Learning how to robustly estimate camera pose in endoscopic videos

PURPOSE

Surgical scene understanding plays a critical role in the technology stack of tomorrow's intervention-assisting systems in endoscopic surgeries. For this, tracking the endoscope pose is a key component, but remains challenging due to illumination conditions, deforming tissues and the breathing motion of organs.

METHOD

We propose a solution for stereo endoscopes that estimates depth and optical flow to minimize two geometric losses for camera pose estimation. Most importantly, we introduce two learned adaptive per-pixel weight mappings that balance contributions according to the input image content. To do so, we train a Deep Declarative Network to take advantage of the expressiveness of deep learning and the robustness of a novel geometric-based optimization approach. We validate our approach on the publicly available SCARED dataset and introduce a new in vivo dataset, StereoMIS, which includes a wider spectrum of typically observed surgical settings.

RESULTS

Our method outperforms state-of-the-art methods on average and more importantly, in difficult scenarios where tissue deformations and breathing motion are visible. We observed that our proposed weight mappings attenuate the contribution of pixels on ambiguous regions of the images, such as deforming tissues.

CONCLUSION

We demonstrate the effectiveness of our solution to robustly estimate the camera pose in challenging endoscopic surgical scenes. Our contributions can be used to improve related tasks like simultaneous localization and mapping (SLAM) or 3D reconstruction, therefore advancing surgical scene understanding in minimally invasive surgery.

A modified Delphi process to establish research priorities in hernia surgery

BACKGROUND

Abdominal wall hernia repair is one of the most commonly performed surgical procedures worldwide, yet despite this, there remains a lack of high-quality evidence to support best management. The aim of the study was to use a modified Delphi process to determine future research priorities in this field.

METHODS

Stakeholders were invited by email, using British Hernia Society membership details or Twitter, to submit individual research questions via an online survey. In addition, questions obtained from a patient focus group (PFG) were collated to form Phase I. Two rounds of prioritization by stakeholders (phases II and III) were then completed to determine a final list of research questions. All questions were analyzed on an anonymized basis.

RESULTS

A total of 266 questions, 19 from the PFG, were submitted by 113 stakeholders in Phase I. Of these, 64 questions were taken forward for prioritization in Phase II, which was completed by 107 stakeholders. Following Phase II analysis, 97 stakeholders prioritized 36 questions in Phase III. This resulted in a final list of 14 research questions, 3 of which were from the PFG. Stakeholders included patients and healthcare professionals (consultant surgeons, trainee surgeons and other multidisciplinary members) from over 27 countries during the 3 phases.

CONCLUSION

The study has identified 14 key research priorities pertaining to abdominal wall hernia surgery. Uniquely, these priorities have been determined from participation by both healthcare professionals and patients. These priorities should now be addressed by well-designed, high-quality international collaborative research.

Click chemistry compared to thiol chemistry for the synthesis of site-selective glycoconjugate vaccines using CRM197 as carrier protein

Conjugation chemistry is one of the main parameters affecting immunogenicity of glycoconjugate vaccines and a rational approach toward a deeper understanding of their mechanism of action will greatly benefit from highly-defined and well-characterized structures. Herein, different conjugation methods were investigated with the aim of controlling glycosylation site and glycosylation density on the carrier protein. S. Typhimurium lipopolysaccharide O-Antigen and CRM₁₉₇ carrier protein were used as models. In particular, thiol and click chemistry were examined, both involving the linkage of the terminal reducing sugar unit of the O-Antigen chain to different amino acids on the carrier protein. Thiol chemistry allowed O-Antigen conjugation only when the carrier protein was activated on the lysines and with a relative high number of linkers, while click chemistry allowed conjugate generation even when just one position on the protein was activated and to both lysine and tyrosine sites. The study highlights click chemistry as a leading approach for the synthesis of well-defined glycoconjugates, useful to investigate the relationship between conjugate design and immune response.

