Bio-knowledge-based filters improve residue-residue contact prediction accuracy.

Motivation: Residue-residue contact prediction through direct coupling analysis has reached impressive accuracy, but yet higher accuracy will be needed to allow for routine modelling of protein structures. One way to improve the prediction accuracy is to filter predicted contacts using knowledge about the particular protein of interest or knowledge about protein structures in general. Results: We focus on the latter and discuss a set of filters that can be used to remove false positive contact predictions. Each filter depends on one or a few cut-off parameters for which the filter performance was investigated. Combining all filters while using default parameters resulted for a test set of 851 protein domains in the removal of 29% of the predictions of which 92% were indeed false positives. Availability and implementation: All data and scripts are available at http://comprec-lin.iiar.pwr.edu.pl/FPfilter/. Supplementary information: Supplementary data are available at Bioinformatics online.

Nonlinear interaction between single photons.

Harnessing nonlinearities strong enough to allow single photons to interact with one another is not only a fascinating challenge but also central to numerous advanced applications in quantum information science. Here we report the nonlinear interaction between two single photons. Each photon is generated in independent parametric down-conversion sources. They are subsequently combined in a nonlinear waveguide where they are converted into a single photon of higher energy by the process of sum-frequency generation. Our approach results in the direct generation of photon triplets. More generally, it highlights the potential for quantum nonlinear optics with integrated devices and, as the photons are at telecom wavelengths, it opens the way towards novel applications in quantum communication such as device-independent quantum key distribution.

Dual-channel, single-photon upconversion detector at 1.3 µm.

We demonstrate a two-channel, upconversion detector for counting 1300-nm-wavelength photons. By using two pumps near 1550 nm, photons near 1300 nm are converted to two spectrally distinct channels near 710 nm using sum-frequency generation (SFG) in a periodically poled LiNbO3 (PPLN) waveguide. We used spectral-conversion engineering to design the phase-modulated PPLN waveguide for simultaneous quasi-phasematching of two SFG processes. The two channels exhibit 31% and 25% full-system photon detection efficiency, and very low dark count rates (650 and 550 counts per second at a peak external conversion efficiency of 70%) through filtering using a volume Bragg grating. We investigate applications of the dual-channel upconversion detector as a frequency-shifting beamsplitter, and as a time-to-frequency converter to enable higher-data-rate quantum communications.

Cascaded frequency upconversion for high-speed single-photon detection at 1550 nm.

We present a device for two-stage frequency upconversion of single-photon-level signals in the 1.55 µm telecom band to the green spectral region with low excess noise, suitable for detection by low-timing-jitter silicon single-photon avalanche photodiodes (APDs). We achieve a net conversion efficiency of 87% and a system timing jitter below 70 ps FWHM, dominated by the jitter of the APD. Modifications of our device are suitable for downconversion of single photons from visible-wavelength quantum emitters into the telecom band.

Long-wavelength-pumped upconversion single-photon detector at 1550 nm: performance and noise analysis.

We demonstrate upconversion-assisted single-photon detection for the 1.55-µm telecommunications band based on a periodically poled lithium niobate (PPLN) waveguide pumped by a monolithic PPLN optical parametric oscillator. We achieve an internal conversion efficiency of 86%, which results in an overall system detection efficiency of 37%, with excess noise as low as 10(3) counts s(-1). We measure the dark count rate versus the upconversion pump-signal frequency separation and find the results to be consistent with noise photon generation by spontaneous anti-Stokes Raman scattering. These results enable detailed design guidelines for the development of low-noise quantum frequency conversion systems, which will be an important component of fiber-optic quantum networks.

Supercontinuum generation in quasi-phasematched waveguides.

We numerically investigate supercontinuum generation in quasi-phase-matched waveguides using a single-envelope approach to capture second and third order nonlinear processes involved in the generation of octave-spanning spectra. Simulations are shown to agree with experimental results in reverse-proton-exchanged lithium-niobate waveguides. The competition between χ((2)) and χ((3)) self phase modulation effects is discussed. Chirped quasi-phasematched gratings and stimulated Raman scattering are shown to enhance spectral broadening, and the pulse dynamics involved in the broadening processes are explained.

Continuous wave monolithic quasi-phase-matched optical parametric oscillator in periodically poled lithium niobate.

