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Background: Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results: A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion: Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality. These results highlight the ongoing need for improvements in assembly methodology. Keywords: next generation sequencing; short read assembly; Mollusca
Background: The ventral midbrain contains a diverse array of neurons, including dopaminergic neurons of the ventral tegmental area (VTA) and substantia nigra (SN) and neurons of the red nucleus (RN). Dopaminergic and RN neurons have been shown to arise from ventral mesencephalic precursors that express Sonic Hedgehog (Shh). However, Shh expression, which is initially confined to the mesencephalic ventral midline, expands laterally and is then downregulated in the ventral midline. In contrast, expression of the Hedgehog target gene Gli1 initiates in the ventral midline prior to Shh expression, but after the onset of Shh expression it is expressed in precursors lateral to Shh-positive cells. Given these dynamic gene expression patterns, Shh and Gli1 expression could delineate different progenitor populations at distinct embryonic time points. Results: We employed genetic inducible fate mapping (GIFM) to investigate whether precursors that express Shh (Shh-GIFM) or transduce Shh signaling (Gli1-GIFM) at different time points give rise to different ventral midbrain cell types. We find that precursors restricted to the ventral midline are labeled at embryonic day (E)7.5 with Gli1-GIFM, and with Shh-GIFM at E8.5. These precursors give rise to all subtypes of midbrain dopaminergic neurons and the anterior RN. A broader domain of progenitors that includes the ventral midline is marked with Gli1-GIFM at E8.5 and with Shh-GIFM at E9.5; these fate-mapped cells also contribute to all midbrain dopaminergic subtypes and to the entire RN. In contrast, a lateral progenitor domain that is labeled with Gli1-GIFM at E9.5 and with Shh-GIFM at E11.5 has a markedly reduced potential to give rise to the RN and to SN dopaminergic neurons, and preferentially gives rise to the ventral-medial VTA. In addition, cells derived from Shh- and Gli1-expressing progenitors located outside of the ventral midline give rise to astrocytes. Conclusions: We define a ventral midbrain precursor map based on the timing of Gli1 and Shh expression, and suggest that the diversity of midbrain dopaminergic neurons is at least partially determined during their precursor stage when their medial-lateral position, differential gene expression and the time when they leave the ventricular zone influence their fate decisions.
Background: Parkinson's disease (PD) is a slowly progressive neurodegenerative disorder which affects widespread areas of the brainstem, basal ganglia and cerebral cortex. A number of proteins are known to accumulate in parkinsonian brains including ubiquitin and alpha-synuclein. Prion diseases are sporadic, genetic or infectious disorders with various clinical and histopathological features caused by prion proteins as infectious proteinaceous particles transmitting a misfolded protein configuration through brain tissue. The most important form is Creutzfeldt-Jakob disease which is associated with a self-propagating pathological precursor form of the prion protein that is physiologically widely distributed in the central nervous system. Discussion: It has recently been found that alpha-synuclein may behave similarly to the prion precursor and propagate between cells. The post-mortem proof of alpha-synuclein containing Lewy bodies in embryonic dopamine cells transplants in PD patient suggests that the misfolded protein might be transmitted from the diseased host to donor neurons reminiscent of prion behavior. The involvement of the basal ganglia and brainstem in the degenerative process are other congruencies between Parkinson's and Creutzfeldt-Jakob disease. However, a number of issues advise caution before categorizing Parkinson's disease as a prion disorder, because clinical appearance, brain imaging, cerebrospinal fluid and neuropathological findings exhibit fundamental differences between both disease entities. Most of all, infectiousness, a crucial hallmark of prion diseases, has never been observed in PD so far. Moreover, the cellular propagation of the prion protein has not been clearly defined and it is, therefore, difficult to assess the molecular similarities between the two disease entities. Summary: At the current state of knowledge, the molecular pathways of transmissible pathogenic proteins are not yet fully understood. Their exact involvement in the pathophysiology of prion disorders and neurodegenerative diseases has to be further investigated in order to elucidate a possible overlap between both disease categories that are currently regarded as distinct entities.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. In statistical spike train analysis, stochastic point process models usually assume stationarity, in particular that the underlying spike train shows a constant firing rate (e.g. [1]). However, such models can lead to misinterpretation of the associated tests if the assumption of rate stationarity is not met (e.g. [2]). Therefore, the analysis of nonstationary data requires that rate changes can be located as precisely as possible. However, present statistical methods focus on rejecting the null hypothesis of stationarity without explicitly locating the change point(s) (e.g. [3]). We propose a test for stationarity of a given spike train that can also be used to estimate the change points in the firing rate. Assuming a Poisson process with piecewise constant firing rate, we propose a Step-Filter-Test (SFT) which can work simultaneously in different time scales, accounting for the high variety of firing patterns in experimental spike