Distinguishing the Uterine Artery, the Ureter, and Nerves in Laparoscopic Surgical Images Using Ensembles of Binary Semantic Segmentation Networks

Performing a minimally invasive surgery comes with a significant advantage regarding rehabilitating the patient after the operation. But it also causes difficulties, mainly for the surgeon or expert who performs the surgical intervention, since only visual information is available and they cannot use their tactile senses during keyhole surgeries. This is the case with laparoscopic hysterectomy since some organs are also difficult to distinguish based on visual information, making laparoscope-based hysterectomy challenging. In this paper, we propose a solution based on semantic segmentation, which can create pixel-accurate predictions of surgical images and differentiate the uterine arteries, ureters, and nerves. We trained three binary semantic segmentation models based on the U-Net architecture with the EfficientNet-b3 encoder; then, we developed two ensemble techniques that enhanced the segmentation performance. Our pixel-wise ensemble examines the segmentation map of the binary networks on the lowest level of pixels. The other algorithm developed is a region-based ensemble technique that takes this examination to a higher level and makes the ensemble based on every connected component detected by the binary segmentation networks. We also introduced and trained a classic multi-class semantic segmentation model as a reference and compared it to the ensemble-based approaches. We used 586 manually annotated images from 38 surgical videos for this research and published this dataset.

Endometrial Biopsy: Indications, Techniques and Recommendations. An Evidence-Based Guideline for Clinical Practice

This practice guideline provides updated evidence for the gynecologist who performs endometrial biopsy (EB) in gynecologic clinical practice. An international committee of gynecology experts developed the recommendations according to AGREE Reporting Guideline. An adequate tissue sampling is mandatory when performing an EB. Blind methods should not be first choice in patients with suspected endometrial malignancy. Hysteroscopy is the targeted-biopsy method with highest diagnostic accuracy and cost-effectiveness. Blind suction techniques are not reliable for the diagnosis of endometrial polyps. In low resources settings, and in absence of the capacity to perform office hysteroscopy, blind techniques could be used for EB. Hysteroscopic punch biopsy allows to collect only limited amount of endometrial tissue. grasp biopsy technique should be considered first choice in reproductive aged women, bipolar electrode chip biopsy should be preferred with hypotrophic or atrophic endometrium. EB is required for the final diagnosis of chronic endometritis. There is no consensus regarding which endometrial thickness cut-off should be used for recommending EB in asymptomatic postmenopausal women. EB should be offered to young women with abnormal uterine bleeding and risk factors for endometrial carcinoma. Endometrial pathology should be excluded with EB in nonobese women with unopposed hyperestrogenism. Hysteroscopy with EB is useful in patients with abnormal bleeding even without sonographic evidence of pathology. EB has high sensitivity for detecting intrauterine pathologies. In postmenopausal women with uterine bleeding, EB is recommended. Women with sonographic endometrial thickness > 4mm using tamoxifen should undergo hysteroscopic EB.

Risk of endometrial cancer in asymptomatic postmenopausal women in relation to ultrasonographic endometrial thickness: systematic review and diagnostic test accuracy meta-analysis

OBJECTIVE

This study aimed to evaluate the risk of endometrial carcinoma and atypical endometrial hyperplasia in asymptomatic postmenopausal women concerning the endometrial thickness measured by stratified threshold categories used for performing subsequent endometrial sampling and histologic evaluation.

DATA SOURCES

MEDLINE, Scopus, ClinicalTrials.gov, SciELO, Embase, the Cochrane Central Register of Controlled Trials, LILACS, conference proceedings, and international controlled trials registries were searched without temporal, geographic, or language restrictions.

STUDY ELIGIBILITY CRITERIA

Studies were selected if they had a crossover design evaluating the risk of atypical endometrial hyperplasia and endometrial carcinoma in postmenopausal asymptomatic women and calculated the diagnostic accuracy of transvaginal ultrasonography thresholds (at least 3.0 mm) confirmed by histopathologic diagnosis.

METHODS

This was a systematic review and diagnostic test accuracy meta-analysis according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses of Diagnostic Test Accuracy and Synthesizing Evidence from Diagnostic Accuracy Tests guidelines. Endometrial thickness thresholds were grouped as follows: from 3.0 to 5.9 mm; between 6.0 and 9.9 mm; between 10.0 and 13.9 mm; and ≥14.0 mm. Quality assessment was performed using the Quality Assessment Tool for Diagnostic Accuracy Studies 2 tool. Publication bias was quantified using the Deek funnel plot test. Coprimary outcomes were the risk of atypical endometrial hyperplasia or endometrial carcinoma according to the endometrial thickness and diagnostic accuracy of each threshold group.

