Miracle-dz/UniFAR-FTUs huggingface dataset:
Richard Kirwan's Phlogiston Theory: Its Success and Fate

Abstract First proposed in the early 1780s, Richard Kirwan's phlogiston theory was the most successful enunciation of the English pneumatic approach to phlogiston. Phlogiston was identified with a material substance, inflammable air. In this paper, I explore the nature of Kirwan's theory, its success in the mid-1780s, the unprecedented collective attack on Kirwan's Essay on Phlogiston by Lavoisier and his colleagues, and Kinvan's ultimate abandonment of phlogistic explanation.
Interactive scenario generation for mission‐based virtual training

For a virtual training system, how to effectively and quickly generate training scenarios has become a challenging issue. A scenario generation system is needed to produce scenarios that can meet different objectives and at the same time be customized for individuals. In this paper, we introduce a scenario generation framework for mission‐based virtual training, which aims to generate scenarios from both trainer and trainee's perspective. The framework allows a trainer to direct the scenario generation process, so that the generated scenarios reflect the trainer's preferences over different mission objectives. It also considers how the scenarios could adapt to different trainees’ skill levels. The representation of scenario beat is proposed, and the scenario generation process adopts a combinatorial optimization approach generating the sequence of scenario beats. The efficacy of the proposed framework is demonstrated through an empirical study of human players in a simple food distribution mission game. The results show that a trainee can achieve better performance improvement when playing the customized scenarios tailored to the trainee's skill level as compared with the uncustomized scenarios. Copyright © 2013 John Wiley & Sons, Ltd.
Nutrient Requirements Early Posthatch Feeding Stimulates Satellite Cell Proliferation and Skeletal Muscle Growth in Turkey Poults 1

The effect of early posthatch feeding on skeletal muscle growth and satellite cell myogenesis was studied in turkey poults. Poults were either fed immediately posthatch or food-deprived for the first 48 h and then refed for the rest of the experiment. Body and breast muscle weights were lower in the starved poults than in fed controls throughout the experiment (P 0.05). Cultures of breast muscle satellite cells revealed significantly higher DNA synthesis in the fed group than in the starved group as early as d 1 (P 0.05). These levels continued to rise, reaching 500-fold those of feed-deprived poults on d 4. In the latter group, thymidine incorporation peaked only on d 6, and then declined. Thereafter, it decreased to the same levels as those in the fed group. Satellite cell number per gram muscle increased until d 4, and was higher in the fed group than in the starved group (P 0.05). Pax7 levels in cell cultures derived from the fed group were markedly higher than in the starved group on d 2 (P 0.05). Myogenin levels in both culture and muscle were higher in the fed than in the starved groups until d 4 (P 0.05). Phosphorylation of the survival factor Akt and cyclin-dependent kinase inhibitor p21 levels were higher in cells derived from the fed group relative to those from the starved group 48 h posthatch (P 0.05). Similarly, Akt phosphorylation and insulin-like growth factor I (IGF-I) levels were significantly higher in the muscles of the fed group (P 0.05). Together, these results suggest that immediate posthatch feeding of poults is critical for satellite cell survival and myogenesis probably via IGF-I. J. Nutr. 133: 1376–1382, 2003.
In vitro selection of DNAs with an increased propensity to form small circles

A protocol was devised to select for DNA molecules that efficiently form circles from a library of 126 base pair DNAs containing 90 randomized base pairs. After six rounds of selection, individual molecules from the library showed 20‐ to 100‐fold greater j‐factors compared with the starting library, validating the selection protocol. High‐throughput sequencing revealed a sinusoidal pattern of enrichment and de‐enrichment of A/T dinucleotides in the random region with a 10.4 base pair period associated with the helicity of DNA. A similar, but more moderate pattern of C/G dinucleotides was offset by precisely half a helical turn. While C/G dinucleotide enrichments were evenly distributed, A/T dinucleotide enrichments displayed a preference to cluster in individual DNA molecules. The most highly enriched 10 base pair sequences in the random region contained adjacent blocks of A/T and C/G trinucleotides present in some, but not all, rapidly cyclizing molecules. The phased dinucleotide enrichments closely match those present in accurately mapped yeast nucleosomes, confirming the importance of DNA bending in nucleosome formation. However, at certain sites the nucleosomal DNAs show dinucleotide enrichments that differ substantially from the cyclization data. These discrepancies can often be correlated with sequence specific contacts that form between histones and DNA. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 303–320, 2015.
Optimal flapping wing for maximum vertical aerodynamic force in hover: twisted or flat?