trains. Formally, we compare the numbers N1=N1(t,h) and N2=N2(t,h) of spikes in the time intervals (t-h,t] and (h,t+h]. By varying t within a fine time lattice and simultaneously varying the interval length h, we obtain a multivariate statistic D(h,t):=(N1-N2)/V(N1+N2), for which we prove asymptotic multivariate normality under homogeneity. From this a practical, graphical device to spot changes of the firing rate is constructed. Our graphical representation of D(h,t) (Figure 1A) visualizes the changes in the firing rate. For the statistical test, a threshold K is chosen such that under homogeneity, |D(h,t)|<K holds for all investigated h and t with probability 0.95. This threshold can indicate potential change points in order to estimate the inhomogeneous rate profile (Figure 1B). The SFT is applied to a sample data set of spontaneous single unit activity recorded from the substantia nigra of anesthetized mice. In this data set, multiple rate changes are identified which agree closely with visual inspection. In contrast to approaches choosing one fixed kernel width [4], our method has advantages in the flexibility of h.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. One of the central questions in neuroscience is how neural activity is organized across different spatial and temporal scales. As larger populations oscillate and synchronize at lower frequencies and smaller ensembles are active at higher frequencies, a cross-frequency coupling would facilitate flexible coordination of neural activity simultaneously in time and space. Although various experiments have revealed amplitude-to-amplitude and phase-to-phase coupling, the most common and most celebrated result is that the phase of the lower frequency component modulates the amplitude of the higher frequency component. Over the recent 5 years the amount of experimental works finding such phase-amplitude coupling in LFP, ECoG, EEG and MEG has been tremendous (summarized in [1]). We suggest that although the mechanism of cross-frequency-coupling (CFC) is theoretically very tempting, the current analysis methods might overestimate any physiological CFC actually evident in the signals of LFP, ECoG, EEG and MEG. In particular, we point out three conceptual problems in assessing the components and their correlations of a time series. Although we focus on phase-amplitude coupling, most of our argument is relevant for any type of coupling. 1) The first conceptual problem is related to isolating physiological frequency components of the recorded signal. The key point is to notice that there are many different mathematical representations for a time series but the physical interpretation we make out of them is dependent on the choice of the components to be analyzed. In particular, when one isolates the components by Fourier-representation based filtering, it is the width of the filtering bands what defines what we consider as our components and how their power or group phase change in time. We will discuss clear cut examples where the interpretation of the existence of CFC depends on the width of the filtering process. 2) A second problem deals with the origin of spectral correlations as detected by current cross-frequency analysis. It is known that non-stationarities are associated with spectral correlations in the Fourier space. Therefore, there are two possibilities regarding the interpretation of any observed CFC. One scenario is that basic neuronal mechanisms indeed generate an interaction across different time scales (or frequencies) resulting in processes with non-stationary features. The other and problematic possibility is that unspecific non-stationarities can also be associated with spectral correlations which in turn will be detected by cross frequency measures even if physiologically there is no causal interaction between the frequencies. 3) We discuss on the role of non-linearities as generators of cross frequency interactions. As an example we performed a phase-amplitude coupling analysis of two nonlinearly related signals: atmospheric noise and the square of it (Figure 1) observing an enhancement of phase-amplitude coupling in the second signal while no pattern is observed in the first. Finally, we discuss some minimal conditions need to be tested to solve some of the ambiguities here noted. In summary, we simply want to point out that finding a significant cross frequency pattern does not always have to imply that there indeed is physiological cross frequency interaction in the brain.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. To truly appreciate the myriad of events which relate synaptic function and vesicle dynamics, simulations should be done in a spatially realistic environment. This holds true in particular in order to explain the rather astonishing motor patterns presented here which we observed within in vivo recordings which underlie peristaltic contractions at a well characterized synapse, the neuromuscular junction (NMJ) of the Drosophila larva. To this end, we have employed a reductionist approach and generated three dimensional models of single presynaptic boutons at the Drosophila larval NMJ. Vesicle dynamics are described by diffusion-like partial differential equations which are solved numerically on unstructured grids using the uG platform. In our model we varied parameters such as bouton-size, vesicle output probability (Po), stimulation frequency and number of synapses, to observe how altering these parameters effected bouton function. Hence we demonstrate that the morphologic and physiologic specialization maybe a convergent evolutionary adaptation to regulate the trade off between sustained, low output, and short term, high output, synaptic signals. There seems to be a biologically meaningful explanation for the co-existence of the two different bouton types as previously observed at the NMJ (characterized especially by the relation between size and Po),the assigning of two different tasks with respect to short- and long-time behaviour could allow for an optimized interplay of different synapse types. As a side product, we demonstrate how advanced methods from numerical mathematics could help in future to resolve also other difficult experimental neurobiological issues.