Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.
Cerebrospinal Fluid Drop Metastases of Canine Glioma: Magnetic Resonance Imaging Classification

Dissemination of glioma in humans can occur as leptomeningeal nodules, diffuse leptomeningeal lesions, or ependymal lesions. Cerebrospinal fluid (CSF) drop metastasis of glioma is not well-recognized in dogs. Ten dogs with at least two anatomically distinct and histologically confirmed foci of glioma were included in this study. The 10 dogs underwent 28 magnetic resonance imaging (MRI) examinations, with distant CSF drop metastasis revealed in 13 MRIs. The CSF drop metastases appeared as leptomeningeal nodules in four dogs, diffuse leptomeningeal lesions in six dogs, and ependymal lesions in seven dogs; six dogs had a combination of lesion types. Primary tumors were generally T2-heterogeneous and contrast-enhancing. Many metastases were T2-homogeneous and non-enhancing. Diffuse leptomeningeal lesions were seen as widespread extra-axial contrast-enhancement, again very dissimilar to the intra-axial primary mass. Primary masses were rostrotentorial, whereas metastases generally occurred in the direction of CSF flow, in ventricles, CSF cisterns, and the central canal or leptomeninges of the cervical or thoracolumbar spinal cord. Seven of the dogs had received therapy limited to the primary mass, such as surgery or stereotactic radiation, then developed metastasis in the following months. CSF drop metastasis of glioma may take a very different appearance on MRI to the primary mass, including periventricular lesions that are more homogeneous and less contrast-enhancing, rostral horn signal changes, or leptomeningeal enhancement ventral to the brainstem or encircling the spinal cord.
Thermo-Rheological Properties of the Ethiopian Lithosphere and Evidence for Transient Fluid Induced Lower Crustal Seismicity Beneath the Ethiopian Rift

Lower crustal earthquakes at plate boundaries and intraplate settings occur at depth where deformation is normally expected to occur in a ductile manner. Here we use the available earthquake catalogs and compute theoretical predictions for a range of conditions for the occurrence of lower crustal earthquakes beneath the Main Ethiopian Rift (MER) and adjacent north-western (NW) plateau. Yield strength envelops are constructed using information on geothermal gradient, strain rate, and composition constrained by geophysical observations. Our models suggest that away from the MER beneath the NW plateau the depth distribution of earthquakes in the lower crust is best explained by strong mafic lower crustal rheology and hydrostatic fluid pore pressure conditions. In the same region the effective elastic thickness is similar to seismogenic thickness showing that the lower crust has long-term strength and hence can physically support brittle deformation. On the contrary, in the central MER the seismogenic thickness is much larger than the effective elastic layer thickness implying that the lower crust has no long-term strength. Here our models show that both hydrostatic and near-lithostatic fluid pore pressures fail to explain the observed seismicity and instead a combination of near-lithostatic pore fluid pressure and transient high strain rate due to the movement of fluids provide a plausible mechanism for the occurrence of seismicity in the lower crust. Our interpretations are supported by occurrence of swarms of deep earthquakes beneath the MER, as opposed to more continuous background deep seismicity away from the rift. Using time-depth progression of earthquakes, we estimate permeability values of 5.9 × 10−15 m2 and 1.8 × 10−14 m2 at lower crustal depth. The range of permeability implies that seismicity can be induced by pore-pressure diffusion, likely from fluids sourced from the mantle that reactivate preexisting faults in the lower crust. Our thermo-rheological models explain the first order differences in lower crustal earthquakes both directly beneath and outboard of the rift valley.
Unified Approach to the Motion Design for a Snake Robot Negotiating Complicated Pipe Structures

A unified method for designing the motion of a snake robot negotiating complicated pipe structures is presented. Such robots moving inside pipes must deal with various “obstacles,” such as junctions, bends, diameter changes, shears, and blockages. To surmount these obstacles, we propose a method that enables the robot to adapt to multiple pipe structures in a unified way. This method also applies to motion that is necessary to pass between the inside and the outside of a pipe. We designed the target form of the snake robot using two helices connected by an arbitrary shape. This method can be applied to various obstacles by designing a part of the target form specifically for given obstacles. The robot negotiates obstacles under shift control by employing a rolling motion. Considering the slip between the robot and the pipe, the model expands the method to cover cases where two helices have different properties. We demonstrated the effectiveness of the proposed method in various experiments.
Utilizing Incentivized Economic Experiments to Test for Social Skills Acquisition Through Physical Education: Study Protocol of the Movigen Project

