Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Future Infrastructure Development on Threat Status and Occurrence of Amazonian Birds

Abstract: Researchers predict that new infrastructure development will sharply increase the rate and extent of deforestation in the Brazilian Amazon. There are no predictions, however, of which species it will affect. We used a spatially explicit model that predicts the location of deforestation in the Brazilian Amazon by 2020 on the basis of historical patterns of deforestation following infrastructure development. We overlaid the predicted deforested areas onto maps of bird ranges to estimate the amount of habitat loss within species ranges. We also estimated the amount of habitat loss within modified ecoregions, which were used as surrogates for areas of bird endemism. We then used the extent of occurrence criterion of the World Conservation Union to predict the future conservation status of birds in the Brazilian Amazon. At current rates of development, our results show that at least 16 species will qualify as threatened or will lose more than half of their forested habitat. We also identified several subspecies and isolated populations that would also qualify as threatened. Most of the taxa we identified are not currently listed as threatened, and the majority are associated with riverine habitats, which have been largely ignored in bird conservation in Amazonia. These habitats and the species they hold will be increasingly relevant to conservation as river courses are altered and hydroelectric dams are constructed in the Brazilian Amazon.
New developments in viral peptides and APL induction.

The associations of antiphospholipid antibodies (aPL) with thrombosis and fetal death are well recognized, but the mechanism(s) that induce their production are not. We demonstrated induction of pathogenic aPL antibodies by immunization with foreign beta(2)-GPI, or synthetic peptides representing the PL-binding site of the beta(2)-GPI. These antibodies caused intrauterine fetal death and transverse myelopathy due to spinal cord infarction in mice, and activated endothelial cells in vitro. We also introduced aPL in mice by immunization with PL-binding viral peptides and observed their pathogenic effects. This study demonstrated that pathogenic effects of aPL antibodies induced by immunization with a human CMV-derived PL-binding synthetic peptide. We hypothesize that in APS patients aPL is induced by beta(2)-GPL-like PL-binding products of human common bacteria or viruses.
Interoperability Standards in the Semantic Web

The growth in the use of the Internet brings with it an increase in the number of interconnections among information systems supporting the manufacturing supply chain as well as other businesses. Each of these interconnections must be carefully prescribed to ensure interoperability. However, the sheer number of interconnections and the resulting complexity threaten to overwhelm the ability of the standards community or industry to provide the necessary specifications—a way out of this impasse must be found. This paper outlines the elements of an approach and the technology to move toward self-integrating systems, wherein the systems negotiate meaningful interfaces as needed in a dynamic environment. DOI: 10.1115/1.1480024
Performing Big Data over Cloud on a Test-Bed

Data analytics has been rapidly growing in a variety of application areas like mining business intellect for processing the huge amount of data. MapReduce programming paradigm adds itself well to these data-intensive analytics jobs, given its one of the well known ability to scale-out and force several machines to parallely process data. This paper introduces a detailed analysis of big data over cloud computing with several mapred techniques from system and application aspects. Here in this work we say that such Mapper and Reducer based analytics provide a better result over cloud platform. However, End-Users in this environment has the ability to use MapReduce applications to minimize the incurred cost, while obtaining the best performance. From the implementation point of view, we describe the key issues and challenges of big data on cloud and on local system as well. At last, the challenges come across in implementing MapReduce functions over Hadoop and the analysis of standalone, clustered and virtualized systems over our testbed. General Terms Mapper, Reducer, Hadoop, Cloud, Virtualization
Evolution of DNA Methylation across Insects

DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects.
Synthesis of Fe3O4 nanoparticles for colour removal of printing ink solution

Fe3O4 nanoparticles can be used as an adsorbent for colour removal of printing ink which contribute as a pollutant in wastewater. Fe3O4 was synthesized by coprecipitation method using FeCl3.6H2O and (NH4)2Fe(SO4)2.6H2O precursors dissolved in distilled water in mol ratio of Fe3+: Fe2+ = 2:1. NaOH solution was added slowly into the iron solution with continuous stirring for 60 minutes in Argon gas atmosphere. After drying, Fe3O4 nanoparticle product is obtained as black crystalline powder with an average particle size about 34 nm. The Fe3O4 nanoparticles (0.1 g) were able to remove blue, red, and yellow colour with percentage of adsorption about 97%, 94%, and 62% for 40 minutes contact time and 100 rpm of stirring speed, respectively. Fe3O4 nanoparticle can be separated from the printing ink solution by an external magnetic field.
Reasoning with contradictory information using quasi-classical logic

