The evolving role of Fourier-transform midinfrared spectroscopy in genetic improvement of dairy cattle

Over the last 100 years,significant advances have been made in the characterisation of milk composition for dairy cattle improvement programs.Technological progress has enabled a shift from labour intensive,on-farm collection and processing of samples that assess yield and fat levels in milk,to large-scale processing of samples through centralised laboratories,with the scope extended to include quantification of other traits.Fourier-transform midinfrared(FT-MIR)spectroscopy has had a significant role in the transformation of milk composition phenotyping,with spectral-based predictions of major milk components already being widely used in milk payment and animal evaluation systems globally.Increasingly,there is interest in analysing the individual FT-MIR wavenumbers,and in utilising the FT-MIR data to predict other novel traits of importance to breeding programs.This includes traits related to the nutritional value of milk,the processability of milk into products such as cheese,and traits relevant to animal health and the environment.The ability to successfully incorporate these traits into breeding programs is dependent on the heritability of the FT-MIR predicted traits,and the genetic correlations between the FT-MIR predicted and actual trait values.Linking FT-MIR predicted traits to the underlying mutations responsible for their variation can be difficult because the phenotypic expression of these traits are a function of a diverse range of molecular and biological mechanisms that can obscure their genetic basis.The individual FT-MIR wavenumbers give insights into the chemical composition of milk and provide an additional layer of granularity that may assist with establishing causal links between the genome and observed phenotypes.Additionally,there are other molecular phenotypes such as those related to the metabolome,chromatin accessibility,and RNA editing that could improve our understanding of the underlying biological systems controlling traits of interest.Here we review topics of importance to phenotyping and genetic applications of FT-MIR spectra datasets,and discuss opportunities for consolidating FT-MIR datasets with other genomic and molecular data sources to improve future dairy cattle breeding programs.

Classification of Toxic Cyanobacterial Blooms by Fourier-Transform Infrared Technology (FTIR)

Cyanobacteria are gram-negative photosynthetic bacteria capable of producing toxins responsible for morbidity and mortality in humans and domestic animals. They are capable of forming concentrated blooms, referred to as harmful algal blooms (HABs). Characterization of HABs is necessary to reduce risks from human and animal exposures to toxins. Current methods used to classify cyanobacteria and cyanotoxins have limitations related to time, analyst skills, and cost. Fourier-Transform Infrared Spectroscopy (FTIR) is a potential tool for rapid, robust cyanobacterial classification that is not limited by these factors. To examine the practicality of this method, library screening with default software algorithms was performed on HAB samples, followed by principle component cluster analyses and dendrogram analysis of samples meeting minimum quality requirements. Two tested spectrometers and software packages were successful at distinguishing cyanobacteria from green algae. Principle component cluster analysis and dendrogram analysis also resulted in clear differentiation between cyanobacteria and green algae. While these methods cannot be used independently to fully characterize HABs, they show the potential and practicality of FTIR as a screening tool.

Optical Frequency Comb-Based Cavity-Enhanced Fourier-Transform Spectroscopy:Application to Collisional Line-Shape Study

Direct-comb spectroscopy techniques uses optical frequency combs(OFCs)as spectroscopic light source.They deliver high sensitivity,high frequency resolution and precision in a broad spectral range.Due to these features,the field has burgeoned in recent years.In this work we constructed an OFC-based cavity-enhanced Fourier-transform spectrometer in the nearinfrared region and used it for a line-shape study of rovibrational transitions of CO perturbed by Ar.The highly sensitive measurements spanned the wavenumber range from 6270 cm^-1 to 6410 cm^-1,which covered both P and R branch of the second overtone band of CO.The spectrometer delivers high-resolution surpassing the Fourier-transform resolution limit determined by interferogram length,successfully removing ringing and broadening effects caused by instrumental line shape function.The instrumental-line-shape-free method and high signal-to-noise ratio in the measurement allowed us to observe collisional effects beyond those described by the Voigt profile.We retrieved collisional line-shape parameters by fitting the speed-dependent Voigt profile and found good agreement with the values given by precise cavity ring-down spectroscopy measurements that used a continuous-wave laser referenced to a stabilized OFC.The results demonstrate that OFC-based cavity-enhanced Fouriertransform spectroscopy is a strong tool for accurate line-shape studies that will be crucial for future spectral databases.