RESULTS

A total of 18 studies provided the data of 10,334 women who were all included in the final analysis. Overall, at an endometrial thickness threshold of at least 3.0 mm, the risk of atypical endometrial hyperplasia or endometrial carcinoma was increased 3-fold relative to women below the cutoff (relative risk, 3.77; 95% confidence interval, 2.26-6.32; I2=74%). Similar degrees of risk were reported for thresholds between 3.0 and 5.9 mm (relative risk, 5.08; 95% confidence interval, 2.26-11.41; I2=0%), 6.0 and 9.9 mm (relative risk, 4.34; 95% confidence interval, 1.68-11.23; I2=0%), 10.0 and 13.9 mm (relative risk, 4.11; 95% confidence interval, 1.55-10.87; I2=86%), and ≥14.0 mm (relative risk, 2.53; 95% confidence interval, 1.04-6.16; I2=78%) with no significant difference among subgroups (P=.885). Regarding diagnostic accuracy, the pooled sensitivity decreased from thresholds below 5.9 mm (relative risk, 0.81; 95% confidence interval, 0.49-0.85) to above 14.0 mm (relative risk, 0.28; 95% confidence interval, 0.18-0.40). Furthermore, the specificity increased from 0.70 (95% confidence interval, 0.61-0.78) for endometrial thickness between 3.0 and 5.9 mm to 0.86 (95% confidence interval, 0.71-0.94) when the endometrial thickness is ≥14.0 mm. For 3.0 to 5.9 mm and 10.0 to 13.9 mm thresholds, the highest diagnostic odds ratios of 10 (95% confidence interval, 3-41) and 11 (95% confidence interval, 2-49), with areas under the curve of 0.81 (95% confidence interval, 0.77-0.84) and 0.82 (95% confidence interval, 0.79-0.86), respectively, were retrieved. The summary point analysis revealed that the 3.0 to 5.9 mm cutoff point was placed higher in the summary receiver operator curve space than the other subgroups, indicating increased endometrial carcinoma or atypical endometrial hyperplasia diagnosis using these cutoffs.

CONCLUSION

Both low and high endometrial thickness thresholds in postmenopausal asymptomatic women seem equally effective in detecting endometrial carcinoma and atypical endometrial hyperplasia. However, although using a 3.0 to 5.9 mm cutoff results in a lower specificity, the offsetting improvement in sensitivity may justify using this cutoff for further endometrial evaluation in patients with suspected endometrial malignancy.

The use of hysteroscopy in endometrial cancer: old questions and novel challenges

Endometrial cancer is the most common gynecological malignancy with a relatively good overall prognosis. It traditionally has two subtypes: type 1 (endometrioid carcinoma) and type 2 (non-endometrioid carcinoma). The prognosis is excellent for stage I endometrioid cancer, with a 5-year survival rate of 96%. However, the prognosis is much worse for women with high-risk endometrial cancer. Effective preoperative staging is important in order to tailor treatment and achieve optimal long-term survival. The majority of asymptomatic polyps detected by ultrasound are treated surgically. Conventionally, dilatation and curettage was performed to obtain a histological diagnosis, but nowadays hysteroscopy with biopsy is starting to be considered as the gold standard. Hysteroscopic resection seems to reduce the risk of underdiagnosed (atypical endometrial hyperplasia) endometrial cancer. To avoid the spread of malignant cells, hysteroscopy should be performed with concern to keep intrauterine pressure low. In comparison with cervical injection, the hysteroscopic method has a better detection rate in the para-aortic area during sentinel lymph node mapping. In the assessment of cervical involvement, the accuracy of magnetic resonance imaging is significantly higher than the accuracy of hysteroscopy. In fertility-sparing cases, hysteroscopic endometrium resection with progesterone therapy is an acceptable option.

Effectiveness of different methods for polypectomy in the menopause: a retrospective study

Introduction: Most endometrial polyps represent focal hyperplasia of the endometrium. Endometrial polyps can be diagnosed by ultrasound, hysterocontrast sonography, hysterosalpingography, endometrial biopsy, and uterine curettage, but diagnostic hysteroscopy is considered the gold-standard method, with the greatest sensitivity and specificity and also with the opportunity for treatment at the same time.Study design: A retrospective study was conducted on 424 patients between 2006 and 2018. The polyps were verified during diagnostic hysteroscopy and were removed by resectoscopy or curettage. All samples underwent histological examination. The effectivity of the type of resection and the recurrence rate were evaluated.Results: The average age of the patients was 60.2 ± 9.3 years. Polyps were excised in 62.97% by resectoscopic polypectomy and in 37.03% by curettage. Malignancy was confirmed in 4.24% of cases. Histological verification of polyps was 79.4% in the resectoscopy group and 69.04% in the curettage group; the difference was significant (p < 0.01). The recurrence rate was 20.47% after resectoscopy and 27.12% following curettage.Conclusion: Hysteroscopy remains the best option and the gold-standard method among diagnostic procedures of endometrial pathology. In this study, there was a significant difference in matching hysteroscopic and histological findings in the two methods of polypectomy. The recurrence rate is also lower following resectoscopy.

