Monitoring the Reaction of the Body State to Antibiotic Treatment against Helicobacter pylori via Infrared Spectroscopy: A Case Study.

The current understanding of deviations of human microbiota caused by antibiotic treatment is poor. In an attempt to improve it, a proof-of-principle spectroscopic study of the breath of one volunteer affected by a course of antibiotics for Helicobacter pylori eradication was performed. Fourier transform spectroscopy enabled searching for the absorption spectral structures sensitive to the treatment in the entire mid-infrared region. Two spectral ranges were found where the corresponding structures strongly correlated with the beginning and end of the treatment. The structures were identified as methyl ester of butyric acid and ethyl ester of pyruvic acid. Both acids generated by bacteria in the gut are involved in fundamental processes of human metabolism. Being confirmed by other studies, measurement of the methyl butyrate deviation could be a promising way for monitoring acute gastritis and anti-Helicobacter pylori antibiotic treatment.

Towards a standard operating procedure for revealing hidden volatile organic compounds in breath: the Fourier-transform IR spectroscopy case.

Human breath contains a large amount of small volatile organic compounds (VOCs) and could therefore be used as a carrier of metabolic information for medical diagnostics. Still, in spite of several promising techniques that have been applied during the last decades to study breath content, there is a lack of breath-based diagnostic tools available for physicians. Among several promising techniques, infrared (IR) spectroscopy has already proved its potential for reliable detection of VOCs in the breath. However, due to the large dynamic range of molecular concentrations and overlapping absorption spectra of different VOCs, many low-absorption molecules stay hidden in spectroscopic measurements. To overcome this obstacle, we propose the Matryoshka method for removing masking effects and revealing the buried spectral structures in any bio-fluid in the gas phase. By exploiting both physical and digital removal steps, we demonstrate how the method reveals methane, acetone, aldehyde, and methyl butyrate in a real breath.

Theory helps experiment to reveal VOCs in human breath.

Volatile organic compounds (VOCs) present in human breath not only provide information about the internal chemistry of the body but can also be specific to diseases. Therefore, detection and analysis of specific VOCs can be used for medical diagnostics. However, up until today in spite of several existing VOC-based detection techniques and significant efforts, breath analysis is not a diagnostic method available for clinicians. Infrared absorption spectroscopy is a promising technique to fill this gap, with tens of identified VOCs in breath. Currently, a lack of digital spectral databases and several masking effects make difficult reliable molecular identification of observed absorption features. We demonstrate that calculations of rotational bands of vibrational spectra could serve as a basic method for molecular identification of spectral features observed in experiment. Results of comparison of several known VOCs spectra with the predictions of the theoretical model are presented.

Breath indeed carries significant information about a disease: Potential biomarkers of cerebral palsy.

Objective and reliable noninvasive medical diagnostics of a large variety of diseases is still a dream. As a step in the direction of realization, a spectroscopic breath study of cerebral palsy (CP) was performed. Principal component analysis revealed data clustering for a healthy group and CP individuals was observed, with a P-value below 10-5 . Learning algorithms resulted in 91% accuracy in distinguishing the groups. With the help of manual analysis of absorption spectral features of breath samples, two volatile organic compounds were identified that demonstrate significant deviations in the groups. These represent two esters of propionic acid (PPAE). A transportation scheme was hypothesized that links the gut where propionic acid (PPA) and PPAE are produced, the brain of CP patients, through which PPA and PPAE transmit, and the lungs where PPAE releases. The results show a possibility to detect one more brain-related disorder via breath, in this case CP.

Molecular identification of bio-fluids in gas phase using infrared spectroscopy.

