Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple allelism at Er locus for powdery mildew resistance in pea (Pisum sativum L.)

Several sources of powdery mildew resistance in pea have been identified in natural germplasm as well as in landraces and cultivated varieties. Genetic studies revealed that all such cases are recessive mutations in a single gene called Er. Many carriers of the powdery mildew resistance trait differ in their phenotype and expression. This indicated existence of multiple alleles at the locus controlling resistance to powdery mildew. Molecular analysis revealed differences in the nature of changes induced in nature or during mutagenesis. A total of nine molecular mutations have been characterized. Many more alleles of different origin are awaiting similar characterization.
Differential expression of 12 NBS-encoding genes in two apple cultivars in response to Alternaria alternata f. sp. mali infection

Abstract: Alternaria blotch, caused by Alternaria alternata f. sp. mali, is a destructive defoliating disease that affects apple worldwide, especially in Asia. Despite previous efforts in characterizing this disease, few have reported on nucleotide binding sites (NBS)-encoding genes in response to pathogen infection. In this study, we characterized the morphological and gene expression response of ‘Golden Delicious’ and ‘Starking’ apples challenged by A. alternata. Inoculation of detached leaves of ‘Golden Delicious’ resulted in a rapid initiation of disease symptoms but a slow spread of the infection from the point of inoculation. In contrast, detached leaves of ‘Starking’ exhibited a delayed visibility of infection but a rapid spread of the infection once it was established. Based upon quantitative reverse transcription polymerase chain reaction data, we characterized the expression of 12 NBS-encoding genes in response to infection by A. alternata. We further characterized the structure, chromosomal location, and physico-chemical properties of the encoded proteins for these 12 NBS-encoding genes. Temporal gene expression profiles following inoculation indicated that the 12 NBS-encoding genes were all involved in the response in the two apple cultivars. The most highly expressed genes, MDP0000127009, MDP0000292810, and MDP0000710999, appear to have great potential for breeding resistant apple cultivars through genetic engineering.
Thalamocortical Projectional Divergence Leads to Complexity in Functional Organizations in Mouse Auditory Cortex

Frequency-related topological projections from the ventral division of the medial geniculate body (MGv) relay the tonotopic organization found in primary auditory cortex (A1). However, relaying circuits of the functional organization to higher-order, secondary auditory field (A2) have not been identified so far. Here, using tracing, we found that A2 receives dense topological projections from MGv in mice, and that tonotopy was established in A2 even when primary fields including A1 were removed. These indicate that thalamic inputs to A2 are sufficient for generating its tonotopy. Moreover, neuronal responses in the thalamocortical recipient layer of A2 showed wider bandwidth and greater heterogeneity of the best frequency distribution than those of A1, which was attributed to larger divergence of thalamocortical projections from MGv to A2 than those from MGv to A1. The current study identifies that the functional organization in the auditory cortex can be determined by the structure of thalamocortical input. Significant Statement Although peripheral input patterns to the primary auditory cortex (A1) of the brain are well understood, how tonal information is relayed to higher-order regions such as the secondary auditory field (A2) remains unclear. This work revealed a new source of auditory information to A2; the tonal map in mouse A2 is primarily produced by orderly projections from the primary auditory thalamus. We also found that the complex behaviour and organization of neurons in A2 is generated by divergent projections from the primary thalamus that converge on neurons in A2. Our findings indicate that thalamocortical projections constitute a major factor that determines the regional properties and functional organization of mouse A2.
Hierarchical, multi‐grain rendezvous site selection by wolves in southern Italy