Multivariate analysis of Brillouin imaging data by supervised and unsupervised learning

Brillouin imaging relies on the reliable extraction of subtle spectral information from hyperspectral datasets. To date, the mainstream practice has been to use line fitting of spectral features to retrieve the average peak shift and linewidth parameters. Good results, however, depend heavily on sufficient signal-to-noise ratio and may not be applicable in complex samples that consist of spectral mixtures. In this work, we thus propose the use of various multivariate algorithms that can be used to perform supervised or unsupervised analysis of the hyperspectral data, with which we explore advanced image analysis applications, namely unmixing, classification and segmentation in a phantom and live cells. The resulting images are shown to provide more contrast and detail, and obtained on a timescale ∼10² faster than fitting. The estimated spectral parameters are consistent with those calculated from pure fitting.

Background-free fibre optic Brillouin probe for remote mapping of micromechanics

Brillouin imaging (BI) has become a valuable tool for micromechanical material characterisation, thanks to extensive progress in instrumentation in the last few decades. This powerful technique is contactless and label-free, thus making it especially suitable for biomedical applications. Nonetheless, to fully harness the non-contact and non-destructive nature of BI, transformational changes in instrumentation are still needed to extend the technology's utility into the domain of in vivo and in situ operation, which we foresee to be particularly crucial for wide spread usage of BI, e.g. in medical diagnostics and pathology screening. This work addresses this challenge by presenting the first demonstration of a fibre-optic Brillouin probe, capable of mapping the micromechanical properties of a tissue-mimicking phantom. This is achieved through combination of miniaturised optical design, advanced hollow-core fibre fabrication and high-resolution 3D printing. Our prototype probe is compact, background-free and possesses the highest collection efficiency to date, thus providing the foundation of a fibre-based Brillouin device for remote, in situ measurements in challenging and otherwise difficult-to-reach environments in biomedical, material science and industrial applications.

Single pixel polarimetric imaging through scattering media

Polarimetric imaging can provide valuable information about biological samples in a wide range of applications. Detrimental tissue scattering and depolarization however currently hamper in vivo polarization imaging. In this work, single pixel imaging is investigated as a means of reconstructing polarimetric images through scattering media. A theoretical imaging model is presented, and the recovery of the spatially resolved Mueller matrix of a test object behind a scattering phantom is demonstrated experimentally.

Minute ventilation stabilization during all pressure-control / support mechanical ventilation modes

The main goal of our prospective randomized study was comparing compare the effectiveness of ventilation control method "Automatic proportional minute ventilation (APMV) "versus manually set pressure control ventilation modes in relationship to lung mechanics and gas exchange. 80 patients undergoing coronary artery bypass grafting (CABG) were randomized into 2 groups. 40 patients in the first group No.1 (APMV group) were ventilated with pressure control (PCV) or pressure support ventilation (PSV) mode with APMV control. The other 40 patients (control group No.2) were ventilated with synchronized intermittent mandatory ventilation (SIMV-p) or pressure control modes (PCV) without APMV. Ventilation control with APMV was able to maintain minute ventilation more precisely in comparison with manual control (p<0.01), similarly deviations of ETCO(2) were significantly lower (p<0.01). The number of manual corrections of ventilation settings was significantly lower when APMV was used (p<0.01). The differences in lung mechanics and hemodynamics were not statistically significant. Ventilation using APMV is more precise in maintaining minute ventilation and gas exchange compared with manual settings. It required less staff intervention, while respiratory system mechanics and hemodynamics are comparable. APMV showed as effective and safe method applicable on top of all pressure control ventilation modes.

SNR enhancement in brillouin microspectroscopy using spectrum reconstruction

Brillouin spectroscopy can suffer from low signal-to-noise ratios (SNRs). Such low SNRs can render common data analysis protocols unreliable, especially for SNRs below ∼10. In this work we exploit two denoising algorithms, namely maximum entropy reconstruction (MER) and wavelet analysis (WA), to improve the accuracy and precision in determination of Brillouin shifts and linewidth. Algorithm performance is quantified using Monte-Carlo simulations and benchmarked against the Cramér-Rao lower bound. Superior estimation results are demonstrated even at low SNRs (≥ 1). Denoising is furthermore applied to experimental Brillouin spectra of distilled water at room temperature, allowing the speed of sound in water to be extracted. Experimental and theoretical values were found to be consistent to within ±1% at unity SNR.