We demonstrate a monolithic and quasi-phasematched singly resonant cw optical parametric oscillator in periodically poled lithium niobate. The threshold is 1.0 W and the OPO delivers up to 0.98 W signal power tunable between 1750 and 1950 nm (2710 and 2340 nm idler, respectively). We identify cascaded parasitic oscillation effects and analyze their behavior theoretically, showing good agreement with our experiment. The analysis of parasitic effects points the way to improved device designs that should enable stable, compact, and frequency-tunable sources.

Efficiency pedestal in quasi-phase-matching devices with random duty-cycle errors.

It is shown that random duty-cycle errors in quasi-phase-matching (QPM) nonlinear optical devices enhance the efficiency of processes far from the QPM peak. An analytical theory is shown to agree well with numerical solutions of second-harmonic generation (SHG) in disordered QPM gratings. The measured efficiency of 1550 nm band SHG in a periodically poled lithium niobate (PPLN) waveguide away from the QPM peak agrees with observations of domain disorder in a PPLN wafer by Zygo interferometry. If suppression of parasitic nonlinear interactions is important in a specific application of QPM devices, control of random duty-cycle errors is critical.

Supercontinuum generation in quasi-phase-matched LiNbO3 waveguide pumped by a Tm-doped fiber laser system.

We demonstrate self-referencing of a Tm-doped fiber oscillator-amplifier system by performing octave-spanning supercontinuum generation in a periodically poled lithium niobate waveguide. We model the supercontinuum generation numerically and show good agreement with the experiment.

Influence of domain disorder on parametric noise in quasi-phase-matched quantum frequency converters.

Ideal quantum frequency conversion (QFC) devices enable wavelength translation of a quantum state of light while preserving its essential quantum characteristics, namely photon statistics and coherence. However, the generation of noise photons due to spontaneous scattering of the strong classical pump used in the three-wave mixing process can limit QFC fidelity. We experimentally and theoretically characterize the noise properties of a difference-frequency generation device for QFC and find that fabrication errors in the quasi-phase-matching grating enhance generation of noise photons by parametric fluorescence.

[Long-term results of revascularization surgery in oblitertive arteriosclerosis of the lower extremities]. / Dlhodobé výsledky revaskularizacných operácií pre obliterujúcu artériosklerózu dolných koncatín.

The authors evaluated their 15-year experience with revascularization operations for atherosclerosis obliterans (ASO) of the lower extremities. Over the period from 1975 to 1990, 1112 patients with ASO were admitted to their department and in 674 (60.6%) of them revascularization operation was performed. Direct revascularization surgery (bypass, desobliteration, angioplasty) was performed in 318 (47.2%) patients and indirect revascularization, sympathectomy in 326 (52.8%) patients. On evaluating the long-term results of aortobifemoral (AF2), femoropopliteal (FP) and femorocrural (FC) bypasses the following long-term patency was established: AF2 bypass--patency up to 2 years 92%, up to 5 years 90%, up to 10 years 76%, up to 15 years 75%; FP bypass--patency up to 2 years 90%, up to 5 years 84%, up to 10 years 62%, up to 15 years 46%; FC bypass--patency up to 2 years 63%, up to 5 years 50%, up to 10 years 25%. Complications developed in 10%, the mortality rate was 2.5% and 8% in FP and AF2, respectively. The obtained results are comparable with the data published in the literature. The authors achieved the best results in the suprainguinal region with AF2 bypasses on using mostly dacron prostheses and in the infrainguinal region FP bypasses on using the autologous great saphenous vein. (Tab. 3, Fig. 4, Ref. 17.)

[Laparoscopic cholecystectomy versus classical cholecystectomy]. / Laparoskopická cholecystektómia versus klasická cholecystektómia.

The authors evaluated the results after classical (CCHE) and laparoscopic cholecystectomies (LCHE) in the period from March 16 1994 to June 30 1995. In this period they operated on 408 patients, out of which 208 were operated by the laparoscopic technique. There were no differences in postoperative morbidity. The mortality after laparoscopic surgery was 0% and the classical cholecystectomy reached the morbidity of 1.4%. Complicated patients were usually operated in the classical way. The time of hospitalisation after LCHE was 5.2 days and after CCHE 8.3 days. The results of LCHE were as follows: morbidity 10.5%, conversions 2.4%, reoperations 1.4%, and no leakage of the bile duct. We saved 40% of costs using LCHE. All these facts show that LCHE is advantageous, secure and well tolerated by patients. The patients prefer comfort after the operation, good cosmetic effect and a short hospital isation. CCHE did not lose its position, especially in complicated cases. (Tab. 5, Ref. 21.)

