Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Study of Length and Growth Rate of Ramie (Boehmeria nivea L. Gaut.) Bast Fiber of Indonesian Clones

The Present research was conducted on five clones of ramie ( Boehmeria nivea L.Gaud.) found in West Sumatra and several other clones from Java. The research objective was to compare the growth, number of fibers per bundles, length and the time until fibers are matured enough for harvesting. The ramie planting was done in Andalas University’s Padang experimental field station from June to October 2016. Microscopic investigation and fiber analysis were carried out in the laboratory of Plant Development and Structure, Department of Biology, Faculty of Mathematics and Natural Science, Andalas University, Padang, Indonesia. The clones investigated were Bandung A, Indochina, Lembang A, Padang 3, and Ramindo. The numbers of fibers per fiber bundle were highest in the Ramindo clone at 69 cell/bundle and the least in Bandung A clone at 40 cell/bundle. The type of fiber was 48% type I, 36% type II and 16% type III. The patterns of fiber-shape in each fiber bundle from the cambium to the outside increases in diameter with the centre being dominantly type I, the middle region type II, and the outer region type III. The length of fiber found in the present study (longest 70 mm) is shorter than in previous reports. Length, diameter, and thickness of cell wall of clone ramie fiber cells grew at similar rates throughout the maturation process. Fastest fiber growth was obtained from Padang 3 clones at 132 μm/day, while the slowest was in Ramindo clones at 48 μm/day. The fastest fiber growth for all clones occured at 2-3 weeks of age. Based on fiber growth, Padang clones should be harvested after six weeks, clones of Indochina, Lembang A, and Ramindo harvested after eight weeks and Lembang A clone after the eighth week. This is sooner than harvesting based on morphological characteristics, which would be between the age of 10-11 weeks. The clones of Padang A were considered superior to the other clones.
Alignment of a circumbinary disc around an eccentric binary with application to KH 15D

We analyse the evolution of a mildly inclined circumbinary disc that orbits an eccentric orbit binary by means of smoothed particle hydrodynamics (SPH) simulations and linear theory. We show that the alignment process of an initially misaligned circumbinary disc around an eccentric orbit binary is significantly different than around a circular orbit binary and involves tilt oscillations. The more eccentric the binary, the larger the tilt oscillations and the longer it takes to damp these oscillations. A circumbinary disc that is only mildly inclined may increase its inclination by a factor of a few before it moves towards alignment. The results of the SPH simulations agree well with those of linear theory. We investigate the properties of the circumbinary disc/ring around KH 15D. We determine disc properties based on the observational constraints imposed by the changing binary brightness. We find that the inclination is currently at a local minimum and will increase substantially before settling to coplanarity. In addition, the nodal precession is currently near its most rapid rate. The recent observations that show a reappearance of star B impose constraints on the thickness of the layer of obscuring material. Our results suggest that disc solids have undergone substantial inward drift and settling towards to disc mid-plane. For disc masses ∼0.001 M⊙, our model indicates that the level of disc turbulence is low (α ≪ 0.001). Another possibility is that the disc/ring contains little gas.
Economic analysis of corn inoculated with Azospirillum brasilense associated with nitrogen sources and doses

Azospirillum brasilense is a bacterium known for its biological nitrogen fixation (BNF) in corn crops. However, there is a lack of comprehensive research defining how much mineral N should be applied to maximize the efficiency of BNF and attain high, economically sustainable yields. Moreover, it would be interesting to investigate whether adding urea with NBPT urease inhibitor might increase BNF in grasses. Therefore, the aim of this study was to determine the effect of inoculation with Azospirillum brasilense associated with N sources and doses in a Cerrado biome soil by evaluating the grain yield of irrigated corn in economic terms. The experiment was conducted in Selviria, MS, Brazil under a no-till system on a Latossolo Vermelho distrofico (Oxisol). The experiment was set up as a randomized block design with four replications in a 2 × 5 × 2 factorial arrangement consisting of two sources of N (urea and urea with NBPT urease enzyme inhibitor) and five N doses applied as top-dressing (0, 50, 100, 150, and 200 kg ha-1), with and without the inoculation of seeds with A. brasilense. Inoculation with Azospirillum brasilense makes corn growth much more profitable, irrespective of the dose and source of N. Addition of 200 kg ha-1 N in the form of conventional urea coupled with inoculation with Azospirillum brasilense increases grain yield; however, the highest economic return is obtained with N applied at 100 kg ha-1 with conventional urea and inoculation.
The effects of authentic English listening and reading materials on EFL learners

