Photo-effects on Current Transport in Back-gate Graphene Field-effect Transistor

Graphene, which has attracted wide attention because of its two-dimensional structure and high carrier mobility, is a promising candidate for potential application in optics and electronics. In this dissertation, the photonic effects on current transport in back-gate graphene field-effect transistor is investigated. Chemical vapor deposition (CVD) on metal provides a promising way for large area, controllability and high quality graphene film. The transfer and back-gate transistor fabrication processes are proposed in this dissertation. The theoretical analysis of photodetector based on back-gate graphene field-effect transistor has been done. It is shown that the photo-electronic current consists of current contributions from photovoltaic, photo-thermoelectric and photo-bolometric effects. A maximum external responsivity close to 0.0009A/W is achieved at 30μW laser power source and 633nm wavelength. The photodiode based on graphene/silicon Schottky barrier is also. A computed 238.8 W-1 photocurrent to dark current ratio normalized by the power source (633nm wavelength and 10mW laser) is obtained. An equivalent circuit model of the graphene/silicon Schottky barrier diode compatible with SPICE simulation is developed and simulated photo-response characteristics are presented using analog behavior modeling which are in close agreement with the theoretical analysis. Besides the optical applications, graphene based-transistors can also be used in applications related to space electronics. The irradiation effects including oxide trap charge and graphene layer traps charges are investigated. A semi-empirical model of graphene back-gate transistors before and after irradiation is predicted

Frequency Fitness Assignment: Optimization without Bias for Good Solutions can be Efficient

A fitness assignment process transforms the features (such as the objective value) of a candidate solution to a scalar fitness, which then is the basis for selection. Under Frequency Fitness Assignment (FFA), the fitness corresponding to an objective value is its encounter frequency in selection steps and is subject to minimization. FFA creates algorithms that are not biased towards better solutions and are invariant under all injective transformations of the objective function value. We investigate the impact of FFA on the performance of two theory-inspired, state-of-the-art EAs, the Greedy (2+1) GA and the Self-Adjusting (1+(lambda,lambda)) GA. FFA improves their performance significantly on some problems that are hard for them. In our experiments, one FFA-based algorithm exhibited mean runtimes that appear to be polynomial on the theory-based benchmark problems in our study, including traps, jumps, and plateaus. We propose two hybrid approaches that use both direct and FFA-based optimization and find that they perform well. All FFA-based algorithms also perform better on satisfiability problems than any of the pure algorithm variants

DEVELOPMENT OF GENOMIC AND GENETIC TOOLS FOR FOXTAIL MILLET, AND USE OF THESE TOOLS IN THE IMPROVEMENT OF BIOMASS PRODUCTION FOR BIOENERGY CROPS

Foxtail millet (Setaria italica L.) is a warm-season, C4 annual crop commonly grown for grain and forage worldwide. It has a relatively short generation time, yet produces hundreds of seeds per inflorescence. The crop is inbred and it has a small-size genome (~500 Mb). These features make foxtail millet an attractive grass model, especially for bioenergy crops. While a number of genomic tools have been established for foxtail millet, including a fully sequenced genome and molecular markers, the objectives of this project were to develop a tissue culture system, determine the best explant(s) for tissue culture, optimize transient gene expression, and establish a stable transformation system for foxtail millet cultivar Yugu1. In optimizing a tissue culture medium for the induction of calli and somatic embryos from immature inflorescences and mature seed explants, Murashige and Skoog medium containing 2.5 mg l-1 2,4-dichlorophenoxyacetic acid and 0.6 mg l-1 6- benzylaminopurine was determined to be optimal for callus induction of foxtail millet. The efficiency of callus induction from explants of immature inflorescences was significantly higher at 76% compared to that of callus induction from mature seed explants at 68%. The calli induced from this medium were regenerated into plants at high frequency (~100%) using 0.2 mg l-1 kinetin in the regeneration media. For performing transient gene expression, immature embryos were first isolated from inflorescences. Transient expression of the GUS reporter gene in immature embryos was significantly increased after sonication, a vacuum treatment, centrifugation and the addition of L-cysteine and dithiothreitol, which led to the efficiency of transient expression at levels greater than 70% after Agrobacterium inoculation. Inoculation with Agrobacterium was also tested with germinated seeds. The radicals of germinated seeds were pierced with needles and dipped into Agrobacterium solution. This method achieved a 10% transient expression efficiency. Throughout these analyses, using plasmids with the hygromycin selectable marker, it was determined that 1.5 mg l-1 hygromycin was the optimal dose for genetic transformation of foxtail millet. In contrast, the nptII selectable marker appeared to yield many escapes. Three methods of transformation were employed in an attempt to produce stable transformants. An in planta transformation experiment, similar to the floral dip method used in Arabidopsis, which utilized a red fluorescent protein pporRFP from coral Porites porites and the hygromycin selectable marker, was tested using immature inflorescences. Although several plants were PCR positive using endpoint and Real-Time PCR and there was transient expression using pporRFP and GUS reporters, no plants were positive on Southern blot. Dipping in Agrobacterium may damage the anther or the pistil because seed production was significantly reduced. Agrobacterium transformation using embryogenic calli was also tested. Although hundreds of plants were regenerated from selection, none were positive using PCR. The third method was to wound germinated seeds with an Agrobacterium coated needle, but none of the plants were PCR positive. Although the Yugu1 genotype was recalcitrant to genetic transformation, several avenues of future research should be considered for foxtail millet. Calli from different foxtail millet genotypes should be screened and selected for regeneration potential, and some genotypes may be more amenable to transformation. Additional selectable markers should also be tested as hygromycin appears to be too stringent and there are too many escapes with nptII. This project has provided training for the following personnel: Dr. Xinlu Chen (postdoc), Xiaomei Liu (postdoc), Jayashree Desai (postdoc) and Kyle Berk (Undergraduate researcher). Conference presentations and peer-reviewed journal articles partly supported by this grant includes the following: 1. Baxter H., Equi R., Chen X, Berk K. and Zale J. Establishing Efficient in vitro Protocols For Foxtail Millet (Setaria italica L. cv. Yugi 1). Plant & Animal Genomes XVIII Conference XVIII, San Diego, California, January 2010 2. Chen X, Zale J and Chen F. The Regeneration and Transformation of Foxtail Millet (Setaria italica), A Model Biofuel Crop. Genomic Science Awardee Meeting IX and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Meeting, Crystal City, Virginia, April 2011 3. Chen, F., Tholl, D., Bohlmann, J., and Pichersky, E. (2011) The family of terpene synthases in plants: A mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom. Plant J. 66: 212-229

