Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the phenotype of aggressiveness

Mixing together unfamiliar pigs is a common husbandry practice in commercial indoor piggeries that causes a period o f intense fighting and aggression between pigs, resulting in elevated stress responses and injuries to those involved. Frequency, duration and intensity of aggressive behaviour have been found to differ between individuals. There is some evidence that these differences are due to trait-aggressiveness, as consistency o f responses to similar challenges has been demonstrated. This trait-aggressiveness may be linked to other behavioural (social and non-social) and physiological traits to fonn part o f personality. To understand aggression in the context o f behavioural trait the prevalence o f aggression was studied throughout the lifetime o f a cohort o f pigs, examining consistency within and between situations at numerous points. M ore specifically, the aims o f this thesis were to investigate: whether the relative magnitude of aggression displayed in response to a repeated social challenge test (Resident Intruder Test) was consistent over time; if this aggressiveness changed with age and experience; whether RIT aggressiveness was comparable to, or predictive o f aggressiveness during social mixing; what strategies were employed by pigs of differing aggressiveness during mixing; and finally, if aggressiveness was linked to the response o f individual pigs to a challenging environment, unconnected to social confrontation (maternal behaviour). Detailed behavioural analysis was performed on the progeny o f 19 gilts. Consistency of aggressiveness was examined using repeated Resident Intruder Tests at various key stages during the lifetime o f male and female growing pigs, and a subset o f female breeding pigs. Behaviour during mixing at weaning and as gilts was examined in detail; information was collected about the way in which these animals behaved in a social context, including nonaggressive social behaviour, and how this related to injuries received (lesions). As social dominance status is often cited as a parameter related to aggressiveness, this was recorded at various stages using a group feeding competition test and compared to behavioural measures from mixing and the RIT. To gain a better understanding o f the interaction between aggressiveness and other traits, the various measures o f aggressiveness were compared with cortisol (as a physiological indicator o f the relative stress responses o f individuals) and the behaviour o f a subset o f female pigs in the period immediately preceding and following farrowing. Maternal behaviour was chosen for comparison to aggressiveness as it is also potentially a trait-behaviour, specific to individuals, that is not obviously linked to social
Hybridization in Four Nigerian Physalis (Linn.) Species

Interspecific reciprocal crosses among four Nigerian Physalis species (Physalis angulata, P. micrantha, P. pubescens and P. peruviana) were carried out by transferring desired pollen grains to ovalate parents, bagged and labelled to prevent contamination by external pollen grains and for easy identification. Pollen cells of the F1 hybrid combination from the only viable cross (P. angulata x P. pubescens) were studied using standard cytogenetic techniques. The F1 hybrid obtained in the current investigation produced few flower buds and no matured fruit was harvested. Its average pollen grain diameter was found within the range of that of the two genitors and the pollen stainability was less than 50%. The hybrid was also characterized by meiotic irregularities. Based on the results obtained, the study concluded that P. pubescens is closely related to P. angulata and P. peruviana, while P. micrantha is more distant from them since the formal individuals were able to cross reciprocally among each other, though no matured fruit was produced except in one cross (P. angulata x P. pubescens).
REGULADORES DEL CRECIMIENTO Y SUSTRATOS EN LA PROPAGACIÓN VEGETATIVA DE NANCHE (Malpighia mexicana A. Juss. y Byrsonima crassifolia (L) H. B. K.)

El nanche es un frutal que produce gran parte del ano y del que poco se conoce sobre su propagacion asexual; por ello, el objetivo de esta investigacion fue evaluar el efecto de sustratos, enraizadores y tipo de estacas en la propagacion vegativa de nanche rojo, rosa y amarillo, recolectadas en Santa Maria Zoquitlan, Oaxaca, Mexico.
Microfluidic pathogen detection, based on continuous bead beating. DNA concentration and aliquoting for multiplex qPCR detection

El objetivo de este trabajo es la deteccion de agentes patogenos por medio de su ADN en un sistema microfluidico que funciona de forma automatica. El sistema consta de tres pasos: en el primero se lisan los microorganismos para extraer su ADN. En el segundo, el ADN extraido se concentra gracias a particulas magneticas. De esta forma, por un lado se consigue mejorar la sensibilidad de la deteccion y por otro se deshacen los restos celulares originados en el paso previo. Por ultimo, el extracto se divide en dos alicuotas y el ADN se detecta en paralelo utilizando la tecnica de qPCR. Mediante la deteccion en paralelo, se pueden hacer medidas en duplicado o bien detectar dos patogenos a la vez.
Bearing the brunt: Mongolian khulan (Equus hemionus hemionus) are exposed to multiple influenza A strains

