Miracle-dz/UniFAR-FTUs huggingface dataset:
Sustainable Harvesting and Conservation of Agarwood: A Case Study from the Upper Baram River in Sarawak, Malaysia

Agarwood is one of the most valuable non-timber forest products harvested from the heart of the mountains of Southeast Asian tropical rain forests. Some species of trees in the genus Aquilaria (Thymelaeaceae) accumulate resins in parts of their trunks. Agarwood has a long history as a trade good, although ecological data and economic assessments regarding agarwood harvesting in natural habitats are lacking. The author performed field surveys in the upper reaches of the Baram River in Sarawak, Malaysia, to assess the possibility of harvesting natural agarwood sustainably. In 2004, the habitat density of Aquilaria beccariana around village L was less than one tree per ha, and only relatively mature trees produced resins in their trunks. The introduction of commercial logging and hill rice cultivation damages the habitat of A. beccariana . Thus, the conservation of primary forests is essential for natural agarwood harvesting. The local Penan people only harvest the portions of the trees where resins accumulate, which allows the trees to survive. However, exploitative agarwood harvesting has begun in this area since the early 2010s, as a result of intrusions by outsiders. Thus, one cannot assume that all agarwood harvesting in Sarawak is being conducted sustainably. Meanwhile, in areas with no traces of outside intruders, the number of mature agarwood-producing trees has been maintained, suggesting that the method of agarwood harvesting used by the villagers is sustainable. To ensure that agarwood harvesting is sustainable, traceability that is based on more strictly defined and more detailed information regarding all of the steps in the agarwood supply chain is required.
Dietary means for enhanced gastrointestinal health and function in weaned pigs: An evaluation of carbohydrase enzymes targeting non-starch polysaccharides

A major challenge for the pig industry is to formulate starter diets that primarily fit the digestive capacity, maintain GIT health and promote growth without recourse to in-feed antimicrobials. Experiments were conducted to evaluate the efficacy of carbohydrase enzymes (CE) targeting non-starch polysaccharides (NSP) in enhancing gut health and function in piglets. First, an experiment was conducted to evaluate the effects of adding CE in piglet diets on growth performance, GIT bacterial activity and nutrient digestibility. Pigs fed diets containing CE had a higher ileal lactobacilli count, total organic acids concentrations, NSP digestibility and low ammonia compared with control. The effectiveness of CE targeting NSP was further evaluated using enterotoxigenic E. coli (ETEC) in a challenge model to evaluate the impact on gut health and function. Two approaches for the ETEC challenge were adopted; an in situ small intestine segments perfusion model and an in vivo model. Initially, a pilot study was conducted to establish and validate the in situ model. In the pilot study, conventional anti-diarrhea agents; fumaric acid, ZnO, egg yolk antibodies against ETEC K88 fimbriae and carbadox, attenuated fluid losses in ETEC-infected jejunal segments. Following the establishment of the in situ model, four experiments were conducted to study the effects NSP hydrolysis products (HP) from various feedstuffs (i.e. wheat, soybean meal, canola meal and flaxseed) on ETEC-induced secretory diarrhea. The results demonstrated that HP protected against ETEC-induced fluid and electrolyte losses. A further study was conducted to investigate the response of piglets fed diets containing HP and EYA singly or in combination upon oral challenge with ETEC. Feeding HP and EYA alone or in combination attenuated ETEC-enteritis symptoms such that piglets fed additives showed
Novel Functions for Neuronal RNA Processing Bodies in the Control of Axon Terminal Growth in Drosophila Melanogaster

