Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental Economics: An Elementary Introduction

1.The big economy 2.Environment and ethics 3.Economic growth, population growth and the environment 4.Sustainable development 5.How markets work and why they fail 6.How governments fail the environment 7.Cost-benefit thinking 8.Valuing concern for nature 9.Coping with uncertainty 10.Using the market to protect the environment 11.Charging for the use of the environment 12.Green taxes 13.Trading environmental permits 14.Setting environmental standards 15.Renewable resources 16.Non-renewable resources 17.Business and the environment 18.Managing waste 19.Climate change 20.Economics and the ozone layer 21.Conserving biological diversity 22.International enivornmental policy: acid rain 23.Environment in the developing world
Are 2D space-use analyses adapted to animals living in 3D environments? A case study on a fish shoal

Lay Summary The way space and resources are shared within a group of animals reveal key aspects of the behavioral ecology of gregarious species. For species using space in 3D, multidimensional analysis would be necessary to accurately describe patterns of spatial partitioning between group-members, however, such analyses are scarce. We used a group of wild fish to test the relevance of multidimensional analysis when space-use is used to infer the feeding behavior of group-members.
Two new species of Dilaridae (Insecta: Neuroptera) with additional notes on Brazilian species

Herein we describe two new species of lacewing in the family Dilaridae from northeastern Brazil: Nallachius furcatus, n. sp. and N. potiguar, n. sp. We also describe range expansions for three species: N. adamsi Penny, 1982 from Manaus to the border of the states of Amazonas and Para; N. dicolor Adams, 1970 from the state of Santa Catarina to the states of Goias and Minas Gerais; N. limai Adams, 1970 from Santa Catarina to Parana. An identification key to adults and a checklist of Brazilian species are presented.
A new melanistic variant of the caterpillar hunter Calosoma wilcoxi LeConte, 1848 from Texas, United States of America and a preliminary phylogeny of the genus Calosoma Weber, 1801 (Coleoptera: Carabidae)

Abstract Two aberrant ground beetle (Coleoptera: Carabidae) specimens from the genus Calosoma Weber, 1801 were collected in Waco, Texas, United States of America, in 2012–2013. The specimens, which are morphologically most similar to Calosoma wilcoxi LeConte, 1848, but are dark blue-black instead of the typical metallic green. We employed DNA barcoding and phylogenetic methods to confirm the identities of the aberrant specimens. Preliminary phylogenetic analyses of cytochrome oxidase subunit 1 (COI) sequences of central Texas and southwestern species place the aberrant specimens with 100% confidence as C. wilcoxi. The new variant of C. wilcoxi presumably occurs at low densities. Frequent collecting from 2011 to 2014 resulted in the discovery of only two of the aberrant coloured individuals among hundreds of typical green specimens. These specimens (to our knowledge) represent the first published record of melanistic Calosoma from North America. While the majority of North American species in the genus are naturally black, two of the most widely distributed and abundant species, C. scrutator (Fabricius, 1775) and C. wilcoxi, are typically green. We sequenced the aberrant form as well as all species co-occurring with the new colour morph at the collection locality and used records from GenBank and the Barcode of Life Data System to generate a preliminary phylogeny of the genus, which suggested that some of the currently established subgenera are likely not monophyletic.
Maintaining Biodiversity in Forest Ecosystems: Contents

Foreword J. Ward Thomas Preface Part I. Introduction: 1. Biological diversity M. Hunter 2. Principles of ecological forestry R. Seymour and M. Hunter Part II. The Macro Approach, Managing Forest Landscapes: 3. Species composition B. Palik and R. Engstrom 4. Dynamic forest mosaics T. Spies and M. Turner 5. Abiotic factors A. Hansen and J. Rotella 6. Forest edges G. Matlack and J. Litvaitis 7. Islands and fragments Y. Haila 8. Riparian zones M. Brinson and J. Verhoeven 9. Forested wetlands A. Calhoun Part III. The Micro Approach, Managing Forest Stands: 10. Dying, dead and down trees W. McComb and D. Lindenmayer 11. Vertical diversity N. Brokaw and R. Lent 12. Production silviculture S. Moore and H. Lee Allen 13. Special species I. Thompson and P. Angelstam 14. Genetic diversity C. Millar Part IV. Synthesis and Implementation: 15. Restoration ecology L. Frelich and K. Puettman 16. Forest reserves D. Norton 17. Forest organization, management and policy C. Oliver, M. Boydak, G. Segura and B. Bare 18. The economic perspective B. Lippke and J. Bishop 19. Social perspectives L. Maguire Taxonomic index Author index, Subject index.
Cold-induced changes in mineral content in leaves of Coffea spp. Identification of descriptors for tolerance assessment