The purpose of this study was to examine Korean EFL university students' perceptions and attitudes toward both authentic listening and reading materials. It also proposed to explore the effects of the implementation of a curriculum with an emphasis on authentic listening and reading materials in EFL classrooms. A total of 146 Korean EFL college students participated in this study and were divided into four groups, two experimental groups and two control groups. For examining the effects of using authentic listening materials on students' listening ability, an experimental group received instruction in which traditional listening materials were replaced by DVD titles during some portions of the listening lessons for the twelve-week period of the treatment. In order to explore the effects of using authentic reading materials on students' reading ability, the other experimental group received instruction in which traditional reading materials were replaced by authentic reading materials during some portions of the reading lessons. The results of the study showed that although the effect of using authentic reading materials in the EFL classroom was not statistically significant, there was a significant positive effect of utilizing DVD titles in EFL classrooms. Implications and suggestions for further research are provided.
LIPEA: Lipid Pathway Enrichment Analysis

Motivation Analyzing associations among multiple omic variables to infer mechanisms that meaningfully link them is a crucial step in systems biology. Gene Set Enrichment Analysis (GSEA) was conceived to pursue this aim in computational genomics, unveiling significant pathways associated to certain gene signatures under investigation. Lipidomics is a rapidly growing omic field, and absolute quantification of lipid abundance by shotgun mass spectrometry is generating high-throughput datasets that depict lipid metabolism in a plethora of conditions and organisms. In addition, high-throughput lipidomics represents a new important ally to develop personalized medicine approaches, investigate the causes and predict effective biomarkers in metabolic diseases, and not only. Results Here, we present Lipid Pathway Enrichment Analysis (LIPEA), a web-tool for over-representation analysis of lipid signatures and detection of the biological pathways in which they are enriched. LIPEA is a new valid resource for biologists and physicians to mine pathways significantly associated to a set of lipids, helping them to discover whether common and collective mechanisms are hidden behind those lipids. LIPEA was extensively tested and we provide two examples where our system gave successfully results related with Major Depression Disease (MDD) and insulin re-sistance. Availability The tool is available as web platform at https://lipea.biotec. tu-dresden.de.
Some faunistic data on the bats of Italy

During a spring trip across Italy in 1998, bats were surveyed using a bat detector and mist nets. The bats were recorded at seven localities, flying and foraging in various habitats or roosting in a shelter. In total, 6 bat species were netted, i.e. Rhinolophus ferrumequinum, Nyctalus leisleri, Pipistrellus pipistrellus, Pipistrellus nathusii, Barbastella barbastellus, and Plecotus auritus. At least 11 bat species were identified using the bat detector, i. e. Myotis daubentonii, Vespertilio murinus, Eptesicus serotinus, Nyctalus leisleri, Hypsugo savii, Pipistrellus pipistrellus, P. pygmaeus, P. nathusii, P. kuhlii, Barbastella barbastellus, and Plecotus sp. P. kuhlii seems to be a common species preferring lower elevations, in contrast with another common species H. savii which was mostly recorded at higher altitudes. The latter two species along with E. serotinus were often found foraging around street lamps. At the time of the survey, records of five species were new to the Gargano National Park. Data concerning V. murinus remain very rare for the whole Italy until now.
Proliferative and positional instructions underliying planarian regeneration and tissue renewal = Instrucciones proliferativas y posicionales subyacentes a la regeneración y el recambio tisular en planaria