[Traumatic rupture of the diaphragm]. / Traumatická ruptúra bránice.

Traumatic ruptures of the diaphragm occur most frequently at blunt injuries of the abdomen or thorax as a component of polytraumatism. At the acute stage they present a serious diagnostic problem since signs of polytrauma are predominant. The authors report 3 cases of traumatic rupture of the diaphragm with thoracotomy as the therapeutic approach. The first patient presented with severe polytraumatism and shock, rupture of the diaphragm, pericardium and lungs, along with serial fracture of the left ribs. The second patient was not in shock, he had suffered serial fracture of the left ribs and fracture of the pelvis. In both these cases of blunt injury to the thorax, careful examination of the patients resulted in early diagnosis and surgery. The third patient presented with open injury of the right side of the thorax, injured diaphragm and liver, serial fracture of the ribs, fractured sternum, and was in a state of deep shock. There was no mortality, all three patients recovered.

[Acute arterial occlusions of the upper extremities--clinical data]. / Akútne uzávery tepien horných koncatín--nás klinický materiál.

The authors describe 30 cases of acute arterial occlusions of upper extremity during the last 10 years (1992-2001) in a group of 27 patients. In 27 cases the occlusions were caused by embolism and in 3 cases by acute thrombosis. In the group were 12 men and 18 women. The embolus was the most frequently located in brachial artery (cubital)--17 times (63%). In one case we were forced to perform amputation of left upper extremity for gangrene. Authors accentuate that early and adequate treatment lead to salvage of extremity in 80-100%.

[Results of surgical treatment of gastric cancer]. / Nase výsledky chirurgickej liecby rakoviny zalúdka.

The authors retrospectively analyse a group (1991-2000) of 129 patients with malignancies of the stomach operated at the Surgical Department of The District Hospital in Lucenec. The operated patients were: males 83 (64%), females 46 (36%), mean age--63.4 years. Elective operations were performed in 78.2% and acute operations in 21.8%. We were able to make resections in 90 (69.8%) patients and palliative operations in 39 (30.2%) patients. On the basis of histologic examinations-adenocarcinomas dominated (120 patients--93%). The postoperative mortality was 4.65% and five-year survival 12%.

[Spontaneous rupture of a renal liposarcoma]. / Spontánna ruptúra liposarkómu oblicky.

The authors describe a rare case of spontaneous rupture of a renal liposarcoma which imitated the clinical picture of an acute abdomen. Urgent transabdominal left nephrectomy was performed. The entire lower half of the kidney was altered by the tumour and ruptured and there was an extensive perirenal and retroperitoneal haematoma. The histological finding confirmed the presence of a primary renal liposarcoma. This is the first case of spontaneous rupture of a liposarcoma of the kidneys described in our literature and the second case in the world literature. The patient survives now for eight years after operation and is in a good condition.

[Personal experience with laparoscopic cholecystectomy in acute cholecystitis]. / Nase skúsenosti s laparoskopickou cholecystektómiou pre akútnu cholecystitídu.

Authors refer about their experiences with operations of acute cholecystitis by laparoscopy. They have evaluated retrospectively 1600 cases of laparoscopic cholecystectomies (LCHE) realized in the period from 1994 to 2000. In 302 (18.8%) cases was realized laparoscopic cholecystectomy for acute cholecystitis, which was confirmed by histopathological finding. During the mentioned period a total number of laparoscopic cholecystectomies for acute cholecystitis (n = 302) rise a number of classical cholecystectomies for the same diagnosis (n = 227). Very important role by authors take early dispatching a patient to a department of surgery and early estimation the diagnosis with consecutive laparoscopic treatment. Rates of peroperation, postoperation complications and reoperations in laparoscopic surgery of acute cholecystitis is comparable with elective laparoscopic cholecystectomy.

Interaction of independent single photons based on integrated nonlinear optics.

The parametric interaction of light beams in nonlinear materials is usually thought to be too weak to be observed when the fields involved are at the single-photon level. However, such single-photon level nonlinearity is not only fundamentally fascinating but holds great potential for emerging technologies and applications involving heralding entanglement at a distance. Here we use a high-efficiency waveguide to demonstrate the sum-frequency generation between a single photon and a single-photon level coherent state. The use of an integrated, solid state, room temperature device and telecom wavelengths makes this type of system directly applicable to future quantum communication technologies such as device-independent quantum key distribution.