Temperature and mineral nutrition are major environmental factors regulating plant growth and development. Yet, cold impact on mineral contents and the ability of the plants to perform changes in specific elements as a part of the acclimation process received little attention. Using five Coffea genotypes previously characterized concerning their cold sensitivity, a mineral analysis was performed considering macro (N, P, K, Ca, Mg, and S) and micro (Na, Fe, Mn, Zn, Cu, and B) nutrients in order to predict their importance in cold tolerance. The results showed a cold-induced dynamics of mineral nutrients in recently mature leaves. The less cold sensitive Icatu and partially Catuai accumulated N, Ca, Mn, Cu, and Zn with potential implications in the maintenance of photosynthetic performance, the reinforcement of the antioxidative defense system, lipid metabolism, and the expression of cold regulated genes, thus constituting interesting traits to evaluate the cold acclimation ability. After a principal component analysis (PCA), N, Fe, Mn, and Cu were further confirmed as strong candidates for an early cold tolerance evaluation due to their dynamics and to specific roles in the activities of superoxide dismutase (Cu), ascorbate peroxidase (Fe), and photosystem II (Mn).
Effect of Omega-3 fatty acids enrichment on performanceand carcass traits of broiler chicken

The experiment was conducted to study the effect of omega-3 fatty acids on performance, carcass traits of broiler chicken. For this purpose, 280 day-old commercial male broiler chicks were randomly divided into seven dietary groups with eight replicates of five birds each (7x8x5) and reared in battery brooders up to 42 days of age following standard management and vaccination schedule. The birds were offered with corn-soya based broiler pre-starter (0-11 days), starter (12-21 days) and finisher (22-42 days) diets. The control diet (T1) was prepared with sunflower oil and diets for remaining treatment groups (T2- T7) were formulated by replacing sunflower oil with different levels of linseed oil and fish oil. The experimental design consists of T1 - Control diet with sunflower oil, T2 - linseed oil @ 33% of sunflower oil, T3 - linseed oil @ 67% of sunflower oil, T4 - linseed oil @ 100%, T5 - fish oil @ 33% of sunflower oil, T6 - fish oil @ 67% of sunflower oil and T7 - fish oil @ 100%. The performance of broiler chicken was evaluated in terms of weekly body weight gain (WBWG) and Feed consumption (FC) as influenced by the supplementation of various levels of Linseed and fish oil. At the end of experiment (42nd day) one bird from each replicate (8 birds per treatment) was randomly selected for estimating slaughter parameters. Significant (P 0.05) influenced whereas, FCR was significantly (P<0.05) influenced. The Carcass traits like dressing yield, breast yield, liver and giblet percentage were not influenced, whereas abdominal fat percentage was significantly (P<0.05) influenced by the inclusion of n-3 fatty acid sources. The study indicated that supplementation of n-3 FA (LO or FO) sources at the level of 3.9 per cent did not cause any adverse effects on performance of broilers, carcass characteristics of meat in addition to decrease in abdominal fat percent.
Maintaining Healthy Population Diversity using Adaptive Cro ssover, Mu tation and Se lection (ACROMUSE)

This paper presents ACROMUSE, a novel Genetic Algorithm (GA) which adapts crossover, mutation and selection parameters. ACROMUSE's objective is to create and maintain a diverse population of highly-fit (healthy) individuals, capable of adapting quickly to fitness-landscape change and well-suited to the efficient optimisation of multimodal fitness landscapes. A new methodology is introduced for determining Standard Population Diversity (SPD) and an original measure of Healthy Population Diversity (HPD) is proposed. The SPD measure is employed to adapt crossover and mutation, while selection pressure is controlled by adapting tournament size according to HPD. In addition to selection pressure control, ACROMUSE tournament selection selects individuals according to healthy diversity contribution rather than fitness. This proposed selection mechanism simultaneously promotes diversity and fitness within the population. The performance of ACROMUSE is evaluated using various multi-modal benchmark functions. Statistically significant results are presented comparing ACROMUSE's fitness and diversity performance to that of several other GAs. By maintaining a diverse population of healthy individuals, ACROMUSE responds to fitness-landscape change by restoring better fitness scores faster than other GAs. Analysis of the adaptive operators illustrates that the key benefit of ACROMUSE is the synergy of the operators working together to achieve an effective balance between exploration and exploitation.
PREDIKSI STRUKTUR 2-DIMENSI NON-CODING RNA DARI BIOMARKER KANKER PAYUDARA TRIPLE-NEGATIVE DENGAN VIENNA RNA PACKAGE