Patch-based adaptive weighting with segmentation and scale (PAWSS) for visual tracking in surgical video

Vision-based tracking in an important component for building computer assisted interventions in minimally invasive surgery as it facilitates estimation of motion for instruments and anatomical targets. Tracking-by-detection algorithms are widely used for visual tracking, where the problem is treated as a classification task and a tracking target appearance model is updated over time using online learning. In challenging conditions, like surgical scenes, where tracking targets deform and vary in scale, the update step is prone to include background information in model appearance or to lack the ability to estimate change of scale, which degrades the performance of classifier. In this paper, we propose a Patch-based Adaptive Weighting with Segmentation and Scale (PAWSS) tracking framework that tackles both scale and background problems. A simple but effective colour-based segmentation model is used to suppress background information and multi-scale samples are extracted to enrich the training pool, which allows the tracker to handle both incremental and abrupt scale variations between frames. Experimentally, we evaluate our approach on Online Tracking Benchmark (OTB) dataset and Visual Object Tracking (VOT) challenge datasets, showing that our approach outperforms recent state-of-the-art trackers, and it especially improves successful rate score on OTB dataset, while on VOT datasets, PAWSS ranks among the top trackers while operating at real-time frame rates. Focusing on the application of PAWSS to surgical scenes, we evaluate on MICCAI 2015 challenge instrument tracking challenge and in vivo datasets, showing that our approach performs the best among all submitted methods and also has promising performance on in vivo surgical instrument tracking.

3-D Pose Estimation of Articulated Instruments in Robotic Minimally Invasive Surgery

Estimating the 3-D pose of instruments is an important part of robotic minimally invasive surgery for automation of basic procedures as well as providing safety features, such as virtual fixtures. Image-based methods of 3-D pose estimation provide a non-invasive low cost solution compared with methods that incorporate external tracking systems. In this paper, we extend our recent work in estimating rigid 3-D pose with silhouette and optical flow-based features to incorporate the articulated degrees-of-freedom (DOFs) of robotic instruments within a gradient-based optimization framework. Validation of the technique is provided with a calibrated ex-vivo study from the da Vinci Research Kit (DVRK) robotic system, where we perform quantitative analysis on the errors each DOF of our tracker. Additionally, we perform several detailed comparisons with recently published techniques that combine visual methods with kinematic data acquired from the joint encoders. Our experiments demonstrate that our method is competitively accurate while relying solely on image data.

Articulated Multi-Instrument 2-D Pose Estimation Using Fully Convolutional Networks

Instrument detection, pose estimation, and tracking in surgical videos are an important vision component for computer-assisted interventions. While significant advances have been made in recent years, articulation detection is still a major challenge. In this paper, we propose a deep neural network for articulated multi-instrument 2-D pose estimation, which is trained on detailed annotations of endoscopic and microscopic data sets. Our model is formed by a fully convolutional detection-regression network. Joints and associations between joint pairs in our instrument model are located by the detection subnetwork and are subsequently refined through a regression subnetwork. Based on the output from the model, the poses of the instruments are inferred using maximum bipartite graph matching. Our estimation framework is powered by deep learning techniques without any direct kinematic information from a robot. Our framework is tested on single-instrument RMIT data, and also on multi-instrument EndoVis and in vivo data with promising results. In addition, the data set annotations are publicly released along with our code and model.

Dissociative electron attachment and electronic excitation in Fe(CO)5

In a combined experimental and theoretical study we characterize dissociative electron attachment (DEA) to, and electronically excited states of, Fe(CO)₅.

Combined 2D and 3D tracking of surgical instruments for minimally invasive and robotic-assisted surgery

PURPOSE

Computer-assisted interventions for enhanced minimally invasive surgery (MIS) require tracking of the surgical instruments. Instrument tracking is a challenging problem in both conventional and robotic-assisted MIS, but vision-based approaches are a promising solution with minimal hardware integration requirements. However, vision-based methods suffer from drift, and in the case of occlusions, shadows and fast motion, they can be subject to complete tracking failure.

METHODS

In this paper, we develop a 2D tracker based on a Generalized Hough Transform using SIFT features which can both handle complex environmental changes and recover from tracking failure. We use this to initialize a 3D tracker at each frame which enables us to recover 3D instrument pose over long sequences and even during occlusions.

RESULTS

We quantitatively validate our method in 2D and 3D with ex vivo data collected from a DVRK controller as well as providing qualitative validation on robotic-assisted in vivo data.