Exploring the Limits of ChatGPT for Query or Aspect-based Text Summarization

Text summarization has been a crucial problem in natural language processing (NLP) for several decades. It aims to condense lengthy documents into shorter versions while retaining the most critical information. Various methods have been proposed for text summarization, including extractive and abstractive summarization. The emergence of large language models (LLMs) like GPT3 and ChatGPT has recently created significant interest in using these models for text summarization tasks. Recent studies \cite{goyal2022news, zhang2023benchmarking} have shown that LLMs-generated news summaries are already on par with humans. However, the performance of LLMs for more practical applications like aspect or query-based summaries is underexplored. To fill this gap, we conducted an evaluation of ChatGPT's performance on four widely used benchmark datasets, encompassing diverse summaries from Reddit posts, news articles, dialogue meetings, and stories. Our experiments reveal that ChatGPT's performance is comparable to traditional fine-tuning methods in terms of Rouge scores. Moreover, we highlight some unique differences between ChatGPT-generated summaries and human references, providing valuable insights into the superpower of ChatGPT for diverse text summarization tasks. Our findings call for new directions in this area, and we plan to conduct further research to systematically examine the characteristics of ChatGPT-generated summaries through extensive human evaluation.Comment: Work in progres

Evolution of an intron-poor cluster of the CIPK gene family and expression in response to drought stress in soybean

Calcium ion is an intracellular messenger that plays a central role in signal transduction pathways. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) signal network have shown different functions in the Ca2+ signaling process. In this work, we identified the entire soybean (Glycine max) CIPK gene family, which comprised 52 genes and divided into four subgroups (I to IV) based on phylogeny. The gene structural analysis separated these 52 genes into an intron-rich clade and an intron-poor clade. Chromosomal location analysis resulted in the identification of 22 duplicated blocks and six tandem duplication events. Phylogenetic classification of 193 CIPK proteins from representative plant species suggested that the intron-poor clade of CIPKs originated in seed plants. Analysis of global gene expression patterns of soybean CIPK family revealed that most intron-poor soybean CIPK genes are drought-inducible; a finding that was further confirmed using qRT-PCR. Our study provides a foundation for further functional analysis to reveal the roles that CIPKs and more specifically the intron-poor clade play in drought tolerance in soybean

AlpaCare:Instruction-tuned Large Language Models for Medical Application

Large Language Models (LLMs) have demonstrated significant enhancements in instruction-following abilities through instruction tuning, achieving notable performances across various tasks. Previous research has focused on fine-tuning medical domain-specific LLMs using an extensive array of medical-specific data, incorporating millions of pieces of biomedical literature to augment their medical capabilities. However, existing medical instruction-tuned LLMs have been constrained by the limited scope of tasks and instructions available, restricting the efficacy of instruction tuning and adversely affecting performance in the general domain. In this paper, we fine-tune LLaMA-series models using 52k diverse, machine-generated, medical instruction-following data, MedInstruct-52k, resulting in the model AlpaCare. Comprehensive experimental results on both general and medical-specific domain free-form instruction evaluations showcase AlpaCare's strong medical proficiency and generalizability compared to previous instruction-tuned models in both medical and general domains. We provide public access to our MedInstruct-52k dataset and a clinician-crafted free-form instruction test set, MedInstruct-test, along with our codebase, to foster further research and development. Our project page is available at https://github.com/XZhang97666/AlpaCare

Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae

Dictyostelids, or social amoebae, have a unique life style in forming multicellular fruiting bodies from unicellular amoeboids upon starvation. Recently, dictyostelids were found to contain terpene synthase (TPS) genes, a gene type of secondary metabolism previously known to occur only in plants, fungi and bacteria. Here we report an evolutionary functional study of dictyostelid TPS genes. The number of TPS genes in six species of dictyostelids examined ranges from 1 to 19; and the model species Dictyostelium purpureum contains 12 genes. Using in vitro enzyme assays, the 12 TPS genes from D. purpureum were shown to encode functional enzymes with distinct product profiles. The expression of the 12 TPS genes in D. purpureum is developmentally regulated. During multicellular development, D. purpureum releases a mixture of volatile terpenes dominated by sesquiterpenes that are the in vitro products of a subset of the 12 TPS genes. The quality and quantity of the terpenes released from D. purpureum, however, bear little resemblance to those of D. discoideum, a closely related dictyostelid. Despite these variations, the conserved clade of dictyostelid TPSs, which have an evolutionary distance of more than 600 million years, has the same biochemical function, catalyzing the formation of a sesquiterpene protoillud-7-ene. Taken together, our results indicate that the dynamic evolution of dictyostelid TPS genes includes both purifying selection of an orthologous group and species-specific expansion with functional divergence. Consequently, the terpenes produced by these TPSs most likely have conserved as well as speciesadaptive biological functions as chemical languages in dictyostelids

A high-throughput transient gene expression system for switchgrass (Panicum virgatum L.) seedlings

<p>Abstract</p> <p>Background</p> <p>Grasses are relatively recalcitrant to genetic transformation in comparison to certain dicotyledons, yet they constitute some of the most important biofuel crops. Genetic transformation of switchgrass (<it>Panicum virgatum </it>L.) has previously been reported after cocultivation of explants with <it>Agrobacterium </it>and biolistics of embryogenic calli. Experiments to increase transient gene expression <it>in planta </it>may lead to stable transformation methods with increased efficiency.</p> <p>Results</p> <p>A high-throughput <it>Agrobacterium</it>-mediated transient gene expression system has been developed for <it>in planta </it>inoculation of germinating switchgrass seedlings. Four different <it>Agrobacterium </it>strains were compared for their ability to infect switchgrass seedlings, and strain AGL1 was found to be the most infective. Wounding pretreatments such as sonication, mixing by vortex with carborundum, separation by centrifugation, vacuum infiltration, and high temperature shock significantly increased transient expression of a reporter gene (GUSPlus, a variation of the β-glucuronidase (GUS) gene). The addition of L-cysteine and dithiothreitol in the presence of acetosyringone significantly increased GUS expression compared with control treatments, whereas the addition of 0.1% surfactants such as Silwet L77 or Li700 decreased GUS expression. 4-Methylumbelliferyl beta-D-galactopyranoside (MUG) assays showed a peak of β-glucuronidase (GUS) enzyme activity 3 days after cocultivation with <it>Agrobacterium </it>harboring pCambia1305.2, whereas MUG assays showed a peak of enzyme activity 5 days after cocultivation with <it>Agrobacterium </it>harboring pCambia1305.1.</p> <p>Conclusion</p> <p><it>Agrobacterium </it>strains C58, GV3101 and EHA105 are less able to deliver transfer DNA to switchgrass seedlings (cultivar Alamo) compared with strain AGL1. Transient expression was increased by double or triple wounding treatments such as mixing by vortex with carborundum, sonication, separation by centrifugation, and heat shock. The addition of thiol compounds such as L-cysteine and dithiothreitol in combination with acetosyringone during cocultivation also increased transient expression. The combination of multiple wounding treatments along with the addition of thiol compounds during cocultivation increased transient expression levels from 6% to 54%. There were differences in temporal GUS expression induced by pCambia1305.1 and pCambia1305.2.</p

Adaptive Routing Forwarding Strategy Based on Neural Network Algorithm

With the profound changes in global digital media, the focus of Internet users has gradually shifted to how to quickly obtain information without paying attention to where the information is stored. However, the current TCP/IP network protocol architecture cannot adapt to the rapid development of today#39s content applications. In order to adapt to the changes in the Internet, information-centric networking (ICN)has received extensive attention. Besides, the optimization of the user service request scheduling problem is the core issue affecting the performance of the ICN , and it is one of the hot research topics in the ICN network. To solve this problem, this paper proposes an adaptive routing forwarding strategy based on neural network algorithm. Through the modeling of the classic architecture named data networking (NDN) network delay model of ICN network, a neural network algorithm is used to delay prediction, and a forwarding strategy mechanism based on predict delay is designed to innovate in the NDN. The interface information Stat is added to the forwarding information base (FIB) of the network component to implement the dynamic selection of the forwarding routing. In addition, routing dynamic self-adaptation adjustment mechanism and fault rerouting function are designed in consideration of the situation of route congestion and interruption. Simulation results show that this strategy effectively reduces network delay and improves network performance