Algunos animales tienen habilidades regenerativas increibles, las cuales han mantenido a los investigadores fascinados durante decadas. Como estos animales son capaces de regenerar partes perdidas y recuperar los tejidos danados podria dar a los investigadores claves en el campo de la medicina regenerativa. Aqui, nosotros usamos la planaria Schmidtea mediterranea, una especie que es capaz de regenerar completamente cada parte perdida, para entender mas profundamente el proceso de regeneracion y recambio tisular. Ambos procesos comparten varios mecanismos los cuales son esenciales para su correcto desarrollo. En esta Tesis, describimos algunos aspectos del balance entre la proliferacion y la apoptosis, la diferenciacion de celulas madre y las instrucciones posicionales, requeridas todos ellos para regenerar cualquier estructura y producir el recambio tisular requerido durante la homeostasis normal de los animales. Para estudiar el balance entre la proliferacion y la apoptosis, nos hemos centrado en la descripcion del factor Kruppel-like 10/11, el cual se ha relacionado con estos procesos en otros organismos. Aqui hemos visto que, klf10/11 se requiere durante la regeneracion para la correcta regulacion de la proliferacion y de la apoptosis y que es necesario para el correcto remodelaje de las estructuras del organismo, probablemente aguas abajo de la kinasa c-Jun N-terminal. Por otra parte, nos hemos centrado en el estudio del complejo transcripcional Nuclear Factor Y para asi comprender su papel durante los eventos de diferenciacion en la planaria. Hemos visto que el NF-Y presente en planaria es esencial para la regeneracion y homeostasis y que su inhibicion produce la acumulacion de neoblastos y la perdida de progenitores epidermicos, lo cual demuestra que NF-Y esta involucrado en la diferenciacion temprana de los progenitores tempranos epidermicos. Finalmente, se han estudiado las instrucciones posicionales, las cuales son esenciales para el correcto posicionamiento de las celulas y organos durante la regeneracion y homeostasis. Aqui, nos hemos centrado en el control de la organizacion medio-lateral del sistema nervioso central en la planaria, donde Wnt5 y Slit juegan un papel esencial. Wnt5, Slit y sus receptores crean un sistema auto-regulativo para establecer el patron medio-lateral en las planarias, el cual guia al SNC para ser posicionado en este eje.
Modelling HIV dynamics and evolution : prospects for viral control

The human immunodeficiency virus (HIV) epidemic is far from over. Antiretroviral therapy (ART) is effective at suppressing viral replication within a patient but it must be taken daily and is life-long. Therefore, the development of a therapy that could induce drug-free remission or constitute a functional cure is a key focus of HIV research. In this thesis I explore three mechanisms which could lead to more individuals being able to control their viraemia in the absence of ART: (1) T-cell immunity, (2) early initiation of ART, and (3) viral evolution. Firstly, a strong HIV-specific T-cell response has been linked to rare cases of spontaneous viral control, but the extent to which this arm of the immune response contributes to viral control is debated. Several types of data are used to answer this question, including the rate at which the virus evolves to escape the CD8+ T-cell response. I study the frequency of incident immune escape in the largest cohort used for this purpose to date. Secondly, some patients, with characteristics dissimilar to spontaneous HIV controllers, are able to control the virus for years after the interruption of ART that was initiated early in infection. I use mathematical models to investigate a new hypothesis for the differing outcomes of early- and late- initiated ART. Thirdly, since HIV is a relatively new infection of humans it is still adapting to its new host. Recent studies suggest that the virus could be evolving towards decreased virulence at the population level. I study whether the widespread administration of ART has the potential to alter the course of virulence evolution and might result in a further attenuated virus. I conclude by discussing the implications of these results for viral control at the individual level and also for population level epidemic control.
Variation in Bird Assemblages Along an Agricultural Intensification Gradient: A Case Study of Olive Orchards in North-Eastern Algeria

