Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of prokaryotic metabolism on suspended particulate organic matter in the dark waters of the subtropical North Atlantic

The distribution of prokaryotic abundance (PA), respiratory activity (ETS), heterotrophic production (PHP), and suspended particulate (POM) and dissolved (DOM) organic matter was determined in the meso‐ and bathypelagic waters of the (sub)tropical North Atlantic. PA decreased by one order of magnitude from the lower euphotic zone to the bathypelagic waters, while ETS decreased by two and PHP by three orders of magnitude. On a section following the Mid‐Atlantic Ridge from 35ºN to 5ºN, ETS below 1000‐m depth increased southwards up to three‐fold. This latitudinal gradient in the deep waters was paralleled by a six‐fold increase in Particulate Organic Carbon (POC), whereas no trend was apparent in the DOM distribution. Significant correlations between POM and ETS were obtained in the water masses between 1000‐m and 3000‐m depth, the Antarctic Intermediate Water and the North East Atlantic Deep Water. A strong imbalance in the dark ocean was found between prokaryotic carbon demand (estimated through two different approaches) and the carbon sinking flux derived from sediment‐trap records corrected with 230Th. The imbalance was greater when deeper in the water column, suggesting that the suspended carbon pool must account for most of the carbon deficit. Our results, together with other recent findings discussed in this paper, indicate that microbial life in the dark ocean is likely more dependent on slowly sinking or buoyant, laterally advected suspended particles than hitherto assumed.
Successional dynamics of woody seedling communities in wet tropical secondary forests

1 Chronosequence studies have found that shrubs and lianas are generally more abundant in early stages of tropical forest succession, whereas canopy trees and palms become more abundant and species‐rich in older stages and mature forests. 2 We analysed changes in woody seedling communities over 5 years in four second‐growth forests (initially 13–26 years after pasture abandonment) in Costa Rica. We recorded community‐level changes in woody seedling density, species density, species richness and composition in six woody life‐forms: canopy trees, subcanopy trees, canopy palms, understorey palms, shrubs and lianas. We evaluated these changes in relation to annualized recruitment and mortality rates for each life‐form. 3 Seedling density declined in all four sites over the 5 years, whereas Shannon diversity and the proportion of rare species increased. Species richness and evenness increased in all but the oldest site. 4 Canopy palm, understorey palm and canopy tree seedlings increased in species richness and relative abundance, whereas shrub and liana relative abundance declined. Canopy trees accounted for 34–42% of all new recruits. Detrended correspondence analysis showed that species composition was initially highly distinct within each forest site and remained distinct over the 5‐year period. 5 Shifts in life‐form were correlated with declining light availability during succession. Across sites, median light availability at the end of the study period in 2003 was positively correlated with recruitment rates of understorey palms, shrubs and lianas, and was negatively correlated with mortality rates of canopy trees and palms. 6 Observed changes among seedling communities mirrored those described in chronosequence studies on plants in larger size classes, lending support to the assumptions of chronosequence studies in Neotropical forests. 7 The results demonstrate the importance of seedling recruitment and mortality in determining the course of succession. Convergence occurs in some community properties, such as relative abundance within life‐forms, but not in others, such as species composition. Finally, the results illustrate the value of studying plant community dynamics at the level of woody life‐forms, especially in hyperdiverse systems such as tropical forests.
Migration of an upper trophic level predator, the salmon shark Lamna ditropis, between distant ecoregions

Knowledge of how animals move through heterogeneous environments is essential to understanding the ecological functions they fulfill in each habitat and their responses to environmen- tal change. Upper trophic level organisms exert structural influences through the food web, so infor- mation on their range, migration and foraging strategy is necessary to understanding ecosystem function. Recent technological advances have enabled researchers to follow individual animals over seasonal and multi-year timescales, revealing long-distance migrations in a variety of taxa. We used satellite telemetry to monitor female salmon sharks Lamna ditropis and remote sensing to character- ize their environment. Salmon sharks ranged throughout the entire eastern North Pacific Ocean dur- ing a seasonal migration cycle. During long-distance migrations, quantitative movement analyses of speed, path straightness and first passage time (FPT) revealed area-restricted search (ARS) behaviors in northern and southern regions, with transiting behaviors at mid-latitudes. Individuals migrating to a highly productive southern region displayed more ARS behaviors than those moving to a low pro- ductivity region. The combination of multi-year time-series of animal behavior with synoptic environ- mental data reveals factors influencing migration and indicates that different life history functions are fulfilled in each habitat.
Taxonomic Diversity of Actinomycetes Isolated from Swine Manure Compost

