Miracle-dz/UniFAR-FTUs huggingface dataset:
Intraspecific Variation in Developmental Characters: The Origin of Evolutionary Novelties1

Abstract Evolutionary developmental biology is inevitably a comparative subject. However, the taxonomic level at which comparisons can be made varies widely, and this greatly affects the kind of information that can be gained from the comparison. Broadly speaking, high-level comparisons (e.g., between phyla) are more informative about phylogenetic pattern and homology, while low-level comparisons (e.g., between congeneric species) are more informative about evolutionary mechanisms, including speciation. However, so far evolutionary developmental biology has had a relatively minor input into the traditional territory of population genetics, namely comparisons within species—both within and between geographic populations. Yet this area is crucial, as all evolutionary novelties ultimately arise from intraspecific variation. Here, I address this issue, focusing on the question of how early in development novelties arise. To shed light on this question, I discuss two examples of developmental polymorphism within species involving two of the main body axes: anteroposterior segmentation in centipedes and left–right asymmetry (chirality) in gastropods.
Activation of Poly(adenosine diphosphate–ribose) Polymerase in Mouse Tumors Treated by Photodynamic Therapy¶

Abstract Poly(adenosine diphosphate–ribose) polymerase (PARP) has recently been characterized as a key regulator of cell death–survival transcriptional programs associated with stress and inflammation. Possible participation of this enzyme in the response of tumors to photodynamic therapy (PDT) was investigated in this study. Immunohistochemical analysis of mouse FsaR tumors treated by PDT based on photosensitizers Photofrin or 5,10,15,20-tetra-(m-hydroxyphenyl)chlorine (mTHPC) revealed a strong positive staining for PARP product poly(ADP-ribose) at 30 min and 1 h after PDT, respectively, and even more intense positivity at 2 h after PDT with both photosensitizers. Flow cytometry–based examination showed the induction of poly-ADP-ribosylation in FsaR tumors at 30 min after PDT, with a trend for a further increase in the intensity by 2 h after PDT in both cancer cells and tumor-associated leukocytes. In FsaR cells treated in vitro by mTHPC-based PDT, flow cytometric analysis indicated that the activation of PARP concentrated in cells undergoing apoptosis and reached a maximum by 30 min after PDT. The administration of PARP inhibitors, 3-aminobenzamide or 1,5-isoquinolinediol, to FsaR tumor–bearing mice before PDT light treatment increased the resistance of these tumors to PDT. PARP appears to control the balance between apoptotic and necrotic cell death in PDT-treated tumors and regulate the progression of PDT-induced inflammatory or innate immune response.
Ultraviolet-B–induced Inactivation of Human OGG1, the Repair Enzyme for Removal of 8-Oxoguanine in DNA†,¶

Abstract The OGG1 proteins are DNA N-glycosylases–apurinic-apyrimidinic lyases that are responsible for the removal of 8-oxo-7,8-dihydroguanine (8-oxoG) base in DNA. The human enzyme (hOGG1) is a monomer of 345 amino acids containing 10 buried tryptophan (Trp) residues that are very sensitive to UVB irradiation. The photolysis quantum yield of these Trp residues is about 0.3 and 0.1 in argon- and air-saturated solutions, respectively. Matrix-assisted laser desorption-ionization–time-of-flight mass spectrometry shows that several cleavage sites are identical under aerobic and anaerobic photolysis of Trp residues; one of them includes the active site. Western blots and polyacrylamide gel electrophoresis indicate that fragments of high molecular size are also formed. In addition to common photochemical paths with argon-saturated solutions, specific reactions occur in air-saturated solutions of hOGG1. The photolysis rate is inhibited by more than 50% on binding of hOGG1 to a 34mer oligonucleotide containing a single 8-oxoG–C base pair. Binding to the oligonucleotide with 8-oxoG–C induced a 20% quenching of the hOGG1 fluorescence, suggesting interaction of nucleic acid bases with the Trp residue(s) responsible for the photolysis. Using 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine (Me-FapyG) and 8-oxoG as substrates, it is shown that protein photolysis induces photoinactivation of the DNA N-glycosylase activities. The excision of 8-oxoG is more affected than that of Me-FapyG at the same dose of UVB irradiation under both air and argon conditions. Besides the role of Trp residues, the possible involvement of Cys 253 in the photoinactivation process of hOGG1 is discussed.
Activation of Heat Shock Protein 70 Promoter with meso-Tetrahydroxyphenyl Chlorin Photodynamic Therapy Reported by Green Fluorescent Protein In Vitro and In Vivo¶

