Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Genetics of a Common Freshwater Mussel, Amblema plicata, in a Southern U.S. River

ABSTRACT Myriad anthropogenic factors have led to substantial declines in North America's freshwater mussel populations over the last century. A greater understanding of mussel dispersal abilities, genetic structure, and effective population sizes is imperative to improve conservation strategies. This study used microsatellites to investigate genetic structure among mussel beds and estimate effective population sizes of a common North American mussel species, Amblema plicata, in the Little River, Oklahoma. We used five microsatellite loci to genotype 270 individuals from nine mussel beds distributed throughout the river and one of its tributaries, the Glover River. Our results indicate that subpopulations of A. plicata in the Little River are genetically similar. Upstream subpopulations had less genetic diversity than sites located downstream of the confluence of the Glover and Little rivers. Downstream subpopulations were primarily assigned to the same genetic group as upstream subpopulations, but they were admixed with a second genetic group. Low flows during droughts likely influenced the observed genetic structuring in A. plicata populations in the Little River. Additionally, downstream subpopulations may be admixed with a genetically distinct population of A. plicata, which may account for the increased genetic diversity. Estimates of effective population sizes (Ne) of large mussel beds were low compared to the total abundance (N) of A. plicata. While our data have limitations, they provide important information on the spatial scale at which conservation plans should focus and the population sizes that should be sustained through relocation and restocking programs.
Estimation of heritability for claw traits in Holstein cattle using Bayesian and REML approaches

The aim of this study was to estimate the heritability of claw conformation traits in Slovak Holstein cattle by using two approaches: the Bayesian method and the restricted maximum likelihood (REML) algorithm. Overall 860 claw trimming records of 716 dairy cows were included in this study. The claw morphometric data were collected after functional trimming between 2012 and 2017. The conformation of claws was evaluated based on eight parameters (angle, length, heel depth, height, diagonal, width, total and functional areas) by digital image analysis and NIS Elements 3.0 software. The heritability of those traits was estimated using a single trait animal model including fixed effects of herd-year-season, stage of lactation and sire. Both of applied approaches indicated low or moderate level of heritability across analysed traits, in average 0.28 ±0.08 (REML) resp. 0.22 ±0.09 (Bayesian). The highest heritability was found for diagonal of claw (0.41), while the lowest one was observed for the total area of claw (0.18) and the claw height (0.12) based on the REML algorithm and Bayesian approach, respectively. The study confirmed previous assumption that the claw conformation traits are inherited in low or moderate mode. Future analysis of genetic correlations between them can be beneficial for construction of new selection indices, better responding to today’s welfare requests and use of new generation indicators made possible.
Max deletion destabilizes MYC protein and abrogates Eµ-Myc lymphomagenesis

Although MAX is widely regarded as an obligate dimerization partner for MYC, its function in normal development and neoplasia is not well defined. We show that B-cell specific deletion of Max has a surprisingly modest effect on B-cell development but completely abrogates Eµ-Myc driven lymphomagenesis. In both contexts, MAX loss leads to a significant reduction in MYC protein levels. This outcome is associated with the downregulation of numerous transcriptional targets of MAX including a subset that regulate MYC stability. Reduction in MYC protein levels is also observed in multiple cell lines treated with a MYC-MAX dimerization inhibitor. Our work uncovers a layer of Myc autoregulation critical for lymphomagenesis yet partly dispensable for normal lymphoid development.
IDENTIFICACIÓN DE DIVERSIDAD PATOGÉNICA DE Phomopsis sp. CAUSAL DEL TIZÓN DEL TALLO Y VAINA EN SOYA (Glycine max) MEDIANTE MARCADORES MOLECULARES