In this thesis we first characterized neuronal functions for HPat/Pat1, a core component of RNA processing bodies or “P bodies”. We show that hpat mutants exhibit a strong synaptic hyperplasia at the developing and acutely stimulated Drosophila larval neuromuscular junctions (NMJs). The synaptic defects observed in hpat mutants are associated with rearrangement of the axonal microtubule cytoskeleton suggesting that HPat negatively regulates presynaptic microtubule-based growth during NMJ development. Interestingly, we also found that both pre-and postsynaptic HPat expression controlled rapid axon terminal growth in response to acute spaced synaptic stimulation. We also demonstrate that HPat interacts genetically with the catalytic subunit of the deadenylase complex (twin/CCR4) and the miRNA pathway (Argonaute 1) to control bouton formation. We propose that HPat is required to target mRNAs involved in the control of microtubule architecture and synaptic terminal growth for repression, presumably in P bodies, via both general and miRNA-mediated mechanisms. Next, we investigated whether HPat interacts with the Drosophila Fragile X Mental Retardation Protein (dFMR1), to regulate neuronal structure in a Drosophila melanogaster fragile X model. First, we demonstrated that HPat interacts biochemically with dFMRP in an RNAse independent manner. Second, we show that HPat genetically interacts with dFmr1 in the Drosophila eye although the phenotype is weak, however we did not see any interaction of hpat and dfmr1 to control synaptic structure at the NMJ. iii Finally, we screened additional P body components that might have function in FMRP mediated translation regulation. Interestingly, a luciferase-based translational repression tethering assays in Drosophila Schneider 2 (S2) cells showed the function of GW182 in FMRP-mediated translation regulation.
The Triple Helix -- University-Industry-Government Relations: A Laboratory for Knowledge Based Economic Development

Universities and industry, up to now relatively separate and distinct institutional spheres, are assuming tasks that were formerly largely the province of the other. The role of government in relation to these two spheres is changing in apparently contradictory directions. Governments are offering incentives, on the one hand, and pressing academic institutions, on the other, to go beyond performing the traditional functions of cultural memory, education and research, and make a more direct contribution to "wealth creation" (HMSO 1993). Governments are also shifting their relationships to economic institutions, becoming both more and less involved. In some countries with a laissez faire capitalist tradition such as the U.S. government is playing a greater role in innovation in the civilian economy (Etzkowitz 1994a) while in former socialist societies government has withdrawn from its previous position of total control of science and technology policy; adopting a stance more in accord with laissez faire principles. Multi-national institutions such as the European Union, the World Bank and the U.N. are also moving to embrace concepts of knowledge based economic development that bring the knowledge, productive and regulatory spheres of society into new configurations. In this conference, we wish to study the role of the sciences in this changing environment with a focus on the university's position in the newly emerging knowledge infrastructure.
INFLUENCE OF INTERSPECIFIC VARIATION ON TREE CARBON STOCK OF A BRAZILIAN CERRADO

http://dx.doi. org/10.1590/1806-90882017000500006 ABSTRACT – Cerrado is a biodiversity hotspot and possibly the most threatened tropical savanna in the world. Although Cerrado has an important role in the global carbon balance, studies about carbon stock in the biome are rare, especially with estimates per species. Thus, we estimated the carbon content and stock by species in a Cerrado area. We destructively sampled 120 trees from 18 species to determine tree aboveground biomass at a cerrado sensu stricto remnant. The carbon content in dry biomass was determined in laboratory and for the species not sampled an average value was used. The biomass of the remaining inventoried trees was estimated using an allometric equation. The carbon content in dry biomass had mean of 50.5 ± 0.20% and the carbon stock for the Cerrado remnant accounted for 22,385.46 kg ha. Results indicated that some species had higher carbon stock than others. The number of individuals, their size and wood density are key points that need to be considered in the evaluation of carbon stock in forests with large number of species. Maintaining species that contribute to higher carbon stock is essential to keep a positive carbon balance in Cerrado areas
Short term Toxicity Profile of ethanol extract of Solanum erianthum leaf in Rats

Introduction: Solanum erianthum is medicinal plant used by folklore all over the world. There is no studies conducted on the toxicological effect of the plant. The present study aims to evaluate the toxicological effect of methanol extract of the leaf of the plant. Methods: The Solanum erianthum leaf was evaluated for toxic effects in Sprague Dawley rats. The extract was given in three doses (125,250,500 mg/kg BW of rats) for 14 days and the effect of the extract on the behaviour and normal physiology was assessed. Results: There was no mortality caused in any of the dosage groups. It was observed that the extract not has affected the normal behaviour and caused no deleterious effect on normal physiology, at all the doses given. Extract has no effect on pattern of weight gain and was comparable to normal control group. Serum biochemical parameters also were not altered and were comparable to normal control group. Conclusion: The results and observations of study it can be proposed that the extract has no mortality and is completely non toxic to the animal system.
Genetic disorders in the growth hormone-IGF-I axis

