large macroaggregates and contents of Cmic and ergosterol.
Developing a Framework to Support the Delivery of Effective Pain Management for Children: An Exploratory Qualitative Study

Two million children are admitted to hospital every year in the UK and between 59% and 94% will experience pain, with 27–40% of them experiencing moderate to severe pain. Currently, there are a number of well-researched guidelines on children's pain available, yet pain prevalence is high. Despite the guidelines, there is a lack of an overall framework that includes the necessary components to deliver effective pain management. This study was built on previous work about key elements that support children's pain management, by exploring their relevance and practical application with 43 healthcare practitioners. We carried out focus groups with band 5 nurses (n = 6) and advanced nurse practitioners (n = 11) and semistructured interviews with pain nurses (n = 16) and consultants (n = 10). We also presented and discussed our findings with an advisory group. Findings demonstrated that the following elements were considered to be important: delivering pain management with confidence, supporting colleagues with protocols and guidance, empowering parents to be involved in pain management, and adopting an individual approach to a child and family. These elements formed the basis of a framework for children's pain management. Some practitioners indicated that pain management required education and more resources, and that the culture of an area could influence pain management practice. The framework brings together elements that have the potential to improve the management of children's pain through its use as an education tool. Each interrelated element of the framework plays an important part in the overall management of children's pain. The need now is to make the dissemination of the findings accessible to health care practitioners, parents, and educators. Next steps include the development of infographic posters, an animation, and a free online course, which will incorporate the use of Bloom's taxonomy.
Trophic interactions between crustacean and protozoan plankton

Previous investigations of the feeding biology of filter feeding crustacean zooplankton have primarily focused on phytoplankton-zooplankton interactions. However, there is increasing evidence that protozoans may contribute to the diet of crustacean zooplankton. For daphnids and calanoid copepods, it has been shown that they are able to prey effectively upon ciliates and heterotrophic nanoflagellates (PORTER et al. 1979, BuRNS & G! LBERT 1993, HARTMANN et al. 1993, ]ACK & G! LBERT 1993, SANDERS & WICKHAM 1993, PACE & VAQUÉ 1994, WICKHAM 1998). H e re we focus o n the species-specific grazing effects of Eudiaptomus graciloides (nauplii, copepodite stages, adults) and D. hyalina, compared to the natural zooplankton community, on the microbial community (protozoans and APP). The study was performed in a mesotrophic lake, by using in situ grazing experiments.
A minority of self-organizing autonomous vehicles significantly increase freeway traffic flow

This study investigates the dynamics of traffic containing human-driven vehicles along with a fraction of self-organized artificial intelligence (AI) autonomous vehicles (AVs) on multilane freeways. We propose guidelines for the development of AI agents, such that a small fraction of AVs forms local constellations that significantly accelerate the entire traffic flow while reducing fuel consumption and increasing safety. Specifically, we report a 40% enhancement in traffic flow efficiency and up to a 28% reduction in fuel consumption even when only 5% of vehicles are autonomous. This scenario does not require changes to current infrastructure or communication between vehicles; it only requires proper regulations. The results indicate that more efficient, safer, faster, and greener traffic flow can be realized in the near future.
Effect of annealing temperature on the microstructure evolution, mechanical and wear behavior of NiCr–WC–Co HVOF-sprayed coatings

In the present work, the effect of annealing temperature on the microstructure, mechanical and tribological properties of NiCr–WC–Co coatings produced by the high-velocity oxy-fuel (HVOF) technique has been investigated. X-ray diffraction and scanning electron microscopy revealed the dissolution of WC into the NiCr matrix to form W_2C and Cr_3C_2 with the annealing process. This dissolution became complete at 800 °C. The mechanical properties of the coatings were investigated using nano-indentation and Vickers fracture toughness measurements. These measurements suggested that the hardness, Young’s modulus, and fracture toughness values increased because of the newly formed carbide phases as a result of the dissolution of the WC particles. The overall properties of the coatings were found to be optimum for annealing temperatures of 800 °C. The wear mechanism appears to be abrasive in the as-sprayed coating, and it becomes a combination of an abrasive and oxidative wear with increasing the annealing temperature.
How Can Smart Mobility Innovations Alleviate Transportation Disadvantage? Assembling a Conceptual Framework through a Systematic Review

Transportation disadvantage is about the difficulty accessing mobility services required to complete activities associated with employment, shopping, business, essential needs, and recreation. Technological innovations in the field of smart mobility have been identified as a potential solution to help individuals overcome issues associated with transportation disadvantage. This paper aims to provide a consolidated understanding on how smart mobility innovations can contribute to alleviate transportation disadvantage. A systematic literature review is completed, and a conceptual framework is developed to provide the required information to address transportation disadvantage. The results are categorized under the physical, economic, spatial, temporal, psychological, information, and institutional dimensions of transportation disadvantage. The study findings reveal that: (a) Primary smart mobility innovations identified in the literature are demand responsive transportation, shared transportation, intelligent transportation systems, electric mobility, autonomous vehicles, and Mobility-as-a-Services. (b) Smart mobility innovations could benefit urban areas by improving accessibility, efficiency, coverage, flexibility, safety, and the overall integration of the transportation system. (c) Smart mobility innovations have the potential to contribute to the alleviation of transportation disadvantage. (d) Mobility-as-a-Service has high potential to alleviate transportation disadvantage primarily due to its ability to integrate a wide-range of services.