Besides cognitive skills, non-cognitive skills—social skills in particular—are crucial for outcomes in various domains of life. The present work describes the design of the Movigen project, an intervention study with children aged 10–13 years using enhanced physical education lessons to foster social skills in a playful way. Utilizing a novel methodological approach various incentivized economic experiments were applied to test for spillover effects of the intervention on social skills. At three points during the course of the study individuals participated in a series of incentivized economic experiments to elicit economic preferences and personality traits. Additional information about physical activity and free time activities, different psychometric scales, and family background were elicited with questionnaires. Furthermore, a subset of individuals was equipped with accelerometers for 7 days to validate the answers on physical activity in the questionnaire. The data set comprises a treatment group which received enhanced physical education lessons and a control group which received regular physical education lessons at school. The comparison of individuals' decision in the economic experiments between both groups allows to study the impact of our intervention on social skills.
Pulmonary Arterial Remodeling Is Related to the Risk Stratification and Right Ventricular-Pulmonary Arterial Coupling in Patients With Pulmonary Arterial Hypertension

Background Pulmonary arterial (PA) stiffness has an essential contribution to the right ventricular (RV) failure pathogenesis. A comprehensive and multiparameter risk assessment allows predicting mortality and guiding treatment decisions in PA hypertension (PAH). We characterize PA remodeling with intravascular ultrasound (IVUS) in prevalent and stable patients with PAH according to the ESC/ERS risk table and analyze the RV-PA coupling consequences. Methods Ten control subjects and 20 prevalent PAH adult patients underwent right heart catheterization (RHC) with simultaneous IVUS study. We estimated cardiac index (CI), pulmonary vascular resistance, and compliance (PVR, PAC) by standard formulas. From IVUS and RHC data, PA diameter, wall thickness/luminal diameter ratio, and indexes of stiffness (pulsatility, compliance, distensibility, incremental elastic modulus - Einc-, and the stiffness index β) were measured. We evaluated RV-PA coupling by the ratio of tricuspid annular plane systolic excursion to systolic pulmonary arterial pressure (TAPSE/sPAP). The individual average risk was calculated by assigning a score of 1 (low-risk -LR-), 2 (intermediate-risk -IR-), and 3 (high-risk -HR-) for each of seven variables (functional class, six-minute walking test, brain natriuretic peptide, right atrial area and pressure, CI, and PA oxygen saturation) and rounding the average value to the nearest integer. Results All PA segments interrogated showed increased vessel diameter, wall cross-sectional area (WCSA), and stiffness in patients with PAH compared to control subjects. 45% corresponded to LR, and 55% corresponded to IR PAH patients. The different measurements of PA stiffness showed significant correlations with TAPSE/sPAP (r = 0.6 to 0.76) in PAH patients. The IR group had higher PA stiffness and lower relative WCSA than LR patients (P < 0.05), and it is associated with a lower PAC and TAPSE/sPAP (P < 0.05). Conclusion In prevalent PAH patients, the severity of proximal PA remodeling is related to the risk stratification and associated with PAC and RV-PA coupling impairment beyond the indirect effect of the mean PA pressure. The concomitant assessment of IVUS and hemodynamic parameters at diagnosis and follow-up of PAH patients could be a feasible and safe tool for risk stratification and treatment response of the PA vasculopathy during serial hemodynamic measurements.
Synthesis of quinoline acetohydrazide-hydrazone derivatives evaluated as DNA gyrase inhibitors and potent antimicrobial agents