Bio-fluids are the source of a large number of metabolites. Identification and quantification of them can be an efficient step for understanding the internal chemistry of the body as well as for developing objective diagnostics of diseases. Several techniques have been developed so far; however, their metabolite identification and/or quantification are not reliable enough for acceptance by clinicians. As another promising step in this direction, we push infrared spectroscopy of bio-fluids in gas phase. Here we discuss features of breath and urine headspace realized with Fourier transform infrared spectroscopy. Molecular identification procedures based on component analysis of gas samples are proposed. In this paper, we show that aggregate data from different bio-fluids in gas phase can strengthen the diagnostics of the body state and disease.

Field-resolved infrared spectroscopy of biological systems.

The proper functioning of living systems and physiological phenotypes depends on molecular composition. Yet simultaneous quantitative detection of a wide variety of molecules remains a challenge1-8. Here we show how broadband optical coherence opens up opportunities for fingerprinting complex molecular ensembles in their natural environment. Vibrationally excited molecules emit a coherent electric field following few-cycle infrared laser excitation9-12, and this field is specific to the sample's molecular composition. Employing electro-optic sampling10,12-15, we directly measure this global molecular fingerprint down to field strengths 107 times weaker than that of the excitation. This enables transillumination of intact living systems with thicknesses of the order of 0.1 millimetres, permitting broadband infrared spectroscopic probing of human cells and plant leaves. In a proof-of-concept analysis of human blood serum, temporal isolation of the infrared electric-field fingerprint from its excitation along with its sampling with attosecond timing precision results in detection sensitivity of submicrograms per millilitre of blood serum and a detectable dynamic range of molecular concentration exceeding 105. This technique promises improved molecular sensitivity and molecular coverage for probing complex, real-world biological and medical settings.

Human beings as islands of stability: Monitoring body states using breath profiles.

By checking the reproducibility of conventional mid-infrared Fourier spectroscopy of human breath in a small test study (15 individuals), we found that a set of volatile organic compounds (VOC) of the individual breath samples remains reproducible at least for 18 months. This set forms a unique individual's "island of stability" (IOS) in a multidimensional VOC concentration space. The IOS stability can simultaneously be affected by various life effects as well as the onset of a disease. Reflecting the body state, they both should have different characteristics. Namely, they could be distinguished by different temporal profiles: In the case of life effects (beverage intake, physical or mental exercises, smoking etc.), there is a non-monotonic shift of the IOS position with the return to the steady state, whereas a progressing disease corresponds to a monotonic IOS shift. As a first step of proving these dependencies, we studied various life effects with the focus on the strength and characteristic time of the IOS shift. In general, our results support homeostasis on a long time scale of months, allostasis on scales of hours to weeks or until smoke quitting for smokers, as well as resilience in the case of recovery from a disease.

Sensitive spectroscopic breath analysis by water condensation.

Breath analysis has great potential for becoming an important clinical diagnosis method due to its friendly and non-invasive way of sample collection. Hundreds of endogenous trace gases (volatile organic compounds (VOCs)) are present in breath, representing different metabolic processes of the body. They are not only characteristic for a person, their age, sex, habit etc, but also specific to different kinds of diseases. VOCs, related to diseases could serve as biomarkers for clinical diagnostics and disease monitoring. However, due to the large amount of water contained in breath, an identification of specific VOCs is a real challenge. In this work we present a technique of water suppression from breath samples, that enables us to identify several trace gases in breath, e.g., methane, isoprene, acetone, aldehyde, carbon monoxide, etc, using Fourier-transform infrared spectroscopy. In the current state, the technique reduces the water concentration by a factor of 2500. Sample preparation and data acquisition take about 25 min, which is clinically relevant. In this article we demonstrate the working principle of the water reduction technique. Further, with specific examples we demonstrate that water elimination from breath samples does not hamper the concentration of trace gases in breath. Preliminary experiments with real breath also indicate that the concentrations of methane, acetone and isoprene remain the same during the sample preparation.

All-fiber highly chirped dissipative soliton generation in the telecom range.