This work presents a parametric study, using the unsteady blade element theory, to investigate the role of twist in a hovering flapping wing. For the investigation, a flapping-wing system was developed to create a wing motion of large flapping amplitude. Three-dimensional kinematics of a passively twisted wing, which is capable of creating a linearly variable geometric angle of attack (AoA) along the wingspan, was measured during the flapping motion and used for the analysis. Several negative twist or wash-out configurations with different values of twist angle, which is defined as the difference in the average geometric AoAs at the wing root and the wing tip, were obtained from the measured wing kinematics through linear interpolation and extrapolation. The aerodynamic force generation and aerodynamic power consumption of these twisted wings were obtained and compared with those of flat wings. For the same aerodynamic power consumption, the vertical aerodynamic forces produced by the negatively twisted wings are approximately 10%–20% less than those produced by the flat wings. However, these twisted wings require approximately 1%–6% more power than flat wings to produce the same vertical force. In addition, the maximum-force-producing twisted wing, which was found to be the positive twist or wash-in configuration, was used for comparison with the maximum-force-producing flat wing. The results revealed that the vertical aerodynamic force and aerodynamic power consumption of the two types of wings are almost identical for the hovering condition. The power loading of the positively twisted wing is only approximately 2% higher than that of the maximum-force-producing flat wing. Thus, the flat wing with proper wing kinematics (or wing rotation) can be regarded as a simple and efficient candidate for the development of hovering flapping-wing micro air vehicle.
The equivalency between a decision tree for classification and a feedback neural network

In machine learning, the learning paradigms of an artificial neural network (ANN) and a decision tree (DT) are different, but they are equivalent in essence. This paper proves the approximate equivalency between feedback neural networks and decision trees. The result provides us a very useful guideline when we perform theoretical research and applications on DT and ANN.
Plasmodium Apicoplast Gln-tRNAGln Biosynthesis Utilizes a Unique GatAB Amidotransferase Essential for Erythrocytic Stage Parasites*

Background: Plasmodium apicoplast protein synthesis is essential for parasite survival, yet few of the enzymes involved have been biochemically characterized. Results: Nucleus-encoded apicoplast GatAB glutamyl-tRNA amidotransferase forms Gln-tRNAGln in concert with a non-discriminating glutamyl-tRNA synthetase. Conclusion: Formation of apicoplast Gln-tRNAGln is via indirect aminoacylation. Significance: The apicoplast indirect aminoacylation pathway is a potential drug target. The malaria parasite Plasmodium falciparum apicoplast indirect aminoacylation pathway utilizes a non-discriminating glutamyl-tRNA synthetase to synthesize Glu-tRNAGln and a glutaminyl-tRNA amidotransferase to convert Glu-tRNAGln to Gln-tRNAGln. Here, we show that Plasmodium falciparum and other apicomplexans possess a unique heterodimeric glutamyl-tRNA amidotransferase consisting of GatA and GatB subunits (GatAB). We localized the P. falciparum GatA and GatB subunits to the apicoplast in blood stage parasites and demonstrated that recombinant GatAB converts Glu-tRNAGln to Gln-tRNAGln in vitro. We demonstrate that the apicoplast GatAB-catalyzed reaction is essential to the parasite blood stages because we could not delete the Plasmodium berghei gene encoding GatA in blood stage parasites in vivo. A phylogenetic analysis placed the split between Plasmodium GatB, archaeal GatE, and bacterial GatB prior to the phylogenetic divide between bacteria and archaea. Moreover, Plasmodium GatA also appears to have emerged prior to the bacterial-archaeal phylogenetic divide. Thus, although GatAB is found in Plasmodium, it emerged prior to the phylogenetic separation of archaea and bacteria.
The Bordering Algorithm and Path Following Near Singular Points of Higher Nullity