Growth is a complex process, regulated by multiple external and internal factors. Deviation from the normal growth pattern can be one of the first manifestations of an underlying disorder, disrupting the normal growth process. The growth hormone – IGF-I axis plays a key role in regulating this growth process. This thesis focuses on growth disorders as a result of genetic defects in the GH-IGF-I axis. The aim of the thesis is to study the genotype-fenotype relationship in patients with a documented genetic defect in one of the components of the GH-IGF-I axis and to unravel the role of the GH-IGF-I axis in the complex process of growth and development throughout life. Two patients with a mutation in the GH releasing hormone receptor gene demonstrate that combined treatment of GH and gonadotropin-releasing hormone antagonists is very effective in increasing final height. The characteristics of the first male patient with a STAT5b mutation are described in detail. The fenotype of the first patient with an inactivating mutation of the IGF-I gene is described, as well as functional characteristics of the mutation. Finally the consequences of a genetic defect of the IGF-I receptor gene are discussed.
De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase

De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase. (May 2010) Sreedhar Reddy Chinnaswamy, B.V. Sc. & A.H. , University of Agricultural Sciences, Bangalore; M.V. Sc. , Indian Veterinary Research Institute; MS, New Mexico State University at Las Cruces. Co-Chairs of Advisory Committee, Dr. Cheng C. Kao Dr. Ryland F. Young Hepatitis C Virus (HCV) is a positive-strand RNA virus that has infected more than 3% of the world population. Chronic infections by the virus lead to cirrhosis and hepatocellular carcinoma. HCV is currently the leading cause for liver transplantation in the US. The nonstructural protein NS5B of HCV is the RNA-dependent RNA polymerase (RdRp) that replicates the viral RNA on host derived membranous structures. Structurally NS5B has the characteristic fingers, thumb and palm domains seen in all polymerase proteins. However, extensive interactions between the fingers and thumb domains completely encircle the active site of NS5B as seen in solved X-ray diffraction crystal structures. These interactions are primarily mediated by a short (35 residues) flexible loop called the ∆1 loop. NS5B produced from heterologous systems can initiate RNA synthesis by a de novo initiation mechanism from 3’ends of RNA templates or can also extend from 3’ ends of primers that are annealed stably to a template RNA in biochemical assays. The closed conformation of NS5B as per X-ray crystal structures can only accommodate a ssRNA but not a dsRNA, hence necessitating a conformational
Genetic diversity, conservation and evolutionary history of the African wild ass (Equus africanus): a non-invasive molecular approach

134 Introduction 134 Material and Methods 136 FCUP – Programa Doutoral em Biodiversidade, Genética e Evolução Genetic diversity, conservation and evolutionary history of the African wild ass xiii Results and Discussion 138 References 141 Chapter VI: General Discussion 6.1 General Discussion 145 6.2 Future Perspectives 151 6.3 References 152 FCUP – Programa Doutoral em Biodiversidade, Genética e Evolução Genetic diversity, conservation and evolutionary history of the African wild ass xiv
Comparative analysis of hemoglobin S and normal populations based on beta-Globin Like Gene Cluster Haplotype Variation in Denizli, Turkey; Historica l- Geographical perspectives and mutation age estimation