Abstract Cellular responses to photodynamic therapy (PDT) include induction of heat shock proteins (HSP). We examined meso-tetrahydroxyphenyl chlorin (mTHPC) PDT–mediated HSP activation in EMT6 cells stably transfected with a plasmid containing the gene for green fluorescent protein (GFP) driven by an hsp70 promoter. mTHPC incubation induced concentration-dependent GFP expression. Irradiation of cells exposed to a sensitizer concentration that induced a slight increase in GFP and no loss of cell viability resulted in fluence-dependent GFP accumulation. In response to drug only and to PDT, GFP levels increased to a maximum of four- to five-fold above control levels with increasing drug or fluence and then decreased at higher doses. A trypan blue–exclusion assay confirmed that decreased GFP levels in both cases were due to a loss of cell viability. For initial evaluation in vivo, HSP70/GFP–transfected EMT6 tumors were grown in BALB/c mice and subjected to mTHPC-PDT with a fluence of 1 J/cm2. Six hours after PDT, GFP fluorescence was imaged in these tumors through the intact skin in vivo. These results indicate that sublethal doses of mTHPC-PDT stimulate GFP expression under the control of an hsp70 promoter and illustrate the potential of noninvasively monitoring reporter protein fluorescence as a measure of molecular response to PDT.
Efficient coding and mapping algorithms for software implementation of a real-time H.263+ compliant low bit rate video coder |

The growing interest in video coding applications led to the development of video coding standards. Several successful standards have emerged, such as the ITU-T H.261, H.263, ISO/EEC MPEG-1 and MPEG-2. ITU-T recently announced its latest low bit rate video coding standard, the H.263 Version 2, also known as the H.263+ standard [25]. While this new low bit rate video coding standard provides better compression performance levels than those of the former ones, it is more complex and is more computationally, demanding. In this thesis, we develop coding and mapping algorithms that improve the video coding speed performance, making a reality the software implementation of interactive real-time low bit rate video coding on the Pentium M M X general purpose processor. First, using statistical properties of low resolution and slowly varying video sequences, we manage to significantly reduce the computation times of the most computationally intensive components of video coding, particularly the DCT, the IDCT, quantization and half pixel motion search. We also map some of the SIMD (Single Instruction Multiple Data) oriented functions onto Intel's M M X architecture. The developed algorithms are implemented using our public-domain H.263+ encoder/decoder software [45]. After the algorithmic optimization and the M M X mapping, the resulting H.263+ video encoder implementation runs approximately 3 times faster than the original unoptimized public-domain encoder implementation. Moreover, our optimized H.263+ compliant video coder implementation can encode/decode more than 15 frames of a QCIF (176x144) video sequence per second without sacrificing video reproduction quality.
Safety properties and memory bound analysis in a functional language without a garbage collector