Abstract Despite the fact that the Mediterranean basin is considered to be a global biodiversity hotspot for flora and fauna, studies investigating the benefits of agri-environmental schemes on biodiversity conservation in perennial agro-ecosystems in this region are scarce, particularly for bird communities in North Africa. This study investigated the effect of agricultural intensification on bird assemblages in olive orchards in north-eastern Algeria. Bird counts were conducted along an agricultural intensification gradient during twelve consecutive months (from March 2014 to February 2015). Accumulation curves and non-parametric estimators for incidence-based data were used to estimate the total species richness of birds. GLMMs, PERMANOVA and non-metric multidimensional scaling analyses were conducted to evaluate and to visualize the variation in species composition among the studied sites during the breeding and non-breeding seasons. Overall, the total species richness of birds decreased with the increasing level of agricultural intensification. Additionally, among the three trophic guilds (insectivore, granivore and omnivore), the frequency of occurrence of insectivorous and granivorous birds tended to decrease with increasing agricultural intensification. We explored possible reasons for the observed patterns, in relation to differences in the intensity of agricultural management, between the olive orchards studied. This study provides the first qualitative data, which suggests that less intensive agriculture can enhance avian diversity, particularly of insectivorous and granivorous birds, in olive orchards in Algeria.
Conservation of four at-risk plant species in sandhill ecosystems of the southeastern Coastal Plain

Understory plants represent the majority of diversity within the longleaf pine ecosystem of the southeastern United States. An understanding of population demography and germination requirements is essential for the creation of ecologically meaningful conservation plans for atrisk understory species in this fire-prone ecosystem. This study quantified density, reproductive success, and seed predation of four herbaceous plants and examined effects of temperature and smoke on germination. No seedlings were found in natural populations surveyed, suggesting that seed germination or seedling establishment may be a limiting factor in population growth. Germination of Baptisia lanceolata was low under all treatments and significantly decreased in response to 15 days of cold stratification and to a combination of smoke and heat. Germination of Carphephorus bellidifolius increased in response to the application of heat, cold and smoke treatments. The greatest increase was in response to 30 days of cold stratification, suggesting an optimal threshold of cold exposure for maximum germination of this species. Although Nolina georgiana had the highest germination percentage of all four species under control conditions, cold stratification for 30 and 45 days increased germination. Stylisma pickeringii had very low
Screening of water-efficient rice genotypes for dry direct seeding in South Asia

ABSTRACT Rice genotypes having high crop water productivity in dry direct-seeded rice (DDSR) need to be assessed while promoting labor- and water-saving technology. The objective of this study was to evaluate the ability of several selection indices to identify genotypes with high crop water productivity in DDSR. A set of 16 genotypes [13 recombinant inbred lines (RILs) and three genotypes as check for control] were evaluated under DDSR for two consecutive years (2013 and 2014) using two irrigation regimes [-10 kPa (non-stress) and -20 kPa (stress)]. Grain yield varied from 5.3 to 8.4 t ha-1 and 5.9 to 8.7 t ha-1 for irrigation regimes of -20 and -10 kPa, respectively. Yield reductions caused by water stress ranged from 2.9 to 25.1%; being lowest in RIL1649 and highest in hybrid SVH-127. The genotypes with high stress-tolerance index (STI), mean productivity (MP), geometric mean productivity (GMP) and harmonic mean productivity (HAR) were identified as the most productive genotypes for high crop water productivity in DDSR. The results implied that selection based on stress tolerance indices likes STI, MP, GMP and HAR was useful in identifying genotypes with high crop water productivity under DDSR and RIL 1649 and SVH-127 were identified as superior genotypes in this regard.
Growth Study, Metabolite Development, and Organoleptic Profile of a Malt-Based Substrate Fermented by Lactic Acid Bacteria