Berdasarkan data WHO, kanker adalah penyakit yang paling berbahaya. Dewasa ini para peneliti sedang berusaha memahami mekanisme molekular kanker. Berdasarkan dogma sentral, hanya protein coding gene yang diketahui fungsinya, sementara non-coding gene belum dapat dijelaskan. Kemudian, diketahui bahwa non-coding RNA (ncRNA) berperan dominan dalam regulasi molekular sel, sehingga berpengaruh secara langsung kepada proliferasi kanker. Dalam hal ini, instrumen RNA-seq maupun Tiling Array sudah mengumpulkan banyak data biologis dan mendeposisikannya kepada database genom. Diketahui bahwa, ncRNA tidak hanya dapat berperan sebagai biomarker untuk diagnostik kanker, namun juga akan dapat dikembangkan sebagai agen terapeutik. Kanker payudara memiliki empat subtipe molekular, yaitu luminal A , luminal B , Her-2 dan triple negative/basal-like . Kanker Payudara Triple-negative (TNBC) merupakan penyakit yang sangat berbahaya dan belum ditemukan pengobatan yang efektif. Memahami mekanisme dan struktur ncRNA pada Biomarker TNBC merupakan langkah awal untuk menentukan agen terapeutik dan propilaksis terbaik. Diketahui bahwa jalur ekspresi lincRNA-RoR/miR-145/ARF6 berperan dalam proliferasi TNBC. Berdasarkan pencarian di GenBank , ditemukan lema-lema ncRNA untuk jalur tersebut. Hasil pencarian diolah dengan software Vienna RNA Package , untuk ditentukan struktur 2 dimensi (2-D) yang solid. Kedepannya, diharapkan dengan mencegah terbentuknya struktur 2-D tersebut, maka semua gen tersebut akan menjadi tidak aktif dan menghentikan proliferasi kanker.
Common Raven (Corvus corax) kleptoparasitism at a Golden Eagle (Aquila chyrsaetos) nest in southern Nevada

ABSTRACT. — The Common Raven (Corvus corax) is a ubiquitous species in the Mojave Desert of southern Nevada and California. From 5 to 24 May 2014, using remote trail cameras, we observed ravens repeatedly kleptoparasitizing food resources from the nest of a pair of Golden Eagles (Aquila chyrsaetos) in the Spring Mountains of southern Nevada. The ravens fed on nine (30%) of the 30 prey items delivered to the nest during the chick rearing period. Kleptoparasitic behavior by the ravens decreased as the eagle nestling matured to seven weeks of age, suggesting a narrow temporal window in which ravens can successfully engage in kleptoparasitic behavior at eagle nests. The observation of kleptoparasitism by Common Ravens at the nest suggests potential risks to young Golden Eagles from Common Ravens.
Poly-β-Hydroxy butyrate depolymerase from Streptomyces lydicus MM10, isolated from wastewater sample.