中国首个地基高分辨率傅里叶变换光谱观测站的大气成分长期观测研究

长期观测主要大气成分的体积混合比(VMR)廓线和柱总量对掌握中国气候变化和碳收支具有重要意义。本文对我国首个TCCON高分辨率傅里叶变换光谱(FTS)地基观测站——合肥观测站开展了系统性研究,该观测站可观测30多种大气成分的柱总量和VMR廓线。本文公布了2014年以来合肥观测站观测到的部分关键大气成分的时间序列,总结了迄今为止该站点取得的主要研究成果,包括光谱反演表征和归一化、关键大气成分的总体演变特征、排放估计、卫星和化学传输模式(CTM)校验以及对大气污染来源和传输的相关研究。同时,本文还对合肥观测站的观测、科学研究和未来研究计划进行了展望。中国明确提出2030年二氧化碳排放达到峰值,2060年实现碳中和。合肥观测站将为中国政府制定绿色经济政策、实现碳中和及《巴黎协定》目标提供科学支撑。

The quantum spectra analysis of the circular billiards in wells

We use a recently defined quantum spectral function and apply the method of closed-orbit theory to the 2D circular billiard system. The quantum spectra contain rich information of all classical orbits connecting two arbitrary points in the well. We study the correspondence between quantum spectra and classical orbits in the circular, 1/2 circular and 1/4 circular wells using the analytic and numerical methods. We find that the peak positions in the Fourier- transformed quantum spectra match accurately with the lengths of the classical orbits. These examples show evidently that semi-classlcal method provides a bridge between quantum and classical mechanics.

The quantum spectral analysis of the two-dimensional annular billiard system

Based on the extended closed-orbit theory together with spectral analysis, this paper studies the correspondence between quantum mechanics and the classical counterpart in a two-dimensional annular billiard. The results demonstrate that the Fourier-transformed quantum spectra are in very good accordance with the lengths of the classical ballistic trajectories, whereas spectral strength is intimately associated with the shapes of possible open orbits connecting arbitrary two points in the annular cavity. This approach facilitates an intuitive understanding of basic quantum features such as quantum interference, locations of the wavefunctions, and allows quantitative calculations in the range of high energies, where full quantum calculations may become impractical in general. This treatment provides a thread to explore the properties of microjunction transport and even quantum chaos under the much more general system.

Optical high-resolution spectroscopic study of Tm^(3+) crystal-field levels in LiLuF_4

We report on the fast high-resohition study of LiLuF4：Tm3＋. The accurate energy level scheme of Tm3＋ in the LiLuF4 matrix was obtained for the 3H6.5.4, 3F4.3.2, and ^1G4 multiplets. It was shown that electric-dipole transitions dominate for all the studied multiplets except the 3H5 one.

Phase-Space Analysis of Wavefront Coding Imaging Systems

We explore the use of the Radon-Wigner transform, which is associated with the fractional Fourier transform of the pupil function, for determining the point spread function （PSF） of an incoherent defocused optical system. Then we introduce these phase-space tools to analyse the wavefront coding imaging system. It is shown that the shape of the PSF for such a system is highly invariant to the defocus-related aberrations except for a lateral shift. The optical transfer function of this system is also investigated briefly from a new understanding of ambiguity function.

Introducing a Novel Approach for Oil-Oil Correlation based on Asphaltene Structure: X-ray Diffraction

Asphaltenes have always been an attractive subject for researchers.However,the application of this fraction of the geochemical field has only been studied in a limited way.In other words,despite many studies on asphaltene structure,the application of asphaltene structures in organic geochemistry has not so far been assessed.Oil-oil correlation is a wellknown concept in geochemical studies and plays a vital role in basin modeling and the reconstruction of the burial history of basin sediments,as well as accurate characterization of the relevant petroleum system.This study aims to propose the Xray diffraction(XRD)technique as a novel method for oil-oil correlation and investigate its reliability and accuracy for different crude oils.To this end,13 crude oil samples from the Iranian sector of the Persian Gulf region,which had previously been correlated by traditional geochemical tools such as biomarker ratios and isotope values,in four distinct genetic groups,were selected and their asphaltene fractions analyzed by two prevalent methods of XRD and Fouriertransform infrared spectroscopy(FTIR).For oil-oil correlation assessment,various cross-plots,as well as principal component analysis(PCA),were conducted,based on the structural parameters of the studied asphaltenes.The results indicate that asphaltene structural parameters can also be used for oil-oil correlation purposes,their results being completely in accord with the previous classifications.The average values of distance between saturated portions(d_(r))and the distance between two aromatic layers(d_(m))of asphaltene molecules belonging to the studied oil samples are 4.69Aand 3.54A,respectively.Furthermore,the average diameter of the aromatic sheets(L_(a)),the height of the clusters(L_(c)),the number of carbons per aromatic unit(C_(au)),the number of aromatic rings per layer(R_(a)),the number of sheets in the cluster(M_(e))and aromaticity(f_(a))values of these asphaltene samples are 10.09A,34.04A,17.42A,3.78A,10.61Aand 0.26A,respectively.The results of XRD parameters indicate that plots of dr vs.d_(m),d_(r) vs.M_(e),d_(r) vs.f_(a),d_(m) vs.L_(c),L_(c) vs.L_(a),and f_(a) vs.L_(a) perform appropriately for distinguishing genetic groups.A comparison between XRD and FTIR results indicated that the XRD method is more accurate for this purpose.In addition,decision tree classification,one of the most efficacious approaches of machine learning,was employed for the geochemical groups of this study for the first time.This tree,which was constructed using XRD data,can distinguish genetic groups accurately and can also determine the characteristics of each geochemical group.In conclusion,the obtaining of structural parameters for asphaltene by the XRD technique is a novel,precise and inexpensive method,which can be deployed as a new approach for oil-oil correlation goals.The findings of this study can help in the prompt determination of genetic groups as a screening method and can also be useful for assessing oil samples affected by secondary processes.