The objective of this study was to investigate the fermentation of barley malt extract by four different lactic acid bacteria (LAB) species and to analyze the effect on biological, physicochemical, and organoleptic attributes of the resulting beverages. Malt and wort were analyzed following the Methodensammlung der Mitteleuropäischen Analysenkommission (MEBAK). Sugars and organic acids were evaluated using HPLC, while aroma compounds and ageing indicators were quantified using a head-space GC-FID. Unhopped wort was able to support the growth of all LAB during the whole experiment time (120 hr), with a cell count increase up to 3.63 log orders. The strain-specific preferences for carbon and nitrogen sources led to significant differences in the accumulation of metabolic byproducts (i.e., organic acids and flavor-active compounds released in the medium). LAB fermentation lowered the amount of some Strecker-aldehydes (2- and 3-methylbutanal and 2-phenylacetaldehyde) carrying “malty” off-flavors and increased dairy-related aroma compounds such as diacetyl and acetoin (“buttery”). The fermented samples were sensorially distinct and described with “bready”, “yeasty”, “yogurty”, or “honey” attributes. In general, LAB fermentation conferred flavor complexity to wort. Forced ageing of the fermented samples led to a large increase of “staling” indicators but these samples improved organoleptic stability compared with the unfermented control.
Biochemical and molecular aspects of Brassica juncea (Indian mustard) genotypes under water-stress conditions

The present investigation was carried out in the Department of Plant Breeding & Genetics, PAU, Ludhiana during rabi 2015-16 to draft a selection criterion for drought tolerance based on morphobiochemical studies, yield and yield attributes for a set of 96 diversity fixed B. juncea genotypes. The crop was raised under two environmental conditions, rainfed (DOS-29/10/2015) and irrigated (DOS24/11/2015) in the field area in two replications for studying various biochemical (enzymatic and nonenzymatic antioxidants) traits at three different plant growth stages viz, vegetative, flowering, podding; morphological and yield traits at the time of maturity. It was observed that the water deficit stress significantly increase the activity of peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) in almost all the genotypes as compared to control (irrigated). Similarly, an increase in the amount of non-enzymatic antioxidants (MDA, proline, reducing sugar, chlorophyll and carotenoid) was observed under stress condition under all the plant growth stages. Among the three growth stages, maximum activity of defense enzymes and amount of non-enzymatic metabolites was observed at the flowering stage. Growth behavior was studied at the maturity stage. Significant decline was recorded in the morphological traits (plant height, number of primary branches) and yield attributes (silique length, siliqua number and yield) under water stress showing that the stress affects the physiological processes in the plant. Correlation studies were carried out among morpho-biochemical and yield attributes to identify the indicators for screening drought tolerant varieties in water stress condition. It was observed that drought tolerance is associated with the more efficient antioxidant system. The response of water deficit on the genotypes varies substantially. Drought tolerant cultivars possess better morphological, physiological and biochemical adaptation to reduce water availability. Selection was made based on STI (stress tolerance index) and a set of ten tolerant genotypes viz, PBR-357, CSR-7, PLM-2, PRG901, MCN-12-42, NRCQR-376-1, DJ-124-1-76, LES-38, PRG-901, JJ-210-5-4 with higher stress tolerance and yield potential were selected. Marker-trait association studies was carried out to identify the quantitative trait loci (QTLs) associated with the traits under water stress. A total of 22 QTLs for various traits were identified, out of which 18 QTLs were associated with biochemical parameters and 4 QTLs were associated with yield and yield attributes. QTLs associated with various traits viz, POD, SOD, CAT, reducing sugars, proline, chlorophyll, siliquae length and yield were mapped on chromosome no. 1,2,3,4,5,7,9,11,14,15 and 17 of B. juncea. As limited information is available for tagging of various biochemical components under stress in Brassica, our study could help in uncovering the details of genetic control of the performance of these biochemical traits in response to water stress.