The fourth extracellular loop of the alpha subunit of Na,K-ATPase. Functional evidence for close proximity with the second extracellular loop.

Na,K-ATPase is the main active transport system that maintains the large gradients of Na(+) and K(+) across the plasma membrane of animal cells. The crystal structure of a K(+)-occluding conformation of this protein has been recently published, but the movements of its different domains allowing for the cation pumping mechanism are not yet known. The structure of many more conformations is known for the related calcium ATPase SERCA, but the reliability of homology modeling is poor for several domains with low sequence identity, in particular the extracellular loops. To better define the structure of the large fourth extracellular loop between the seventh and eighth transmembrane segments of the alpha subunit, we have studied the formation of a disulfide bond between pairs of cysteine residues introduced by site-directed mutagenesis in the second and the fourth extracellular loop. We found a specific pair of cysteine positions (Y308C and D884C) for which extracellular treatment with an oxidizing agent inhibited the Na,K pump function, which could be rapidly restored by a reducing agent. The formation of the disulfide bond occurred preferentially under the E2-P conformation of Na,K-ATPase, in the absence of extracellular cations. Using recently published crystal structure and a distance constraint reproducing the existence of disulfide bond, we performed an extensive conformational space search using simulated annealing and showed that the Tyr(308) and Asp(884) residues can be in close proximity, and simultaneously, the SYGQ motif of the fourth extracellular loop, known to interact with the extracellular domain of the beta subunit, can be exposed to the exterior of the protein and can easily interact with the beta subunit.

Sex determination in dioecious Mercurialis annua and its close diploid and polyploid relatives.

Separate sexes have evolved on numerous independent occasions from hermaphroditic ancestors in flowering plants. The mechanisms of sex determination is known for only a handful of such species, but, in those that have been investigated, it usually involves alleles segregating at a single locus, sometimes on heteromorphic sex chromosomes. In the genus Mercurialis, transitions between combined (hermaphroditism) and separate sexes (dioecy or androdioecy, where males co-occur with hermaphrodites rather than females) have occurred more than once in association with hybridisation and shifts in ploidy. Previous work has pointed to an unusual 3-locus system of sex determination in dioecious populations. Here, we use crosses and genotyping for a sex-linked marker to reject this model: sex in diploid dioecious M. annua is determined at a single locus with a dominant male-determining allele (an XY system). We also crossed individuals among lineages of Mercurialis that differ in their ploidy and sexual system to ascertain the extent to which the same sex-determination system has been conserved following genome duplication, hybridisation and transitions between dioecy and hermaphroditism. Our results indicate that the male-determining element is fully capable of determining gender in the progeny of hybrids between different lineages. Specifically, males crossed with females or hermaphrodites always generate 1:1 male:female or male:hermaphrodite sex ratios, respectively, regardless of the ploidy levels involved (diploid, tetraploid or hexaploid). Our results throw further light on the genetics of the remarkable variation in sexual systems in the genus Mercurialis. They also illustrate the almost identical expression of sex-determining alleles in terms of sexual phenotypes across multiple divergent backgrounds, including those that have lost separate sexes altogether.

Colorectal cancer and thoracic surgeons: close encounters of the third kind.

Resection of lung metastases from colorectal cancer (CRC) is increasingly performed with a curative intent. This strategy was made possible in the 1990s by the development of new chemotherapeutic approaches, improved surgical techniques and better imaging modalities. However, evidence-based data showing clinical benefits of lung metastasectomy in this setting are nonexistent, and there are no prospective randomized trials to support the routine performance of these procedures for stage IV CRC. Current evidence suggests that resection of pulmonary metastases in combination with new cytotoxic agents, such as oxaliplatin, irinotecan and bevacizumab, may result in prolonged survival for many, and cure for a small minority of CRC patients who experienced tumor spread beyond the limits of the abdomen. This review focuses on the results of surgical management of CRC patients with lung metastases: we report the outcome of published series according to the presence or the absence of liver metastasis (and hepatic resection) prior to lung resection.

Spatial analysis of corresponding fingerprint features from match and close non-match populations

The development of statistical models for forensic fingerprint identification purposes has been the subject of increasing research attention in recent years. This can be partly seen as a response to a number of commentators who claim that the scientific basis for fingerprint identification has not been adequately demonstrated. In addition, key forensic identification bodies such as ENFSI [1] and IAI [2] have recently endorsed and acknowledged the potential benefits of using statistical models as an important tool in support of the fingerprint identification process within the ACE-V framework. In this paper, we introduce a new Likelihood Ratio (LR) model based on Support Vector Machines (SVMs) trained with features discovered via morphometric and spatial analyses of corresponding minutiae configurations for both match and close non-match populations often found in AFIS candidate lists. Computed LR values are derived from a probabilistic framework based on SVMs that discover the intrinsic spatial differences of match and close non-match populations. Lastly, experimentation performed on a set of over 120,000 publicly available fingerprint images (mostly sourced from the National Institute of Standards and Technology (NIST) datasets) and a distortion set of approximately 40,000 images, is presented, illustrating that the proposed LR model is reliably guiding towards the right proposition in the identification assessment of match and close non-match populations. Results further indicate that the proposed model is a promising tool for fingerprint practitioners to use for analysing the spatial consistency of corresponding minutiae configurations.