Spectroscopy of compounds from the family of rare-earth orthoborates

This paper is devoted to the rare-earth borates described by the general formula RM3（BO3）4, M = Al, Fe, and Cr, that have non-centrosymmetric trigonal slructure of the natural mineral huntite. It give a brief review of a spectroscopic research on YbAI3（BO3）4 （YbAB）, on a large group of magnetic iron borates, and on NdCra（BO3）4.

Effect of metal fluorides on chromium ions doped bismuth borate glasses for optical applications

Fluoride based glasses with composition CaF_2-ZnF_2-Bi_2 O_3-B_2 O_3 doped with chromium ions have been investigated using physical, optical, electron paramagnetic resonance(EPR), Fourier-transform infrared spectroscopy(FTIR), and Raman studies. The amorphous nature of samples was confirmed from x-ray diffraction spectra. The density is evaluated from the Archimedes principle and the values of optical band gap and Urbach energy values were evaluated from the optical absorption spectra. Thus, molar volume, refractive index, etc., were also evaluated. The observed decrease in density and the optical band gap with CaF2 is explained using the crystalline density of metal fluorides and the ionicity of fluorine ions,respectively. The three peaks near 450 nm, 606 nm, and 720 nm, which are shown in the absorption spectra, are accredited to ~4 A)(2 g) → ~4 T_(1 g), ~4 A_(2 g)→ ~4 T_(2 g), ~4 A_(2 g)→~2 E transitions, respectively. Resonance signals at g≈ 4.82 and g≈ 1.99 were observed in EPR spectra which are assigned. FTIR and Raman analysis were carried out to examine the impact of metal fluorides on the structure of bismuth borate glasses.

Application of Cosine Zone Plates to Image Encryption

We analyse the diffraction result of optical field after Cosine zone plate, and theoretically deduce its transform matrix. Under some conditions, its diffraction distribution is a mixture of fractional Fourier spectra. Then we use Cosine zone plate and its diffraction result to image encryption. Possible optical image encryption and decryption implementations are proposed, and some numerical simulation results are also provided.

Optical Image Encryption with Simplified Fractional Hartley Transform

We present a new method for image encryption on the basis of simplifed fractional Hartley transform （SFRHT）. SFRHT is a real transform as Hartley transform （HT） and furthermore, superior to HT in virtue of the advantage that it can also append fractional orders as additional keys for the purpose of improving the system security to some extent. With this method, one can encrypt an image with an intensity-only medium such as a photographic film or a CCD camera by spatially incoherent or coherent illumination. The optical realization is then proposed and computer simulations are also performed to verify the feasibility of this method.

Tm^(3+) interactions in LiYF_4 studied by high-resolution spectroscopy

We used the high-resolution spectroscopy to study the interactions that Tm3＋ ion in a LiYF4 crystal is subjected to. Several crystal field transitions with low integral intensity were found not registered before by means of ordinary spectroscopy. Spectral evidences for interionic, hyperfine, isotopic interactions, and for a resonant broadening of the ground state are presented.