Fine-scale knowledge of how anthropogenic effects may alter habitat selection by wolves (Canis lupus) is important to inform conservation management, especially where wolf populations are expanding into more populated areas or where human activity and development are increasingly encroaching on formerly pristine environments. From 1999 to 2003, we documented rendezvous sites (n1⁄4 31) used by wolves (n1⁄4 6 packs) in a previously unstudied wolf population in the southern Apennines, Italy (Pollino National Park [PNP]), where conditions are ideal to unveil behavioral adaptations of wolves living in human-dominated landscapes.We adopted a hierarchical, multi-scale habitat selection approach by using a set of environmental, topographic, and anthropogenic factors within multi-grain resource selection functions (MRSFs) at the landscape and the territory extent. Habitat selection by wolves was scale-dependent and different habitat components affected wolves at different grains. When establishing a territory at the landscape scale, wolves avoided areas featuring high densities of humans, paved roads, and trails, and they preferentially located territories where higher forest cover and rough terrain enhanced concealment and ensured reduced accessibility by humans. Concurrently, wolves also selected open areas and, at coarse grain, areas of high density of dirt roads and trails to enhance hunting and traveling efficiency. When selecting rendezvous sites within territories, wolves still selected for forest cover and lessened avoidance of anthropogenic features apparent at the lower order of selection. When choosing rendezvous sites, wolves also avoided low-use anthropogenic linear features and rough terrain, unveiling trade-offs in selection decisions across different spatial and temporal scales. Our results reinforce the notion that occurrence of wolves in human-modified landscapes is shaped by avoidance of anthropogenic pressure, but they also indicate that rendezvous site selection by wolves conform to a hierarchical decision-making process that is extentand grain-dependent. Spatially explicit models of rendezvous site selection such as the one we developed for PNP enhance management effectiveness for strategies such as regulating human access and activity during the pup rearing seasons, preventing human persecution, mitigating livestock depredations, and designing cost-effective monitoring programs. 2018 The Wildlife Society.
Embryonic gene transcription in the spiny mouse (Acomys cahirinus): an investigtion into the embryonic genome activation

Our understanding of genetic mechanisms driving early embryonic development is primarily based on experiments conducted on mice, however translation of findings can be limited by physiological differences between mice and humans. To address this, we investigated whether the spiny mouse (Acomys cahirinus) is a closer model of early human embryonic development due to their more human-like endocrine profile. We therefore characterised the initiation of gene transcription in the spiny mouse embryo and compared the pattern of gene expression during the embryonic genome activation (EGA) with common mouse and human embryos. Naturally-mated spiny mouse embryos were obtained at the 2-cell, 4-cell and 8-cell stages of development (n=4 biological replicates per stage). RNA-Seq of these samples produced 709.1M paired-end reads in total. De novo assembly of reads was conducted using Trinity. Embryo-specific transcripts were extracted from the de novo assembly and added to the reference spiny mouse transcriptome. Transcription was first detected between the 2-cell and 4-cell stages for the majority of genes (n=3,428), with fewer genes first transcribed between the 4-cell and 8-cell stages (n=1,150). The pattern of gene expression in spiny mouse embryos during this period of development is more human-like than common mouse embryos. This is the first evidence the spiny mouse may provide a more suitable model of human embryonic development. The improved reference Acomys cahirinus transcriptome is publically accessible, further increasing the value of this tool for ongoing research. Further investigation into early development in the spiny mouse is warranted.
Connecting conceptual and spatial search via a model of generalization

The idea of a “cognitive map” was originally developed to explain planning and generalization in spatial domains through a representation of inferred relationships between experiences. Recently, new research has suggested similar principles may also govern the representation of more abstract, conceptual knowledge in the brain. We test whether the search for rewards in conceptual spaces follows similar computational principles as in spatial environments. Using a within-subject design, participants searched for both spatially and conceptually correlated rewards in multi-armed bandit tasks. We use a Gaussian Process model combining generalization with an optimistic sampling strategy to capture human search decisions and judgments in both domains, and to simulate human-level performance when specified with participant parameter estimates. In line with the notion of a domain-general generalization mechanism, parameter estimates correlate across spatial and conceptual search, yet some differences also emerged, with participants generalizing less and exploiting more in the conceptual domain.
Compendiums of Cancer Transcriptome for Machine Learning Applications

