Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Formation of Cyclobutane Pyrimidine Dimers in UV-irradiated DNA: Why are Thymines More Reactive?¶

Abstract The reaction pathways for thermal and photochemical formation of cyclobutane pyrimidine dimers in DNA are explored using density functional theory techniques. Although it is found that the thermal [2 + 2] cycloadditions of thymine + thymine (T + T → T⋄T), cytosine + cytosine (C + C → C⋄C) and cytosine + thymine (C + T → C⋄T) all are similarly unfavorable in terms of energy barriers and reaction energies, the excited-state energy curves associated with the corresponding photochemical cycloadditions display differences that—in line with experimental findings—unanimously point to the predominance of T⋄T in UV-irradiated DNA. It is shown that the photocycloaddition of thymines is facilitated by the fact that the S1 state of the corresponding reactant complex lies comparatively high in energy. Moreover, at a nuclear configuration coinciding with the ground-state transition structure, the excited-state energy curve displays an absolute minimum only for the T + T system. Finally, the T + T system is also associated with the most favorable excited-state energy barriers and has the smallest S2–S0 energy gap at the ground-state transition structure.
UVB-activated Psoralen Reduces Luminal Narrowing After Balloon Dilation Because of Inhibition of Constrictive Remodeling¶

Abstract In this study we have explored the potential of PUVB (8-MOP + UVB) therapy for the reduction of luminal narrowing after arterial injury. In 15 rabbits, balloon dilation of iliac arteries was performed. In 20 arteries, dilation was combined with the delivery of pulsed ultraviolet light B (UVB) irradiation with 10 arteries being previously subjected to sensitizer infusion. Changes in vessel diameter, proliferation and extracellular matrix protein content at 6 weeks were evaluated by means of angiography and histomorphometry–immunohistochemistry. We found that PUVB, applied at the time of dilation, induced reduction in late loss (LL) at 6 weeks (percutaneous transluminal angioplasty vs UVB vs PUVB: 0.64 ± 0.15 mm vs 0.61 ± 0.05 mm vs 0.29 ± 0.05 mm; p = 0.018). The same holds true for constrictive remodeling (0.53 ± 0.15 mm vs 0.45 ± 0.06 mm vs 0.15 ± 0.05 mm; p = 0.016). In the irradiation groups, LL was independent of acute gain (AG), as opposed to the control. Collagen content increased significantly after PUVB in media and adventitia, without increased cellular proliferation in all vessel layers. Thus, PUVB at the time of dilation reduced luminal narrowing at follow-up without effecting proliferation. This effect was independent of AG and was associated with increased collagen content in media and adventitia.
Identification of a Vibrational Frequency Corresponding to H-atom Translocation in Hypericin¶

Abstract Using time-resolved infrared spectroscopy, ab initio quantum mechanical calculations and synthetic organic chemistry a region in the infrared spectrum of triplet hypericin has been found between 1400 and 1500 cm−1 corresponding to the translocation of the hydrogen atom between the enol and the keto oxygens, O···H···O. This result is discussed in the context of the photophysics of hypericin and of eventual measurements to observe directly the excited-state H-atom transfer.
EVOLUTION OF GENOME SIZE IN PINES (PINUS) AND ITS LIFE-HISTORY CORRELATES: SUPERTREE ANALYSES