A high-energy (0.93 nJ) all-fiber erbium femtosecond oscillator operating in the telecom spectral range is proposed and realized. The laser cavity, built of commercially available fibers and components, combines polarization maintaining (PM) and non-PM parts providing stable generation of highly chirped (chirp parameter 40) pulses compressed in an output piece of standard PM fiber to 165 fs. The results of the numerical simulation agree well with the experiment. The analyzed intracavity pulse dynamics enables the classification of the generated pulses as dissipative solitons.

Carrier-envelope-phase stabilization via dual wavelength pumping.

A power-scalable concept for carrier-envelope-phase stabilization is presented. It takes advantage of simultaneous pumping of the zero- and first-phonon absorption line of Yb:YAG at 969 and 940 nm. The concept was implemented to lock the carrier-envelope-offset frequency of a 45 W average power Kerr-lens mode-locked thin-disk oscillator. The lock performance is compared to previous experiments where carrier-envelope-stabilization was realized by means of cavity loss modulation.

Cascaded generation of coherent Raman dissipative solitons.

The cascaded generation of a conventional dissipative soliton (at 1020 nm) together with Raman dissipative solitons of the first (1065 nm) and second (1115 nm) orders inside a common fiber laser cavity is demonstrated experimentally and numerically. With sinusoidal (soft) spectral filtering, the generated solitons are mutually coherent at a high degree and compressible down to 300 fs. Numerical simulation shows that an even higher degree of coherence and shorter pulses could be achieved with step-like (hard) spectral filtering. The approach can be extended toward a high-order coherent Raman dissipative soliton source offering numerous applications such as frequency comb generation, pulse synthesis, biomedical imaging, and the generation of a coherent mid-infrared supercontinuum.

Feedback-controlled Raman dissipative solitons in a fiber laser.

Energy of chirped dissipative solitons (DS) generated in fiber lasers may exceed a threshold of stimulated Raman scattering (SRS) leading to formation of a noisy Raman pulse (RP). As we demonstrated recently, a feedback loop providing re-injection of the Raman pulse into the laser cavity can form a Raman dissipative soliton (RDS) with similar characteristics to those of the main dissipative soliton. Here, we present the results of feedback optimization of the generated RDS spectra. First experimental results of coherent combining of DS and RDS are also shown.

260-megahertz, megawatt-level thin-disk oscillator.

A Kerr-lens mode-locked (KLM) Yb:YAG thin-disk oscillator delivering 215-fs pulses with 75-W average power and 1.4-MW peak power at a repetition rate of 260 MHz is presented. Self-starting KLM is demonstrated at an output power of 68 W. This is the highest repetition rate of any mode-locked thin-disk oscillators so far. Concepts for scaling the repetition rate up to 1 GHz are discussed.

Multicolour nonlinearly bound chirped dissipative solitons.

The dissipative soliton regime is one of the most advanced ways to generate high-energy femtosecond pulses in mode-locked lasers. On the other hand, the stimulated Raman scattering in a fibre laser may convert the excess energy out of the coherent dissipative soliton to a noisy Raman pulse, thus limiting its energy. Here we demonstrate that intracavity feedback provided by re-injection of a Raman pulse into the laser cavity leads to formation of a coherent Raman dissipative soliton. Together, a dissipative soliton and a Raman dissipative soliton (of the first and second orders) form a two (three)-colour stable complex with higher total energy and broader spectrum than those of the dissipative soliton alone. Numerous applications can benefit from this approach, including frequency comb spectroscopy, transmission lines, seeding femtosecond parametric amplifiers, enhancement cavities and multiphoton fluorescence microscopy.

Large-mode enhancement cavities.