In this study, we investigated the taxonomic diversity of actinomycetes isolated from swine manure compost that had undergone self-heating. Pretreatment with sodium dodecyl sulfate and subsequent cultivation of the compost sample on humic acid-vitamin agar at 30 and 50°C resulted in the selective isolation of 125 actinomycete strains. These isolates were classified using a combination of morphological characterization and 16S rDNA sequence analysis, with sequence similarities of ≥97% and ≥99% used to identify isolates at genus and species level, respectively. The isolated actinomycete assemblage consisted of a diverse array of species, with the 125 isolates falling into 10 families, 15 genera, and 22 species. The most dominant thermophilic actinomycetes were Saccharomonospora (Sam.) viridis and Thermobifida fusca, followed by Actinomadura spp. Other species that were frequently isolated at 30°C included Glycomyces spp. , Nocardiopsis (Nop.) alba, Nop. composta, Rhodococcus rhodochrous, and Sam. azurea.
ASSIMILATION OF 15 NH4 + BY BEECH (FAGUS SYLVATICA L.) ECTOMYCORRHIZAS.

Ammonia assimilation has been followed in ectomycorrhizal roots of Fagus sylvatica. The absorption of ammonium ions was associated with a rapid synthesis of free amino acids in mycorrhizal tissues, glutamine being the most prominent. In the presence of [15 N]ammonium, glutamate, glutamine and alanine became the most strongly labelled metabolites of ectomycor-rhizas. Nitrogen-15 nuclear magnetic resonance spectroscopy demonstrated that the glutamine amide-N was the most highly enriched component of the extracts. Methionine sulphoximine and albizine, inhibitors of glutamine synthetase and glutamate synthase, almost completely blocked the incorporation of 15 N label into amino acids and induced an accumulation of NH4 + . These observations suggest that in the ammonia-fed beech ectomycorrhizas, ammonia assimilation occurs mainly via the glutamine synthetase/glutamate synthase pathway, and that glutamate dehydrogenase plays little, if any, part in this process. Alternative models for the nitrogen assimilation pathways in fungal and host tissues are presented.
Effect of selenium sources on performance and meat characteristics of broiler chickens

SUMMARY Selenium is an important mineral, required for many functions within animals, where it interacts with vitamin E, maximizing the efficiency of the vitamin as an antioxidant. In chickens, adequate intake of organic forms of Se may be linked to reduced drip loss in the final meat and to improved feather production. The present trial was conducted to examine the impact of feeding organic Se (Sel-Plex, Alltech Inc., Nicholasville, KY) to broilers on their productive performance, feather growth, and meat characteristics. Birds fed 0.3 ppm of organic Se had decreased drip loss from breast meat and lower levels of apparent liver damage (indicated by lower plasma concentrations of indicator enzymes). Feathering was improved at 21 d by feeding organic Se.
CDS-RSRAM: a Reconfigurable SRAM Architecture to Reduce Read Power with Column Data Segmentation

SRAM access takes a significant part of on-chip power consumption in many signal processing systems. Reconfigurable data-adaptive SRAMs (RSRAM) can save considerable read power by utilizing data patterns. In these RSRAM designs, the column size (i.e., the number of cells in one column) of the cell array defines the granularity of data pattern exploitation. However, the column size cannot be too small due to circuit constraints, which makes finer-grained data features hidden and suppresses RSRAM's advantage of low-power read. In this paper, we propose a reconfigurable SRAM architecture with column data segmentation (CDS-RSRAM) to break this limitation to exploit better data patterns without decreasing the column size. We partition data in one column into several segments and perform statistical analysis on every segment respectively. Each data segment has one exclusive flag bit to control its working mode while reading. This architecture can leverage data patterns at finer granularity and magnify RSRAM's advantage of low-power read. We also make a thorough overhead analysis and improve the mode decision strategy to minimize the power overheads. The simulation results show that compared with the original RSRAM, the proposed architecture saves up to 36.8% read power with 8.8% area overhead. Compared with 8T SRAM, the total power saving can be up to 77.1%.
A Survey of DMFBs Security: State-of-the-Art Attack and Defense