Genome size has been suggested to be a fundamental biological attribute in determining life-history traits in many groups of organisms. We examined the relationships between pine genome sizes and pine phylogeny, environmental factors (latitude, elevation, annual rainfall), and biological traits (latitudinal and elevational ranges, seed mass, minimum generation time, interval between large seed crops, seed dispersal mode, relative growth rate, measures of potential and actual invasiveness, and level of rarity). Genome sizes were determined for 60 pine taxa and then combined with published values to make a dataset encompassing 85 species, or 70% of species in the genus. Supertrees were constructed using 20 published source phylogenies. Ancestral genome size was estimated as 32 pg. Genome size has apparently remained stable or increased over evolutionary time in subgenus Strobus, while it has decreased in most subsections in subgenus Pinus. We analyzed relationships between genome size and life-history variables using cross-species correlations and phylogenetically independent contrasts derived from supertree constructions. The generally assumed positive relation between genome size and minimum generation time could not be confirmed in phylogenetically controlled analyses. We found that the strongest correlation was between genome size and seed mass. Because the growth quantities specific leaf area and leaf area ratio (and to a lesser extent relative growth rate) are strongly negatively related to seed mass, they were also negatively correlated with genome size. Northern latitudinal limit was negatively correlated with genome size. Invasiveness, particularly of wind-dispersed species, was negatively associated with both genome size and seed mass. Seed mass and its relationships with seed number, dispersal mode, and growth rate contribute greatly to the differences in life-history strategies of pines. Many life-history patterns are therefore indirectly, but consistently, associated with genome size.
TERTIARY MARINE MOLLUSCAN ASSEMBLAGES OF EASTERN PATAGONIA (ARGENTINA): A BIOSTRATIGRAPHIC ANALYSIS

Abstract Pectinids are the most abundant and widely distributed taxa in the Tertiary marine beds of Patagonia. Along with other very common molluscan species, they characterize five assemblages, from oldest to youngest: 1) the Oligocene Panopea sierrana– Parinomya patagonensis Assemblage; 2) the Late Oligocene–Early Miocene Jorgechlamys centralis–Reticulochlamys borjasensis Assemblage; 3) the Early Miocene Reticulochlamys zinsmeisteri–Struthiolarella patagoniensis–Pleuromeris cruzensis Assemblage; 4) the Early Miocene Pseudoportlandia glabra–Antimelatoma quemadensis Assemblage; and 5) the latest Early Miocene–earliest Middle Miocene Nodipecten sp. –Venericor abasolensis–Glycymerita camaronesia Assemblage. A brief analysis of the origin and composition of these Tertiary Patagonian molluscan faunas is provided. Striking compositional changes occurred through time, recorded mainly in the Late Paleocene, Late Eocene, Late Oligocene–Early Miocene, and Late Miocene.
Swim Initiation Neurons in Tritonia diomedea1

Abstract Two groups of interneurons, Tr1 and DRI, have been identified in the escape swim circuit of the marine mollusc Tritonia diomedea that have important roles in behavioral initiation. DRI functions as a command neuron, receiving direct excitatory input from the afferent neurons, and in turn directly exciting the DSI neurons of the central pattern generator. DRI fires throughout the swim motor program, and activity in DRI is both necessary and sufficient for sensory input to elicit the swim motor program. Tr1 is an excitatory interneuron that fires briefly in response to sensory input and then remains silent during the motor program. Tr1 excites DRI with an excitatory connection that has fast and slow components and thus appears to have a role in converting brief afferent neuron activity to long-lasting firing in downstream circuit elements. These neurons complete the description of a continuous synaptic pathway from afferent to flexion neurons in the Tritonia swim circuit. Their identification should facilitate studies of motor program initiation, as well as of how various forms of experience, including simple forms of learning, act to influence neuronal decision-making processes.
SEED LONGEVITY IN THREE PAIRS OF NATIVE AND NON-NATIVE CONGENERS: ASSESSING INVASIVE POTENTIAL

Abstract The goal of this study was to determine whether seed longevity is an indicator of invasive potential. We studied annual (Polygonum) and woody perennial (Celastrus, Parthenocissus) non-native species and their native congeners in a three-year buried seed experiment. The woody perennial species formed a transient seed bank lasting only one year. In year one, both perennial non-native species had significantly greater germination than their native congeners. Both Polygonum species formed a persistent seed bank, but the invasive P. perfoliatum had greater longevity than the native P. sagittatum. The study demonstrated that seed bank strategies of invasive species are qualitatively similar to their less abundant native congeners, but there were significant quantitative differences.
Albedo-enhanced Maximum UV Irradiance—Measured on Surfaces Oriented Normal to the Sun¶

