Incomplete Spectra Research Articles

Identification of three novel P450 enzymes involved in the oxidative modification of a newly discovered fusicoccane diterpene

Fusicoccane (FC)-type diterpenoids are a class of diterpenoids characterized by a unique 5–8–5 ring system and exhibit diverse biological activities. Recently, we identified a novel FC-type diterpene synthase MgMS, which produces a myrothec-15(17)-en-7-ol (1) hydrocarbon skeleton, however, its tailoring congeners have not been elucidated. Here, we discovered two additional gene clusters Bn and Np, each encoding a highly homologous terpene synthase to MgMS but distinct tailoring enzymes. Heterologous expression of the terpene synthases BnMS and NpMS yielded the same product as MgMS. Subsequent introduction of three P450 enzymes MgP450, BnP450 and NpP450 from individual gene clusters resulted in four new FC-type diterpenoids 2–5. Notably, MgP450 serves as the first enzyme responsible for hydroxylation of the C19 methyl group, whereas NpP450 functions as a multifunctional P450 enzyme involved in the oxidations at C5, C6, and C19 positions of the 5–8–5 tricyclic skeleton. C5 oxidation of the hydrocarbon skeleton 1 led to broadening of the NMR signals and incomplete spectra, which was resolved by high-temperature NMR spectral analysis.

A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics.

Antibody sequences can be determined at 99% accuracy directly from the polypeptide product by using bottom-up proteomics techniques. Sequencing accuracy at the peptide level is limited by the isobaric residues leucine and isoleucine, incomplete fragmentation spectra in which the order of two or more residues remains ambiguous due to lacking fragment ions for the intermediate positions, and isobaric combinations of amino acids, of potentially different lengths, for example, GG = N and GA = Q. Here, we present several updates to Stitch (v1.5), which performs template-based assembly of de novo peptides to reconstruct antibody sequences. This version introduces a mass-based alignment algorithm that explicitly accounts for mass coincidence errors. In addition, it incorporates a postprocessing procedure to assign I/L residues based on secondary fragments (satellite ions, i.e., w-ions). Moreover, evidence for sequence assignments can now be directly evaluated with the addition of an integrated spectrum viewer. Lastly, input data from a wider selection of de novo peptide sequencing algorithms are allowed, now including Casanovo, PEAKS, Novor.Cloud, pNovo, and MaxNovo, in addition to flat text and FASTA. Combined, these changes make Stitch compatible with a larger range of data processing pipelines and improve its tolerance to peptide-level sequencing errors.

Cenopopulation of Epipactis helleborine (Orchidaceae) in forest ecosystems that have been anthropogenically transformed to various degrees

Because of developed symbiotic connections of the root system of trees, mycorrhiza-forming fungi and the orchid family Orchidaceae in forest ecosystems of the northeast Polissia Region – cultivated Pinus sylvestris, which are now 100–120 years old, recovery of cenopopulations of Epipactis helleborine has been observed in locations of mixed and broad-leaved forests. In natural plant cover of mature pines of the region, indigenous vegetation is gradually recovering – there occur young Quercus robur, Tilia cordata, Acer platanoides of various ages, crown density of understory formed by Coryllus avellana has reached 0.6, above-ground organic leaf foliage that is able to sustain moisture and increase fertility of soil accumulates, creating sufficient conditions of shading for seedlings and juvenile individuals of forest orchids. Special studies revealed a relationship between density of E. helleborine specimens and crown density of the tree stand, shrub strata, structure of soil cover, expressed in cenoses under various degrees of recreational pressure. Density of individuals of forest orchids in the studied populations ranges 10.0 to 0.1 ind./10 m2. Dynamics were seen in groupings of Betuleto-Pineta corylosa, Querceta (roboris) corylosa, Querceto-Pineta corylosa, Acereto (platanoidis) –Tilieto (cordatae) – Quercetum (roboris) aegopodiosum in the territory of the nature-reserve fund and structurally similar anthropogenically pressurized cenoses. We determined that all examined cenopopulations in old indigenous zonal cenoses in the territory of the nature reserve fund are normal, they may be considered relatively stable, ontogenetic spectra are incomplete, mostly with right-sided age spectrum – maximum numbers of virgin and generative individuals of various stages. Low density of individuals and incomplete spectra of cenopopulations in light oak forests are natural, and now the largest share of generative and virgin individuals is concentrated in this area. Impact of recreation, unavoidable due to proximity to a road, is a negative factor directly decreasing their density. Ontogenetic spectra of all cenopopulations are incomplete – no seedlings were found in the natural conditions due to underground type of germination. Much more interesting data may be obtained by monitoring studies of age and morphometric dynamic changes during several years.