CONCLUSIONS

We demonstrate from our extended sequences that our method provides drift-free robust and accurate tracking. Our occlusion-based sequences additionally demonstrate that our method can recover from occlusion-based failure. In both cases, we show an improvement over using 3D tracking alone suggesting that combining 2D and 3D tracking is a promising solution to challenges in surgical instrument tracking.

Electron-impact vibrational excitation of cyclopropane

We report a very detailed test of the ab initio discrete momentum representation (DMR) method of calculating vibrational excitation of polyatomic molecules by electron impact, by comparison of its results with an extensive set of experimental data, covering the entire range of scattering angles from 10° to 180° and electron energies from 0.4 to 20 eV. The DMR calculations were carried out by solving the two-channel Lippmann-Schwinger equation in the momentum space, and the interaction between the scattered electron and the target molecule was described by exact static-exchange potential corrected by a density functional theory (DFT) correlation-polarization interaction that models target's response to the field of incoming electron. The theory is found to quantitatively reproduce the measured spectra for all normal modes, even at the difficult conditions of extreme angles and at low energies, and thus provides full understanding of the excitation mechanism. It is shown that the overlap of individual vibrational bands caused by limited experimental resolution and rotational excitation must be properly taken into account for correct comparison of experiment and theory. By doing so, an apparent discrepancy between published experimental data could be reconciled. A substantial cross section is found for excitation of the non-symmetric HCH twisting mode ν4 of A1 (″) symmetry by the 5.5 eV A2 (') resonance, surprisingly because the currently accepted selection rules predict this process to be forbidden. The DMR theory shows that the excitation is caused by an incoming electron in an f-wave of A2 (') symmetry which causes excitation of the non-symmetric HCH twisting mode ν4 of the A1 (″) symmetry and departs in p- and f-waves of A2 (″) symmetry.

Experimental evidence on the mechanism of dissociative electron attachment to formic acid

Two mechanisms for dissociative electron attachment in HCOOH, the formation of HCOO(-)+H, were proposed in the literature: (i) via a direct electron attachment into a σ* resonance, augmented by dipole binding of the incident electron [G. A. Gallup et al., Phys. Rev. A 79, 042701 (2009)], and (ii) with the 1.8 eV π* resonance as a doorway state, linked to the products by symmetry lowering-distortion of the temporary anion, primarily the C-H bond, from the planar symmetry [T. N. Rescigno et al., Phys. Rev. Lett. 96, 213201 (2006)]. The later mechanism implies a reduction of the cross section upon deuteration of the hydrogen bonded to the C atom, whereas the former mechanism would leave the cross section unaffected. Our experimental absolute cross sections for the four isotopomers of formic acid show that deuteration on the C atom reduces the cross section value only marginally (by 12%) compared to deuteration on the O atom (reduction by a factor of 16), and thus favor mechanism (i).

Autodetachment dynamics of acrylonitrile anion revealed by two-dimensional electron impact spectra

Two-dimensional electron energy-loss spectra of acrylonitrile are presented in the incident energy range 0.095-0.9 eV, where the incoming electron is temporarily captured in the lowest π* orbital. The cross section is plotted as a function of the incident electron energy that determines which vibrational resonant anion state is populated, and of the electron energy loss, that shows into which final vibrational states each resonance decays. The striking result is that besides the expected horizontal (for given resonances) and vertical (for given final states) patterns of peaks, diagonal arrangements of peaks are observed. They reveal restrictive selectivity with respect to which vibrations are deexcited in the detachment process, with ν(4) (C ≡ N stretch) and ν(7) (C-H rocking) dominating. Surprisingly, all spectral features could be assigned to vibrational levels of the valence π* resonance, and none to dipole-bound vibrational Feshbach resonance, although the latter must also exist in this energy range.