The proof theory of quasi-classical logic (QC logic) allows the derivation of non-trivializable classical inferences from inconsistent information. A non-trivializable, or paraconsistent, logic is, by necessity, a compromise, or weakening, of classical logic. The compromises on QC logic seem to be more appropriate than other paraconsistent logics for applications in computing. In particular, the connectives behave in a classical manner. Here we motivate the need for QC logic, present a proof theory, and semantics for the logic, and compare it to other paraconsistent logics.
Complete genome sequence of Nakamurella multipartita type strain (Y-104T)

Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the monospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein-coding and 56 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project.
Powernet for distributed energy resource networks

We propose Powernet as an end-to-end open source technology for economically efficient, scalable and secure coordination of grid resources. It offers integrated hardware and software solutions that are judiciously divided between local embedded sensing, computing and control, which are networked with cloud-based high-level coordination for real-time optimal operations of not only centralized but also millions of distributed resources of various types. Our goal is to enable penetration of 50% or higher of intermittent renewables while minimizing the cost and address security and economical scalability challenges. In this paper we describe the basic concept behind Powernet and illustrate some components of the solution.
Evolutionary Dynamics of the Mitochondrial Genome in the Evaniomorpha (Hymenoptera)—A Group with an Intermediate Rate of Gene Rearrangement

We determined the complete mitochondrial (mt) genomes of three evaniomorph species, Ceraphron sp. (Ceraphronoidea), Gasteruption sp. (Evanioidea), and Orthogonalys pulchella (Trigonalyoidea) as well as the nearly complete mt genome from another evaniomorph species, Megalyra sp. (Megalyroidea). Each of them possesses dramatic gene rearrangements, including protein-coding or rRNA genes. Gene inversions were identified in all of these mt genomes; for example, the two rRNA genes have inverted and moved into the nad2-cox1 junction in the Megalyra sp. mt genome. In addition, we found two copies of a 10-bp complementary repeat at the beginning of rrnS and at the end of trnL2 in the Gasteruption sp. mt genome, consistent with recombination as the possible mechanism for gene inversion and long-range movement. Although each of the genomes contains a number of repeats of varying size, there was no consistent association of the size or number of repeats with the extent or type of gene rearrangement. The breakpoint distance analysis showed the Evaniomorpha has an intermediate rate of gene rearrangement. Sequence-based phylogenetic analyses of 13 protein-coding and 2 rRNA genes in 22 hymenopteran taxa recovered a paraphyletic Evaniomorpha with the Aculeata nested within it. Within the Evaniomorpha, our analyses confirmed the Trigonalyoidea + Megalyroidea as the sister group to the Aculeata and recovered a novel clade, Ceraphronoidea + Evanioidea. In contrast to previous hymenopteran phylogenetic studies, the internal relationships of the Evaniomorpha were highly supported and robust to the variation of alignment approach and phylogenetic inference approach.
Parallel digraphs-building algorithm for polynomial realisations of one-dimensional positive systems with delays

In this paper, the new method of the determination of entries of the state matrices of the positive one-dimensional systems with delay using multidimensional digraphs theory D(n) has been presented. For the proposed method, parallel computing algorithm was constructed. This algorithm is based on GPGPU (General-Purpose Computing on Graphics Processing Units) computing method to gain needed speed and computational power for such a solution. The proposed method was discussed and illustrated with numerical examples. The proposed solution allows minimal digraphs construction for any positive one-dimensional system with delays, regardless of its complexity.
Antiplatelet antibody [7E3 F(ab')2] prevents rethrombosis after recombinant tissue-type plasminogen activator-induced coronary artery thrombolysis in a canine model.