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. Parallel multiunit recordings from V1 in anesthetized cat were collected during the presentation of random sequences of drifting sinusoidal gratings at 12 fixed orientations while gamma oscillations were present. In agreement with the seminal work [1], most units were orientation selective to varying degrees and synchronization was evident in spike train crosscorrelograms computed between units with similar preferred orientations, particularly during the presentation of optimal stimuli. Interestingly, a subset of units, which we refer to as synchronization hubs, were additionally found to synchronize with units having differing preferred orientations which was consistent with a previous study [2]. Moreover, oscillatory patterning in spike train autocorrelograms was also found to be strongest in units denoted as synchronization hubs, and synchronization hubs also tended to have narrower tuning curves relative to other units. We used simplified computational models of small networks of V1 neurons to demonstrate that neurons subject to a sufficiently strong level of inhibitory input can function as synchronization hubs. Neurons were endowed either with integrate-and-fire or conductance-based dynamics and each neuron received a combination of excitatory (AMPA) synaptic inputs that were Poisson-distributed and inhibitory (GABA) inputs that were coherent at a gamma-frequency range. If the strength of rhythmic inhibition was increased for a subset of neurons in the network, and excitation was increased simultaneously to maintain a fixed firing rate, then these neurons produced stronger oscillatory patterning in their discharge probabilities. The oscillations in turn synchronized these neurons with other neurons in the network. Importantly, the strength of synchronization increased with neurons of differing orientation preferences even though no direct synaptic coupling existed between the hubs and the other neurons. Enhanced levels of inhibition account for the emergence of synchronization hubs in the following way: Inhibitory inputs exhibiting a gamma rhythm determine a time window within which a cell is likely to discharge. Increased levels of inhibition narrow down this window further simultaneously leading to (i) even stronger oscillatory patterning of the neuron's activity and (ii) enhanced synchronization with other neurons. This enables synchronization even between cells with differing orientation preferences. Additionally, the same increased levels of inhibition may be responsible for the narrow tuning curves of hub neurons. In conclusion, synchronization hubs may be the cells that interact most strongly with the network of inhibitory interneurons during gamma oscillations in primary visual cortex.
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. Background: Oscillatory activity in high-beta and gamma bands (20-80Hz) is known to play an important role in cortical processing being linked to cognitive processes and behavior. Beta/gamma oscillations are thought to emerge in local cortical circuits via two mechanisms: the interaction between excitatory principal cells and inhibitory interneurons – the pyramidal-interneuron gamma (PING) [1], and in networks of coupled inhibitory interneurons under tonic excitation – the interneuronal gamma (ING) [2]. Experimental evidence underlines the important role of inhibitory interneurons and especially of the fast spiking (FS) interneurons [3,4]. We show in simulation that an important property of FS neurons, namely the membrane resonance (frequency preference), represents an additional mechanism – the resonance induced gamma (RING), i.e. modulation of oscillatory discharge by resonance. RING promotes frequency stability and enables oscillations in purely excitatory networks. Methods: Local circuits were modeled with small world networks of 80% excitatory and 20% inhibitory neuron populations interconnected in small-world topology by realistic conductance-based synapses. Neuron populations were leaky integrate and fire (LIF) or Izhikevich resonator (RES) neurons. We also tested networks of purely inhibitory and purely excitatory RES neurons. Networks were stimulated with miniature postsynaptic potentials (MINIs) [5] and with low frequency sinusoidal (0.5 Hz) input that mimics the effect of gratings passing trough the visual field. The activity was calibrated to match recordings from cat visual cortex (firing rate, oscillatory activity). Results: Sinusoidal input modulates network oscillation frequency. This effect is most prominent in IF excitatory and IF inhibitory (IF-IF) networks and less prominent (about 4 times) in IF-RES or RES-IF networks where frequency remains relatively stable. The most stable frequency was observed in networks of pure resonators (RES-RES, None-RES, RES-None). Interestingly, purely excitatory RES networks (RES-None) were also able to exhibit oscillations through RING. By contrast purely excitatory or inhibitory IF networks (IF-None, None-IF) were not able to express oscillations under these conditions, matching experimental parameters. Conclusions: In both PING and ING, adding membrane resonance to principal cells or inhibitory interneurons stabilizes network oscillation frequency via the RING mechanism. Notably, in networks of purely excitatory networks, where ING and PING are not defined, oscillations can emerge via the RING mechanism if membrane resonance is expressed. Thus, RING appears as a potentially important mechanism for promoting stable network oscillations.