We study the behavior of the bordering algorithm (a form of block elimination) for solving nonsingular linear systems with coefficient matrices in the partitioned form $\left( {\begin{array}{*{20}c} A & B \\ {C^ * } & D \\ \end{array} } \right)$ when $\dim \mathcal{N}(A) \geqq 1$. Systems with this structure naturally occur in path following procedures. We show that under appropriate assumptions, the algorithm, which is based on solving systems with coefficient matrix A, works as A varies along a path and goes through singular points. The required assumptions are justified for a large class of problems coming from discretizations of boundary value problems for differential equations.
Shared Tasks on German Sentiment Analysis ( GESTALT )

We present the German Sentiment Analysis Shared Task (GESTALT) which consists of two main tasks: Source, Subjective Expression and Target Extraction from Political Speeches (STEPS) and Subjective Phrase and Aspect Extraction from Product Reviews (StAR). Both tasks focused on fine-grained sentiment analysis, extracting aspects and targets with their associated subjective expressions in the German language. STEPS focused on political discussions from a corpus of speeches in the Swiss parliament. StAR fostered the analysis of product reviews as they are available from the website Amazon.de. Each shared task led to one participating submission, providing baselines for future editions of this task and highlighting specific challenges. The shared task homepage can be found at https://sites.google. com/site/iggsasharedtask/.
Epidemiology of osteosarcoma and Ewing's sarcoma in childhood

The Children's Cancer Group conducted a case‐control study to determine the role of a broad range of environmental and familial factors in the etiology of Ewing's sarcoma and osteosarcoma in children. These factors included radiation exposure and, for children with osteosarcoma, parental exposure to beryllium.
Experimental Performance of Shared Path Protection With Flooded Versus Collected Sharing Resource Information in GMPLS WSON Networks

In generalized multiprotocol label switching (GMPLS)-enabled wavelength-switched optical networks (WSONs), shared path protection (SPP) attains 100% survivability with an acceptable recovery time, for lightpaths affected by a single-link failure. This is achieved by sharing backup resources. Nevertheless, neither the standard OSPF-TE nor the RSVP-TE protocols support the respective flooding/collection of shareable resource information for SPP purposes. This prevents the source node from computing backup paths exploiting the SPP advantages, and the destination node from performing optimal wavelength assignment (WA) favoring the reuse of shareable resources. In this paper, we experimentally evaluate, in the GMPLS control plane of the ADRENALINE testbed, the performance improvements when shareable resource information is either flooded (by enhanced OSPF-TE) and/or collected (by enhanced RSVP-TE), under the wavelength continuity constraint. Additionally, we propose efficient SPP path computation and WA algorithms, considering three information dissemination strategies: aggregated unreserved bandwidth, aggregated shared bandwidth, and wavelength-channel granularity.
Comparison of the in vivo efficiency of photofrin II‐, mTHPC‐, mTHPC‐PEG‐ and mTHPCnPEG‐mediated PDT in a human xenografted head and neck carcinoma

One of the approaches to enhance the selectivity and efficiency of photodynamic therapy (PDT) was the conjugation of the photosensitizer meta‐tetrahydroxyphenylchlorin (mTHPC) to the water‐soluble polymer polyethylene glycol (PEG). Several studies have demonstrated that mTHPC‐PEG has a higher selectivity and a longer circulating half‐life than free mTHPC, whereas no in vivo effect of this benefit could be seen.
Suppression of grp78 core promoter element-mediated stress induction by the dbpA and dbpB (YB-1) cold shock domain proteins