Missing-level statistics in a dissipative microwave resonator with partially violated time-reversal invariance.

We report on the experimental investigation of the fluctuation properties in the resonance frequency spectra of a flat resonator simulating a dissipative quantum billiard subject to partial time-reversal-invariance violation (TIV) which is induced by two magnetized ferrites. The cavity has the shape of a quarter bowtie billiard of which the corresponding classical dynamics is chaotic. Due to dissipation it is impossible to identify a complete list of resonance frequencies. Based on a random-matrix theory approach we derive analytical expressions for statistical measures of short- and long-range correlations in such incomplete spectra interpolating between the cases of preserved time-reversal invariance and complete TIV and demonstrate their applicability to the experimental spectra.

Missing-level statistics in classically chaotic quantum systems with symplectic symmetry.

We present experimental and theoretical results for the fluctuation properties in the incomplete spectra of quantum systems with symplectic symmetry and a chaotic dynamics in the classical limit. To obtain theoretical predictions, we extend the random-matrix theory (RMT) approach introduced in Bohigas and Pato [O. Bohigas and M.P. Pato, Phys. Rev. E 74, 036212 (2006)PLEEE81539-375510.1103/PhysRevE.74.036212] for incomplete spectra of quantum systems with orthogonal symmetry. We validate these RMT predictions by randomly extracting a fraction of levels from complete sequences obtained numerically for quantum graphs and experimentally for microwave networks with symplectic symmetry and then apply them to incomplete experimental spectra to demonstrate their applicability. Independently of their symmetry class, quantum graphs exhibit nongeneric features which originate from nonuniversal contributions. Part of the associated eigenfrequencies can be identified in the level dynamics of parameter-dependent quantum graphs and extracted, thereby yielding spectra with systematically missing eigenfrequencies. We demonstrate that, even though the RMT approach relies on the assumption that levels are missing at random, it is possible to determine the fraction of missing levels and assign the appropriate symmetry class by comparison of their fluctuation properties with the RMT predictions.

An approach to gas sensors based on tunable diode laser incomplete saturated absorption spectra* *Project supported by the Guangdong Province Key Laboratory of Efficient and Clean Energy Utilization (Grant No. 2013A061401005) and the Key Laboratory of Efficient and Clean Energy Utilization of Guangdong Higher Education Institutes (Grant No. KLB10004).

A spectral profile reconstruction method that can be applied to incomplete saturated-absorption spectra is proposed and demonstrated. Through simulation and theoretical calculation, it is proved that compared with the traditional whole-profile fitting method, this new method can increase the concentration detection upper limit of a single absorption line by about 8.7 times. High-concentration water vapor is measured using TDLAS technology, the total water vapor pressure and the self-broadened half-width coefficient of the spectrum were simultaneously measured from incomplete saturated-absorption spectra and compared with high-precision pressure sensors and the HITRAN databases. Their maximum relative deviations were about 4.63% and 9.10%, respectively. These results show that the spectral profile reconstruction method has great application potential for expanding the dynamic range of single-line measurements to higher concentrations, especially for in-situ online measurements under complex conditions, such as over large temperature and concentration dynamic ranges.

Sensitivity of the spectral form factor to short-range level statistics.

The spectral form factor is a dynamical probe for level statistics of quantum systems. The early-time behavior is commonly interpreted as a characterization of two-point correlations at large separation. We argue that this interpretation can be too restrictive by indicating that the self-correlation imposes a constraint on the spectral form factor integrated over time. More generally, we indicate that each expansion coefficient of the two-point correlation function imposes a constraint on the properly weighted time-integrated spectral form factor. We discuss how these constraints can affect the interpretation of the spectral form factor as a probe for ergodicity. We propose a probe, which eliminates the effect of the constraint imposed by the self-correlation. The use of this probe is demonstrated for a model of randomly incomplete spectra and a Floquet model supporting many-body localization.