Operating limits and features of direct air capture on K_(2)CO_(3)/ZrO_(2) composite sorbent

Potassium carbonate-based sorbents are prospective materials for direct air capture(DAC).In the present study,we examined and revealed the influence of the temperature swing adsorption(TSA)cycle conditions on the CO_(2) sorption properties of a novel aerogel-based K_(2)CO_(3)/ZrO_(2) sorbent in a DAC process.It was shown that the humidity and temperature drastically affect the sorption dynamic and sorption capacity of the sorbent.When a temperature at the sorption stage was 29℃ and a water vapor pressure P_(H2O) in the feed air was 5.2 mbar(1 bar=105 Pa),the composite material demonstrated a stable CO_(2) sorption capacity of 3.4%(mass).An increase in sorption temperature leads to a continuous decrease in the CO_(2) absorption capacity reaching a value of 0.7%(mass)at T=80℃.The material showed the retention of a stable CO_(2) sorption capacity for many cycles at each temperature in the range.Increasing PH2O in the inlet air from 5.2 to 6.8 mbar leads to instability of CO_(2) sorption capacity which decreases in the course of 3 consecutive TSA cycles from 1.7%to 0.8%(mass)at T=29℃.A further increase in air humidity only facilitates the deterioration of the CO_(2) sorption capacity of the material.A possible explanation for this phenomenon could be the filling of the porous system of the sorbent with solid reaction products and an aqueous solution of potassium salts,which leads to a significant slowdown in the CO_(2) diffusion in the composite sorbent grain.To investigate the regeneration step of the TSA cycle in situ,the macro ATRFTIR(attenuated total reflection Fourier-transform infrared)spectroscopic imaging was applied for the first time.It was shown that the migration of carbonate-containing species over the surface of sorbent occurs during the thermal regeneration stage of the TSA cycle.The movement of the active component in the porous matrix of the sorbent can affect the sorption characteristics of the composite material.The revealed features make it possible to formulate the requirements and limitations that need to be taken into account for the practical implementation of the DAC process using the K_(2)CO_(3)/ZrO_(2) composite sorbent.

Nonclassical Plane-crystallographic Groups and Their Applications Ⅲ

Six kinds of nonclassical periodic lattices with locally 10-fold rotational symmetries are proposed. They can be delineated via nonclassical plane-crystallographic groups. The projections on the planes of corresponding unit cells consisting of embedding polyhedra generate the periodic lattices, respectively. The Fourier-transform patterns of the periodiclattices have almost perfect 10-fold rotational symmetries, which are very similar to those displaying in the electron-diffraction patterns of so-called quasicrystals.

Techniques to elucidate the conformation of prions

Proteinaceous infectious particles(prions) are unique pathogens as they are devoid of any coding nucleic acid.Whilst it is assumed that prion disease is transmitted by a misfolded isoform of the cellular prion protein, the structural insight of prions is still vague and research for high resolution structural information of prions is still ongoing. In this review, techniques that may contribute to the clarification of the conformation of prions are presented and discussed.

Nonclassical Plane-crystallographic Groups and Their Applications IV

Eight kinds of nonclasslcal periodic lattices with locally 8-fold rotational symmetries are introduced.They can be described via nonclassical Planc-crystallographic groups. The periodic lattices may be interpreted bythe projections on the plane of the corresponding unit cells consisting of embedding polyhedrons, respectively. TheFourier-transform patterns of the Periodic lattices have striking approximate'8-fold rotational symmetries', some ofwhich are similar to those displaying in the electrton-diffraction patterns of so-called quasicrystals.

Infrared-Spectral Characteristics of <i>Camellia oleifera</i>Shell/Meal during Composting

The compost products of Camellia oleifera shell/meal mixed at different mass ratios were characterized by Fourier-transform infrared spectroscopy (FTIR) at different composting stages to monitor the structural changes of their components. The results showed that the amount of Camellia oleifera meal significantly affected the composting rate of the shell, but did not change the degradation order and decomposition of the related compounds. During the composting process, microorganisms used the highly decomposable carbon source materials, such as proteins and sugars, first to grow and multiply, and then decomposed hemicellulose, cellulose and lignin by oxidative cleavage after these nutrients were consumed to a certain extent. The decomposition products were then condensed into more stable humic acids. The degradation rates of the compounds were directly proportional to the amount of Camellia oleifera?meal. The compounds in Camellia oleifera shell were composted faster with higher amounts of Camellia oleifera meals, resulting in less lignocellulose in the final products.

Visualization of decreased docosahexaenoic acid in the hippocampus of rats fed an n – 3 fatty acid-deficient diet by imaging mass spectrometry

The present study employed an imaging mass spectrometry (IMS) method to evaluate the effect of dietary n – 3 fatty acids on the fatty acid composition in rat brain. Rats were divided into two groups and fed either an n – 3 fatty acid-deficient or adequate diet. We determined the decreased n – 3 fatty acids in the hippocampus of rats fed an n – 3 fatty acid-deficient diet compared to the control. IMS visualization was achieved at a resolution of 100 m in rat brain, and showed decreased docosahexaenoic acid (DHA)-containing phosphatidyl choline (PC) or phosphatidyl ethanolamine (PE) in the hippocampus of rats fed an n – 3 fatty acid-deficient diet.