The highly conserved grp78 core promoter element plays an important role in the induction of grp78 under diverse stress signals. Previous studies have established a functional region in the 3' half of the core (stress-inducible change region [SICR]) which exhibits stress-inducible changes in stressed nuclei. The human transcription factor YY1 is shown to bind the SICR and transactivate the core element under stress conditions. Here we report that expression library screening with the core element has identified two new core binding proteins, YB-1 and dbpA. Both proteins belong to the Y-box family of proteins characterized by an evolutionarily conserved DNA binding motif, the cold shock domain (CSD). In contrast to YY1, which binds only double-stranded SICR, the Y-box/CSD proteins much prefer the lower strand of the SICR. The Y-box proteins can repress the inducibility of the grp78 core element mediated by treatment of cells with A23187, thapsigargin, and tunicamycin. In gel shift assays, YY1 binding to the core element is inhibited by either YB-1 or dbpA. A yeast interaction trap screen using LexA-YY1 as a bait and a HeLa cell cDNA-acid patch fusion library identified YB-1 as a YY1-interacting protein. In cotransfection experiments, the Y-box proteins antagonize the YY1-mediated enhancement of transcription directed by the grp78 core in stressed cells. Thus, the CSD proteins may be part of the stress signal transduction mechanism in the mammalian system.
Facilitation of cortical responses by competing stimuli

During investigations of transmission in the sensory pathway of the rat, it was found that when an electrical test stimulus was applied to a forefoot the response to it, recorded from the dorsal surface of the medulla near the cuneate nucleus, could be reduced in size by stimulation of the cerebral cortex on the opposite side (Dawson, 1958). This effect occurred even when the animal was deeply anaesthetized. Similar results have been described in unanaesthetized, curarized, cats by Scherrer & Hern6andez-Peon (1955). Modifications of transmission in the spinothalamic pathways have been investigated by Hagbarth & Kerr (1954) and the alteration of responses of single units in the cuneate nucleus have been examined by Towe & Jabbur (1961) and Jabbur & Towe (1961). An electrical stimulus to the cerebral cortex, such as that used to modify the response of the cuneate nucleus to a test stimulus (Dawson, 1958) is unlikely to produce a natural pattern of discharge in the cerebral cortex itself, or in the pathways leaving it. Investigations were therefore begun to see whether similar alterations of the responses in the cuneate nucleus could be produced by stimulating the body surface instead of the cerebral cortex. This also allowed records to be made of the cortical responses to the test stimuli, to see how far their size was related to the size of the responses in the cuneate nucleus. The evidence to be presented shows that, under the conditions of these experiments, stimuli applied to various parts of the body surface have little or no effect on the responses of the cuneate nucleus to test stimuli applied subsequently to a forefoot. On the other hand, as has been reported elsewhere in abstract (Dawson, Podachin & Schatz, 1959), the responses of the cerebral cortex to the test stimuli were
The temporal and spatial pattern of histone H3 phosphorylation at serine 28 and serine 10 is similar in plants but differs between mono- and polycentric chromosomes

Immunolabeling using site-specific antibodies against phosphorylated histone H3 at serine 10 or serine 28 revealed in plants an almost similar temporal and spatial pattern of both post-translational modification sites at mitosis and meiosis. During the first meiotic division the entire chromosomes are highly H3 phosphorylated. In the second meiotic division, like in mitosis, the chromosomes contain high phosphorylation levels in the pericentromeric region and very little H3 phosphorylation along the arms of monocentric species. In the polycentric plant Luzula luzuloides phosphorylation at both serine positions occurs along the whole chromosomes, whereas in monocentric species, only the pericentromeric regions showed strong signals from mitotic prophase to telophase. No phosphorylated serine 10 or serine 28 was detectable on single chromatids at anaphase II resulting from equational segregation of rye B chromosome univalents during the preceding anaphase I. In addition, we found a high level of serine 28 as well as of serine 10 phosphorylation along the entire mitotic monocentric chromosomes after treatment of mitotic cells using the phosphatase inhibitor cantharidin. These observations suggest that histone H3 phosphorylation at serine 10 and 28 is an evolutionarily conserved event and both sites are likely to be involved in the same process, such as sister chromatid cohesion.
Regional topography of rod and immunocytochemically characterized “blue” and “green” cone photoreceptors in rabbit retina