Robust input layer for neural networks for hyperspectral classification of data with missing bands

Hyperspectral classification using artificial neural networks is commonly applied on camera dependent interpolated data, or on the results of a dimensionality reduction algorithm. While these methods usually produce satisfactory results, they have severe limitations when part of the spectrum is missing, for example when parts of the image are overexposed or affected by bad pixels. This article presents an input layer based on the Haar transform for artificial neural networks used for hyperspectral data classification. This input layer is designed to perform efficiently with incomplete data and is independent of the specific bands used by the camera. This could enable providing pre-trained neural networks, which can be used with a camera with different specifications than the one used for training. This paper shows that a classifier for mineral identification built using this approach performs better than standard normalization on incomplete spectra, and similarly on complete spectra. Additionally, it shows that such a classifier matches local spectral features, and therefore that the artificial neural network is matching the spectrum shape.

Three-nucleon force effects in inclusive spectra of the neutron-deuteron breakup reaction

We investigate the sensitivity of the non-exclusive nucleon induced deuteron breakup reaction to the three-nucleon interaction and distributions of three-nucleon force effects in inclusive spectra. To this end we solve the three-nucleon Faddeev equation at a number of incoming nucleon laboratory energies using the CD Bonn nucleon-nucleon interaction alone or combined with the 2{\pi}-exchange Tucson-Melbourne three-nucleon force. Based on these solutions energy spectra of an outgoing nucleon, at a specified detection angle as well as spectra integrated over that angle, are calculated. By integrating the spectra at a given angle over the energy of the outgoing nucleon the angular distributions of three-nucleon force effects in the breakup process are additionally obtained. Contrary to elastic nucleon-deuteron scattering, where at higher energies significant three-nucleon force effects were encountered for scattering angles around the minimum of the cross section, for the breakup process only moderate effects are found and they are restricted to forward angles. Results of the present investigation show that the large three-nucleon force effects found for some specific complete breakup configurations are reduced substantially in the incomplete spectra when averaging over contributing complete geometries is performed.

Research and development of a method for determining the dimensional characteristics of sea waves with measurements made by a wave buoy

The problem of determining the spatial characteristics of sea waves with incomplete measurement information obtained by modern wave buoys is discussed. Information about wave ordinates, slopes and curvature of the waves in two perpendicular directions is needed to evaluate the full directional spectrum. Since the direct measurement of wave curvature by buoys is difficult due to technical reasons, their manufacturers decided to correct incomplete spectra using mathematical methods, such as maximum entropy, maximum likelihood methods, etc. The current study shows that the curvature of the waves can be estimated by using additional information on the parameters of the wave propagation, which can be obtained using ordinary wave buoys. Such an approach will make it possible to obtain more reliable spatial spectra.

Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding

Nowadays, most biodiversity assessments involving meiofauna are mainly carried out specimen by specimen based on morphological identifications, which is very time-consuming and demands comprehensive taxonomic knowledge. Specimens have to be examined for minor differences of setae compositions, mouthpart morphology or number of segments for various extremities. DNA-based methods such as metabarcoding as well as recently emerged rapid analyses using MALDI-TOF mass spectrometry to identify specimens based on a proteome fingerprint could vastly accelerate the process of specimen identification in biodiversity assessments. However, these techniques depend on reference libraries to connect assessed data to morphologically described species. In this study the success rate of both approaches have been tested based on reference libraries constructed using part of the samples from a new study area to identify unknown samples. Using MALDI-TOF MS we found, that species not contained in an incomplete mass spectra reference library only have minor impact on the results, when employing a post hoc test for Random Forest classifications. This test reveals specimens that demand morphological re-examination for the final species assignment. Metabarcoding however strongly demands a rich reference library to provide correct MOTU assessments in congruence with morphological determination. Nevertheless, with a complete library and a suitable data transformation (herein log(x+1)), the number or reads per MOTU reflects relative species abundances in metabarcoding inference. Furthermore, a single gene barcoding approach on selected specimens was performed here in order to provide a cost comparison among the three techniques. The results of this study facilitate specimen identification by using MALDI-TOF MS, which is incomparably cheap for specimen-by-specimen identification, but when it comes to sample wise analyses, metabarcoding outperforms other techniques by far.