In passive enhancement cavities the achievable power level is limited by mirror damage. Here, we address the design of robust optical resonators with large spot sizes on all mirrors, a measure that promises to mitigate this limitation by decreasing both the intensity and the thermal gradient on the mirror surfaces. We introduce a misalignment sensitivity metric to evaluate the robustness of resonator designs. We identify the standard bow-tie resonator operated close to the inner stability edge as the most robust large-mode cavity and implement this cavity with two spherical mirrors with 600 mm radius of curvature, two plane mirrors and a round trip length of 1.2 m, demonstrating a stable power enhancement of near-infrared laser light by a factor of 2000. Beam radii of 5.7 mm × 2.6 mm (sagittal × tangential 1/e(2) intensity radius) on all mirrors are obtained. We propose a simple all-reflective ellipticity compensation scheme. This will enable a significant increase of the attainable power and intensity levels in enhancement cavities.

Long-term carrier-envelope-phase-stable few-cycle pulses by use of the feed-forward method.

The feed-forward technique has recently revolutionized carrier-envelope phase (CEP) stabilization, enabling unprecedented values of residual phase jitter. Nevertheless, its demonstrations have hitherto remained in a proof-of-principle state. Here we show that pulse quality and power issues can be solved, leading to few-cycle pulses with good beam quality. Making use of stable interferometers, we achieve day-long CEP-stable operation of the setup. Out-of-loop RMS phase noise amounts to less than 30 mrad in 20 s, with more than 24 h of CEP-locked operation being demonstrated.

Pump-seed synchronization for MHz repetition rate, high-power optical parametric chirped pulse amplification.

We report on an active synchronization between two independent mode-locked lasers using a combined electronic-optical feedback. With this scheme, seed pulses at MHz repetition rate were amplified in a non-collinear optical parametric chirped pulse amplifier (OPCPA). The amplifier was seeded with stretched 1.5 nJ pulses from a femtosecond Ti:Sapphire oscillator, while pumped with the 1 ps, 2.9 µJ frequency-doubled output of an Yb:YAG thin-disk oscillator. The residual timing jitter between the two oscillators was suppressed to 120 fs (RMS), allowing for an efficient and broadband amplification at 11.5 MHz to a pulse energy of 700 nJ and an average power of 8 W. First compression experiment with 240 nJ amplified pulse energy resulted in a pulse duration of ~10 fs.

Ultrabroadband efficient intracavity XUV output coupler.

We report an efficient intracavity XUV output coupler based on an anti-reflection-coated grazing incidence plate (GIP). Conceptually, GIP is an extension of a Brewster plate, affording low loss of the circulating fundamental light and serving as a highly efficient, extremely broadband output coupler for XUV. Due to the grazing incidence geometry, the short wavelength reflectivity can be extended to the keV range. The first GIP realized shows parameters close to the design. We discuss both the limitations of the GIP in comparison with other XUV output couplers and the applicability of the GIP extension at longer wavelengths, down to the MIR.

Energy scalability of mode-locked oscillators: a completely analytical approach to analysis.

A completely analytical approach to analysis of energy-scalable ultrashort-pulse oscillators operating in both normal- and anomalous-dispersion regimes is developed. The theory, based on the approximated solutions of the generalized complex nonlinear Ginzburg-Landau equation allows the problem to be reduced to a purely algebraic model, so that the oscillator characteristics are easy to trace and are completely characterized by only two parameters defining the so-called master diagram of the pulse energy scalability. The proposed theory covers all types of energy-scalable oscillators: all-normal-dispersion fiber, chirped-pulse and thin-disk solid-state ones and is validated by numerical simulations.

Power scaling of a high-repetition-rate enhancement cavity.

A passive optical resonator is used to enhance the power of a pulsed 78 MHz repetition rate Yb laser providing 200 fs pulses. We find limitations relating to the achievable time-averaged and peak power, which we distinguish by varying the duration of the input pulses. An intracavity average power of 18 kW is generated with close to Fourier-limited pulses of 10 W average power. Beyond this power level, intensity-related effects lead to resonator instabilities, which can be removed by chirping the seed laser pulses. By extending the pulse duration in this way to 2 ps, we could obtain 72 kW of intracavity circulating power with 50 W of input power.