Abstract Evidence from several sources indicates that the photoreceptors of rabbit retina include rods, green cones and blue cones, and that blue-green color opponency occurs in select retinal ganglion cells. One of us (Famiglietti) has identified wide-field cone bipolar cells as probable blue-cone-selective bipolars, and type C horizontal cells as possibly connected to blue cones. We wished to extend the analysis of blue cone pathways in rabbit retina and to characterize the topographic distribution of blue and green cones. Two monoclonal antibodies raised against chicken visual pigments are reported to label medium- and long-wavelength cones (COS-1) and short-wavelength cones (OS-2) in all mammalian retinas studied thus far (Szél and colleagues). Using selective labeling with these two antibodies and a nonselective method in nasal and temporal halves of the same retinas, we have found that densities of photoreceptors vary systematically, depending upon the size of the eye and age of the animal. In ‘standard’ New Zealand rabbits of 2–3 kg (2–3 months old), rods reached a peak density of about 300,000/mm2 just dorsal to the visual streak, while cones exhibit peak density at mid-visual streak of about 18,000/mm2. Published measurements of visual acuity in rabbit are less than predicted by this calculation. The ratio of cones to rods is significantly higher in ventral retina, where the density of cones declines to a plateau of 10,000–12,000/mm2, when compared to dorsal retina, where cones are uniformly distributed at a density of about 7000/mm2. The density of OS-2 labeled (presumably “blue”) cones is uniformly low, 1000–1500/mm2, in a wide expanse that includes dorsal retina, the visual streak, and much of ventral retina, except for a region of higher density along the vertical midline. We confirm that there is a far ventral horizontal region near the perimeter that is populated exclusively by a high density (about 13,000/mm2) of OS-2-positive cones (Juliusson and colleagues). This region does not extend to the ventral retinal margin, however, where cone density drops precipitously. Transitional zones between COS-1 and OS-2 labeling, in a region of relatively high and uniform cone density, where sums of COS-1 and OS-2 labeling are higher than expected and in which weakly and strongly labeled cones are intermixed, raise questions about the identities of the visual pigment epitopes, the possibility of double labeling, and therefore the possibility of dual expression of pigments in single cones. The “inverted- T -shaped” topography of higher density OS-2 labeling raises doubts about the significance of a ventral concentration of blue cones for visual function in rabbit retina.
School of IT Technical Report WALKABOUT: AN ASYCHRONOUS INTERNET MESSAGING ARCHITECTURE TAILORED TO MOBILE DEVICES

Walkabout is an architecture that provides network support for message transfer between mobile devices communicating across the Internet. In order to cope with changing addresses and device disconnections, devices send messages to each other across a peer-to-peer overlay network, via peers which are located in the same local network segments as they are. This enables them to transfer messages at local network speeds, maximising their usage of transient network connectivity. The overlay uses a transfer protocol that makes use of parallel downloads wherever possible. Messages migrate to follow destination devices as they move, and are cached when the destination is not available. We have designed an approach that is robust and efficient and intend to prove this through simulation and a series of
In vivo imaging of the mouse model of X-linked juvenile retinoschisis with fourier domain optical coherence tomography.

PURPOSE The purpose of this study was to investigate Fourier domain optical coherence tomography (FD OCT) as a noninvasive tool for retinal imaging in the Rs1h-knockout mouse (model for X-linked juvenile retinoschisis). METHODS A prototype spectrometer-based FD OCT system was used in combination with a custom optical beam-scanning platform. Images of the retinas from wild-type and Rs1h-knockout mice were acquired noninvasively with FD OCT with the specimen anesthetized. At the completion of the noninvasive FD OCT imaging, invasive retinal cross-sectional images (histology) were acquired from a nearby region for comparison to the FD OCT images. RESULTS The retinal layers were identifiable in the FD OCT images, permitting delineation and thickness measurement of the outer nuclear layer (ONL). During FD OCT in vivo imaging of the Rs1h-knockout mouse, holes were observed in the inner nuclear layer (INL), and retinal cell disorganization was observed as a change in the backscattering intensity profile. Comparison of the ONL measurements acquired noninvasively with FD OCT to measurements taken using histology at nearby locations showed a degeneration of roughly 30% of the ONL by the age of 2 months in Rs1h-knockout mice relative to wild-type. CONCLUSIONS FD OCT was demonstrated to be effective for noninvasive imaging of retinal degeneration and observation of retinal holes in Rs1h-knockout mice.