Detection of proteoglycan loss from articular cartilage using Brillouin microscopy, with applications to osteoarthritis

The degeneration of articular cartilage (AC) occurs in osteoarthritis (OA), which is a leading cause of pain and disability in middle-aged and older people. The early disease-related changes in cartilage extra-cellular matrix (ECM) start with depletion of proteoglycan (PG), leading to an increase in tissue hydration and permeability. These early compositional changes are small (<10%) and hence difficult to register with conventional non-invasive imaging technologies (magnetic resonance and ultrasound imaging). Here we apply Brillouin microscopy for detecting changes in the mechanical properties and composition of porcine AC. OA-like degradation is mimicked by enzymatic tissue digestion, and we compare Brillouin microscopy measurements against histological staining of PG depletion over varying digestion times and enzyme concentrations. The non-destructive nature of Brillouin imaging technology opens new avenues for creating minimally invasive arthroscopic devices for OA diagnostics and therapeutic monitoring.

Precision and informational limits in inelastic optical spectroscopy

Using Fisher information and the Cramér-Rao lower bound, we analyse fundamental precision limits in the determination of spectral parameters in inelastic optical scattering. General analytic formulae are derived which account for the instrument response functions of the dispersive element and relay optics found in practical Raman and Brillouin spectrometers. Limiting cases of dispersion and diffraction limited spectrometers, corresponding to measurement of Lorentzian and Voigt lineshapes respectively, are discussed in detail allowing optimal configurations to be identified. Effects of defocus, spherical aberration, detector pixelation and a finite detector size are also considered.

Relationship between dynamic expiratory time constant tau(edyn) and parameters of breathing cycle in pressure support ventilation mode

Study of the relationship between ventilation parameters: monitored expiratory time constant - tau(edyn) and breathing - trigger frequency (f(trig)) and time of breathing cycle (T(cy)) are main goals of this article. Parameters were analyzed during last 4+/-2 h before weaning from ventilation in 66 patients ventilated in pressure support mode (PSV). We have found out, that there exist mathematical relationships, observed during adequate gas exchange, yet not described. Monitored parameters are represented by tau(edyn), f(trig) and T(cy). The analysis showed close negative correlation between T(cy) and f(trig) (R(2)=0.903). This implies that each increasing of tau(edyn) causes decreasing of f(trig) and vice versa. The calculation of regression equation between tau(edyn) and T(cy) outlined that T(cy) = 5.2625 * tau(edyn) + 0.1242 (R(2)=0.85). Regulation of respiratory cycles by the respiratory center in the brain is probably based on evaluation of tau(edyn) as the tau(edyn) probably represents a regulatory element and T(cy) regulated element. It can be assumed, that respiratory center can optimize the work of breathing in order to minimize energy in system patient + ventilator. The unique relationship, described above could be useful in clinical practice for development of new ventilation modes.

Both trait-neutrality and filtering effects are validated by the vegetation patterns detected in the functional recovery of sand grasslands

Neutral theory of species assembly means that species assembly is governed by stochastic dispersal processes and fluctuations in established populations. An alternative theory suggests that assembly is strongly determined by functional trait filtering governed by abiotic and biotic filtering selecting species from the local species pool. To test these assumptions, in the current paper we analysed vegetation changes in the first 12 years of succession after heavy goose grazing on acidic sand. With trait-based analyses using permanent plots we addressed the following hypotheses: (i) High fluctuations in the trait values are typical in the first years; later a temporally divergent change in the trait patterns of sites with different vertical position became characteristic. (ii) In the functional diversity of regenerative and vegetative traits we expected different temporal patterns. We confirmed the first hypothesis, as in the first few years most traits displayed high fluctuations with no clear patterns. Our findings weakly supported the second hypothesis; while there were distinct patterns detected in the functional richness of traits, functional divergence and evenness displayed no clear distinctive patterns. We can conclude that both trait neutrality and filtering effects operate in the vegetation changes of the first period of secondary succession.

Comparison of different theories for focusing through a plane interface: reply

The correction pointed out by Kim et al. [J. Opt. Soc. Am. A35, 591 (2018)JOAOD60740-323210.1364/JOSAA.35.000591] to our paper [J. Opt. Soc. Am. A14, 1482 (1997)JOAOD60740-323210.1364/JOSAA.14.001482] is welcome. A few additional remarks are included in this reply.

Probing the internal micromechanical properties of Pseudomonas aeruginosa biofilms by Brillouin imaging

Biofilms are organised aggregates of bacteria that adhere to each other or surfaces. The matrix of extracellular polymeric substances that holds the cells together provides the mechanical stability of the biofilm. In this study, we have applied Brillouin microscopy, a technique that is capable of measuring mechanical properties of specimens on a micrometre scale based on the shift in frequency of light incident upon a sample due to thermal fluctuations, to investigate the micromechanical properties of an active, live Pseudomonas aeruginosa biofilm. Using this non-contact and label-free technique, we have extracted information about the internal stiffness of biofilms under continuous flow. No correlation with colony size was found when comparing the averages of Brillouin shifts of two-dimensional cross-sections of randomly selected colonies. However, when focusing on single colonies, we observed two distinct spatial patterns: in smaller colonies, stiffness increased towards their interior, indicating a more compact structure of the centre of the colony, whereas, larger (over 45 μm) colonies were found to have less stiff interiors.