Phomopsis longicolla (Plo) y P. phaseoli var. sojae (Pps) son causantes del tizón del tallo y vainas (TTV) y decaimiento de semillas (DS) en soja (Glycine max). El objetivo fue estudiar la variabilidad genética y patogénica de Phomopsis al interactuar con cultivares con resistencia variada o susceptibilidad; así como conocer la asociación entre el perfil molecular y patogénico en las interacciones estudiadas. La hipótesis fue que existe variabilidad genética en los germoplasmas fúngico y vegetal que incrementa la diversidad de reacciones específicas durante el desarrollo del TTV. Por lo tanto, en este estudio se propone una metodología para analizar la asociación entre atributos patogénicos (expresión fenotípica de la enfermedad) y marcadores moleculares. Seis aislamientos de Plo y uno de Pps se inocularon en seis cultivares de soja. La variabilidad genética fúngica se evaluó mediante marcadores tipo RAPD e ITS y el comportamiento patogénico de los aislamientos fúngicos a través de la severidad (S%) de la enfermedad generada en los cultivares de soja. La caracterización molecular separó a los aislamientos de Plo de Pps. Las interacciones específicas evidenciaron comportamientos diferenciales entre aislamientos fúngicos y entre cultivares de soja. El estudio permitió identificar asociaciones entre la variabilidad molecular de los patógenos y los comportamientos diferenciales en el conjunto de aislamientos de Phomopsis y cultivares de soja frente a TTV en G. max.
Diversity analysis of Sweet Potato (Ipomoea batatas[L.] Lam) genotypes using morphological, biochemical and molecular markers

Sweet potato [ Ipomea batatas (L.) Lam. ] is a nutritious food crop primarily grown by small and marginal farmers. Successful breeding and germplasm conservation programs demands characterization of its germplasm. Here, we tried to determine genetic diversity among 21 sweet potato genotypes using morphological, biochemical and molecular markers. Ten morphological traits were studied and subjected to analysis of variance (ANOVA). Mean square due to germplasm were highly significant as well as wide mean range performance was observed for tuber number per plant, individual tuber weight, tuber fresh yield per plant, tuber dry yield per plant, tuber yield per plot and tuber length. UPGMA (Unweighted Pair Group Method Arithmetic Average) cluster analysis based on morphological traits separated the germplasm into three groups. The genotypes Gautam, Shree Arun, RS-92 and CO-3-4 appeared promising with regard to yield characters. Total phenol was maximum in in V-12 genotype (1.39 mg), while minimum was recorded in Samrat genotype (0.95 mg). The highest total antioxidant was observed in the genotype Samrat (0.30 mg), while minimum was recorded in the genotype Navsari Local (0.16 mg). Molecular diversity analysis was carried out using 25 RAPD (Random Amplified Polymorphic DNA) primers, out of which 13 primers produced 117 reproducible amplicons (106 polymorphic, 7 monomorphic and 4 unique amplicons). UPGMA dendogram based on RAPD data separated the genotypes into two major clusters having the similarity coefficient ranged from 0.56 to 0.76. The results can be used for sweet potato crop improvement through molecular breeding and marker assisted selection of for desired traits in future.
Freshwater Adaptation at the Molecular Scale in the Unique Sponges of Lake Baikal

The Lake Baikal ecosystem is unique. The largest, oldest and deepest lake in the world presents a variety of rare evolutionary opportunities and ecological niches to the species that inhabit it, and as a result the lake is a biodiversity hotspot. More than 80% of the animals found there are endemic, and they often exhibit unusual traits. The freshwater sponge Lubomirskia baicalensis and its relatives are good examples of these idiosyncratic organisms. Lake Baikal sponges are unusually large for freshwater sponges, and possess particular symbiotic microorganisms which aid their survival and growth. As sponges are the most abundant benthic organisms in Lake Baikal, with 13 extant species (and 2 subspecies), they play a variety of key roles in the maintenance of this unusual ecosystem. In recent years the flora and fauna of Lake Baikal have been challenged by human activity in the region. Pollution, invasive species, temperature increases, eutrophication and falling water levels have all had deleterious effects. Sponges have suffered in particular from bleaching events, where their symbiotes are no longer retained, with knock-on effects to their survival and that of the ecosystem as a whole. To better understand the unique biology of these sponges we have established here a variety of resources for understanding these sponges at a molecular level. We have sequenced transcriptomes from three species of Lubomirskiidae. We have also assembled a draft genome resource for L. baicalensis. With these resources in place, a sizable addition to our knowledge of freshwater sponge genetics, we have investigated the adaptations of these and other freshwater sponge species to their environment, investigated their symbioses, and established a range of molecular tools for understanding the molecular and population-level biology of these key species across their habitat in Lake Baikal.
A thorny issue: Woody plant defence and growth in an East African savanna