The digital microfluidic biochips (DMFBs) have the advantages of high precision, small consumption of samples/reagents, and high flexibility in experimental places. Nowadays, DMFB technology has been implemented in industry, such as by illumina. However, similar to the situation faced in integrated circuits, DMFBs also suffer from various security risks and end users usually know little about these security threats. Accordingly, in this paper, we propose a survey on DMFBs security in the research community. First, we prevent an overview of the attack behaviors in DMFBs and list them according to the design and manufacture flow. Then, we outline the current defense techniques and classify them into several categories according to their corresponding purposes and functions. Finally, the comparison between security threats faced in DMFBs and the corresponding defense techniques are provided and analyzed in detail, thus presenting the future research trends in DMFBs security.
Methods for protein identification using expressed sequence tags and peptide mass fingerprinting for seed crops without complete genome sequences

Abstract Proteomic approaches based on two-dimensional gel electrophoresis, mass spectrometry and database search are widely used to address questions about the development, physiology and quality of seeds. Identification of proteins is of great importance in proteomic analyses. For seed crops without full genome information, cross-species protein identification by mass spectrometry-driven sequence similarity search can be used. However, this approach is risky due to protein polymorphism between different species. Species-specific expressed sequence tag (EST) databases are an invaluable resource, which complements mass spectrometry data analysis for protein identification. Here, we illustrate a modified method of protein identification and characterization using species-specific EST databases and peptide mass fingerprinting with an example of protein identification. This method is reliable, supplements the existing methods, and improves the efficiency and accuracy of protein identification for seed crops for which complete genome information is not available.
Enhancing Performance of FSO Communication Link using Coherent Optical OFDM with Cascaded EDFA

Orthogonal Frequency Division Multiplexing (OFDM) and Quadrature Amplitude Modulation (QAM) are the recent existing techniques that are being investigated in Free Space Optical (FSO) communication for the enhancement of Quality of Service (QoS) in provision for longer ranges and higher data rates. Coherent Optical OFDM (CO-OFDM) is capable of providing improved receiver sensitivity and spectral efficiency. The scintillations, atmospheric turbulences and attenuations induced by varying weather (such as rain, fog etc.) conditions pose a serious impact on the link performance. The optical amplifiers and their configuration used in the FSO link design pose an influencing impact on the link performance. The present work incorporates the evaluation of designed FSO communication link using CO-OFDM with Cascaded Erbium Doped Fiber Amplifier (CEDFA) at 30Gbps under the influence of moderate turbulences and geometric attenuations for Clear weather, Heavy rain and Fog (Moderate to Dense) attenuations. The system performance is analyzed for Quality (Q)-Factor, Bit Error Rate (BER), Signal-to-Noise Ratio (SNR) and Constellation diagram as parametric metrics. This novel thought of utilizing cascaded amplifier configuration with CO-OFDM has enabled the implementation of FSO communication over longer distances of 24, 3.9, 1.43 and 0.672 Km for Clear weather, Heavy rain, and Moderate and Dense fog conditions respectively that has not been investigated earlier.
Isolation and characterization of polymorphic microsatellite markers in the white-winged chough (Corcorax melanorhamphos)

We have isolated and characterized seven polymorphic microsatellite loci in the white-winged chough (Corcorax melanorhamphos), a highly social, cooperatively breeding bird of Australian eucalypt woodlands. In analyses of 100 samples from 16 family groups, the number of alleles per locus ranged from four to 18, and observed heterozygosity ranged between 0.46 and 0.93. One locus appears to be sex-linked. The primers were also tested in apostlebirds (Struthidera cinerea), the only other species in the subfamily Corcoracinae. Five loci were successfully amplified and three were polymorphic.
Functional studies of purifi ed transmembrane proteases, omptins, of Yersinia pestis and Salmonella enterica.