The majority of influenza A virus strains are hosted in nature by several Anseriformes and Charadriformes birds. A minority of strains have been able to cross species boundaries and establish themselves in novel non-avian hosts. Influenza viruses of horses, donkeys, and mules represent successful cases of avian to mammal influenza virus adaptation. Mongolia has over 3 million domestic horses and is home to two wild equids, the Asiatic wild ass (Equus hemionus hemionus), and Przewalski horse (Equus ferus przewalskii). Domestic and wild equids are sympatric across most of their range in Mongolia. Epizootic influenza A virus outbreaks among Mongolian domestic horses have been frequently recorded. However, the exposure, circulation and relation to domestic horse influenza A virus outbreaks among wild equids is unknown. We evaluated serum samples of Asiatic wild asses in Mongolia for antibodies against influenza A viruses, using a serological assay. We detected antibodies against hemagglutinin (H) H1, H3, H5, H7, H8 and H10 influenza A viruses. Asiatic wild asses may represent a previously unidentified influenza A virus reservoir in an ecosystem shared with populations of domestic horses in which influenza strains circulate.
The axon initial segment drives the neuron’s extracellular action potential

Extracellular voltage fields produced by a neuron’s action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron’s soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology. Key points summary The neuron’s soma and dendrites are thought to give rise to its extracellular voltage signal, while signals from the axon are usually considered negligible. Instead, we found that the largest amplitude of the extracellular signal originates from the axon initial segment, not from the soma. This finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology. Abbreviations ACSF artificial cerebrospinal fluid AIS axon initial segment AnkG ankyrin-G CMOS complementary-metal-oxide-semiconductor DMEM Dulbecco’s modified eagle medium EAP extracellular action potential GAD67-GFP glutamic acid decarboxylase 67-green fluorescent protein MAP2 microtubule-associated protein 2.
The development and application of a transposon insertion sequencing methodology in Escherichia coli BW25113

Escherichia coli is one of the most studied model organisms in biology. Even with decades of research, there are a substantial number of genes with an as yet unknown function. Previously, to determine the link between gene function and phenotype took significant experimental effort. However, newer methods are capable of providing large amounts of biological data in short timeframes. One such method, transposon insertion sequencing, is a powerful research tool, which couples transposon mutagenesis and next generation sequencing to identify genes that have important or essential functions. Here, three transposon insertion sequencing methods were compared. The techniques were adapted from previously published literature. Based on a number of metrics one technique was shown to be superior for data generation. This method was chosen for application in further transposon-insertion sequencing experiments. Subsequently, the optimised method was used to assess which genes were essential for the viability of the model organism E. coli K12. The results of this work were compared with the literature and other databases of gene essentiality. A high degree of concordance was observed between our datasets and those generated previously through other methods. Indeed, the method described here was shown to have several benefits over previously used approaches. Finally, genes involved with maintenance of the outer membrane were identified by using markers for membrane permeability in tandem with the chosen method. In keeping with previous literature multiple genes involved with many aspects of the cell envelope were reported. Many of the reported genes were shown to be involved with metabolic processes related to the biogenesis and maintenance of the cell envelope.
Xenotropic Murine leukemia virus-related virus (XMRV) in Iranian HIV Patients

Background and Aims: Despite isolation of Xenotropic murine leukaemia related virus (XMRV) from the patients with prostate cancer in 2006 and patients with chronic fatigue syndrome in 2009, there have been controversial findings about its potential role in human diseases and frequencies in different population groups. The aim of this study was to determine the frequency of XMRV genome in Iranian HIV-infected patients for the first time. Materials and Methods: We performed a cross-sectional study on the prevalence of XMRV nucleic acid among 150 patients diagnosed with HIV infection in Tehran’s hospitals. After extracting the viral RNA from plasma samples, nucleic acid was amplified by Real-Time PCR using XMRV specific primers. HIV viral load testing was performed for all of the patients as well. Results: Out of 150 patients, XMRV RNA was found in 13 (8.6 %) of patient's specimens, including 9 males (69/2%) and 4 females (30/8%). Average HIV viral load was 14471.92 and 17016.66 copies/ml in positive and negative XMRV patients, respectively. Conclusions: Our results showed the presence of XMRV infection in HIV-infected patients. No other significant association was observed between XMRV with gender, age and HIV viral load of the patients. However, more studies are needed to demonstrate the actual prevalence of XMRV infection by geographical regions and different populations.
TARGET ANALYSIS BY FOCUSING ELLIPSOMETRY

Reflection ellipsometry is a proven optical measurement method often used to measure film thicknesses. Classical ellipsometers use an unfocused measurement beam, which causes a low lateral resolution in the order of 1 mm. To determine microstructures ellipsometrically (e.g. in the semiconductor industry), an improved lateral resolution in the order of micrometers is essential. We discuss the problems of focusing ellipsometry, occurring when a reflection ellipsometer is used to measure surface characteristics (topography, material). Different measurement setups are analyzed and compared. Simulating calculations show that particularly the measured values of the phase difference ∆ are influenced by beam focusing. This leads to errors particularly in the attenuation index k of the surface material.
The tryptophan salvage pathway is dynamically regulated by the iron-dependent repressor YtgR in Chlamydia trachomatis