Aim: Our study aimed to understand the genetic origin of Hb S based on comparative analysis with normal population haplotype data in the Denizli province of Turkey. Materials and Methods: We performed data obtained from previously published articles. We studied DNA samples from 12 unrelated patients with heterozygous abnormal hemoglobin S (Hb S) and 59 unrelated healthy subjects from published articles. The association of population genetic parameters such as haplotypes, diversity, differentiation, HWE and demographic analysis for two populations were performed by latest version of the Arlequin software (ver. 3.5). Results: Our results show that normal and Hb S populations have different genetic parameters based on haplotype diversity through the history. The obtained results are highly associated with frequency haplotype [+ ---+ + +] (20.8%) in the Hb S population and the Mediterranean haplotype I [+ ----+ +] (14.4%) in the Normal population. According to historical population growth and mutation age parameter of τ values for normal and Hb S populations dated approximately 42,000 to 26,000 ybp, respectively. Conclusions: Historically, two populations exhibit different genetic parameters and unimodal growth distribution. Our results are consistent with the Hb S mutation which occured in this region about 26,000 years ago.
Spatial extinction date estimation: a novel method for reconstructing spatiotemporal patterns of extinction and identifying potential zones of rediscovery

The estimation of extinction dates from limited and incomplete sighting records is a key challenge in conservation (when experts are uncertain whether a species has gone extinct) and historical ecology (when the date and mechanism of extinction is controversial). We introduce a spatially-explicit method of interpolating extinction date estimators, allowing users to estimate spatiotemporal surfaces of population persistence from georeferenced sighting data of variable quality. We present the R package spatExtinct, which produces spatially-explicit extinction date surfaces from geolocated sightings, including options for custom randomization schemes to improve accuracy with limited datasets. We use simulations to illustrate the sensitivity of the method to parameterization, and apply the method to identify potential areas where Bachman’s warbler (Vermivora bachmanii) might be rediscovered. Our method, and the spatExtinct package, has the potential to help describe and differentiate different drivers of extinction for historical datasets, and could be used to identify possible regions of population persistence for species with an uncertain extinction status, improving on non-spatial or imprecise methods that are currently in use.
Lactobacillus pentosus en la alimentación animal. Artículo de revisión.

Esta revision tuvo el objetivo de evaluar la participacion de Lactobacillus pentosus en la esfera de la produccion de alimentos. Se consultaron revistas especializadas en la produccion avicola y otras relacionadas con la produccion animal en general, cuyo descriptor principal fue Lactobacillus. Se constato que L. pentosus es una especie versatil encontrada en varios nichos; presentes tambien en la preparacion de muchos alimentos fermentados y en la secrecion de diversas sustancias de caracter antimicrobiano. La especie, ademas, contribuye a disminuir la contaminacion ambiental. Existen pocas investigaciones sobre su participacion en la produccion agropecuaria de carne y aves. Lactobacillus pentosus in Animal Feeding. Review . ABSTRACT This review aimed to assess the involvement of Lactobacillus pentosus in the field of food production. Journals specialized in poultry and animal production in general were reviewed. The main descriptor used was Lactobacillus. It was found that L. pentosus is a versatile species found in a variety of environmental niches, which has a significant presence in the preparation of many fermented foods; also in the secretion of various substances of antimicrobial character, and it contributes to reduce environmental pollution. There are very few researches on the participation of L. pentosus in the agricultural production of meat and poultry.
DEGRADABILITY OF MYCOTOXINS USING IN VITRO METHOD

Barley is classified as one of the most important cereals in the Czech Republic. Fusarium Head Blight (FHB) is a worldwide grain disease caused by microscopic filamentous Fusarium fungi, infecting crops in the course of vegetation. The following mycotoxin levels such as nivalenol, deoxynivalenol, 3-acyl-deoxynivalenol, 15-acetyldeoxynivalenol, deoxynivalenol-3-glukosid, betazearalenon, zearalenon, alternariol-methylether, enniatin (B, B1, A, A1), HT-2 toxin were determined in this study. It was based on the hypothesis that the enzyme preparations can eliminate the occurrence of mycotoxins. In vitro method called Daisy II was used in this study. All monitored parameters were significantly reduced. The aim was to create an alternative method for mycotoxin degradation using in vitro method.
Invaders among locals: Alien species decrease phylogenetic and functional diversity while increasing dissimilarity among native community members