Background: In many species males face a higher predation risk than females because males display elaborate traits that evolved under sexual selection, which may attract not only females but also predators. Females are, therefore, predicted to avoid such conspicuous males under predation risk. The present study was designed to investigate predator-induced changes of female mating preferences in Atlantic mollies (Poecilia mexicana). Males of this species show a pronounced polymorphism in body size and coloration, and females prefer large, colorful males in the absence of predators. Results: In dichotomous choice tests predator-naïve (lab-reared) females altered their initial preference for larger males in the presence of the cichlid Cichlasoma salvini, a natural predator of P. mexicana, and preferred small males instead. This effect was considerably weaker when females were confronted visually with the non-piscivorous cichlid Vieja bifasciata or the introduced non-piscivorous Nile tilapia (Oreochromis niloticus). In contrast, predator experienced (wild-caught) females did not respond to the same extent to the presence of a predator, most likely due to a learned ability to evaluate their predators' motivation to prey. Conclusions: Our study highlights that (a) predatory fish can have a profound influence on the expression of mating preferences of their prey (thus potentially affecting the strength of sexual selection), and females may alter their mate choice behavior strategically to reduce their own exposure to predators. (b) Prey species can evolve visual predator recognition mechanisms and alter their mate choice only when a natural predator is present. (c) Finally, experiential effects can play an important role, and prey species may learn to evaluate the motivational state of their predators. Keywords: Sexual selection; female choice; non-independent mate choice; predator recognition; Poecilia mexicana
The molecular conformation of the title compound, C18H18N2O3S, is stabilized by an intramolecular N—H ... O hydrogen bond. The crystal packing shows centrosymmetric dimers connected by N—H ... S hydrogen bonds. The terminal ethoxy substituents are statistically disordered [occupancy ratio 0.527 (5):0.473 (5)].
The title compound, C20H22O4S2, was synthesized by the reaction of 1,4-dibromobutene with methyl thiosalicylate. The aliphatic segment of this ligand is in an all-trans conformation. The bridging chain, –S-(CH2)4-S–, is almost planar (r.m.s. deviation for all non-H atoms: 0.056 Å) and its mean plane forms dihedral angles of 16.60 (7) and 5.80 (2)° with the aromatic rings. In the crystal, the molecules are linked by weak C—H ... O interactions into chains with graph-set notation C(14) along [0 0 1]. The crystal studied was a racemic twin, the ratio of the twin components being 0.27 (9):0.73 (9).
The title compound, C14H11NO4, crystallizes with two molecules in the asymmetric unit. The major conformational difference between these two molecules is the dihedral angle between the aromatic rings, namely 36.99 (5) and 55.04 (5)°. The nitro groups are coplanar with the phenyl rings to which they are attached, the O—N—C—C torsion angles being -1.9 (3) and 1.0 (3)° in the two molecules.
The 3,5-methoxy groups in the title compound, C16H23NO4, are almost coplanar with the aromatic ring, whereas the 4-methoxy group is bent out of this plane. The three CH3—O—C—C torsion angles are -1.51 (18), 0.73 (19) and 75.33 (15)°. The cyclohexane ring adopts a chair conformation. In the crystal, molecules are connected by intermolecular N—H ... O hydrogen bonds into chains running along the b axis.
The title compound. C15H14N2O4, (I), has a gauche–gauche (O/C/C/C—O/C/C/C or GG) conformation and is a positional isomer of propane-1,3-diyl bis(pyridine-3-carboxylate), (II). The molecule of (I) lies on a twofold rotation axis, which passes through the central C atom of the aliphatic chain, giving one half-molecule per asymmetric unit. There is excellent agreement of the geometric parameters of (I) and (II). The most obvious differences between them are the O/C/C/C—O/C/C/C torsion angles [56.6 (2)° in (I) and 174.0 (3)/70.2 (3)° in (II) for GG and TG conformations, respectively] and the dihedral angle between the planes of the aromatic rings [80.3 (10)° in (I) and 76.5 (3)° in (II)]. The crystal structure is stabilized by weak C—H ... N and C—H ... O hydrogen bonding.
4-Nitrophenyl 1-naphthoate
(2010)
In the title compound, C17H11NO4, the dihedral angle between the two benzene rings is 8.66 (3)°. The nitro group is twisted by 4.51 (9)° out of the plane of the aromatic ring to which it is attached. The presence of intermolecular C—H ... O contacts in the crystal structure leads to the formation of chains along the c axis.
The title compound, C6H5NO2·C6H6O2, crystallizes with one pyridinium-2-carboxylate zwitterion and one molecule of benzene-1,2-diol in the asymmetric unit. The crystal structure is characterized by alternating molecules forming zigzag chains running along the a axis: the molecules are connected by O—H ... O and N—H ... (O,O) hydrogen bonds.