A specialized microscopy technique can monitor biofilm stiffness in a non-destructive manner, yielding insights into biofilm structure and development. The technique, called Brillouin imaging, uses changes in the frequency of light interacting with a substance to reveal fine detail about the material’s mechanical properties. Peter Török and colleagues at Imperial College London, with co-workers in Singapore, used Brillouin imaging to study biofilms of Pseudomonas aeruginosa bacteria at different stages in their life cycle. In young colonies, stiffness increased towards the interior of the biofilm, while mature colonies had less stiff interiors. The older biofilms may therefore have hollow interiors or may have been moving towards a phase of bacterial dispersal from the biofilm state. This non-disruptive method to study mechanical variations within and between living biofilms may help efforts to combat biofilms in clinical, environmental and industrial situations.

Decoupling absorption and emission processes in super-resolution localization of emitters in a plasmonic hotspot

The absorption process of an emitter close to a plasmonic antenna is enhanced due to strong local electromagnetic (EM) fields. The emission, if resonant with the plasmonic system, re-radiates to the far-field by coupling with the antenna via plasmonic states, whose presence increases the local density of states. Far-field collection of the emission of single molecules close to plasmonic antennas, therefore, provides mixed information of both the local EM field strength and the local density of states. Moreover, super-resolution localizations from these emission-coupled events do not report the real position of the molecules. Here we propose using a fluorescent molecule with a large Stokes shift in order to spectrally decouple the emission from the plasmonic system, leaving the absorption strongly resonant with the antenna's enhanced EM fields. We demonstrate that this technique provides an effective way of mapping the EM field or the local density of states with nanometre spatial resolution.

Reporting the position of molecules and the electromagnetic enhancement in a plasmonic hotspot is difficult. Here Mack et al. use a large Stokes-shifted molecule to spectrally decouple the emission process of the dye from the plasmonic system, keeping the absorption on resonance with the plasmon resonance of the antenna.

Quantification of plaque stiffness by Brillouin microscopy in experimental thin cap fibroatheroma

Plaques vulnerable to rupture are characterized by a thin and stiff fibrous cap overlaying a soft lipid-rich necrotic core. The ability to measure local plaque stiffness directly to quantify plaque stress and predict rupture potential would be very attractive, but no current technology does so. This study seeks to validate the use of Brillouin microscopy to measure the Brillouin frequency shift, which is related to stiffness, within vulnerable plaques. The left carotid artery of an ApoE(-/-)mouse was instrumented with a cuff that induced vulnerable plaque development in nine weeks. Adjacent histological sections from the instrumented and control arteries were stained for either lipids or collagen content, or imaged with confocal Brillouin microscopy. Mean Brillouin frequency shift was 15.79 ± 0.09 GHz in the plaque compared with 16.24 ± 0.15 (p < 0.002) and 17.16 ± 0.56 GHz (p < 0.002) in the media of the diseased and control vessel sections, respectively. In addition, frequency shift exhibited a strong inverse correlation with lipid area of -0.67 ± 0.06 (p < 0.01) and strong direct correlation with collagen area of 0.71 ± 0.15 (p < 0.05). This is the first study, to the best of our knowledge, to apply Brillouin spectroscopy to quantify atherosclerotic plaque stiffness, which motivates combining this technology with intravascular imaging to improve detection of vulnerable plaques in patients.

Integrated plasmonic metasurfaces for spectropolarimetry

Plasmonic metasurfaces enable simultaneous control of the phase, momentum, amplitude and polarization of light and hence promise great utility in realization of compact photonic devices. In this paper, we demonstrate a novel chip-scale device suitable for simultaneous polarization and spectral measurements through use of six integrated plasmonic metasurfaces (IPMs), which diffract light with a given polarization state and spectral component into well-defined spatial domains. Full calibration and characterization of our device is presented, whereby good spectral resolution and polarization accuracy over a wavelength range of 500-700 nm is shown. Functionality of our device in a Müller matrix modality is demonstrated through determination of the polarization properties of a commercially available variable waveplate. Our proposed IPM is robust, compact and can be fabricated with a single photolithography step, promising many applications in polarization imaging, quantum communication and quantitative sensing.

Polarization-multiplexed encoding at nanometer scales

Optical data storage was developed using binary encoding primarily due to signal to noise ratio considerations. We report on a multiplexing method that allows a seven fold storage increase, per storage layer, per side, and propose one that can yield theoretically a 20+ fold increase. Multiplexing is achieved by encoding information in polarization via appropriately oriented nanostructures that emit strongly polarized light when excited by unpolarized light. The storage increase is possible due to the significantly reduced crosstalk that results form using unpolarized light.