Pharmacokinetics of tildipirosin in porcine plasma, lung tissue, and bronchial fluid and effects of test conditions on in vitro activity against reference strains and field isolates of Actinobacillus pleuropneumoniae

The pharmacokinetics of tildipirosin (Zuprevo(®) 40 mg/mL solution for injection for pigs), a novel 16-membered-ring macrolide for the treatment for swine respiratory disease (SRD), was investigated in studies collecting blood plasma and postmortem samples of lung tissue and bronchial fluid (BF) from swine. In view of factors influencing the in vitro activity of macrolides, and for the interpretation of tildipirosin pharmacokinetics in relation to minimum inhibitory concentrations (MIC), additional experiments were conducted to study the effects of pH, carbon dioxide-enriched atmosphere, buffers, and serum on tildipirosin MICs for various reference strains and Actinobacillus (A.) pleuropneumoniae field isolates. After single intramuscular (i.m.) injection at 4 mg/kg body weight, maximum plasma concentration (Cmax) was 0.9 μg/mL observed within 23 min (Tmax ). Mean residence time from the time of dosing to the time of last measurable concentration (MRTlast) and terminal half-life (T1/2) both were about 4 days. A dose-response relationship with no significant sex effect is observed for area under the plasma concentration-time curve from time 0 to the last sampling time with a quantifiable drug concentration (AUClast) over the range of doses up to 6 mg/kg. However, linear dose proportionality could not be proven with statistical methods. The time-concentration profile of tildipirosin in BF and lung far exceeded that in blood plasma. In lung, tildipirosin concentrations reached 3.1 μg/g at 2 h, peaked at 4.3 μg/g at day 1, and slowly declined to 0.8 μg/g at day 17. In BF, tildipirosin levels were 14.3, 7.0, and 6.5 μg/g at days 5, 10, and 14. T1/2 in lung was ∼7 days. Tildipirosin is rapidly and extensively distributed to the respiratory tract followed by slow elimination. Culture media pH and carbon dioxide-enriched atmosphere (CO2 -EA) had a marked impact on in vitro activity of tildipirosin in reference strains of various rapidly growing aerobic and fastidious bacteria including Histophilus (H.) somni ATCC 700025 and A. pleuropneumoniae ATCC 27090. For A. pleuropneumoniae ATCC 27090 testing conditions without CO2 -EA resulted in reduced acidification of culture media pH and a reduction in the minimum inhibitory concentrations compared to standard in vitro test conditions by 2 log2 dilution steps (4-fold) from 8 to 2 μg/mL. Supplementary buffering of standard culture media resulted in a reduction in the A. pleuropneumoniae (n = 8) MIC range by 4 log2 dilution steps (16-fold) from 8-16 to 0.5-1 μg/mL. Incremental supplementation of culture media with 50% serum resulted in noticeable shifts to lower minimum or maximum MICs by at least 2 log2 dilution steps (≥4-fold) in all aerobic and fastidious reference strains tested except for Pasteurella (P.) multocida. The MIC of A. pleuropneumoniae ATCC 27090 decreased by 2-4 log2 dilution steps (4 to 16-fold) from 8 to 0.5-2 μg/mL when 50% serum was added to the standard assay. Considering a higher presence of serum and the rather neutral pH conditions maintained in vivo, it is suggested to take the influence of these factors on in vitro activity into account when interpreting tildipirosin MICs for A. pleuropneumoniae in relation to pharmacokinetics.

Elimination of arctic variant rabies in red foxes, metropolitan Toronto

To control the arctic variant of rabies virus in red foxes, 332,257 bait doses containing live, attenuated Evelyn-Rokitnicki-Abelseth rabies vaccine were distributed in greater metropolitan Toronto during 1989–1999. Human and pet contact with bait was minimal, and no adverse reactions to the vaccine were noted. Significantly fewer rabid foxes were found during the 17 years after fox baiting (5 cases during 1990–2006) than in the 17 years before (96 cases during 1973–1989). The last report of a rabid fox in metropolitan Toronto was in 1996 (reporting period through September 2006), which confirms that distributing oral rabies vaccine bait is a feasible tactic for the control of rabies in foxes in urban environments.

Nuclear magnetic resonance as a quantitative tool to study interactions in biomacromolecules

High-resolution nuclear magnetic resonance (NMR) has emerged as one of the most versatile tools for the quantitative study of structure, kinetics, and thermodynamics of biomolecules and their interactions at atomic resolution. Traditionally, nuclear Overhauser enhancements (NOEs) and chemical shift perturbation methods are used to determine molecular geometries and to identify contact surfaces, but more recently, weak anisotropic orientation, anisotropic diffusion, and scalar couplings across hydrogen bonds provide additional information.