4/2006 Kari Kreander A Study on Bacteria-Targeted Screening and in vitro Safety Assessment of Natural Products 5/2006 Gudrun Wahlstrom From Actin Monomers to Bundles: The Role of Twinfi lin and a-Actinin in Drosophila melanogaster Development 6/2006 Jussi Joensuu Production of F4 Fimbrial Adhesin in Plants: A Model for Oral Porcine Vaccine against Enterotoxigenic Escherichia coli 7/2006 Heikki Vilen Mu in vitro Transposition Technology in Functional Genetics and Genomics: Applications on Mouse and Bacteriophages 8/2006 Jukka Pakkanen Upregulation and Functionality of Neuronal Nicotinic Acetylcholine Receptors 9/2006 Antti Leinonen Novel Mass Spectrometric Analysis Methods for Anabolic Androgenic Steroids in Sports Drug Testing 10/2006 Paulus Seitavuopio The Roughness and Imaging Characterisation of Different Pharmaceutical Surfaces 11/2006 Leena Laitinen Caco-2 Cell Cultures in the Assessment of Intestinal Absorption: Effects of Some Co-Administered Drugs and Natural Compounds in Biological Matrices 12/2006 Pirjo Wacklin Biodiversity and Phylogeny of Planktic Cyanobacteria in Temperate Freshwater Lakes 13/2006 Antti Alaranta Medication Use in Elite Athletes 14/2006 Anna-Helena Saariaho Characterization of the Molecular Components and Function of the BARE-1, Hin-Mu and Mu Transposition Machineries 15/2006 Jaana Vaitomaa The Effects of Environmental Factors on Biomass and Microcystin Production by the Freshwater Cyanobacterial Genera Microcystis and Anabaena 16/2006 Vootele Voikar Evaluation of Methods and Applications for Behavioural Profi ling of Transgenic Mice 17/2006 Paivi Lindfors GDNF Family Receptors in Peripheral Target Innervation and Hormone Production 18/2006 Tarja Kariola Pathogen-Induced Defense Signaling and Signal Crosstalk in Arabidopsis 19/2006 Minna M. Jussila Molecular Biomonitoring During Rhizoremediation of Oil-Contaminated Soil 20/2006 Bamidele Raheem Developments and Microbiological Applications in African Foods: Emphasis on Nigerian Wara Cheese 21/2006 Jiri Lisal Mechanism of RNA Translocation by a Viral Packaging Motor 22/2006 Roosa Laitinen Gerbera cDNA Microarray: A Tool for Large-Scale Identifi cation of Genes Involved in Flower Development 23/2006 Lari Lehtio Enzymes with Radical Tendencies: The PFL Family
Characterization of WAP2 gene in Aegilops tauschii and comparison with homoeologous loci in wheat

Abstract The Q/q gene, also known as WAP2, is an important gene for wheat domestication and is a member of the AP2 (APETALA2) class of transcription factors. In the present study, we first isolated the WtAP2 allele (where the superscript “t” refers to the speciese source, in this case “tauschii”) on chromosome 5D from Aegilops tauschii Coss. , the D‐genome donor species of common wheat. We found that WtAP2 and the AP2 gene from Arabidopsis share a central core of the AP2 polypeptide, a highly basic 10‐amino acid domain, and an AASSGF box, although there are many differences in the 37‐amino acid serine‐rich acidic domain and the remaining regions. In addition, WtAP2 was highly homologous to the homoeologous loci on 5A and 5B of wheat at both the nucleotide and amino acid level. However, there were some variations that are probably related to gene function. In the first AP2 domain, the amino acids VYL on the 5D and 5A loci were replaced with LLR on 5B. In the 37‐amino acid serine‐rich acidic domain, WtAP2 on 5D had an extra amino acid insertion. There was also a variation at the 329 amino acid position, which is thought to be related to the appearance of free‐threshing wheat. At this position, the amino acid is isoleucine on 5A for the Q allele and valine for the q allele, whereas the amino acid is leucine on 5D and 5B. Furthermore, a Stowaway miniature terminal inverted repeat element (MITE) insertion was present in the ninth intron of WAP2 on 5B of all common wheats and partial tetraploid Triticum turgidum wheats. These results provide new clues for studies into the evolutionary biology of WAP2 and the origin of common wheat.
Universal Adaptive Stabilization-Based Trend Filtering for Impending Battery Voltage Collapse Detection