Abstract UV radiation measured on normal-to-the-sun-oriented surfaces can show significantly higher global UV irradiance values compared to measurements on horizontal receivers. The direct component is amplified by the inverse cosine of the zenith angle, but over surfaces with high local albedo this accounts for only about half of the signal rise of global irradiance. The signal rise of the diffuse component, however, is strongly related to local albedo and solar elevation, which is demonstrated by 2 years of measurements of direct, diffuse, global, reflected and global normal-to-the-sun erythemal effective UV irradiance (UVery). Global UVery signal rises, on normal-to-the-sun-oriented versus horizontal receivers, of up to 65% were measured on fresh snow and solar elevation angles below 30°. An empirical expression has been deduced from the measurements relating the ratio of normal-to-the-sun versus horizontal measurements of global UVery to surface albedo and solar elevation. This allows one to calculate the maximum global UVery irradiance levels which are to be expected on normal-to-the-sun-oriented surfaces with respect to horizontal measurements or model calculations.
Middle Eocene to Middle Miocene planktonic foraminiferal biostratigraphy for internal basins (Monferrato and northern Apennines, Italy)

Abstract A planktonic foraminiferal zonal scheme is proposed for the internal basinal successions of the Monferrato and Northern Apennines (late Bartonian-early Serravallian). This scheme is based on a synthesis of quantitative analyses performed on the foraminiferal assemblages from 30 stratigraphic sections, cropping out over a distance of 300 km, between the Piedmont and the Northern Apennines. The proposed zonal scheme represents the synthesis, with minor changes, of the biozonations proposed by Novaretti et al. (1995) and Mancin and Pirini (2001) with the addition of unpublished data from some new sections, spanning a broader temporal and geographical range. With respect to the previous regional and standard biozonations, this scheme shows a better biostratigraphical resolution resulting from the replacement of missing or unreliable standard bioevents with new “reproducible” and reliable regional biohorizons. These new events are: LO of muricate species, which identifies the top of the Acarinina spp. , Globigerinatheka spp. and Turborotalia cerroazulensis Assemblage Zone because Truncorotaloides rohri is very rare to absent; LO of Turborotalia cerroazulensis lineage, which marks the top of the Turborotalia cerroazulensis Interval Zone because the Hantkenina group is absent; LO of psuedohastigerinids, which marks the upper boundary of the Pseudohastigerina spp. Interval Zone because Cassigerinella chipolensis and Pseudohastigerina micra do not co-occur; the former appears later, in the Globigerina ampliapertura Zone, whereas the latter often disappears near the Eocene/Oligocene boundary; FCO of Paragloborotalia opima opima, which identifies the Paragloborotalia opima opima Subzone boundary (IFP21a/IFP21b) because the LO of Chiloguembelina cubensis is a weakly reliable event; FO of Globoquadrina dehiscens, which marks the Paragloborotalia kugleri Subzone boundary (IFN1a/IFN1b) because the FCO of the Globigerinoides group occurs later; LO of Paragloborotalia kugleri, which identifies the top of the P. kugleri Total Range Zone because the FO of Globigerinoides altiaperturus occurs later and finally, the FO of Globigerinoides trilobus, used to subdivide the interval between the LO of P. kugleri and the LO of Catapsydrax dissimilis, because Globigerinatella insueta is absent. Other homotaxial biohorizons have also been recognized and introduced among the primary bioevents. These “secondary events” can help in better placing zonal and subzonal boundaries when the primary events cannot be used and in the refinement of the correlations among the different sections. The validity of this proposal, in our view, consists in the general correspondence between the adopted bioevents and the standard zonal boundaries and therefore in an easy correlation with the various standard schemes. Moreover, the area of applicability of this biozonation could be extended to the surrounding basins and also to coeval Mediterranean successions.
THE MAINTENANCE OF REPRODUCTIVE ISOLATION IN A MOSAIC HYBRID ZONE BETWEEN THE FIRE-BELLIED TOADS BOMBINA BOMBINA AND B. VARIEGATA