In most functional languages, memory management is delegated to the runtime system. There usually exists a garbage collector in charge of determining, at runtime, which parts of the memory are no longer needed and can be disposed of. The main advantage of this approach is that programmers are not bothered about memory management issues. However, this purely implicit approach makes it difficult to predict, at compile time, the lifetimes of the data structures at runtime. Other languages delegate the task of memory management to the programmer. In this way, the lifetimes of data structures are known at compile time. However, this is an error-prone approach, since the programmer might try to access to memory areas which have been disposed of previously (dangling pointers), mainly due to unexpected sharing between data structures. Safe is a first-order functional language that provides a semiexplicit approach to memory management by means of two mechanisms: regions (inferred by the compiler), and destructive pattern matching (controlled by the programmer). In this way, we can do without a garbage collector to destroy the data structures that are no longer used. As a consequence, the behaviour of programs (regarding memory usage) becomes more predictable, and eases the task of developing a static analysis to infer upper bounds on the memory needs of a program. The incorporation of explicit mechanisms for memory destruction implies the risk of accessing dangling pointers. The first goal of this thesis is to develop a static analysis for guaranteeing the safety of a program with regard to its memory accesses (specifically, the absence of dangling pointers). Once the compiler has checked the presence of this property for a given program, our next goal is to formalize this property as a certificate, so the latter can be automatically checked by the code receiver. Finally, we will develop an abstract interpretation-based analysis for inferring upper bounds to the memory needs of a program. Since the final aim of the Safe project is the certification of pointer-safety properties and bounded memory execution, we have put emphasis on the formal correctness of each analysis.
Vertical Stratification and Caloric Content of the Standing Fruit Crop in a Tropical Lowland Forest1

ABSTRACT Fruit abundance in tropical forests thus far has been studied in relation to consumer populations. Area-based surveys that focus on the quantity and quality of the standing fruit crop of an entire plant community, however, are lacking. This paper presents the results of a four-month study on the seasonality and vertical distribution of the standing fruit crop within a tropical forest during the dry season in southern Venezuela. Fruit numbers ranged from 262,000 to 424,000 fruits/ha. The standing crop was between 39 and 92 kg/ha, yielding 67,000 to 126,000 kJ. Fruits were not evenly distributed in different forest layers. They were most abundant in the canopy above 16 m and scarce between 4 and 12 m above the ground. Despite a scarcity of fruits in the mid-strata, the caloric value of the total fruit supply peaked within a narrow layer of subcanopy at 12 to 16 m above ground due to a high amount of energy per fruit. Palms fruited mostly in this layer, their fruits contributing 59 percent of the energy supplied by all fruits. Above 12 m, we found a broader range of fruit sizes than in the forest below 12 m. Small-sized fruits were distributed in the understory and in the canopy but were nearly absent from the mid-story. Corresponding to the abundance of small-sized fruits in the canopy, small frugivorous species, such as members of the Thraupidae, limited their foraging to the canopy strata whereas larger avian frugivores foraged mainly in the mid-story.
PARASITE-HOST SPECIFICITY: EXPERIMENTAL STUDIES ON THE BASIS OF PARASITE ADAPTATION

Abstract Specificity in parasitic interactions can be defined by host genotypes that are resistant to only a subset of parasite genotypes and parasite genotypes that are infective on a subset of host genotypes. It is not always clear if specificity is determined by the genotypes of the interactors, or if phenotypic plasticity (sometimes called acclimation) plays a larger role. Coevolutionary outcomes critically depend on the pervasiveness of genetic interactions. We studied specificity using the bacterial parasite Pasteuria ramosa and its crustacean host Daphnia magna. First, we tested for short-term adaptation of P. ramosa lines that had been rapidly shifted among different host genotypes. Adaptation at this time-scale would demonstrate the contribution of phenotypic plasticity to specificity. We found that infectivity was stable across lines irrespective of recent passage history, indicating that in the short term infection outcomes are fixed by genetic backgrounds. Second, we studied longer-term evolution with two host clones and two parasite lines. In this experiment, P. ramosa lines had the possibility to evolve adaptations to the host genotype (clone) in which they were serially passaged, which allowed us to test for a genetic component to specificity. Substantial differences arose in the two passaged lines: one parasite line gained infectivity on the host clone it was grown on, but it lost infectivity on the other host genotype (this line evolved specificity), while the other parasite line evolved higher infectivity on both host clones. We crossed the two host genotypes used in the serial passage experiment and found evidence that the number of host genes that underlies resistance variation is small. In sum, our results show that P. ramosa specificity is a stably inherited trait, it can evolve rapidly, and it is controlled by few genes in the host. These findings are consistent with the idea of a rapid, ongoing arms race between the bacterium and its host.
Factors Contributing to Variation in Seed Production among Remnant Populations of the Endangered Daisy Gerbera aurantiaca1