Background There exist massive transcriptome profiles in the form of microarray, enabling reuse. The challenge is that they are processed with diverse platforms and preprocessing tools, requiring considerable time and informatics expertise for cross-dataset or cross-cancer analyses. If there exists a single, integrated data source consisting of thousands of samples, similar to TCGA, data-reuse will be facilitated for discovery, analysis, and validation of biomarker-based clinical strategy. Findings We present 11 merged microarray-acquired datasets (MMDs) of major cancer types, curating 8,386 patient-derived tumor and tumor-free samples from 95 GEO datasets. Highly concordant MMD-derived patterns of genome-wide differential gene expression were observed with matching TCGA cohorts. Using machine learning algorithms, we show that clinical models trained from all MMDs, except breast MMD, can be directly applied to RNA-seq-acquired TCGA data with an average accuracy of 0.96 in classifying cancer. Machine learning optimized MMD further aids to reveal immune landscape of human cancers critically needed in disease management and clinical interventions. Conclusions To facilitate large-scale meta-analysis, we generated a newly curated, unified, large-scale MMD across 11 cancer types. Besides TCGA, this single data source may serve as an excellent training or test set to apply, develop, and refine machine learning algorithms that can be tapped to better define genomic landscape of human cancers.
Natural Dynamics of Multi-Species Flowering Annuals in Tropical Landscape

This study investigate the growth performance and the dynamic community of multi-species annual flowers in tropical landscape. The multi-species plant community produce an attractive colour of flowers according to their flowering peak of each species that have been tested. At the first growth cycle, the earliest species to bloom were Gomphrena globosa and Zinnia elegans which took 8 weeks after seed were sown. Meanwhile, Cosmos spp and Tithonia rotundifolia were the late species to bloom which took 14 weeks after seeds were sown. At the second growth cycle, the multi-species annual plants bloom much earlier which is only 3 weeks after pruning. The mean plant height and dry weight of several species on both growth cycles show a significant difference (P<0.05). Cosmos sulphureus and Cosmos caudatus recorded maximum heights on both growth cycles with C. sulphureus recording a maximum dry weight of about 172.5 gm/plant in the first growth cycle. Overall, the established multi-species plant community developed, had a lifespan of 5- 6 months in each growth cycle. The second growth cycle plant community was formed through self-sowing and vegetative part after pruning.
The impact of predation on the evolution of hosts and parasites.

The study of infectious diseases, particularly those transmitted by parasites, is vital to improving our understanding of the evolutionary and population dynamics which may arise during an epidemic outbreak or ongoing endemic. The evolution of host-parasite systems within complex communities is not fully understood. With the use of mathematical models, I build upon our theoretical knowledge of this area. By including a predator population in these systems, I determine how this impacts the evolution of host resistance against infection and multiple enemies, specifically parasites and predators. I also determine when parasite populations are likely to evolve intermediate host manipulation in order to reach a final host. Additionally, trade-offs are included within the host and parasite populations as evolving such defences or manipulation is likely to come at a cost. The presence of the predator increases the potential for host diversity to arise. Experimental work is used to determine the existence of trade-offs occurring in the Plodia interpunctella (Indian meal moth) host system. My results reveal the underlying ecological feedbacks, created by relative population densities and growth rates, which drive host-parasite evolution, whilst uncovering the key effects of the predator population. The inclusion of such complexities is important as they clearly affect host-parasite evolution. Overall, I provide an insight into the interesting dynamics arising in these systems. Future studies in this area will continue to develop and improve our understanding of these complex systems.
Phytochemical analysis and antioxidant activities of Trigona Apicalis propolis extract