Mammalian hosts restrict cellular nutrient availability to starve invading pathogens and successfully clear an infection by a process termed ″nutritional immunity″. For the obligate intracellular pathogen Chlamydia trachomatis , nutritional immunity likely encompasses the simultaneous limitation of the amino acid tryptophan and the essential biometal iron. Unlike other model bacteria, C. trachomatis lacks many global stress response systems, such as ″stringent response″ homologs, adapted to these host insults. However, a physiological response by Chlamydia that is common to both stresses is the development of an aberrant, ″persistent″ state, suggesting that tryptophan and iron starvation trigger a coordinated developmental program. Here, we report that the trpRBA operon for tryptophan salvage in C. trachomatis serovar L2 is regulated at the transcriptional level by iron. The expression of the tryptophan synthase encoding genes, trpBA , is induced following iron limitation while that of the repressor trpR is not. We show that this specific induction of trpBA expression initiates from a novel promoter element within an intergenic region flanked by trpR and trpB . YtgR, a DtxR-homolog and the only known iron-dependent transcriptional regulator in Chlamydia , can bind to the trpRBA intergenic region upstream of the alternative trpBA promoter to repress transcription. This binding also likely attenuates transcription from the primary promoter upstream of trpR by blocking RNA polymerase read-through. These data illustrate a dynamic and integrated method of regulating tryptophan biosynthesis in an iron-dependent manner, which has not been described in any other prokaryote, underscoring the uniqueness of Chlamydia .
Treatment of benign prostatic hyperplasia with finasteride: Evidence from a meta-analysis

Purpose : To clarify the usefulness and safety of finasteride in the treatment of patients with benign prostatic hyperplasia (BPH) compared to placebo group or controls. Methods : In a meta-analysis, PubMed and Web of Science were searched to include relevant studies. The results were combined with a random effect model. Publication bias was evaluated using Egger regression asymmetry test. Results : Fourteen publications involving 17,364 patients were included in the study. Pooled results indicated that International Prostate Symptom Score (IPSS) in the finasteride group was lower [weighted mean difference (WMD) = -0.77, 95% CI= -0.97 to -0.57] compared to the placebo group. The usefulness of finasteride was higher in total prostate volume (TPV) [WMD= 0.13, 95%CI= 0.00 to 0.26] but lower in serum DHT [WMD= -1.18, 95%CI= -1.51 to -0.86] when compared to the placebo group. Drug-related adverse event was higher in the finasteride treatment group when compared to placebo group [summary RR= 1.95, 95%CI= 1.31-2.90]. Conclusion : Finasteride could improve the symptom score (IPSS and TPV) and reduce serum DHT. However, the potential adverse events, especially the drug-related adverse events in Finasteride treatment should be attention. Keywords : Benign prostatic hyperplasia, Finasteride, Meta-analysis
The pre-Linnaean herbarium of Paolo Boccone (1633–1704) kept in Leiden (the Netherlands) and its connections with the imprinted one in Paris

Abstract The subject of this paper is the study of the pre-Linnaean herbarium of Paolo Boccone (1633–1704) which is kept in Leiden (the Netherlands) and its connections with two works of the same author: the imprinted herbarium kept in Paris in the Bibliothèques Interuniversitaires de Médecine and the printed volume “Icones et Descriptiones” of 1674. By means of the comparative analysis of the three works we have verified the existence of numerous similarities (even a complete overlap) between the samples of the Leiden herbarium (some with visible traces of ink), the imprints of the Paris herbarium and the figures of “Icones et Descriptiones”. The drawings to be found in this work, thanks to the realistic fidelity that distinguishes them, have been used by various authors until quite recent times for the description of new taxa. This shows the importance and the usefulness of the herbarium in question for the processes of typification. The taxonomic identification of the specimens (121 angiosperms and 1 alga) allowed us to designate the lectotype and the epitype of Daucus gingidium subsp. polygamus (Gouan) Onno and of Daucus carota subsp. commutatus (Paol.) Thell.
What proteomic analysis of the apoplast tells us about plant–pathogen interactions

A. P. Mart ınez-Gonz alez, H. D. Ardila* , S. T. Mart ınez-Peralta, L. M. Melgarejo-Mu~ noz, M. A. Castillejo-S anchez and J. V. Jorr ın-Novo Laboratory Research in Vegetal Metabolic Activities, Department of Chemistry, Faculty of Science, Universidad Nacional de Colombia; Laboratory of Plant Physiology and Biochemistry, Department of Biology, Faculty of Science, Universidad Nacional de Colombia, Cra. 30 No. 45-03, Bogot a, Colombia; and Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of C ordoba, Agrifood Campus of International Excellence (ceiA3), C ordoba, 14071, Spain
The ongoing invasion of translocated sleepy cod (Oxyeleotris lineolata) in the Lake Eyre Basin, central Australia