Crystals of the title compound, C12H8N2·C7H8O2, were obtained during cocrystallization experiments of a compound with two hydrogen-bond donors (2-hydroxybenzyl alcohol) with another compound containing two hydrogen-bond acceptors (phenanthroline). Unexpectedly, the two molecules do not form dimers with two O—H ... N hydrogen bonds connecting the two molecules. However, one of the hydroxy groups forms a bifurcated hydrogen bond to both phenanthroline N atoms, whereas the other hydroxy group forms an O—H ... O hydrogen bond to a symmetry-equivalent 2-hydroxybenzyl alcohol molecule. In addition, the crystal packing is stabilized by Pi – Pi interactions between the two phenanthroline ring systems, with a centroid–centroid distance of 3.570 Å.
In the crystal of the title compound [systematic name: 2-(3,5-diamino-6-chloropyrazin-2-ylcarbonyl)guanidinium chloride methanol disolvate], C6H9ClN7O+·Cl-·2CH3OH , the components are connected by N—H ... N, N—H ... Cl, N—H ... O, O—H ... Cl and O—H ... O hydrogen bonds into a three-dimensional network. The dihedral angle between the aromatic ring and the guanidine residue is 6.0 (2)°.
In contrast to the previous structure determinations of the title structure, (NH4)2[MoS4], the present determination at 173 K localized the positions of the H atoms. The title structure belongs to the beta-K2SO4 family and all the ions are located on crystallographic mirror planes. The ions are held together by N—H ... S hydrogen bonds (some of which are bifurcated), forming a three-dimensional network. One of the N atoms has nine contacts to the S atoms shorter than 4 Å, and the other has ten.
The title compound (also know as azorellanone), C20H32O2, is built up from three fused carbocycles, one five-membered ring and two six-membered rings. The five membered-ring has an envelope conformation, whereas the six-membered rings have a distorted half-chair and a twist–boat conformation. In the crystal, molecules are linked by O—H ... O interactions into zigzag chains with graph-set notation C(8) along [010]. The absolute configuration was assigned on the basis of earlier chemical studies.
The dihydropyrimidine ring of the title compound, C13H15ClN2S, adopts an envelope conformation with five almost coplanar atoms (r.m.s. deviation = 0.054 Å) and the C atom bearing the two methyl substituents deviating from this plane by 0.441 (2) Å. The best plane through the five almost coplanar atoms forms a dihedral angle of 89.56 (5)° with the benzene ring. The crystal packing is characterized by centrosymmetric dimers connected by pairs of N—H ... S hydrogen bonds.
9-Bromo-9-borafluorene
(2010)
The title compound, C12H8BBr, crystallizes with three essentially planar molecules (r.m.s. deviations = 0.018, 0.020 and 0.021Å) in the asymmetric unit: since the title compound is rigid, there are no conformational differences between these three molecules. The crystal packing resembles a herringbone pattern.
The title compound, C22H28N2O6, crystallizes with four half-molecules in the asymmetric unit: each molecule is located about a crystallographic inversion centre. The central methylene groups of two molecules are disordered over two sets of equally occupied sites. The crystal packing is characterized by sheets of molecules parallel to (114).
In the title compound, C27H19N3O4, the phenol and pyrazole rings are almost coplanar [dihedral angle = 0.95 (12)°] due to an intramolecular O—H ... N hydrogen bond, whereas the phenyl ring is tilted by 40.81 (7)° with respect to the plane of the pyrazole ring. The aromatic ring with a nitrophenoxy substituent makes a dihedral angle of 54.10 (7)° with the pyrazole ring.
The title compound, C8H11FN5 +·Cl-, crystallized with a monoprotonated 1-(4-fluorophenyl)biguanidinium cation and a chloride anion in the asymmetric unit. The biguanidium group is not planar [dihedral angle between the two CN3 groups = 52.0 (1)°] and is rotated with respect to the phenyl group [tau = 54.3 (3)°]. In the crystal, N—H ... N hydrogen-bonded centrosymmetric dimers are connected into ribbons, which are further stabilized by N—H ... Cl interactions, forming a three-dimensional hydrogen-bonded network.
The title compound, [Na(CF3O3S)(C12H24O6)], features a sodium cation that is coordinated by eight O atoms in an irregular hexagonal bipyramidal environment. The equatorial positions are occupied by the six O atoms of an 18-crown-6 ether ring. In the axial positions, there is one O atom of a trifluoromethanesulfonate anion and an ether O atom of a symmetry-equivalent crown ether ring. In this way, centrosymmetric dimers are formed.