Propolis is a resinous substance found in beehives. It provides beneficial effects on human health and has been used to treat many diseases since ancient times. The objectives of this study were to analyze the phytochemical profile of propolis derived from local T. apicalis species and its antioxidant activities. The ethanolic extract of propolis was subjected to HPLC analysis to analyze its phytochemical profile. The propolis extract was later tested for antioxidant capacities by using DPPH radical scavenging assay. TPC and TFC were performed to determine the correlation with its antioxidant activities. TEAC for each serial dilution sample was 2621.15 (4.76 mg/mL), 2050.85 (2.38 mg/mL), 1883.27 (1.19 mg/mL), 1562.67 (0.59 mg/mL), 1327.82 (0.29 mg/mL), 1164.49 (0.15 mg/mL), 983.27 (0.07 mg/mL), and 944.79 (0.04 mg/mL). The results demonstrated that the antioxidant activities of propolis extract were dose dependent. The IC50 of propolis for DPPH assay was 4.27 mg/ml. Correlation values of TPC and TFC again.
Mechanisms of Horizontal Gene Transfer

Horizontal gene transfer plays important roles in the evolution of S. aureus, and indeed, a variety of virulence factors and antibiotic resistance genes are embedded in a series of mobile genetic elements. In this chapter, we review the mechanisms of horizontal gene transfer, including recent findings on the natural genetic competence. Then, we consider the transfer of two important antibiotic resistance genes: the methicillin resistance gene, mecA (in Staphylococcal Cassette Chromosome) and the linezolid resistance gene, cfr (in plasmid). In either case, distinct mechanisms driving the gene dissemination support the prominent evolutionary ability of this important human pathogen.
Gut microbiota dynamics in the weaner pig in response to experimental Escherichia coli challenge and dietary manipulation

v Lay summary . vii List of abbreviations . ix List of tables . x List of figures . xii Table of contents . xv Chapter 1: Introduction . 1.1 General Introduction . 1 1.2 Weaning the pig . 2 1.2. 1 Weaning age . 3 1.2. 2 Housing. 4 1.2. 3 Feed intake . 5
Brucella Abortus Vaccines: Use in Control Programs and Immune Response

Brucella spp. is a highly infectious pathogen that affects numerous livestock and wild animal species besides humans, and that although eradicated in some countries, remains one of the most economically important zoonosis worldwide. Strain 19 and RB51 are the two Brucella abortus vaccine strains more largely used in the control of brucellosis in cattle worldwide, being effective in the prevention of abortion and infection, besides offering long lasting protection. Here, we reviewed the main aspects of the B. abortus vaccines and their use in brucellosis control and eradication programs over the years and the current understanding in the immune response triggered by these two B. abortus vaccines, especially in cattle.
The Concept of Environmental Education

I Tithin the past 50 years the United States has become a predominantly urban nation, both in thought and in physical character. Large and middle-sized communities, many within complex urban regions, have evolved to where over 70% of this country's population resides on 1.5% of the nation's land surface. By 1980, eight out of ten Americans will probably live in an urban environment. Consequently, the independent rural-oriented living that once characterized this country's social and political heritage is no longer a dominating influence in the lives of most Americans. In rural surroundings, direct daily contact with the basic natural resources was prevalent, especially within man's immediate environment. As man became progressively urbanized, his intimate association and interaction with natural resources diminished and, with it, his awareness of his dependency on them. Yet it is imperative that man, wherever he lives, comprehend that his welfare is dependent upon the proper management and use of these resources. Man should also have an awareness and understanding of his community and its associated problems. Our communities are being plagued with problems such as: lack of comprehensive environmental planning; indiscriminate use of pesticides; community blight; air and water pollution; traffic congestion; and the lack of institutional arrangements needed to cope effectively with environmental problems. While these problems are legitimate concerns of community governmental officials and planners, the responsibility for their solution rests, to a large extent, with citizens. To an increasing extent citizens are being asked to make decisions that affect (directly and indirectly) their environment. Specifically, citizens make these decisions as they cast votes on community issues; as they elect representatives to policy-making bodies; as they directly act upon the environment itself. Citizens can be effective in influencing sound policy in other ways. They can ask informed questions, at the proper time, of the right people. They can serve on advisory and policy-making committees. They can support sound legislation directed at resolving environmental problems. To perform these tasks effectively, it is vital that the citizenry be knowledgeable concerning their biophysical environment and associated problems, aware of how they can help solve these problems, and motivated to work toward effective solutions. Most current programs in conservation education are oriented primarily to basic resources; they do not focus on community environment and its associated problems. Furthermore, few programs emphasize the role of the citizen in working, both individually and collectively, toward the solution of problems that affect our well-being. There is a vital need for an educational approach that effectively educates man regarding his relationship to the total environment. The Supreme Court decision regarding the one-
Endometritis subclínica en ganado vacuno lechero: etiopatogenia y diagnóstico. Revisión Bibliográfica