Evidence against close linkage of the loci for fraXq of Martin-Bell syndrome and for factor IX.

Linkage between the loci for fraXq of Martin-Bell syndrome and factor IX was studied in nine families exhibiting this syndrome by means of a restriction fragment length polymorphism at the factor IX locus. Computer analysis of the data indicates there to be no evidence for close linkage between the syndrome and the factor IX locus.

Long-term close follow-up of chorioretinal lesions in presumed ocular tuberculosis

Purpose: To evaluate the long-term outcome (up to 7 years) of presumed ocular tuberculosis (TB) when the therapeutic decision was based on WHO guidelines. Methods: Twelve out of 654 new uveitic patients (1998-2004) presented with choroiditis and positive tuberculosis skin test (TST) (skin lesion diameter >15 mm). Therapy was administered according to WHO recommendations after ophthalmic and systemic investigation. The area size of ocular lesions at presentation and after therapy, measured on fluorescein and indocyanine green angiographies, was considered the primary outcome. Relapse of choroiditis was considered a secondary outcome. The T-SPOTTB test was performed when it became available. Results: Visual acuity (VA) significantly improved after therapy (p=0.0357). The mean total surface of fluorescein lesions at entry was 44.8±20.9 (arbitrary units) and decreased to 32.5±16.9 after therapy (p=0.0165). The mean total surface of indocyanine green lesions at entry was 24.5±13.3 and decreased to 10.8±5.4 after therapy (p=0.0631). The T-SPOT TB revealed 2 false TST-positive results. The mean follow-up was 4.5±1.5 years. Two relapses out of 10 confirmed ocular TB was observed after complete lesion healing, 2.5 years and 4.5 years after therapy, respectively. Conclusions: A decrease of ocular lesion mean size and a mean improvement of VA were observed after antituberculous therapy. Our long-term follow-up of chorioretinal lesions demonstrated relapse of ocular tuberculosis in 10% of patients with confirmed ocular TB, despite complete initial retinal scarring.

Full-waveform inversion of cross-hole ground-penetrating radar data to characterize a gravel aquifer close to the Thur River, Switzerland

Cross-hole radar tomography is a useful tool for mapping shallow subsurface electrical properties viz. dielectric permittivity and electrical conductivity. Common practice is to invert cross-hole radar data with ray-based tomographic algorithms using first arrival traveltimes and first cycle amplitudes. However, the resolution of conventional standard ray-based inversion schemes for cross-hole ground-penetrating radar (GPR) is limited because only a fraction of the information contained in the radar data is used. The resolution can be improved significantly by using a full-waveform inversion that considers the entire waveform, or significant parts thereof. A recently developed 2D time-domain vectorial full-waveform crosshole radar inversion code has been modified in the present study by allowing optimized acquisition setups that reduce the acquisition time and computational costs significantly. This is achieved by minimizing the number of transmitter points and maximizing the number of receiver positions. The improved algorithm was employed to invert cross-hole GPR data acquired within a gravel aquifer (4-10 m depth) in the Thur valley, Switzerland. The simulated traces of the final model obtained by the full-waveform inversion fit the observed traces very well in the lower part of the section and reasonably well in the upper part of the section. Compared to the ray-based inversion, the results from the full-waveform inversion show significantly higher resolution images. At either side, 2.5 m distance away from the cross-hole plane, borehole logs were acquired. There is a good correspondence between the conductivity tomograms and the natural gamma logs at the boundary of the gravel layer and the underlying lacustrine clay deposits. Using existing petrophysical models, the inversion results and neutron-neutron logs are converted to porosity. Without any additional calibration, the values obtained for the converted neutron-neutron logs and permittivity results are very close and similar vertical variations can be observed. The full-waveform inversion provides in both cases additional information about the subsurface. Due to the presence of the water table and associated refracted/reflected waves, the upper traces are not well fitted and the upper 2 m in the permittivity and conductivity tomograms are not reliably reconstructed because the unsaturated zone is not incorporated into the inversion domain.

Chemotherapy in patients with advanced pancreatic cancer: too close to death?