The (E)-N′-(substituted-benzylidene)-2-(7-fluoro-2-methoxyquinolin-8-yl)acetohydrazide-hydrazone derivatives reported in this manuscript represent a new series of antibacterial agents, as well as DNA gyrase inhibitors. Efforts were made to synthesize these quinolone-acetohydrazide-hydrazone derivatives (9a–n) in excellent yields. All the target compounds were evaluated for their in vitro antimicrobial activity against Escherichia coli (MTCC 443) and Pseudomonas aeruginosa (MTCC 424), as specimens of Gram-negative bacteria, and Staphylococcus aureus (MTCC 96) and Staphylococcus pyogenes (MTCC 442), as specimens of Gram-positive bacteria. Excellent antibacterial activity was observed for compounds substituted with R = 3,4,5-trimethoxy, 4-F, 4-OCF3, 4-CF3, and 3-CF3 moieties. Derivatives 9a–n were docked into the active sites of DNA gyrase A and DNA gyrase B in order to obtain more insight into the binding modes of the compounds. Among all the derivatives, 9n showed the lowest binding energy of −91.6 kcal mol−1 with DNA gyrase A. A DNA gyrase enzyme inhibition assay favors compounds 9m and 9n, which were substituted with di-fluorine moieties (R = 2,4-difluoro and 3,4-difluoro) in the quinoline scaffold, as the most potent inhibitors of S. aureus DNA gyrase A (9m, IC50 0.14 mg mL−1 and 9n, IC50 0.19 mg mL−1).
Isolation and characterization of polysaccharides and lignin from medium density fibreboard effluent water

The dry matter from medium density fibreboard (MDF) effluent water was fractionated into extractives (33.5%), pectic substances (4.2%), hemicelluloses (32.6%), cellulose (7.0%), and lignin (8.7%) by extraction with chloroform-methanol (2:1, v/v), hot water, dilute HCl, 5% NaOH, and 18% NaOH, respectively. Acid hydrolysis, alkaline nitrobenzene oxidation, ultraviolet (UV), gel-permeation chromatography (GPC), Fourier transform infrared (FT-IR), and carbon-13 nuclear magnetic resonance (NMR) spectroscopy were used to investigate the chemical compositions and structural features of the isolated polysaccharides and lignins. Sugar analyses indicated that galactose was the predominant sugar component in the hot water soluble polysaccharides, and glucose, mannose, xylose, and galactose were the major sugar constituents both in the pectic substances and in the 5% and 18% NaOH soluble hemicelluloses. The results showed that the three lignin fractions were composed of a large amount of guaiacyl (G) units, which can be justified as G-lignin from softwood.
Low-cost high-order-mode cavity backed slot array antenna using empty substrate integrated waveguide for the 5G n260 band

毫米波天线设计面临高增益、宽带、低成本等诸多挑战,在该频段基片集成波导(Substrate Integrated Waveguide,SIW)由于其辐射损耗低和易集成的优势而被广泛应用。 然而在毫米波频段SIW的介质损耗直接降低了天线辐射效率,若采用低损耗介质材料会导致较高的制造成本。 基片集成空腔波导(Empty Substrate Integrated Waveguide,ESIW)结构通过去除SIW中介质,可实现电磁波低损耗传输,在毫米波频段具有广阔应用前景。 本文面向5G n260频段应用,提出一款采用低成本FR-4 PCB板材设计的缝隙天线阵。 天线采用基片集成空腔波导结构设计,消除了介质损耗,并引入高次模腔体结构,减小馈电网络复杂度,在保证天线性能前提下,实现了毫米波天线低成本制造,为低成本毫米波天线设计提供了技术参考。 天线由5层FR-4 PCB板组成,从顶层往下依次为缝隙辐射层、高次模腔体层、耦合缝隙层、功分馈电网络层以及同轴馈电层。 天线底部由2. 4 mm同轴馈电,通过ESIW功分馈电网络,缝隙耦合激励4×4个腔体中的TE340模式,每个TE340模式的腔体通过顶层的3×4个缝隙辐射,形成12×16的缝隙阵列。 每层PCB板都将ESIW部分的介质去除并进行内壁覆铜处理,加工完成的PCB板通过周围的定位孔用螺钉组装。 给出了测试S参数与仿真S参数以及测试增益与仿真增益的对比结果。 S参数−8 dB带宽可覆盖n260的37–40 GHz频率范围。 测试的最大实际增益为27 dBi,通过与仿真的方向性系数对比,可估计得到天线辐射效率约为72. 4%。 从天线在37、38、39、40 GHz处的辐射方向图看,测试的方向图与仿真结果具有很好一致性。
City Commercial Banks and Credit Allocation: Firm-Level Evidence