Coronary artery rethrombosis can complicate initially effective thrombolytic therapy. Platelets interacting with injured vascular endothelium in a region along the coronary artery with reduced luminal cross-sectional area contribute to rethrombosis. The purpose of this study was to investigate the potential of the F(ab')2 fragment of the murine monoclonal antibody 7E3 [7E3 F(ab')2] to prevent rethrombosis after intracoronary clot lysis with recombinant tissue-type plasminogen activator (rt-PA) in an experimental model. The 7E3 F(ab')2 binds to the platelet glycoprotein IIb/IIIa complex (GPIIb/IIIa), thereby preventing platelet-fibrinogen interaction and intravascular thrombus formation. Experimental coronary artery thrombosis was produced in the anesthetized dog by application of direct anodal current to the intimal surface of the left circumflex coronary artery in the region of an external stenosis. Lysis of the established intracoronary thrombus was achieved with the intravenous administration of rt-PA (25 mg) after which the animals were randomized into two groups. Group 1 (n = 10) served as the control, receiving the saline diluent, and group 2 (n = 9) received 7E3 F(ab')2, given as a single intravenous injection (0.8 mg/kg). The times required for occlusive thrombus formation, rt-PA-induced thrombolysis, and rethrombosis (if it occurred) were similar in the animals treated with saline and those treated with 7E3 F(ab')2. The initial left circumflex coronary artery blood flow was similar in both groups but decreased to a negligible level in group 1. In group 2, left circumflex coronary artery blood flow declined modestly (24 +/- 2 to 10 +/- 2 ml/min). Rethrombosis occurred in all animals in group 1 but in only two of nine animals in group 2 (p less than 0.05). Oscillations in coronary blood flow preceded rethrombosis in group 1, whereas 7E3 F(ab')2 stabilized left circumflex coronary artery blood flow patterns during the course of teh experimental protocol (5.2 +/- 0.9 vs. 0.7 +/- 0.4 oscillations, respectively; p less than 0.05). Thrombus mass recovered from the left circumflex coronary artery at the conclusion of each experiment was greater in group 1 as compared with group 2 (7.0 +/- 2.3 vs. 1.5 +/- 0.7 mg, respectively; p less than 0.05). The area of left ventricle at risk for infarction was similar in both groups but infarct size, infarction/at risk assessed histochemically, was larger in group 1 than group 2 (35 +/- 9% vs. 6 +/- 4%, respectively; p less than 0.05). Platelet aggregation induced by ADP and arachidonic acid was similar at baseline for all of the animals. (ABSTRACT TRUNCATED AT 400 WORDS)
Lightweight SLAM and Navigation with a Multi-Camera Rig

An interesting recent branch of SLAM algorithms using vision has taken an appealing approach which can be characterised as simple, robust and lightweight when compared to the more established and complex geometrical methods. These lightweight approaches typically comprise mechanical odometry or simple visual odometry for local motion estimation; appearance-based loop closure detection using either whole image statistics or invariant feature matching; and some type of efficient pose graph relaxation. However, such algorithms have so far been proven only as localisation systems, since they have not offered the semantic demarcation of free space and obstacles necessary to guide fully autonomous navigation and exploration. In this paper we investigate how to apply and augment such approaches with other lightweight techniques to permit fully autonomous navigation and exploration around a large and complicated room environment. Our approach uses only odometry and visual sensing, the latter being provided by a rig of multiple standard cameras without the need for precise inter-camera calibration. A particular focus of our work is to investigate the camera configurations which are most valuable to permit the capabilities needed by autonomous navigation, and our solution neatly assigns each camera a well-defined specialist role.
Effects of Fentanyl and Low Doses of Alcohol on Neuropsychological Performance in Healthy Subjects

The effects of the opioid fentanyl and low doses of alcohol on neuropsychological functions in healthy volunteers were measured. Twenty-four healthy male volunteers participated in this study. Two randomised placebo-controlled cross-over trials were conducted. In group 1, 6 subjects received fentanyl (0.2 µg/kg body weight) in the order of fentanyl/placebo and 6 subjects in the order of placebo/fentanyl. Group 2 received alcohol in a similar procedure by continuous intravenous infusion, leading to a blood alcohol concentration (BAC) of 0.03%. Impairment was measured via different neuropsychological tests. The results indicate that fentanyl in concentrations commonly used in out-patient surgical procedures produces pronounced cognitive impairment (auditory reaction time, signal detection, sustained attention, recognition) in comparison to placebo. After application of low doses of alcohol (BAC 0.03%) only visual reaction time was impaired in comparison to placebo.
Reevaluating the Prognostic Significance of Age in Differentiated Thyroid Cancer