PURPOSE: We evaluated the attitude in using chemotherapy near the end of life in advanced pancreatic adenocarcinoma (PAC). Clinical and laboratory parameters recorded at last chemotherapy administration were analyzed, in order to identify risk factors for imminent death. METHODS: Retrospective analysis of patients who underwent at least one line of palliative chemotherapy was made. Data concerning chemotherapy (regimens, lines, and date of last administration) were collected. Clinical and laboratory factors recorded at last chemotherapy administration were: performance status, presence of ascites, hemoglobin, white blood cell (WBC), platelets, total bilirubin, albumin, LDH, C-reactive protein (C-rp), and Ca 19.9. RESULTS: We analyzed 231 patients: males/females, 53/47 %; metastatic/locally advanced disease, 80/20 %; and median age, 66 years (range 32-85). All patients died due to disease progression. Median overall survival was 6.1 months (95 % CI 5.1-7.2). At the last chemotherapy delivery, performance status was 0-1 in 37 % and 2 in 63 %. Fifty-nine percent of patients received one chemotherapy line, while 32, 8, and 1 % had second-, third-, and fourth line, respectively. The interval between last chemotherapy administration and death was <4 weeks in 24 %, ≥4-12 in 47 %, and >12 in 29 %. Median survival from last chemotherapy to death was 7.5 weeks (95 % CI 6.7-8.4). In a univariate analysis, ascites, elevated WBC, bilirubin, LDH, C-rp and Ca 19.9, and reduced albumin were found to predict shorter survival; however, none of them remained significant in a multivariate analysis. CONCLUSIONS: A significant proportion of patients with advanced PAC received chemotherapy within the last month of life. The clinical and laboratory parameters recorded at last chemotherapy delivery did not predict shorter survival.

Long-term close follow-up of chorioretinal lesions in presumed ocular tuberculosis.

PURPOSE: To evaluate the long-term outcome (up to 7 years) of presumed ocular tuberculosis (TB) when the therapeutic decision was based on WHO guidelines. METHODS: Twelve out of 654 new uveitic patients (1998-2004) presented with choroiditis and positive tuberculosis skin test (TST) (skin lesion diameter >15 mm). Therapy was administered according to WHO recommendations after ophthalmic and systemic investigation. The area size of ocular lesions at presentation and after therapy, measured on fluorescein and indocyanine green angiographies, was considered the primary outcome. Relapse of choroiditis was considered a secondary outcome. The T-SPOT TB test was performed when it became available. RESULTS: Visual acuity significantly improved after therapy (p=0.0357). The mean total surface of fluorescein lesions at entry was 44.8 ± 20.9 (arbitrary units) and decreased to 32.5 ± 16.9 after therapy (p=0.0165). The mean total surface of indocyanine green lesions at entry was 24.5 ± 13.3 and decreased to 10.8 ± 5.4 after therapy (p=0.0631). The T-SPOT TB revealed 2 false TST-positive results. The mean follow-up was 4.5 ± 1.5 years. Two relapses out of 10 confirmed ocular TB was observed after complete lesion healing, 2.5 years and 4.5 years after therapy, respectively. CONCLUSIONS: A decrease of ocular lesion mean size and a mean improvement of VA were observed after antituberculous therapy. Our long-term follow-up of chorioretinal lesions demonstrated relapse of ocular tuberculosis in 10% of patients with confirmed ocular TB, despite complete initial retinal scarring.

Patent foramen ovale in patients with ischaemic stroke of unknown cause: to close? "pro closure" position

There is ample epidemiological and anecdotal evidence that a PFO increases the risk of stroke both in young and elderly patients, although only in a modest way: PFOs are more prevalent in patients with cryptogenic (unexplained) stroke than in healthy subjects, and are more prevalent in cryptogenic stroke than in strokes of other causes. Furthermore, multiple case series confirm an association of paradoxical embolism across a PFO in patients with deep vein thrombosis and/or pulmonary emboli.2. Is stroke recurrence risk in PFO-patients really not elevated when compared to PFO-free patients, as suggested by traditional observational studies? This finding is an epidemiological artifact called "the paradox of recurrence risk research" (Dahabreh & Kent, JAMA 2011) and is due to one (minor) risk factor, such as PFO, being wiped out by other, stronger risk factors in the control population.3. Having identified PFO as a risk factor for a first stroke and probably also for recurrences, we have to treat it, because treating risk factors always has paid off. No one would nowadays question the aggressive treatment of other risk factors of stroke such as hypertension, atrial fibrillation, smoking, or hyperlipidemia.4. In order to be effective, the preventive treatment has to control the risk factor (i.e. close effectively the PFO), and has to have little or no side effects. Both these conditions are now fulfilled thanks to increasing expertise of cardiologists with technically advanced closure devices and solid back up by multidisciplinary stroke teams.5. Closing a PFO does not dispense us from treating other stroke risk factors aggressively, given that these are cumulative with PFO.6. The most frequent reason why patients have a stroke recurrence after PFO closure is not that closure is ineffective, but that the initial stroke etiology is insufficiently investigated and not PFO related, and that the recurrence is due to another mechanism because of poor risk factor control.7. Similarly, the randomized CLOSURE study was negative because a) patients were included who had a low chance that their initial event was due to the PFO, b) patients were selected with a low chance that a PFO-related recurrence would occur, c) there was an unacceptable high rate of closure-related side effects, and d) the number of randomized patients was too small for a prevention trial.8. It is only a question of time until a sufficiently large randomized clinical trial with true PFO-related stroke patients and a high PFO-related recurrence risk will be performed and show the effectiveness of this closure9. PFO being a rather modest risk factor for stroke does not mean we should prevent our patients from getting the best available prevention by the best physicians in the best stroke centers Therefore, a PFO-closure performed by an excellent cardiologist following the recommendation of an expert neurovascular specialist after a thorough workup in a leading stroke center is one of the most effective stroke prevention treatments available in 2011.