ABSTRACT The species-rich mist-belt grasslands of southern Africa have been severely reduced in extent as a result of commercial afforestation, thus confining many endemic plants and animals to small populations in habitat fragments. We investigated the influence of various environmental factors on seed production and seedling recruitment in remnant populations of the endangered grassland herb Gerbera aurantiaca (Asteraceae). Experiments with color traps showed that Eriesthis beetles, which appear to be the primary pollinators of G. aurantiaca, were most abundant in the two largest extant populations. Seeds are produced in a very small proportion (typically <10%) of the ca 80 female florets in a capitulum. The mean number of seeds produced in undamaged capitula was found to be significantly lower in small than in large populations. Pollen limitation was evident from a significant overall increase in seed set after supplemental pollination in three populations over two seasons. The proportion of capitula containing seed predators did not differ markedly among populations or years, but lepidopteran larvae, which destroy all of the seeds in a capitulum, were most abundant in the two largest populations in 2003. The presence of juvenile plants varied markedly among populations, but this could not be linked firmly to estimates of seed production. Clonal growth is likely to contribute to the persistence of small isolated populations of G. aurantiaca, even when seed production is severely compromised by pollen limitation and predation.
ANIMAL SIGNALS AND THE OVERLOOKED COSTS OF EFFICACY1

The most striking aspects of many animals are signals. Thus one might expect Animal Signals by John Maynard Smith and David Harper to discuss the detailed biology of this half of the communication dyad. Not so. Instead, they concentrate on a single question, why signals are reliable, and emphasize one methodology to its solution: game theory. Although not embracing the entire biology of signaling, the book grapples with a continuing problem. Signals evolved to communicate information and manipulate receivers to the signaler’s benefit. Similarly, the receiver’s response to signals is under selection to promote its fitness. The issue at hand is the conflict between signal and receiver: what keeps the signaler from providing false information to the receiver? Zahavi (1975) explained signal reliability with the handicap principle: males evolve costly signals to indicate their underlying genetic quality for survivorship. The authors detail how this theory was rejected enthusiastically by modelers, including Maynard Smith (1976; see also Kirkpatrick 1986), and resurrected as enthusiastically a decade later (Pomiankowski 1987; Grafen 1990). Maynard Smith and Harper, however, argue convincingly that although sufficient, the handicap principle is hardly necessary to explain reliable signals because not all signals are costly, and not all costs are handicaps. Several situations enforce signal reliability without handicaps: signalers and receivers share common interests, both parties have conflicting interests yet agree on preferences for outcomes, cheaters are punished, or signals cannot be faked. In this last and most interesting case, signals are constrained to be reliable by morphology and physiology—this type of signal is an index (p. 60; see also Enquist 1985). The authors offer as an example the frequency of a red deer’s call being constrained by larynx size. Males can evolve larger larynges and behaviors to expand its size, but once such innovations are fixed in the population, call frequency again becomes a reliable index (p. 46). Many signals that are not indices are costly to the signaler. Is this cost prima facie evidence for a handicap, as Zahavi might suggest? No. ‘‘Demonstrating that a signal is costly, therefore, is not evidence that it is a handicap. ’’ (p. 16; see also Ryan 1998a) Why? The authors point out that there is more to signaling than reliability, and they identify a dichotomy of signal costs. Efficacy costs are those required to ensure that signals can be transmitted efficiently to the receiver (p. 73). Strategic costs are additional costs that ensure signal reliability—Zahavi’s handicaps. Effective signaling is
A Weight Voltage DAC been Chained by Weight Resistance