Examples of such technologies are shown as applied to the quantitative characterization of function and thermodynamics of several biomacromolecules. In particular, (1) the structural and dynamical changes of the TipA multidrug resistance protein are followed upon antibiotic binding, (2) the trimer-monomer equilibrium and thermal unfolding of foldon, a small and very efficient trimerization domain of the T4 phagehead, is described in atomic detail, and (3) the changes of individual protein hydrogen bonds during thermal unfolding are quantitatively followed by scalar couplings across hydrogen bonds.

Effects of interchannel coupling in associative detachment: electron spectra for H+Cl- and H+Br- collisions

We present experimental and theoretical energy spectra of the electrons detached in collisions of slow Cl- and Br- ions with atomic hydrogen. Nonlocal resonance theory predicts two kinds of features in the spectra: steplike structures associated with rovibrational onsets and steep rises associated with interchannel coupling, the latter being absent in a calculation using the simpler local-complex potential theory. Our experimental spectra confirm the presence of both types of structures and thus the necessity of including interchannel coupling to properly describe the product-state distribution.

Selectivity in the excitation of fermi-coupled vibrations in CO2 by impact of slow electrons

Improvement of resolution of a gas phase hemispherical electron spectrometer (to 7 meV FWHM) permitted separate measurements of the excitation of each member of the well known Fermi dyad in CO2 by impact of slow electrons. Absolute differential cross sections at a scattering angle of 135 degrees were measured as a function of electron energy. The excitation was found to be highly selective both via the 2Pi(u) shape resonance around 3.6 eV and via the virtual CO2- state at low energy. The selectivity is surprising because both vibrational states ensuing from the Fermi resonance involve the same type of nuclear motion (bending and stretch) and excitation of both is symmetry allowed.

Emergency response to raccoon rabies introduction into Ontario

During 15 July to 4 October, 1999, rabies control programs were implemented with the objective being to contain the first three confirmed cases of raccoon rabies in Canada. The strategy, called point infection control (PIC) involved the use of three tactics: population reduction (PR), trap-vaccinate-release (TVR) and oral rabies vaccination with baits (ORV), to control the spread of raccoon rabies. A total of 1,202 raccoons (Procyon lotor) and 337 skunks (Mephitis mephitis) were captured and euthanized using 24,719 trap-nights in the three PR zones around the location of the three rabies cases, near Brockville, Ontario. That represented an 83% to 91% reduction in the raccoon populations in an approximate 225 km2 area around the three rabies cases. Raccoon density in the PR zones declined from 5.1-7.1/km2 to 0.6-1.1/km2 following control. All tested specimens were negative for rabies by the fluorescent antibody test (FAT). In addition, 1,759 raccoons and 377 skunks were intramuscularly vaccinated against rabies and released using 27,956 trap-nights in an approximate 485 km2 TVR zone implemented outside of the PR zones. A total of 856 cats from both PR and TVR areas were also captured, vaccinated and released. Cost for the three PIC operations was $363,000.00 Cdn or about $500.00 Cdn/km2. To further contain the outbreak, about 81,300 baits containing Raboral V-RG oral rabies vaccine were aerially distributed on 8 and 27 September 1999, to create an 8 to 15 km wide buffer zone (1,200 km2 area) of vaccinated raccoons immediately beyond the PR and TVR zones. This was the first time that V-RG was used in Canada to orally vaccinate free ranging raccoons against rabies. Baiting costs were $241,000.00 Cdn or about $200.00 Cdn/km2 including post baiting assessment costs. As of 31 August, 2000, thirty-five additional cases (38 in total) of raccoon rabies have occurred in the control and vaccination zones. This number is far below the level of rabies prevalence in USA jurisdictions where raccoon rabies was epizootic. In the future, PIC methodologies will continue to be used in Ontario to contain isolated cases of raccoon rabies.