Recent work suggests that savanna woody plant species utilise two different strategies based on their defences against herbivory; a low nutrient/high chemical defence strategy and a nutrition paired with mostly architectural defences strategy. The concept that chemical and structural defences can augment each other and do not necessarily trade‐off has emanated from this work. In this study, we examine woody plant defence strategies, how these respond to herbivore removal and how they affect plant growth in an East African savanna. At three paired long‐term exclosure sites with high browser and mixed‐feeder densities at Mpala Ranch, Kenya, we investigated: (a) whether defences employed by the dominant fine‐ and broad‐leaved woody savanna species form defence strategies and if these align with previously proposed strategies, (b) how nine key plant defence traits respond to herbivore removal and (c) how effective the different defence strategies are at protecting against intense herbivory (by measuring plant growth with and without herbivores present). We identified three defence strategies. We found a group (a) with high N, short spines and high N‐free secondary metabolites, a group (b) with high N, long spines and low N‐free secondary metabolites and a group (c) with moderate N, no spines and low N‐free secondary metabolites (most likely defended by unmeasured chemical defences). Structural defences (spine length, branching) were generally found to be induced by herbivory, leaf available N increased or did not respond, and N‐free secondary metabolites decreased or did not respond to herbivory. Species with long spines combined with increased “caginess” (dense canopy architecture arising from complex arrangement of numerous woody and spiny axis categories) of branches, maintained the highest growth under intense browsing, compared to species with short spines and high N‐free secondary metabolites and species with no spines and low N‐free secondary metabolites. Synthesis. At our study site, structural traits (i.e. spines, increased caginess) were the most inducible and effective defences against intense mammalian herbivory. We propose that high levels of variability in the way that nutrient and defence traits combine may contribute to the coexistence of closely related species comprising savanna woody communities.
Preliminary Study on Magnetic Resonance Temperature Measurement using Brain-Metabolite Phantom

In this study, we measured the chemical shift change of metabolite peaks in the brain-metabolite phantom according to the temperature variation using nuclear magnetic resonance(NMR). The temperature range in NMR system was controled from 25 to 80 (5 step) by internal temperature controller. Temperature coefficients of each metabolite peaks were also calculated from the measured chemical shift depending on the temperature. The chemical shift changes depending on temperature were validated by linear regression method for each metabolite peaks. The temperature coefficients of , Cho, Cr, NAA, and Lac were 0.0086, 0.0088, 0.0091, 0.0089, and 0.0088ppm/, respectively. This study shows that chemical shift change of brain metabolite and temperature variation have linear relationship each other. This also makes authors believe that brain temperature measurement is possible using MR spectroscopic imaging technique.
A Generic method for assembling software product line components