This article brings forward a kind of Weight Voltage DAC which is been chained by Weight Resistances,a n bits DAC is based on n Weight Resistances(20r,21r,22 r,…,2n-1r) which formed a resistance-chain and crossed connecting to anode and cathode of the power source,whichever Weight Resistance could be linked up or down output point according to the controlling digital signals,thus makes the output voltage becoming Weight Voltage combination corresponded to digital signal,achieving a Weight Voltage Digital-Analog Convert(DAC). Weight Voltage DAC,its conversion precision only depends on the precision of resistance.Such DAC has following characters: abandon the traditional Weight Current principle by adopting the Weight Voltage principle;compared with Weight Current DAC,its maximum current streaming drops two orders of magnitude;More likely to improve the precision of conversion.
Alien Abduction: Disruption of Native Plant-Pollinator Interactions by Invasive Species1

ABSTRACT The indirect impacts of Shorea siamensis-logging on the reproductive ecology of Dipterocarpus obtusifolius, a self- incompatible butterfly-, moth-, and bird-pollinated tree, were studied in tropical dry forest in Thailand. Pollinator activity at D. obtusifolius trees and subsequent seed production were recorded in three forest areas subject to differing intensities of S. siamensis extraction. The pollinator and plant understory communities in these areas were also noted. Forest areas subject to high S. siamensis extraction intensities had very high understory flowering plant cover, dominated by the exotic invader Chromolaena odorata. Activity of butterfly pollinators at D. obtusifolius trees decreased in these disturbed areas, although their abundance remained comparable to other forest areas subject to only moderate or no extraction. For sphingid moth pollinators, there was no difference across differentially disturbed forest areas in either abundance or in the proportion bearing pollen. Pollinator activity by birds increased at highly disturbed locations but was not sufficient to offset a decline in overall pollinator activity at D. obtusifolius canopies in areas of heavy S. siamensis extraction. Thus, extraction of S. siamensis indirectly affected the pollination of D. obtusifolius, primarily by causing changes in the foraging behavior of butterfly pollinators rather than their abundance. A shift in the relative abundance of floral nectar resources from the canopy to the understory, a consequence of S. siamensis extraction and invasion by C. odorata, led to a parallel shift in foraging location of the principal diurnal pollinators, the butterflies, toward the understory. Despite reduced pollination at disturbed sites, behavioral changes did not translate into a D. obtusifolius seed set effect, possibly because pollination by birds (or moths) at the disturbed site compensated for reduced butterfly pollination.
CONSTRAINTS ON THE MORPHOLOGICAL EVOLUTION OF MARSUPIAL SHOULDER GIRDLES

Abstract Throughout their evolutionary histories, marsupial mammals have been taxonomically and morphologically less diverse than their sister taxa the placentals. Because of this, it has been proposed that the evolution of marsupials has been constrained by the functional requirements of their mode of reproduction. Marsupials give birth after short gestation times to immature neonates that immediately crawl, under the power of their precociously developed shoulder girdles, to the teat where they attach and complete their early development. Using a novel approach incorporating adult and embryological morphological data, this study is the first to both: (1) statistically support adult patterns of morphological divergence consistent with the constraint hypothesis, and (2) identify ontogenetic patterns of morphological change that demonstrate that the constraint was responsible, at least in part, for their formation. As predicted by the marsupial constraint, the shoulder girdles of adult marsupials are less diverse than those of adult placentals, and adult marsupial scapulae are less morphologically diverse than adult marsupial pelves. Furthermore, marsupials that complete an extensive crawl to the teat are restricted to a common pattern of ontogenetic scapular shape change, strongly supporting the hypothesis that the morphological development of the marsupial scapula has been limited evolutionarily by its obligate role in the crawl to the teat. Because this study establishes that ontogenetic and evolutionary morphological change is correlated within mammalian scapulae, it is probable that the marsupial constraint also restricted the morphological divergence of the scapula over evolutionary time by limiting ontogenetic change in the scapula. These findings, coupled with the importance of the shoulder girdle in mammalian locomotor specialization, support the conclusion that the low morphological diversity of marsupial forms over evolutionary time could be directly due to the constraint on marsupial morphological evolution caused by the functional requirements of the crawl to the teat.