Abstract Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 × 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.
Within-year variation in the vegetative spread of five temperate grasses

Abstract Questions: Do species planted outdoors in native soil differ in the timing of their period of vegetative spread during the growing season? Location: Cleish Hills, Fife, Scotland, UK. Methods: Patches (20 cm × 20 cm) of Agrostis capillaris, Festuca rubra, Holcus lanatus, Lolium perenne and Poa trivialis were arranged in plots so that every species patch had all the remaining species as neighbours. The plots were cut every 14 days at 3 cm and photographed monthly from above. The photographs of species boundaries were traced and digi-tised. Measurements were made on the digitised images of the distances each species spread and of the area occupied by each species. Results: Fitting some simple models to the data indicated firstly that species varied in their vegetative competitive ability, with A. capillaris and P. trivialis being the most and least competitive respectively, and secondly that the ability of a species to colonize can differ from its ability to resist colonization, the most discrepant species being H. lanatus. Our analysis also indicated statistically significant variation in the data over and above the simple models, providing evidence of additional, genuine, complexity in the seasonal patterns of spread. Conclusion: This study provides evidence to support the hypothesis that clonal grass species do not spread vegetatively at the same times within a growing season. Since sward height is known to affect species spread, there is some opportunity for the manipulation of species composition simply through temporal control of sward height. Nomenclature: Stace (1991). Abbreviations: s.e. d. =standard error of difference.
Ultraviolet A Radiation Induces Rapid Apoptosis of Human Leukemia Cells by Fas Ligand–Independent Activation of the Fas Death Pathway¶

Abstract Endogenous cellular chromophores absorb ultraviolet A radiation (UVA, 290–320 nm), the major UV component of terrestrial solar radiation, leading to the formation of reactive oxidizing species that initiate apoptosis, gene expression and mutagenesis. UVA-induced apoptosis of T helper cells is believed to underlie the UVA phototherapy for atopic dermatitis and other T cell–mediated inflammatory skin diseases. We have evaluated the involvement of the Fas–Fas ligand (FasL) pathway in rapid UVA-induced apoptosis in human leukemia HL-60 cells. UVA-induced apoptosis was not inhibited by pretreatment with a neutralizing anti-Fas antibody, although the same UVA treatment initiated cleavage of caspase-8 and subsequent processing of Bid and caspase-3–like proteases. Inhibition of caspase-8 by Lle-Glu (OMe)-Thr-Asp(OMe)-fluoromethyl ketone completely blocked caspase-3 cleavage and apoptosis in UVA-treated cells, suggesting that apoptosis was initiated by the Fas pathway. This inference was supported by demonstrating that immunoprecipitates obtained from UVA-treated cells using anti-Fas antibody contained caspase-8 and Fas-associating protein with death domain (FADD). In addition, Fas clustering in response to UVA treatment was observed by immunofluorescence microscopy. These data support a mechanism for rapid, UVA-induced apoptosis in HL-60 cells involving initial formation of the Fas–FADD–caspase-8 death complex in an FasL-independent manner.
Control of the Cranio-Cervical System During Feeding in Birds1