Confocal polarization imaging in high-numerical-aperture space

In this work we describe theoretical and experimental physical aspects of high-resolution imaging polarimetry and its application to polarization-multiplexed encoding. We theoretically demonstrate that it is possible to resolve the orientation of two fixed dipole-like emitters placed significantly below the resolution limit if their emission is uncorrelated. Furthermore, we experimentally demonstrate this phenomenon by illuminating closely spaced asymmetric nanopits with unpolarized light and subsequently determining their individual orientation and position from the measured spatial distributions of the azimuth angle of the polarization and degree of polarization, respectively. Reduction of the optical resolution of the imaging system is also shown to only weakly affect resolution obtainable via polarization measurements.

Phase-retrieved pupil function and coherent transfer function in confocal microscopy

This work reports on the retrieval of the pupil function and coherent transfer function of a coherent reflection type confocal microscope from simulated measurements of the intensity point spread function. Two phase retrieval algorithms are presented in this vein, which incorporate the multiple pupil dependence of image formation in confocal microscopy. Verification of the algorithms follows by numerical simulations.

Stokes vector based polarization resolved second harmonic microscopy of starch granules

We report on the measurement and analysis of the polarization state of second harmonic signals generated by starch granules, using a four-channel photon counting based Stokes-polarimeter. Various polarization parameters, such as the degree of polarization (DOP), the degree of linear polarization (DOLP), the degree of circular polarization (DOCP), and anisotropy are extracted from the 2D second harmonic Stokes images of starch granules. The concentric shell structure of a starch granule forms a natural photonic crystal structure. By integration over all the solid angle, it will allow very similar SHG quantum efficiency regardless of the angle or the states of incident polarization. Given type I phase matching and the concentric shell structure of a starch granule, one can easily infer the polarization states of the input beam from the resulting SH micrograph.

[Is there a relationship between inflammatory markers, oxidative stress and postoperative atrial fibrillation?]

INTRODUCTION

Atrial fibrillation (AF) is one of the most common complications following heart surgery. The aim of this work was to verify the relationship between inflammatory markers, oxidative stress and postoperative arrhythmia.

METHODS

45 patients with ischemic heart disease (12 women and 33 men, mean age 62.3 ± 9.4 years) underwent surgical myocardial revascularization. The extracorporeal circulation (ECC) was used in 30 patients, without ECC was 15 patients. During the first 3 postoperative days was determining the incidence and duration of the AF, laboratory markers of inflammation (CRP, leukocytes, TNFα), malondialdehyde (MDA).

RESULTS

Demographic data and associated disease were in this patients similar. The incidence of AF we documented in 30 patients (66.7%). In patients with postoperative AF were significantly higher levels of inflammatory markers (leukocytes 13.6 ± 3.6 vs 11.3 ± 3.6; 14.7 ± 3.9 vs 12.5 ± 2.9; 13.7 ± 4.1 vs 11.4 ± 13.7; p 0.05; CRP 138.1 ± 41.1 vs 69.9 ± 25.8; p 0.001; TNFα 11.3 ± 14.3 vs 8.7 ± 3.6; 12.1 ± 14.5 vs 8.7 ± 3.1; p 0.05) compared with patients who were free from AF. Values of MDA were not significantly different.

CONCLUSION

Patients with post-operative atrial fibrillation were higher levels of inflammatory markers compared with patients with sinus rhythm but no significant differences in the levels of oxidative stress.

Polarization-resolved second harmonic generation microscopy with a four-channel Stokes-polarimeter

We developed a four-channel photon counting based Stokes-polarimeter for spatial characterization of polarization effects in second harmonic generation (SHG). We have implemented a calibration technique allowing quantitative measurement of polarization parameters, such as the degree of polarization (DOP), degree of linear polarization (DOLP), degree of circular polarization (DOCP), as well as anisotropy from the acquired Stokes parameters. The technique is used as contrast mechanism to characterize the polarization properties from two potassium dihydrogen phosphate (KDP) micro-crystals and collagen type-I in SHG microscopy.

Spatial and temporal variations in vector fields

We introduce a new metric to characterise spatial variations occurring in a time varying vector field, and we derive a rotationally invariant formula that quantifies temporal fluctuations within a consistent framework. So as to highlight the physics behind these metrics, both are derived from a well-known experiment in polarimetry. The derivation yields a set of expressions in a two-dimensional space, which is subsequently expanded to n-dimensions for special cases. The resulting expressions of the temporal and spatial metrics are incorporated into the electromagnetic theory of coherence and polarisation. Examples are given in the context of single molecule detection when measuring asymmetrically and radially polarised beams.