Objective To determine the impact of age on disease-specific survival in differentiated thyroid cancer. Study Design Retrospective analysis of a large population database. Setting Surveillance, Epidemiology, and End Results (SEER) database/multiple settings. Subjects and Methods The SEER database was examined to identify patients diagnosed with either papillary or follicular carcinoma of the thyroid between the years 1988 and 2003. Information obtained included patient age, sex, tumor type, size, extension, and nodal or distant metastases. Kaplan-Meier survival analyses were used to estimate disease-specific survival based on patient age range, and the log-rank test was used to assess for statistical differences between survival curves. A multivariate analysis was performed including the variables listed above to determine disease-specific hazard ratios of death for various age cutoffs. Results A total of 42,209 patients were identified. Patients 45 years and older had significantly worse survival than younger patients (P < .0001). A significant decrease in disease-specific survival was first seen in patients aged 35 years and older, and survival continued to steadily decrease with each additional decade of age (P < .001). Patients aged 35 years and older were 14 times more likely to die from differentiated thyroid cancer than patients younger than 35 years. Conclusion Increasing age is associated with poorer survival in differentiated thyroid cancer. This relationship represents a continuum with an initial decrease in survival starting at age 35 years that continues to decline with further advancing age.
Identification of sequences required for the efficient localization of the focal adhesion kinase, pp125FAK, to cellular focal adhesions

The integrin family of heterodimeric cell surface receptors play critical roles in multiple biological processes by mediating cellular adhesion to the extracellular matrix (ECM). Adhesion triggers intracellular signaling cascades, including tyrosine phosphorylation and elevation of [Ca2+]i. The Focal Adhesion Kinase (FAK or pp125FAK), a protein tyrosine kinase that colocalizes with integrins in cellular focal adhesions, is a prime candidate for a mediator of integrin signaling events. Here we report an analysis of the domain structure of FAK in which we have identified a contiguous stretch of 159 amino acids within the COOH terminus essential for correct subcellular localization. When placed in the context of an unrelated cytosolic protein, this Focal Adhesion Targeting (FAT) sequence functions to efficiently mediate the focal adhesion localization of this fusion protein. Furthermore, this analysis suggests that pp125FAK cannot be activated oncogenically by mutation. This result could be explained if pp125FK either exhibits a narrow substrate specificity or is diametrically opposed by cellular phosphatases or other cellular processes.
Regenerating human-like arm motions of humanoid robots for a movable object

A method to regenerate a new human-like arm motion by modifying and scaling a human arm motion is presented. The humanoid robot may not obtain all the necessary human-like motions from motion capture data. When the robot communicates with a person, the robot has to keep attention to the person by aligning the direction of the motion. The robot needs to modify human arm motions and regenerate new human-like arm motions without loosing the original meanings. The developed method modifies and scales the wrist trajectory of a human arm motion and reproduces the human-like arm. The motion of drawing multiple circles with a various radius and direction is examined.
Dynamic Changes in Gene Expression along the Rat Epididymis1

Abstract In the epididymis a series of complex, sequential events transform immature, spermatozoa into mature, motile sperm with fertilizing ability. These events are not intrinsic to germ cells but rather are a direct result of exposure to, and interaction with, the environment created by the epididymal epithelium. Regional differences along the epididymis are essential in the establishment of the environment required for sperm maturation. Although parts of this process have been identified, the molecular basis for the segment-specific differences and how they contribute to the process of sperm maturation, are not yet resolved. The identification of genes expressed in a region-specific manner will provide valuable insight into the functional differences between the regions. To characterize gene expression in the different regions of the epididymis, microarrays containing 1176 rat cDNAs were used to examine gene expression in the initial segment, caput, corpus, and cauda epididymidis of the adult Brown Norway rat. Overall, the cauda epididymidis expressed the most genes and the corpus epididymidis the fewest. A small percentage of genes (3%) were expressed highly (greater than fivefold the average expression on the array) along the tissue. Segment-specific gene expression for genes expressed at high levels was observed in all epididymal segments except the corpus epididymidis. Of the genes on the array, 36% were expressed in all four epididymal segments; expression changes that were a minimum of twofold in either direction between adjacent segments are discussed. The expression of cathepsins and oxidative stress-related genes was investigated. Six of the eight cathepsins on the array (B, C, E, H, L, and K) were expressed above twofold background and showed different levels of expression along the duct with cathepsin K showing the most dramatic change (i.e., a decrease of 87% between the initial segment and the corpus epididymidis). There was also differential expression along the epididymis of many genes associated with oxidative stress defenses. Using the power of expression array technology, we have identified novel transcripts expressed in a segment-specific manner and been able to assess how the expression of several selected gene families is modulated along the epididymis.