This paper investigates how government-led banking liberalization affects credit allocation by banks using as a quasi-natural experiment the establishment of city commercial banks (CCBs) in China. Based on more than three million corporate financial statements spanning over 16 years, we find that the establishment of CCBs led to a 6–14 % drop in debt funding for private firms, as well as a 1–2 % rise in their funding costs. At the same time, private infrastructure firms enjoyed a nearly 6 % increase in debt funding and more than 100-basis-point drop in interest costs despite their inferior credit quality. The debt financing of private firm appears most severely affected in municipalities where officials face high promotional pressures or fiscal constraints.
Qualitative phytochemical assessment of Leucas aspera (willd.) Link using various solvent extracts

Leucas aspera (Willd.) Linn. belonging to family Lamiaceae is well-known as ‘Thumbai' in Tamil Nadu with traditional medicinal value as an antipyretic and insecticide. The current research work has been carried out to screen the phytochemical content of the aqueous, hexane, ethanol and methanol extract from the whole plant of Leucas aspera. The percentage of yield of the extracts varied according to the organic solvents used in which aqueous yielded 5.4% and methanol yielded 7.8%, respectively. Among the 11 phytochemicals screened, the whole-plant extract showed the presence of 10 phytochemicals. The phytochemical screening result showed that the carbohydrate, protein, lipids, alkaloids, saponins, glycosides, tannins, flavonoids, triterpenoids and phenols were present in the plant sample. Among the different solvent extract, methanol extract exhibited more number of phytochemical presence, and aqueous extract showed the least number of phytochemical presence. Among the different phytochemicals screened, carbohydrates, alkaloids, saponins, glycosides, tannins were present in all the solvent extracts. In contrast, steroids were absent in all the solvent extracts, and lipid was present only in methanol extract. The result suggested that the presence of secondary metabolites of Leucas aspera could be a potential source for antimicrobial, antioxidant activity and cytotoxic activity and the methanolic extract of Leucas aspera could be explored for its potent pharmacological activities.
Wood-decaying fungi in old-growth boreal forest fragments: extinctions and colonizations over 20 years

According to ecology theory, isolated habitat fragments cannot maintain populations of specialized species. Yet, empirical evidence based on monitoring of the same fragments over time is still limited. We studied the colonization–extinction dynamics of eight wood-decaying fungal species in 16 old-growth forest fragments (<14 ha) over a 20-year period (1997–2017). We observed 19 extinctions and 5 colonizations; yet, the distribution of extinctions and colonizations did not differ from the one expected by chance for any of the species. Twenty-six percent of the extinctions took place in two natural fragments amid large forest–peatland complexes. Phellinus nigrolimitatus (Romell) Bourdot and Galzin decreased and Phellinus ferrugineofuscus (P. Karst.) Bourdot increased in abundance (number of logs occupied). The volume of living spruce trees in the forest fragments correlated positively with the number of logs inhabited in five of the study species. Because fragment characteristics did not affect species turnover, it seems that stochastic processes governed colonizations and extinctions. Although the least abundant species in 1997 had declined, and the most abundant species had become more abundant, it appears that specialized wood-decaying fungi can persist for decades in isolated old-growth forest fragments, if suitable dead wood is continuously available.
Running head: SEX DIFFERENCES IN ADDICTION Sex Differences in Addiction: The Effects of Cocaine Self-Administration and Abstinence on Astrocytes in the Nucleus Accumbens of Female Rats