Battery operated devices are common in everyday life. Deciding when a warning for impending battery voltage collapse should be triggered is not trivial. This letter develops an impending battery terminal voltage collapse detection system using a universal adaptive stabilizer (UAS) and a well-known trend filter. This eliminates requiring knowledge of battery model parameter values, or initial state-of-charge (SOC). The proposed approach overcomes the need for extensive training when compared to using neural-networks based techniques. Also, the developed trend filter when used with a UAS, eliminates the need for selecting windows of data to be processed. This is advantageous compared to earlier work, which uses a different trend filtering mechanism, because selection of window sizes is not straightforward. Further, the approach used in this letter shows that the UAS based technique is implementable on a cell phone. Associated mathematical results, and experimental data from such an implementation are presented. Additionally, the technique is also applied to other larger capacity Li-ion batteries showing its versatility. The developed technique can also be used to detect when the state-of-health (SOH) of a Li-ion battery is about to enter an unsafe region.
Efficacy and Economics of Summer Fallow Conventional and Reduced-Tillage Programs for Sugarcane

Abstract During the summer fallow period of the sugarcane production cycle, glyphosate in conjunction with frequent tillage is used to destroy sugarcane regrowth and reduce perennial weed infestations. For tillage to be reduced or eliminated in fallowed fields, weed control must be maintained and sugarcane must be completely destroyed so as not to interfere with the subsequent planting operation. Field studies were conducted to evaluate glyphosate rates and formulations for control of sugarcane, bermudagrass, and johnsongrass. Glyphosate (isopropylamine salt) applied in April at 1.68, 2.24, and 2.80 kg ai/ha controlled 15-cm sugarcane at least 95% 42 d after treatment (DAT). Control of 25- and 40-cm sugarcane was maximized at 1.68 kg/ha (91 and 86% control, respectively). In another study, 25-cm sugarcane was controlled equally with isopropyl amine and potassium salt glyphosate formulations. Bermudagrass control 40 d after glyphosate was applied at 1.12 kg/ha was 86% and increased to 98% when the same rate was applied sequentially. In fallowed sugarcane fields, conventional-tillage, reduced-tillage, and no-tillage programs were implemented from mid-April through mid-August to evaluate weed control and economics. When a glyphosate application was substituted for a tillage operation, bermudagrass and johnsongrass control was increased compared with the conventional tillage alone program, but differences in sugarcane and sugar yield among the various programs the following year were not observed. Based on 2006 costs, elimination of a single tillage operation reduced cost $18.49/ha and addition of glyphosate (2.8 kg/ha plus application cost) increased cost $43.47/ha. Total cost for the conventional tillage–alone fallow program was $110.94/ha; where herbicide was used in the reduced-tillage and no-tillage programs, total cost was $19.47 to $77.38/ha more. Nomenclature: Diuron; glyphosate; hexazinone; bermudagrass, Cynodon dactylon L. Pers. CYNDA; johnsongrass, Sorghum halepense L. Pers. SORHA; sugarcane, Saccharum spp. hybrids ‘LCP 85-384’.
Modified Rectangular Microstrip Antenna for Wideband Response with Conical Radiation Pattern

Broadband behavior of antennas with gap coupled configurations has been reported so far. But most of the configurations explained about broadside radiation pattern. This paper puts forward the idea of a novel compact antenna configuration for broadband response with conical radiation pattern. A rectangular microstrip antenna is truncated along its width and pairs of sectoral patches are gap coupled along truncated edges to obtain broadband response. The resonant frequency modes are identified through the study of surface current distributions. Bandwidth improvement is observed due to nearness of TM20 mode of truncated microstrip antenna and TM10mode of the pairs of parasitic sectors. A simulated bandwidth of 642 MHz (37%) has been realized with a gain of nearly 8 dBi. The novelty of the work lies in achieving conical radiation pattern with uni polar currents at the band edge frequencies.