Plant invasions can drastically change the structure of native communities, but it is not fully understood whether alien species occupy phylogenetic and functional space within the range occupied by natives, or provide a novel set of evolutionary origins and traits to the invaded communities. Here, we evaluated this open question with data on a large number of plant communities from different terrestrial habitats. We used ~27,000 vegetation plots from 26 terrestrial habitats in the Czech Republic and compared phylogenetic and functional diversity (PD and FD, respectively) and community trait means in invaded and non‐invaded plots. We tested for differences (1) between invaded vs. non‐invaded plots, (2) among natives in invaded vs. non‐invaded plots, and (3) in invaded plots only, with and without aliens. To minimize habitat filtering effects on PD and FD, we ran these tests within the habitat‐specific species pools of the 26 vegetation types. In general, PD, FD and trait mean values changed with invasion, with changes being rather consistent across the habitats considered. Invaded plots were less phylogenetically, but more functionally diverse than non‐invaded plots. The greater FD in invaded plots, compared to non‐invaded ones, was due to greater dissimilarity between natives. In fact, native species in invaded plots showed higher PD and FD than native species in non‐invaded plots, while alien species reduced PD and FD in invaded plots. Changes in the trait means with invasion were due to differences in native species in invaded and non‐invaded plots, rather than to an effect of alien species. Within most habitats, the trait means and variance of all aliens were similar to those of all natives, while in some habitats, the variability in traits was greater between aliens that belonged to phylogenetically closer clades. Synthesis. Our results suggest that alien species more often occupy a phylogenetic and functional space within the range formed by the native species in a community. They do so either by filling empty gaps or by excluding natives from the existing phylogenetic and functional space, rather than occupying or creating a phylogenetic and trait space outside of it.
First record of a ctenophore in lakes: the comb-jelly Mnemiopsis leidyi A. Agassiz, 1865 invades the Fayum, Egypt.

In 2013, the invasive marine ctenophore Mnemiopsis leidyi was first recorded in a true lake, Birket Qarun in the Fayum, Egyptian Desert. In 2014, it expanded in numbers and was also recorded in lake El Rayan II, south of Birket Qarun. Both lakes are saline, with Birket Qarun currently more concentrated than seawater. In the hot summer of 2015, a huge mortality was recorded, with only few larvae surviving. Whereas previous invasions were made possible by transportation in ship ballast water, trucks transporting mullet fry from aquaculture facilities in the Nile Delta to Birket Qarun and Lake Rayan II triggered the Fayum invasion. This is the first ever record of a ctenophore in an inland environment. We do not expect this invasion to be permanent, but it may damage the lake fisheries in the years ahead.
The bud midge Prodiplosis floricola in citrus crops in Colombia

Sampling performed in flower buds of citrus in Colombia allowed the detection of the presence of Prodiplosis longifila Gagné and Prodiplosis floricola Felt (Diptera: Cecidomyiidae). The polyphagous P. longifila is a pest of Solanaceae, but whether both species cause economic losses in citrus is unknown. These congeneric species are indistinguishable in the larval stage, and their morphological identification, which is complex, is performed on adult males. This study comprises a morphological description and characterization of the damage generated by P. floricola larvae feeding on the flowers of key lime, Citrus × aurantiifolia (Christm.) Swingle (pro. sp.), and Tahiti lime, Citrus × latifolia Tanaka ex Q. Jiménez (Rutaceae), as well as a population genetical analysis of the insect. Prodiplosis floricola was found in the localities of Támesis (Antioquia), Garzón (Huila), and Palmira and Zarzal (Valle del Cauca). These populations were characterized by COI and ITS2 molecular markers, with a moderate genetic structure found that cannot be explained by the geographic distance between the populations. The haplotype distribution pattern indicates that the populations are composed of highly differentiated haplotypes of equivalent frequencies, which suggests that the Colombian populations of P. floricola are products of multiple introductions and that their dispersion between populations is attributable to anthropic transport. Citrus in Colombia constitutes a new host for P. floricola and increases the known geographical range of the insect, as it has only been previously reported in Brazil and the USA. The molecular markers used in the present study are useful for early diagnosis of P. floricola in the larval stage and for future research on the population dynamics in citrus.