The asymmetric unit of the title compound, [K(C5HF6N2)(H2O)2]n, is composed of two 3,5-bis(trifluoromethyl)pyrazolide anions, two potassium cations and four water molecules. The water molecules and 3,5-bis(trifluoromethyl)pyrazolide anions act as bridges between the potassium cations. Each potassium cation is surrounded by four O atoms [K—O = 2.705 (3)–2.767 (3) Å] and four F atoms [K—F = 2.870 (7)–3.215 (13) Å]. The water molecules and the 3,5-bis(trifluoromethyl)pyrazolide anions are connected by O—H ... N hydrogen bonds, forming layers in the ab plane. All –CF3 groups show rotational disorder between two orientations each.
The two rings in the title compound, C11H12N2O4S, are roughly coplanar [dihedral angle = 6.77 (8)°]. Whereas the two outer methyl groups of the three methoxy groups are almost coplanar with the aromatic ring to which they are attached [C—C—O—C torsion angles = 8.5 (3) and -8.3 (3)°], the methyl group of the central methoxy substituent is not [C—C—C—C = -78.4 (3)°]. The crystal packing is stabilized by N—H ... O hydrogen bonding.
In the title compound, C11H11N3O2, the dihedral angle between the central ethanone fragment and the 4-methoxyphenyl group is 2.9 (2)°, while that between the ethanone fragment and the triazole ring is 83.4 (2)°. The dihedral angle between the planes of the triazole and benzene rings is 81.7 (1)°. The 4-methoxyphenyl group is cis with respect to the ethanone fragment O atom across the exocyclic C—C bond. In the crystal, molecules are linked by C—H ... N interactions into C(9) chains along [001].
The central structural element of the title compound, C24H29NO2, is a carbazole unit substituted with two acetyl residues and an octyl chain. The acetyl residues are nearly coplanar [dihedral angles = 5.37 (14) and 1.0 (3)°] with the carbazole unit which is essentially planar (r.m.s. deviation for all non-H atoms = 0.025 Å). The octyl chain adopts an all-trans conformation. The crystal packing is stabilized by C—H ... O hydrogen bonds.
17-Acetoxymulinic acid
(2010)
The title compound, [systematic name: 5a-acetoxymethyl-3-isopropyl-8-methyl-1,2,3,3a,4,5,5a,6,7,10,10a,10b-dodecahydro-7,10-endo-epidioxycyclohepta[e]indene-3a-carboxylic acid], C22H32O6 (I), is closely related to methyl 5a-acetoxymethyl-3-isopropyl-8-methyl-1,2,3,3a,4,5,5a,6,7,10,10a,10b-dodecahydro-7,10-endo-epidioxycyclohepta[e]indene-3a-carboxylate, (II) [Brito et al., (2008 [triangle]). Acta Cryst. E64, o1209]. There are two molecules in the asymmetric unit, which are linked by two strong intramolecular O—H ... O hydrogen bonds with graph-set motif R 2 2(8). In both (I) and (II), the conformation of the three fused rings are almost identical. The five-membered ring has an envelope conformation, the six-membered ring has a chair conformation and the seven-membered ring has a boat conformation. The most obvious differences between the two compounds is the observed disorder of the acetoxymethyl fragments in both molecules of the asymmetric unit of (I). This disorder is not observed in (II). The crystal structure and the molecular conformation is stabilized by intermolecular C—H ... O hydrogen bonds. The ability to form hydrogen bonds is different in the two compounds. The crystal studied was a non-merohedral twin, the ratio of the twin components being 0.28 (1):0.72 (1)
In the title compound, C4H7N3O·C2H6OS, creatinine [2-amino-1-methyl-1H-imidazol-4(5H)one] exists in the amine form. The ring is planar (r.m.s. deviation for all non-H atoms = 0.017 Å). In the crystal, two creatinine molecules form centrosymmetric hydrogen-bonded dimers linked by pairs of N—H[cdots, three dots, centered]N hydrogen bonds. In addition, creatinine is linked to a dimethyl sulfoxide molecule by an N—H[cdots, three dots, centered]O interaction. The packing shows layers parallel to (120).
The title compound, [Li3(C4F9O)3(C3H6O)3], features an open Li/O cube with an Li ion missing at one corner. Three of the four bridging O atoms of the cube carry a fluorinated tert-butyl residue, whereas the fourth is part of an acetone molecule. Two of the Li atoms are further bonded to a non-bridging acetone molecule. Two of the lithium ion coordination geometries are very distorted LiO4 tetrahedra; the third could be described as a very distorted LiO3 T-shape with two distant F-atom neighbours. The Li[cdots, three dots, centered]Li contact distances for the three-coordinate Li+ ion [2.608 (14) and 2.631 (12) Å] are much shorter that the contact distance [2.940 (13) Å] between the tetrahedrally coordinated species.