espanolUno de los factores que determinan la rentabilidad economica de las explotaciones de vacuno lechero es la eficiencia reproductiva. Esta dependera a su vez de otros muchos factores, y dentro de estos, tienen gran relevancia las patologias uterinas. La prevalencia de alteraciones uterinas en vacas de leche es elevada y causa de numerosos fallos reproductivos. En los ultimos anos, los investigadores han mostrado un gran interes en las endometritis subclinicas dada su elevada prevalencia en el postparto del vacuno lechero, y en consecuencia, se han desarrollo metodos sencillos para su diagnostico. Sin embargo, a pesar del elevado numero de trabajos publicados al respecto en las ultimas decadas, existen todavia muchas incognitas al respecto. Por ejemplo, existen diferencias de opinion respecto al metodo de diagnostico: la citologia, la ecografia o la biopsia. En el caso de la primera, que es la mas utilizada, no hay un criterio unanime en relacion al porcentaje de polimorfonucleares neutrofilos (PMN) que deberia tomarse como punto de corte, a partir del cual se considera que una vaca padece endometritis subclinica. Esto lleva a que, dependiendo del punto de corte utilizado por los distintos autores, la prevalencia del proceso pueda ser muy variable. Por otra parte, los efectos de la endometritis subclinica sobre la reproduccion son tambien muy variables dependiendo del trabajo consultado y no esta totalmente claro como se producen. En esta revision, se abordaran estos aspectos EnglishOne of the main factors determining profitability of dairy farms is the reproductive efficiency of cows. Reproductive performance depends on many factors, being the existence of uterine pathologies one of the most relevant. Incidence of uterine diseases in dairy cattle is high and it is believed to be the cause of numerous reproductive failures. During the last years, researchers have shown great interest in subclinical endometritis because of the high incidence in the postpartum of dairy cows, and it has lead to the development of simple diagnosis methods. However, despite the high number of studies on subclinical endometritis published in the last years, many unknown aspects still exist. For example, there are different opinions concerning the best diagnosis method: endometrial cytology, uterine ultrasound or biopsy. In the case of cytology, the most used method, there is no unanimous opinion regarding the percentage of PMN that should be considered the cut-off point for diagnosing subclinical endometritis. Therefore, depending on the PMN cut off considered, the incidence of the process reported by the different authors may widely differ. On the other hand, effects of subclinical endometritis on reproduction may also differ in different studies, and it is still unclear how those effects are generated. In this review, main aspects on subclinical endometritis will be addressed.
“Hello? Are You Still There?” The Impact of Social Media on Self-Disclosure and Reciprocity in Interpersonal Relationships: A Literature Review

Social Media sites have become increasingly popular platforms for developing and maintaining interpersonal relationships. Although the usage of computer-mediated communication is normal in dayto-day life, the understanding behind how and why these relationships grow is scarce. This literature review considers relational elements such as self-disclosure and reciprocity, and how they are impacted by online elements such as an asynchronous context, controllability, and the disinhibition effect. Contrary to interpersonal relationships that develop in a physical context, the law of reciprocity is fulfilled and replaced by affirmation and recognition from relational partners, while self-disclosure continues to be a vital element within relationships. Developing an online relationship isn’t difficult, but the factors involved are varied and worth exploring in further study.