Plastics are an integral part in our daily life activities and it is difficult to conceive how we could function without them. Burning or chemical treatments of these plastic materials destroys the environment and have many dangerous effects on, water air and human health. Thus, other sources of plastic (biodegradable plastic) must be introduced. Under unfavorable growth conditions Poly s-hydroxybutyrate (PHB) is accumulated intracellular by many bacteria and the principal enzyme for the degradation of PHB is PHB depolymerase. A number of thermophilic actinomycetes have been screened for PHB degradation on agar plats. All these isolates were recovered from soil, sand and wastewater samples on starch nitrate agar at incubation temperature of 45. Five isolates (50%) out of 10 showed degradation activities, detected by the diameter of the clear zone. The Actinomycete isolate MM10 was the most PHB degrader and it was identified using morphological, physiological and biochemical characters. According to 16SrRNA analysis, it was identified as Streptomyces lydicusMM10. Growth at 45oC, in minimal medium (pH7.0) containing glucose and0.3% PHB as enzyme inducer, enhanced enzyme production and maximum activity was obtained after 24 h of incubation. The PHB depolymerase was precipitated and purified using column chromatography. The optimum temperature and pH of the pure enzyme were 45°C and pH 8, respectively. However, production of bioplastics is cost effective as compared to synthetic plastics they were non-toxic and completely biodegradable by some actinomycete isolates. © 2015 Friends Science Publishers
Investigation of the coeliac immunogenicity of cereal peptides and their quantification using monoclonal antibodies

2 ACKNOWLEDGEMENTS 4 LIST OF ABBREVIATIONS 5 CODE FOR AMINO ACIDS 7 TABLE OF CONTENTS 8 LIST OF FIGURES 14 LIST OF TABLES 16 CHAPTER ONE: GENERAL INTRODUCTION 1.1 History of CD 20 1.2 The prevalence of CD 21 1.3 Presentation of CD 1.3. 1 Terminology and associations 23 1.3. 2 Paediatric presentation of CD 25 1.3. 3 Adults presentation of CD 26 1.4 Pathogenesis 1.4. 1 Genetic susceptibility 27 1.4. 2 Adaptive immune response 29 1.4. 2.1 Interaction between HLA molecules peptide binding groove and epitopes 30 1.4. 2.2 Role of tTG 31 1.4. 3 Innate immune response 33
Cancer risk associated single nucleotide polymorphisms of mitochondrial D-loop and 8-hydroxy-2'-deoxyguanosine levels in gastric cancer

ABSTRACT The accumulation of mutations and single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) is related to gastric carcinogenesis. To evaluate the potential relationships between DNA damage and D-loop SNPs, we measured the 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in the gastric cancer tissue by immmunostaining. Our data showed that the gastric cancer susceptibility SNP of 16519C was associated with higher 8-OHdG levels. Taken together, the cancer-risk associated D-loop SNPs might initiate carcinogenesis through increasing oxidative damage.
Conectividade e variabilidade genética do tubarão galha-branca oceânico, Carcharhinus longimanus, usando DNA mitocondrial

Until few decades ago, shark catching was considered to be only incidental and with no significant effects on their populations. However, the great increase in the fins market value combined with declining levels of traditional fish population for human consumption, sharks have become targets of the fisheries worldwide. Among these, the whitetip shark Carcharhinus longimanus shows strong signs of population depletion, and is currently listed as globally "Vulnerable" according to the Red List of Threatened Species of the International Union for Conservation of Nature. Regarding conservation plans, acquiring knowledge about the population genetic structure of the species is a fundamental step towards establishing effective conservation policies. Considering the limited information about population dynamics of the oceanic whitetip shark, were used partial sequences of the mitochondrial DNA (mtDNA) control region to determine its population genetic structure across the Atlantic Ocean and the Indian Ocean. Were sampled 215 specimens of C. longimanus and obtained 724 base pairs (bp), identifying nine polymorphic sites, which resulted in 12 distinct haplotypes. The total nucleotide diversity was π = 0.0013 and haplotype diversity h = 0.5953. These results show a genetic variability slightly below the observed average among other species of pelagic sharks. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (FST = 0.1039, P<0.001) with restriction of gene flow between the Western and Eastern Atlantic Ocean with a strong relationship of this latter with the Indian Ocean. Thus, for the expansion of conservation plans of the species, also for the maintenance of their genetic stocks, should be considered at least two populations in the Atlantic Ocean and more attention to areas where the greatest genetic diversity indexes were found. As the acquisition of information about the environmental causes that are associated to species extinction can induce behavioral changes and, therefore, contribute to biodiversity conservation, the present project also included the development of educational strategy gathering information about the extinction risks, genetics identification and elasmobranch conservation. (Appendix I).
Effect of increased doses of final gonadotropin-releasing hormone (GnRH) of Ovsynch on luteinizing hormone (LH) peak and corpus luteum (CL) function in lactating dairy cows and buffaloes