The title compound, [Tl4(C4H9O)4], featuring a (Tl—O)4 cube, crystallizes with a quarter-molecule (located on a special position of site symmetry An external file that holds a picture, illustration, etc. Object name is e-66-m1621-efi1.jpg..) and a half-molecule (located on a special position of site symmetry 23.) in the asymmetric unit. The Tl—O bond distances range from 2.463 (12) to 2.506 (12) Å. All O—Tl—O bond angles are smaller than 90° whereas the Tl—O—Tl angles are wider than a rectangular angle.
In the crystal of the title compound, C8H8ClN3S, molecules are connected by N—H[cdots, three dots, centered]S hydrogen bonds into strips parallel to the (112) planes and running along [110]. One of the amino H atoms is not involved in a classical hydrogen bond. In addition, there is a rather short intermolecular Cl ... S distance of 3.3814 (5) Å.
In the title compound, C15H14N2O4, (I), the molecule lies on a twofold rotation axis which passes through the central C atom of the aliphatic chain, giving one half-molecule per asymmetric unit. The structure is a monoclinic polymorph of the triclinic structure previously reported [Brito, Vallejos, Bolte & López-Rodríguez (2010). Acta Cryst. E66, o792], (II). The most obvious difference between them is the O/C/C/C—O/C/C/C torsion angle [58.2 (7)° in (I) and 173.4 (3)/70.2 (3)° in (II) for GG and TG conformations, respectively]. Another important difference is observed in the dihedral angle between the planes of the aromatic rings [86.49 (7)° for (I) and 76.4 (3)° for (II)]. The crystal structure features a weak pi–pi interaction [centroid–centroid distance = 4.1397 (10)Å]; this latter kind of interaction is not evident in the triclinic polymorph.
The title compound, C15H25N5, is an aminalization product between 2,6-diacetylpyridine and 1,3-diaminopropane. It crystallizes with two independent molecules in the asymmetric unit with different conformations. In the first molecule, the methyl groups are cis oriented with respect to the pyridine ring [N—C—C—C torsion angles = 72.5 (1) and 80.3 (1)°], while they are trans oriented in the second molecule [N—C—C—C torsion angles = 82.6 (1) and -90.8 (1)°]. Each of the two molecules forms centrosymmetric dimers held together by N—H[cdots, three dots, centered]N hydrogen bonds, thus forming R 2 2(16) rings. The two dimers are interlinked by additional N—H[cdots, three dots, centered]N bonds into R 4 4(14) rings, building chains along the a axis. These patterns influence the orientation (either equatorial or axial) of the N—H bonds.
Neanderthal diets are reported to be based mainly on the consumption of large and medium sized herbivores, while the exploitation of other food types including plants has also been demonstrated. Though some studies conclude that early Homo sapiens were active hunters, the analyses of faunal assemblages, stone tool technologies and stable isotopic studies indicate that they exploited broader dietary resources than Neanderthals. Whereas previous studies assume taxon-specific dietary specializations, we suggest here that the diet of both Neanderthals and early Homo sapiens is determined by ecological conditions. We analyzed molar wear patterns using occlusal fingerprint analysis derived from optical 3D topometry. Molar macrowear accumulates during the lifespan of an individual and thus reflects diet over long periods. Neanderthal and early Homo sapiens maxillary molar macrowear indicates strong eco-geographic dietary variation independent of taxonomic affinities. Based on comparisons with modern hunter-gatherer populations with known diets, Neanderthals as well as early Homo sapiens show high dietary variability in Mediterranean evergreen habitats but a more restricted diet in upper latitude steppe/coniferous forest environments, suggesting a significant consumption of high protein meat resources.
Carbon-13 and oxygen-18 abundances were measured in large mammal skeletal remains (tooth enamel, dentine and bone) from the Chiwondo Beds in Malawi, which were dated by biostratigraphic correlation to ca. 2.5 million years ago. The biologic isotopic patterns, in particular the difference in carbon-13 abundances between grazers and browsers and the difference in oxygen-18 abundances between semi-aquatic and terrestrial herbivores, were preserved in enamel, but not in dentine and bone. The isotopic results obtained from the skeletal remains from the Chiwondo Beds indicate a dominance of savannah habitats with some trees and shrubs. This environment was more arid than the contemporaneous Ndolanya Beds in Tanzania. The present study confirms that robust australopithecines were able to live in relatively arid environments and were not confined to more mesic environments elsewhere in southern Africa.