Astrocytes are the most numerous glial cell of the brain, and are implicated in various psychiatric disorders including addiction. Previous research on male rats demonstrates cocaine-induced changes in surface area, volume, and synaptic colocalization in astrocytes of the nucleus accumbens (NAc), a reward center of the brain. However, it is unknown whether the effects of cocaine on astrocytes in male rats are also observed in females. Thus, the goal of my Honors Thesis was to test the hypothesis that prolonged abstinence following cocaine self-administration (SA) would lead to a reduction in morphometric features and synaptic colocalization of NAc astrocytes in female rats. Twenty-four female Sprague-Dawley rats underwent 10-days of longaccess (6 h/day) self-administration of cocaine or saline, followed by 45 days of abstinence. Fluorescently-labelled astrocytes in the NAc were imaged and analyzed for morphological properties and synaptic colocalization. My results revealed no significant differences between saline and cocaine groups in astrocyte morphology and synaptic contact, suggesting the effects of cocaine on astrocytes in male rats do not extend to females. This study demonstrates a sex difference in the cellular effects of cocaine self-administration, and indicates that female astrocytes may display protective factors against cocaine-induced astrocyte retraction. SEX DIFFERENCES IN ADDICTION 4
THE INSTITUTE OF INTELLIGENT SYSTEMS AND ROBOTICS* INTERNSHIP OFFER Augmented reality for a surgical cockpit

: Minimally invasive surgery is known for its benefits to the patient. These benefits result mainly from the smaller incisions it requires compared to open surgery. These incisions allow the insertion of an endoscope and instruments into the patient's body through trocars. Despite its advantages, minimally invasive surgery presents several challenges for the surgeon. The trend is increasing with the generalization of minimally invasive access to almost all
Prognostic lncRNAs, miRNAs, and mRNAs Form a Competing Endogenous RNA Network in CESC

Background: Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tumorigenesis involves a combination of multiple genetic alteration processes. Constructing a survival-associated competing endogenous RNA (ceRNA) network and a multi-mRNA-based prognostic signature model can help us better understand the complexity and genetic characteristics of CESC.Methods: The RNA-seq data and clinical information of CESC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed mRNAs, lncRNAs and miRNAs were identified by edgeR package. Constructing prognostic model used the differentially expressed RNAs. The Kaplan-Meier method and log-rank test were performed to assess survival rates. The relationships between overall survival (OS) and clinical parameters were evaluated by Cox regression analysis. A survival-associated ceRNA network was constructed by multiMiR package and miRcode database. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Ontology (GO) were used to identify the functional role of the ceRNA network in the prognosis of CESC.Results: Differentially expressed 298 mRNAs, 8 miRNAs, and 29 lncRNAs were significantly associated with the prognosis of CESC. The prognostic signature model based on 4 mRNAs (OPN3, DAAM2, HENMT1, and CAVIN3) was constructed. The prognostic ability was 0.726 for this model. Patients in the high-risk group were significantly associated with worse OS. The KEGG pathways were significantly enriched in the TGF-β and Cell adhesion molecules signaling pathways.Conclusion: This study identified several potential prognostic biomarkers to construct a multi-mRNA-based prognostic model for CESC.
PROPOSAL FOR A HIGHER EDUCATION ADMISSION MANAGEMENT SYSTEM WITH THE USE OF OPEN SOURCE TECHNOLOGIES

Higher education institutions are characterized by the growth of the student population, the need to align their programs with market demand, and the adoption of new management and service delivery techniques, making it essential to use information technologies. This research project aims to design an information system prototype for a higher education admission management information system and propose open source software engineering tools that can assist its development. This paper presents the main concepts related to information systems, higher education and open source software. The prototype was designed following the object-oriented software development methodology and the software engineering tools were based on the comparison of two tools to three information system software elements namely forms, reports and web portal.
How Novelists Use Generative Language Models: An Exploratory User Study

Generative language models are garnering interest as creative tools. We present a user study to explore how fiction writers use generative language models during their writing process. We had four professional novelists complete various writing tasks while having access to a generative language model that either finishes their sentence or generates the next paragraph of text. We report the primary ways that novelists interact with these models, including: to generate ideas for describing scenes and characters, to create antagonistic suggestions that force them to hone their descriptive language, and as a constraint tool for challenging their writing practice. We identify six criteria for evaluating creative writing assistants, and propose design guidelines for future co-writing tools.