EFFECT OF INCREASED DOSES OF FINAL GONADOTROPIN-RELEASING HORMONE (GnRH) OF OVSYNCH ON LUTEINIZING HORMONE (LH) PEAK AND CORPUS LUTEUM (CL) FUNCTION IN LACTATING DAIRY COWS AND BUFFALOES By Srijana Manandhar Fertility of dairy cows has been decreasing with a corresponding increase in milk productivity. Synchronization protocols using gonadotropin releasing hormone (GnRH) and prostaglandin F2 alpha (PG) have been designed to synchronize ovulation to allow timed artificial insemination (AI). To tackle challenges of lesser concentration of steroid hormones in higher producing cows, studies focused on increasing steroid hormones to imitate that of heifers have been reported. The objective of this thesis was to assess the effect of increased doses of final GnRH of Ovsynch in dairy cows on the LH peak and CL function [CL size and progesterone (P4) secretion]. Dairy cows (N=70) were enrolled in an Ovsynch protocol. Selected cows (n=24) were divided to receive three different doses of final GnRH (100 vs 200 vs 400 μg) of Ovsynch followed by timed artificial insemination (TAI). The LH peak and P4 per CL volume of the three treatment doses were not significantly different (p > 0.05) except for P4 per CL volume of 200 vs. 400 μg on day 7 (p =0.04). Similarly, in n=6 buffaloes, two doses (100 vs 400 μg) of final GnRH was used in Ovsynch. There was no significant difference in P4 per CL volume (p > 0.3) post treatment between the two treatment doses. Due to unforeseen shortcomings, our data is not adequate to conclude the effect of greater GnRH dose on CL function in cow and buffalo and we suggest further studies on GnRH doses in cow and buffalo synchronization protocols.
Mapping goliath grouper aggregations in the southwestern Atlantic

(Lichtenstein, 1822), is the largest reef fish in the western Atlantic Ocean, reaching up to 2.5 meters long and > 400 kg (BULLOCK et al., 1992). The species matures at 5-8 years with a maximum age of 37 years (BULLOCK et al., 1992). Some characteristics of goliath grouper that make them particularly vulnerable to overfishing include their large body size, slow growth, high longevity, late maturity, and the formation of predictable seasonal spawning aggregations (SADOVY; EKLUND, 1999). Consequently, the species has suffered sharp population declines across its entire distribution range (CRAIG et al., 2009; McCLENACHAN, 2009; GIGLIO et al., 2015) and currently is classified as Critically Endangered by the International Union for the Conservation of Nature (CRAIG, 2011). In Brazil, the species have been fully protected by a federal law since 2002, however, illegal fisheries threaten the population’s recovery (GIGLIO et al., 2014a). During the reproductive season, goliath grouper form relatively small (10 to 100 individuals) spawning aggregations (SADOVY; EKLUND, 1999) with individuals migrating distances up to 300 km to specific spawning areas (PINA-AMARGOS; GONZALEZ-SANSON, 2009). Data on the spatial and temporal distributions of spawning aggregations are mostly available for the northern hemisphere (SADOVY; EKLUND, 1999; MANN et al., 2009; KOENIG et al., 2011; 2016). In Brazil, anecdotal reports of aggregation sites have been described using fishers’ knowledge (GERHARDINGER et al., 2009; FERREIRA et al., 2014) and
Protein Fold Recognition with Representation Learning and Long Short-Term Memory

: Predicting the 3D structure of a protein from its amino acid sequence is an important challenge in bioinformatics. Since directly predicting the 3D structure is hard to achieve, classifying a protein into one of the “folds”, which are pre-deﬁned structural labels in protein databases such as SCOP and CATH, is generally used as an intermediate step to determine the 3D structure. This classiﬁcation task is called protein fold recognition (PFR), and much research has addressed the problem of either (i) feature extractions from amino acid sequences or (ii) classiﬁcation methods of the protein folds. In this paper, we propose a new approach for PFR with (i) learning feature representations with unsupervised methods from a large protein database instead of manual feature selection and using external tools. (ii) learning deep neural architectures, recurrent neural networks (RNNs) with long short-term memory (LSTM) units, and re-training the representations instead of ﬁxing the extracted features. On a benchmark dataset, our approach outperforms existing methods that use various physicochemical features.