A thick Middle and Late Pleistocene loess/palaeosol sequence is exposed at the gravel quarry Gaul located east of Weilbach in the southern foreland of the Taunus Mountains. The loess/palaeosol sequence correlates to the last three glacial cycles. Seven samples were dated by luminescence methods using an elevated temperature IRSL (post-IR IRSL) protocol for polymineral fine-grains to determine the deposition age of the sediment and to set up a more reliable chronological framework for these deposits. The fading corrected IR50 and the pIRIR225 age estimates show a good agreement for almost all samples. The fading corrected IRSL ages range from 23.7 ± 1.6 ka to >350 ka indicating that the oldest loess was deposited during marine isotope stage (MIS) 10 or earlier and that the humic-rich horizon (Weilbacher Humuszone) was developed during the late phase of MIS 7. Loess taken above the fCc horizon most likely accumulated during MIS 6 indicating that the remains of the palaeosol are not belonging to the last interglacial soil. The two uppermost samples indicate that the youngest loess accumulated during MIS 2 (Upper Würmian). Age estimates for the loess-palaeosol sequence of the gravel quarry Gaul/Weilbach could be obtained up to ~350 ka using the pIRIR225 from feldspar. Keywords: loess, luminescence dating, IRSL, fading, Weilbach, chronostratigraphy
We present simulations with the Chemical Lagrangian Model of the Stratosphere (CLaMS) for the Arctic winter 2002/2003. We integrated a Lagrangian denitrification scheme into the three-dimensional version of CLaMS that calculates the growth and sedimentation of nitric acid trihydrate (NAT) particles along individual particle trajectories. From those, we derive the HNO3 downward flux resulting from different particle nucleation assumptions. The simulation results show a clear vertical redistribution of total inorganic nitrogen ( ), with a maximum vortex average permanent removal of over 5ppb in late December between 500 and 550K and a corresponding increase of of over 2ppb below about 450K. The simulated vertical redistribution of is compared with balloon observations by MkIV and in-situ observations from the high altitude aircraft Geophysica. Assuming a globally uniform NAT particle nucleation rate of 7.8x10-6cm-3h-1 in the model, the observed denitrification is well reproduced.
In the investigated winter 2002/2003, the denitrification has only moderate impact (≤14%) on the simulated vortex average ozone loss of about 1.1ppm near the 460K level. At higher altitudes, above 600K potential temperature, the simulations show significant ozone depletion through -catalytic cycles due to the unusual early exposure of vortex air to sunlight.
Background: The aim of this study was to develop a child-specific classification system for long bone fractures and to examine its reliability and validity on the basis of a prospective multicentre study. Methods: Using the sequentially developed classification system, three samples of between 30 and 185 paediatric limb fractures from a pool of 2308 fractures documented in two multicenter studies were analysed in a blinded fashion by eight orthopaedic surgeons, on a total of 5 occasions. Intra- and interobserver reliability and accuracy were calculated. Results: The reliability improved with successive simplification of the classification. The final version resulted in an overall interobserver agreement of kappa=0.71 with no significant difference between experienced and less experienced raters. Conclusions: In conclusion, the evaluation of the newly proposed classification system resulted in a reliable and routinely applicable system, for which training in its proper use may further improve the reliability. It can be recommended as a useful tool for clinical practice and offers the option for developing treatment recommendations and outcome predictions in the future.
Dynamics of relativistic heavy-ion collisions is investigated on the basis of a simple (1+1)-dimensional hydrodynamical model in light-cone coordinates. The main emphasis is put on studying sensitivity of the dynamics and observables to the equation of state and initial conditions. Low sensitivity of pion rapidity spectra to the presence of the phase transition is demonstrated, and some inconsistencies of the equilibrium scenario are pointed out. Possible non-equilibrium effects are discussed, in particular, a possibility of an explosive disintegration of the deconfined phase into quark-gluon droplets. Simple estimates show that the characteristic droplet size should decrease with increasing the collective expansion rate. These droplets will hadronize individually by emitting hadrons from the surface. This scenario should reveal itself by strong non-statistical fluctuations of observables. Critical Point and Onset of Deconfinement 4th International Workshop July 9-13 2007 GSI Darmstadt,Germany
Event-by-event multiplicity fluctuations in nucleus-nucleus collisions from low SPS up to RHIC energies have been studied within the HSD transport approach. Fluctuations of baryonic number and electric charge also have been explored for Pb+Pb collisions at SPS energies in comparison to the experimental data from NA49. We find a dominant role of the fluctuations in the nucleon participant number for the final hadron multiplicity fluctuations and a strong influence of the experimental acceptance on the final results. Critical Point and Onset of Deconfinement - 4th International Workshop July 9 - 13, 2007 Darmstadt, Germany
Yuniyanti Chuzaifah is one of the founders of "Voice of Concerned Mothers" (Suara Ibu Peduli or SIP) and later joined the "Coalition of Indonesian Women" (Koalisi Perempuan Indonesia or KPI). She studied at the Universities of Leiden and Amsterdam in the Netherlands, and later returned to Indonesia. Since March 2010 she has been the Director of the "Indonesian National Commission on Violence against Women" (Komnas Perempuan). This interview was conducted on 15 March 2010 at the organisation’s premises in Jakarta.