Las lineas de productos de software (LPS) promueven la industrializacion del desarrollo de software mediante la definicion y ensamblaje de componentes reutilizables de software. Actualmente existen diferentes propuestas para implementar y ensamblar estos componentes. Sin embargo, su construccion y ensamblaje continua siendo un proceso complejo y que requiere mucho tiempo. Esta tesis analiza las ventajas y desventajas de las diferentes estrategias actuales para implementacion y ensamblaje de componentes de LPS. Con base en esto y con el objetivo de desarrollar un metodo generico (el cual se pueda aplicar a multiples componentes de software desarrollados en diferentes lenguajes), esta tesis desarrolla la programacion orientada a fragmentos (FragOP), la cual define un marco de trabajo para disenar, implementar y reutilizar componentes de dominio de LPS. FragOP se basa en: (i) componentes de dominio, (ii) archivos de dominio, (iii) puntos de fragmentacion, (iv) fragmentos, (v) puntos de personalizacion, y (vi) archivos de personalizacion. Ademas, se realizo una implementacion de FragOP en una herramienta llamada VariaMos, y se llevaron a cabo tres evaluaciones: (i) se creo una LPS de tiendas de ropa, se derivaron cinco productos y se discutieron los resultados. (ii) Se realizo una discusion acerca de la comparacion de FragOP y otras propuestas actuales. Y (iii) se diseno una prueba de usabilidad acerca del soporte de VariaMos para FragOP. Los resultados muestran evidencia preliminar de que el uso de FragOP reduce la intervencion manual cuando se ensamblan componentes, y que FragOP puede usarse como un metodo generico para el ensamblaje de componentes.
cDNA-AFLP analysis of transcript derived fragments during seed development in castor bean (Ricinus communis L.)

Abstract Ricinoleic acid, one of the biggest components in castor oil, is an unusual fatty acid with numerous industrial applications. Despite much research on the oil content of Ricinus communis L. , the genes encoding the oil biosynthesis function in the seed developmental stages are still poorly known. Here, we analyzed differentially expressed transcripts during seed development using cDNA-amplified fragment length polymorphism. Almost all ingredients significantly decreased along with seed maturation, except for ricinoleic acid, which increased greatly from 6.7% to 86.8%. A total of 534 distinguished fragments were differentially expressed in six development stages. Among these, 67 fragments showed high homology with known-function genes, and 26 sequences were successfully annotated with fatty acid synthesis or storage proteins in castor and other species. The results showed that fatty acid synthesis and accumulation in castor seeds displayed various temporal patterns. Different cDNA-fragment patterns were mainly found in later development stages, coinciding with the onset of oil synthesis.
Cell and protoplast culture of Indica javanica elite rice breeding lines IR 65597-134-2 and IR 65598-112-2

Rice (Orvza saliva L.) is one of the world's most important food crop species with an increasing demand Therefore, high yielding new rice breeding lines have been produced by IRRI to raise the rice production. These breeding lines require further crop improvement. Genetic transformation provides efficient methods of crop improvement, complementing the conventional methods of plant breeding.
Selective Isolation of Mammalian Genes by TAR Cloning

This unit describes procedures for selective isolation of specific chromosomal regions and entire mammalian genes as circular yeast artificial chromosomes (YACs). The isolation is based on transformation‐associated recombination (TAR) in yeast between genomic DNA and a linearized vector containing targeting sequences homologous to a region of interest. The details preparation of highly competent yeast spheroplasts and transformation of the spheroplasts by genomic DNA along with a TAR vector. Support protocols describe preparation of chromosome‐sized genomic DNA in solid agarose plugs, identification of positive clone pools among primary yeast transformants using PCR, and a quick method for preparing PCR templates from lysed spheroplasts. PCR analysis of each clone in the positive pool is performed to identify individual clones containing the gene of interest. A final support protocol describes retrofitting TAR‐isolated YACs into bacterial artificial chromosomes (BACs).
Selection and Characterization of a Nanobody Biosensor of GTP-Bound RHO Activities

RHO (Ras HOmologous) GTPases are molecular switches that activate, in their state bound to Guanosine triphosphate (GTP), key signaling pathways, which involve actin cytoskeleton dynamics. Previously, we selected the nanobody RH12, from a synthetic phage display library, which binds the GTP-bound active conformation of RHOA (Ras Homologous family member A). However, when expressed as an intracellular antibody, its blocking effect on RHO signaling led to a loss of actin fibers, which in turn affected cell shape and cell survival. Here, in order to engineer an intracellular biosensor of RHOA-GTP activation, we screened the same phage nanobody library and identified another RHO-GTP selective intracellular nanobody, but with no apparent toxicity. The recombinant RH57 nanobody displays high affinity towards GTP-bound RHOA/B/C subgroup of small GTPases in vitro. Intracellular expression of the RH57 allowed selective co-precipitation with the GTP-bound state of the endogenous RHOA subfamily. When expressed as a fluorescent fusion protein, the chromobody GFP-RH57 was localized to the inner plasma membrane upon stimulation of the activation of endogenous RHO. Finally, the RH57 nanobody was used to establish a BRET-based biosensor (Bioluminescence Resonance Energy Transfer) of RHO activation. The dynamic range of the BRET signal could potentially offer new opportunities to develop cell-based screening of RHOA subfamily activation modulators.
Raspberry Pi-based Finger Vein Recognition System using PCANet