On the analysis of incomplete spectra in random matrix theory through an extension of the Jimbo–Miwa–Ueno differential

Several distribution functions in the classical unitarily invariant matrix ensembles are prime examples of isomonodromic tau functions as introduced by Jimbo, Miwa and Ueno (JMU) in the early 1980s [45]. Recent advances in the theory of tau functions [41], based on earlier works of B. Malgrange and M. Bertola, have allowed to extend the original Jimbo–Miwa–Ueno differential form to a 1-form closed on the full space of extended monodromy data of the underlying Lax pairs. This in turn has yielded a novel approach for the asymptotic evaluation of isomonodromic tau functions, including the exact computation of all relevant constant factors. We use this method to efficiently compute the tail asymptotics of soft-edge, hard-edge and bulk scaled distribution and gap functions in the complex Wishart ensemble, provided each eigenvalue particle has been removed independently with probability 1−γ∈(0,1].

Missing-level statistics and analysis of the power spectrum of level fluctuations of three-dimensional chaotic microwave cavities.

We present an experimental study of missing-level statistics of three-dimensional chaotic microwave cavities. The investigation is reinforced by the power spectrum of level fluctuations analysis, which also takes into account the missing levels. On the basis of our data sets we demonstrate that the power spectrum of level fluctuations in combination with short- and long-range spectral fluctuations provides a powerful tool for the determination of the fraction of randomly missing levels in systems that display wave chaos such as the three-dimensional chaotic microwave cavities. The experimental results are in good agreement with the analytical expressions that explicitly take into account the fraction of observed levels φ. We also show that in the case of incomplete spectra with many unresolved states the above procedures may fail. In such a case the random matrix theory calculations can be useful for the determination of missing levels.

An Algorithm for Determining the Peak Frequency of BOTDR Under the Case of Transient Interference

An algorithm based on spectra splicing is proposed to determine the peak frequency of Brillouin spectrum under a transient interference. The peak frequency calculated is only 0.79 MHz lower than that obtained based on the whole Brillouin spectrum when the frequency interval is 5 MHz. Discussions on the performance of our algorithm with and without spectral shift are conducted in light of the practical situation. Imposing a random shift on the primal Brillouin spectrum between −5 and 5 MHz, only 200 incomplete Brillouin spectra are required for splicing to gain a reliable value of the peak frequency with a frequency interval of 5 MHz. Moreover, the efficiency can be significantly improved by increasing the frequency interval, but the improvement is limited since higher frequency interval means more information loss of the whole Brillouin spectrum. This method is helpful in deciding the Brillouin frequency shift when the external interference lasts for a very short time, such as sound barriers and wind tunnel tests. It provides guidelines for the design of distributed optical fiber sensing systems.

Exploring protein solution structure: Second moments of fluorescent spectra report heterogeneity of tryptophan rotamers

Trp fluorescent spectra appear as a log-normal function but are usually analyzed with λmax, full width at half maximum, and the first moment of incomplete spectra. Log-normal analyses have successfully separated fluorescence contributions from some multi-Trp proteins but deviations were observed in single Trp proteins. The possibility that disparate rotamer environments might account for these deviations was explored by moment spectral analysis of single Trp mutants spanning the sequence of tear lipocalin as a model. The analysis required full width Trp spectra. Composite spectra were constructed using log-normal analysis to derive the inaccessible blue edge, and the experimentally obtained spectra for the remainder. First moments of the composite spectra reflected the site-resolved secondary structure. Second moments were most sensitive for spectral deviations. A novel parameter, derived from the difference of the second moments of composite and simulated log-normal spectra correlated with known multiple heterogeneous rotamer conformations. Buried and restricted side chains showed the most heterogeneity. Analyses applied to other proteins further validated the method. The rotamer heterogeneity values could be rationalized by known conformational properties of Trp residues and the distribution of nearby charged groups according to the internal Stark effect. Spectral heterogeneity fits the rotamer model but does not preclude other contributing factors. Spectral moment analysis of full width Trp emission spectra is accessible to most laboratories. The calculations are informative of protein structure and can be adapted to study dynamic processes.