Abstract The avian neck is a complex, kinematically redundant system, which plays a role during inter alia food prehension and manipulation. Kinematical analysis shows that chickens (Gallus domesticus) move their vertebrae according to a geometric principle that maximizes angular rotation efficiency. The movement pattern shows simultaneous rotations in some joints, while not in the others. Anseriformes show a pattern of successive, rather than simultaneous rotations in the rostral part of the neck. A kinematical model indicates that the geometric principle produces an anseriform-like pattern only if a constraint on the movement of the caudal vertebrae is introduced. The strength of this constraint, required for a realistic simulation, is related to the amount of stretch in the long dorsal neck muscles (M. biventer and M. longus colli dorsalis), which have a different configuration in Anseriformes compared to the chicken. To investigate whether the difference in movement pattern is a result of differences in anatomy only, or also of differences in neuromotor patterns, the EMG-patterns of the neck muscles of the mallard and chicken during drinking and pecking were studied. Considerable overlap in the activity of antagonists is found in mallards, but not in chickens. Muscles in the rostral part of the neck are activated successively in mallards, but simultaneously in chickens. We conclude that the difference in movement patterning between chickens and Anseriformes, results from both a difference in the control system of the neck, and a difference in the anatomy. The anseriform pattern is found in water as well as on land, which suggests that neck movement in both environments is controlled by the same neuromotor patterns. The modifications in motor control system and anatomy of the Anseriformes may have evolved as an adaptation to aquatic feeding, since the anseriform pattern is energetically more beneficial in an aquatic environment than on land.
Talking Back: Sending Soil Vibration Signals to Lekking Prairie Mole Cricket Males1

Abstract The male prairie mole cricket, Gryllotalpa major, native of the tallgrass prairie of the south central U.S., constructs a specialized acoustical burrow in the spring in the prairie soil from which he generates an airborne calling song that attracts flying females for mating. Males do not phonorespond to manipulations involving playbacks of airborne sounds. At the same time, vibrations with the same temporal scale and pattern as the airborne signal are produced in the substrate through an unknown mechanism. These ground vibrations can be distinguished from background vibrations in the soil at distances up to 3 m depending on soil conditions and conditions that control the background vibration environment (e.g., wind, highway traffic). We hypothesize that males use the vibration component of the call as information for spacing as they form display arenas, or leks. We used modified field recordings of soil vibrations from singing males with an electromechanical vibration exciter to simulate the vibration component of a calling song in playback experiments. Airborne sounds of males were monitored for two minutes before and two minutes after the introduction of the ground vibration stimulus with a tape recorder microphone placed 20 cm from the burrow opening. Males did respond to the manipulation experiment; although, we observed individual variation in the level of response.
Influence of virtual networks to internet collective behavior

A virtual network is defined as a logical network, in which users exhibit their access behaviors. Virtual networks rely on physical computer networks like the Internet, but have different topologies, and cause significant influence on the physical networks. In this paper, a novel two-tier model is proposed to study influences of virtual networks to Internet collective behavior. It is shown that the queue lengths of the node data packets present phase transition characteristics. Moreover, the phase transition critical point moves to the left and network performance is deteriorated. In a free flow, the nodes are independent of each other or short-range correlative. In the critical state, the nodes are long-range correlative, and there exists a higher power exponent H which means stronger long-range correlation. When the system state is on the right of critical point, virtual network behaviors make the network to present consistent long-range correlative characteristic.
EVALUATION OF d 2, A MICROSATELLITE MEASURE OF INBREEDING AND OUTBREEDING, IN WOLVES WITH A KNOWN PEDIGREE

We have evaluated a microsatellite measure proposed as an indicator of inbreeding and outbreeding using a captive wolf population with known inbreeding levels and founder sources. The measure, which is based on the difference in the repeat number for microsatellite alleles within an individual, was not more predictive of the known inbreeding coefficient than microsatellite heterozygosity (it was actually less predictive). We also found no support that the measure was predictive of the level of outbreeding. However, we could not determine if the measure was predictive of very low levels of inbreeding due to matings between remote relatives. Overall, it appears that the usefulness of this measure to identify individuals on the inbred-outbred continuum beyond that of heterozygosity and identify biologically important associations with fitness-related traits may be limited. We suggest that the measure be examined theoretically to determine when (and how much) the predictive value of the measure is different from that of heterozygosity for inbreeding or outbreeding levels in a variety of different scenarios.