The role of seed bank in the dynamics of understorey in an oak forest in Hungary

We studied the potential role of seed bank in the dynamics of the understorey in a turkey oak-sessile oak forest (Querceteum petraeae-cerris) in Hungary. We used long-term records of the herb layer (1973-2006) and the seed bank composition of 2006 to assess the role of seed bank in the regeneration of herb layer. The total cover of herb layer decreased from 22% (1973) to 6% (1988), and remained low (<10%) till 2006; coinciding with the increasing cover of secondary canopy dominated by Acer campestre. We found a low density seed bank (ca. 1300 seeds/m2). Altogether 33 species were germinated from the soil samples. A few generalist weed species composed the majority of seed bank. It was possible to assign a seed bank type for 19 species; 14 species out of 19 was long-term persistent. We found that the characteristic perennial forest herbs and grasses had only sparse seed bank. The Jaccard similarity between vegetation and seed bank was low (<30%). Our results suggest that the continuous establishment of forest herbs are not based on local persistent seed bank; it should be based on vegetative spreading and/or seed rain.

Synthesis of structured partially spatially coherent beams

We report on the generation and rapid characterization of structured beams of arbitrary spatial coherence. An experimental setup is introduced capable of generating partially coherent fields by incoherently superposing fully coherent fields. The characterization is performed using the spectral information in the interferogram produced when using a two-dimensional nonredundant array of pinholes. An example of a partially coherent "doughnut" beam is given and proved to be partially coherent.

[Why there is atrial fibrillation after cardiac operations?]

Atrial fibrillation (AF) is the most frequent arrhythmias after cardiac operations. Its incidence ranges from 10-65%. Often there is a patient discomfort, prolongs hospitalization, increases costs of operation and may be permanent or recurrent course. The cause of postoperative AF is multifactorial. The prevention of non-pharmacological and pharmacological interventions. The conventional treatment strategies include monitoring ventricular rate, restoration of sinus rhythm and prevention of thromboembolic events. The development of effective therapies designed to decrease the high incidence of postoperative AF may be important in the future.

Early vegetation development after grassland restoration by sowing low-diversity seed mixtures in former sunflower and cereal fields

We studied the early vegetation dynamics in former croplands (sunflower and cereal fields) sown with a low-diversity seed mixture (composed of 2 native grass species) in Egyek-Pusztakócs, Hortobágy National Park, East-Hungary. The percentage cover of vascular plants was recorded in 4 permanent plots per field on 7 restored fields between 2006 and 2009. Ten aboveground biomass samples per field were also collected in June in each year. We addressed two questions: (i) How do seed sowing and annual mowing affect the species richness, biomass and cover of weeds? (ii) How fast does the cover of sown grasses develop after seed sowing? Weedy species were characteristic in the first year after sowing. In the second and third year their cover and species richness decreased. From the second year onwards the cover of perennial grasses increased. Spontaneously immigrating species characteristic to the reference grasslands were also detected with low cover scores. Short-lived weeds were suppressed as their cover and biomass significantly decreased during the study. The amount of litter and sown grass biomass increased progressively. However, perennial weed cover, especially the cover of Cirsium arvense increased substantially. Our results suggest that grassland vegetation can be recovered by sowing low diversity mixtures followed up by yearly mowing. Suppression of perennial weed cover needs more frequent mowing (multiple times a year) or grazing.

Focusing of spatially inhomogeneous partially coherent, partially polarized electromagnetic fields

We report a general framework capable of describing the focusing of electromagnetic waves with spatially varying coherence and polarization properties in optical systems of arbitrary numerical aperture and Fresnel number. We also investigate the reduction of the dimensionality of the requisite integrals by use of a coherent mode expansion. We find that coherent mode expansions treating each component of the electric field vector individually are unsuitable for describing focusing systems because of the inter-component mixing that can occur in high numerical aperture systems. In addition, we show that the assumption of harmonic angular dependence allows the azimuthal integration to be performed analytically, providing further simplification of the analysis. We also find that the effective degree of spectral coherence of an electromagnetic beam is unchanged upon focusing. Finally, as an illustration of the developed framework, we calculate the transverse and axial focal distributions for a partially coherent source formed by incoherent superposition of radially and azimuthally polarized Laguerre-Gauss modes.

Properties of high-numerical-aperture Mueller-matrix polarimeters

To our knowledge there has been very little work done to establish the theoretical basis of high-NA Mueller matrix polarimetry. We consider how high-NA polarimetry differs from traditional wide-field polarimetry. We show that confocal polarimetry leads to an averaging of the sample Jones matrices, each of which is associated with one of the incident plane waves comprising the incident focused field and that a conventional polarimeter leads to an averaging of sample Mueller matrices. We conclude with an example.

A priori information and optimisation in polarimetry

Polarimetric measurements are designed to obtain information pertaining to the system under study, however noise in the system limits the precision and hence information obtainable. Exploitation of a priori knowledge of the system allows for an improvement in the precision of experimental data. In this vein we present a framework for system design and optimisation based upon the Fisher information matrix, which allows easy incorporation of such a priori information. As such the proposed figure of merit is more complete than the commonly used condition number. Conditions of equivalence are considered, however a number of examples highlight the failings of the condition number under more general scenarios. Bounds on the achievable informational gains via multiple polarimeter arms are also given. Finally we present analytic results concerning error distribution in a Mueller matrix polar decomposition, allowing for a more accurate noise analysis in polarimetric experiments.