Restricted Boltzmann machine: a non-linear substitute for PCA in spectral processing

Context. Principal component analysis (PCA) is widely used to repair incomplete spectra, to perform spectral denoising, and to reduce dimensionality. Presently, no method has been found to be comparable to PCA on these three problems. New methods have been proposed, but are often specific to one problem. For example, locally linear embedding outperforms PCA in dimensionality reduction. However, it cannot be used in spectral denoising and spectral reparing. Wavelet transform can be used to denoise spectra; however, it cannot be used in dimensionality reduction.

Diversity of bacterial forms in ice wedge of the Mamontova Gora glacial complex (Central Yakutiya)

Electron microscopic investigation of four samples of ancient ice wedge from the Pleistocene glacial complex of Mamontova Gora (Yakutiya, Russia) revealed high diversity of bacteriomorphic particles. Their structural features included the presence of electron-transparent zones, presumably inclusions containing storage compounds, and microenvironment (capsules or external sheaths). These features may be a result of adaptive strategies providing for microbial survival under permafrost conditions. Predominance of rod-shaped forms morphologically resembling coryneform actinobacteria was found. X-ray microanalysis revealed organic origin of bacteriomorphic particles. Some particles were characterized by incomplete spectra of the major biogenic elements, resulting probably from low-temperature damage to the cellular structures. Total numbers of aerobic heterotrophic bacteria determined by plating on nutrient media were comparable to the values obtained for permafrost soils and Arctic ice. Predominance of coryneform actinobacteria was observed. Abundance of these evolutionarily early groups of actinobacteria may indicate the ancient origin of the microflora of the relic frozen rocks.

Differential (14)N/(15)N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing.

While de novo peptide sequencing is essential in many situations, it remains a difficult task. This is because peptide fragmentation results in complicated and often incomplete product ion spectra. In a previous study, we demonstrated that N-terminal charge derivatization with 4-amidinobenzoic acid (Aba) resulted in improved peptide fragmentation under low-energy CID conditions. However, even with this derivatization, some ambiguity exists, due to difficulties in discriminating between N- and C-terminal fragments. In this study, to specifically identify b-ions from complex product ion spectra, the differential (14)N/(15)N-labeling of peptides was performed using Aba derivatization. (15)N-Labeled Aba was synthesized in the form of a succinimide ester. Peptides were derivatized individually with (14)N-Aba or (15)N-Aba and analyzed by ESI-MS/MS using a linear ion trap-Orbitrap hybrid FTMS system. The N-terminal fragments (i.e., b-ions) were then identified based on m/z differences arising from isotope labeling. By comparing the spectra between (14)N- and (15)N-Aba derivatized peptides, b-ions could be successfully identified based on the m/z shifts, which provided reliable sequencing results for all of the peptides examined in this study. The method developed in this study allows the easy and reliable de novo sequencing of peptides, which is useful in peptidomics and proteomics studies.

The Kadanoff–Baym approach to double excitations in finite systems

We benchmark many-body perturbation theory by studying neutral, as well as non-neutral, excitations of finite lattice systems. The neutral excitation spectra are obtained by time-propagating the Kadanoff–Baym equations in the Hartree–Fock and the second Born approximations. Our method is equivalent to solving the Bethe–Salpeter equation with a high-level kernel while respecting self-consistency, which guarantees the fulfillment of a frequency sum rule. As a result, we find that a time-local method, such as Hartree–Fock, can give incomplete spectra, while already the second Born approximation, which is the simplest time-non-local approximation, reproduces well most of the additional excitations, which are characterized as double excitations.

Incomplete Brillouin-zone spectra and controlled Bragg reflection with ionic-type photonic lattices

We demonstrate ionic-type photonic lattices consisting of alternating positive and negative lattice potentials akin to those of ionic crystals in solids. A modified geometrical structure factor is developed for describing Bragg scattering in these non-Bravais photonic lattices. We show that lattice reconfiguration leads to incomplete Brillouin zone spectra due to selective band-gap closures. Experimentally, incomplete Brillouin zone spectra and associated Bragg-reflection suppression are observed in such ionic-type lattices optically induced in a bulk nonlinear crystal. Our experimental results agree well with our theoretical analysis.