Abstract Context. Present-day distribution records show that Oxyeleotris lineolata (sleepy cod) has colonised many ephemeral streams and refugial waterholes of the Cooper Creek catchment in the Lake Eyre Basin within a decade of the first record or capture. When introduced to new habitats outside its natural range, this species is considered to be a serious conservation risk to native fish species. Aims. The present study aims to document the transport, establishment, colonisation and integration of O. lineolata in the Lake Eyre Basin, and quantify its impact on native fish assemblages. Methods. Fish samples were taken annually in 21 waterholes between 2011 and 2016, by using a combination of single- and double-winged fyke nets. We collected novel diet and life-history information from 242 O. lineolata individuals across their known distribution. Key results. Abundance, length distribution and life-history information suggested a ‘colonising front’ moving downstream, across state jurisdictional boundaries and into the Coongie Lakes Ramsar site. Oxyeleotris lineolata diet is most similar to that of two native generalist invertivore–piscivores and preys on several native fish species. With a derived longevity in excess of 15 years and a life-history strategy that combines batch spawning, high fecundity and parental care (i.e. high juvenile survivorship), there is real potential for O. lineolata to dominate fish assemblages in waterholes that provide refuge for native fishes during dry periods. Conclusions. The present study showed that O. lineolata has the potential to negatively influence native fish assemblages through both competition and predation in refugial waterholes. Eradication of O. lineolata from the Cooper Creek catchment in central Australia is highly unlikely, given its widespread distribution, the remoteness of the receiving landscape and a current lack of resources to monitor spread and attempt eradication at the moving front of the Cooper Creek population. Implications. Achieving greater awareness of the potential impacts of introducing or spreading non-native species is an important first step towards preserving the native fish fauna of the Lake Eyre Basin. Further research is warranted to fully understand the current and potential future distribution of O. lineolata in the basin, its biological and ecological requirements, and influence on native fish species and assemblages.
Advanced Design of a Full-Scale Active Morphing Droop Nose

This paper describes the design of a morphing droop nose conceived to increase the performance in high-lift conditions of a twin-prop regional aircraft, while ensuring the natural flow laminarity of the wing. Starting from the results obtained in a previous phase, mainly concerned with the performance augmentation, a detailed structural design is conducted. The main aim is the achievement of a feasible solution based on the use of conventional materials, such as aluminium alloy for the internal structure and glass-fibre for the skin. A finite element model of the complete device is generated for the three-dimensional shape quality evaluation and for the skin structural verification. Stress analyses on high-fidelity models of the single adaptive ribs are also performed. At the same time, various design aspects are evaluated, such as installation and inspection issues, actuation power, and weight considerations. All these requirements contribute to the definition of an advanced and complete solution for the device, up to the realization of a detailed CAD model. Final verification on the virtual prototype assesses the functionality of the device when attached to the wing-box. Moreover, the bird impact safety of the leading edge is demonstrated according to the certification rules.
Complete mitochondrial genome of Bombus breviceps (Hymenoptera: Apidae)

Abstract The complete mitochondrial genome of Bombus breviceps, which belongs to the subgenus of Alpigenobombus in Bombus genus, was sequenced. This circular mitogenome is 16,743 bp (83.5% AT) in length, with two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. All protein-coding genes are initiated with the common invertebrate initiation codon except TTA for ND2, and terminated by the typical stop codon TAA or TAG. tRNA-Ser (TCT) lacks a dihydrouridine (DHU) arm while other tRNA genes form a cloverleaf structure. Phylogenetic analysis shows that genus Bombus has a closer relationship with genus Melipona than any other genera in Apidae family, and B. breviceps clusters closer to B. lapidarius than any other bumblebees with sequenced mitogenome.
Effect of Oxalic Acid on Sensory Evaluation of ‘Gola’ Ber (Ziziphus mauritiana Lamk.) Fruit during Storage

Ber (Ziziphus mauritiana Lamk.) is an important fruit of arid and semi-arid regions. Native place of Z. mauritiana is central Asia (Morton, 1987). It belongs to the Rhamnaceae family. Ber fruit is very perishable during storage at room temperature due to rapid ripening and high susceptibility. Fresh ber fruits deteriorate fast and cannot be kept for more than 5 days under ambient conditions without serious deterioration (Kadam et al., 1993), even though some improved cultivars in India are known to store for up to 15 days without loss of organoleptic quality (Pareek, 2001).