Determination of the three-dimensional orientation of single molecules

A simple method for real-time determination of the full three-dimensional orientation of the emission dipole of single molecules is presented. Introduction of a pi phase step in the back focal plane of the collector lens breaks the inherent symmetry, allowing the longitudinal dipole component to be measured. Experimental tolerances and the consequence of a nonzero bandwidth emission spectrum are also discussed. The scheme also allows for the longitudinal component of an electric field to be found experimentally.

Inversion of the Debye-Wolf diffraction integral using an eigenfunction representation of the electric fields in the focal region

The forward problem of focusing light using a high numerical aperture lens can be described using the Debye-Wolf integral, however a solution to the inverse problem does not currently exist. In this work an inversion formula based on an eigenfunction representation is derived and presented which allows a field distribution in a plane in the focal region to be specified and the appropriate pupil plane distribution to be calculated. Various additional considerations constrain the inversion to ensure physicality and practicality of the results and these are also discussed. A number of inversion examples are given.

Eigenfunction expansion of the electric fields in the focal region of a high numerical aperture focusing system

The Debye-Wolf electromagnetic diffraction integral is now routinely used to describe focusing by high numerical (NA) lenses. We obtain an eigenfunction expansion of the electric vector field in the focal region in terms of Bessel and generalized prolate spheroidal functions. Our representation has many optimal and desirable properties which offer considerable simplification to the evaluation and analysis of the Debye- Wolf integral. It is potentially also useful in implementing two-dimensional apodization techniques to synthesize electromagnetic field distributions in the focal region of a high NA lenses. Our work is applicable to many areas, such as optical microscopy, optical data storage and lithography.

High numerical aperture vectorial imaging in coherent optical microscopes

Imaging systems are typically partitioned into three components: focusing of incident light, scattering of incident light by an object and imaging of scattered light. We present a model of high Numerical Aperture (NA) imaging systems which differs from prior models as it treats each of the three components of the imaging system rigorously. It is well known that when high NA lenses are used the imaging system must be treated with vectorial analysis. This in turn requires that the scattering of light by the object be calculated rigorously according to Maxwell's equations. Maxwell's equations are solvable analytically for only a small class of scattering objects necessitating the use of rigorous numerical methods for the general case. Finally, rigorous vectorial diffraction theory and focusing theory are combined to calculate the image of the scattered light. We demonstrate the usefulness of the model through examples.

Photon statistics in single molecule orientational imaging

Optical techniques in single molecule imaging rely heavily on photon counting for data acquisition. Extraction of information from the recorded readings is often done by means of statistical signal processing, however this requires a full knowledge of the photoelectron statistics. In addition to counting statistics we include a specific form of random signal variations namely reorientational dynamics, or wobble to derive the general probability density function of the number of detected photons. The relative importance of the two factors is dependent upon the total number of photons in the system and results are given in all regimes.

Rigorous analysis of spheres in Gauss-Laguerre beams

In this paper we develop a rigorous formulation of Gauss- Laguerre beams in terms of Mie scattering coefficients which permits us to quasi-analytically treat the interaction of a spherical particle located in the focal region of a possibly high numerical aperture lens illuminated by a Gauss-Laguerre beam. This formalism is used to study the scattered field as a function of the radius of a spherical scatterer, as well as the translation of a spherical scatterer through the Gauss-Laguerre illumination in the focal plane. Knowledge of the Mie coefficients provides a deeper insight to understanding the scattering process and explaining the oscillatory behaviour of the scattered intensity distribution.

Calculation of the image of an arbitrary vectorial electromagnetic field

In order to rigorously calculate the image of a scattered field, it must be propagated into the far-field before vectorial focusing theory is applied. This approach may become difficult when, for example, the scattering object is embedded in a stratified medium, requiring calculation of the appropriate Green's tensor. We present a method for calculating the image of an arbitrary vectorial field by decomposing the field into a superposition of magnetic-dipole waves. We show that this technique can significantly simplify the calculation of the image of arbitrary vectorial fields even when the field is known within a stratified medium. The technique is more computationally efficient than existing methods however we also show that the method retains accuracy.

Rigorous near- to far-field transformation for vectorial diffraction calculations and its numerical implementation

A rigorous method for transforming an electromagnetic near-field distribution to the far field is presented. We start by deriving a set of self-consistent integral equations that can be used to represent the electromagnetic field rigorously everywhere in homogeneous space apart from the closed interior of a volume encompassing all charges and sinks. The representation is derived by imposing a condition analogous to Sommerfeld's radiation condition. We then examine the accuracy of our numerical implementation of the formula, also on a parallel computer cluster, by comparing the results with a case when the analytical solution is also available. Finally, an application example is shown for a nonanalytical case.