Finger Vein Recognition System (FVRS) is a biometric technology that identifies or verifies an individual identity based on unique vein patterns. Compared with other biometrics, it is more secure, anti-forgery and hygiene. Thus, it successfully utilized in many authentications nowadays. A feature extraction process is mandatory in maximizing recognition rate of the system. However, majority of feature extraction techniques utilized in FVRS only can provide low-level features, which return an unsatisfied result. A simple deep learning network is proposed in this paper, namely Principal Component Analysis Network (PCANet). PCANet composed of three basic data processing components: 1) PCA filter, 2) binary hashing 3) histograms. PCA is employed for learning multistage filter banks. Binary hashing and block histograms are the steps for indexing and pooling. The features extracted are represented in block-wise histograms. In this paper, PCANet is compared with PCA in term of performance and effectiveness. PCANet retrieved an accuracy of 98.5% under limited training samples, an increase of 21.3% than that of PCA. Factors which impact PCANet are studied to identify the limitations of PCANet. Classifier utilized in FVRS is kNN with Euclidean distance. OpenCV image processing library and C++ language are used in the development. The results returned prove that PCANet performance does not easily influenced by intra-class variability and limited training datasets. Meanwhile, the research noticed about the difficulty in recognition as age increased. The performance evaluation shows that the accuracy of FVRS is 92.67% with the utilization of PCANet. Concluded that PCANet is a promising technique in finger vein recognition.
Design of PCIe-DMA bridge interface for High Speed Ethernet Applications

Modern applications requires system to be scalable and computationally intensive. These requirements have driven the need for systems with more than one processing element. Traditional architecture includes one or more Central Processing Unit (CPU) where as present scenario demands for more accelerating devices such as Graphics Processing Unit (GPU), General Purpose Graphics Processing Unit (GPGPU) or custom accelerators with Field Programmable Gate Array (FPGA). FPGA device reconfigurablity and high speed Serializer Deserializer(SERDES) makes it more preferable. Designers find it difficult to couple FPGA to CPU, because of complex communication schemes such as Peripheral Component Interconnect (PCIe) needs to be implemented to fully utilize the potential of FPGA. This Paper proposes system architecture for PCIe-DMA bridge interface for high speed Ethernet applications, based on Intel FPGA platform. The system mainly comprises of PCIe AVMM DMA bridge, Avalon FIFO Memory, Tri-Speed Ethernet. The host processing system consist of Linux operating system, which uses PCIe AVMM DMA Bridge to communicate to end point device. The bridge provides conversion logic from PCIe address domain to Avalon address domain. This paper uses a custom designed Gigabit Ethernet (GBE) Card form factor VITA 74 standard to implement the proposed architecture. It discusses hardware and software flow for portable server.
THE RELATIONSHIP BETWEEN PHYSICAL ACTIVITY AND DEPRESSION OF CHINESE STUDENTS STUDYING IN RUSSIA

To understand the effect of physical activity on the depression status of Chinese students studying in Russia.The authors used the SDS depression self-assessment scale and physical exercise assessment scale to survey350 Chinese students in some Russian universities, and collected the questionnaires on their mobile phones.The basic situation was investigated and the data was analyzed statistically. Use SPSS to assess the correlationbetween physical activity and depression. It was found that appropriately increasing the amount of physicalactivity can effectively improve depression and be beneficial to the development of mental health of Chinesestudents studying in Russia.