Locomotor sensitization to quinpirole: environment-modulated increase in efficacy and context-dependent increase in potency

This study examines whether behavioural sensitization to the dopamine agonist, quinpirole, reflects an increase in the drug's potency and/or efficacy to induce locomotion, and how these parameters are influenced by environmental context. Three experiments were conducted in which animals received either chronic quinpirole (10 x 0.5 mg/kg, twice weekly) or saline injections in either the home cage environment, an alternate environment or the testing environment (activity monitors), followed by a dose-response test for the expression of sensitization in the activity monitors. Compared to the acute dose-response relationship, chronic quinpirole increased the maximum response. This increase in efficacy was significantly higher in animals treated with quinpirole in a non-home cage environment compared to those that received chronic treatment in the home cage. A leftward shift in the dose-effect function was observed only in animals with prior drug experience in the testing environment. Results indicate that locomotor sensitization to quinpirole reflects an environment-modulated increase in the drug's efficacy, and an environment-dependent increase in drug potency. Efficacy and potency may be subject to sensitization by non-associational and associational mechanisms, respectively.

Associational and nonassociational mechanisms in locomotor sensitization to the dopamine agonist quinpirole

A pairing paradigm was employed to explore the contribution of associational mechanisms to the expression of sensitization to the dopamine agonist quinpirole. Rats received ten quinpirole injections in the test environment (Group Paired) or in the home cage (Group Unpaired), and saline in the alternate environment. A third group received saline injections in both environments (Group Acute). Subjects received quinpirole on the 11th injection as a test for locomotor sensitization, and saline on the next injection as a test for conditioned activity. The range of discriminative stimuli predicting a drug versus a non-drug injection was increased across three independent experiments in an effort to detect a possible associational effect. Regardless of the strength of discriminative stimuli, both Paired and Unpaired groups showed locomotor sensitization to 0.5 mg/kg quinpirole compared with the Acute group. However, the Paired group showed more locomotion than the Unpaired group in the last minutes of the sensitization test. With a lower sensitizing dose of quinpirole (0.1 mg/kg) used in one experiment, only the Paired group showed locomotor sensitization. For both doses, the Paired, but not the Unpaired groups showed conditioned locomotion. It is suggested that with moderate doses of quinpirole, expression of locomotor sensitization does not require drug-signalling cues though such signals may have a modulatory influence. With lower quinpirole doses, however, quinpirole sensitization is context-dependent.

Retinoids and retinoid-binding protein expression in rat adipocytes

Adipose tissue has been reported to contain relatively high levels of the specific mRNA for retinol-binding protein (RBP) (Makover A., Soprano, D.R., Wyatt, M. L., and Goodman, D.S. (1989) J. Lipid Res. 30, 171-180). Studies were conducted to explore retinoid and retinoid-binding protein storage and metabolism in adipose tissue. In these studies, we measured RBP and cellular retinol-binding protein (CRBP) mRNA levels and retinoid levels in 6 adipose depots in male rats. Total RNA was isolated from inguinal, dorsal, mesenteric, epididymal, perinephric, and brown adipose tissue, and average RBP and CRBP mRNA levels were determined by Northern blot analysis. The relative levels of RBP mRNA in these 6 anatomically different adipose depots averaged, respectively, 6.3, 6.7, 16, 34, 37, and 21% of the level in a rat liver RNA standard. Retinoid levels in the 6 depots were similar and averaged approximately 6-7 micrograms of retinol eq/g of adipose tissue. Since adipose tissue contains several cell types, the cellular localizations of RBP and CRBP expression and retinoid storage were examined. RNA was prepared from isolated rat adipocytes and stromal-vascular cells. Cellular levels of the mRNAs for RBP, CRBP, apolipoprotein E (apoE), lipoprotein lipase, adipocyte P2, and adipsin were measured by Northern blot analysis. RBP was expressed almost exclusively in the adipocytes and only weakly in the stromal-vascular cells. Both CRBP and apoE mRNA levels were relatively high in the stromal-vascular cell preparations and only very low mRNA levels were found in the adipocytes. Lipoprotein lipase, adipsin, and adipocyte P2 mRNAs were found in substantial levels in both the adipocytes and stromal-vascular cells, but with higher levels present in the adipocytes. Cultured adipocytes synthesized RBP protein and secreted it into the medium. Only adipocytes (not stromal-vascular cells) contained retinol, at levels between 0.65-0.8 micrograms of retinol eq/10(6) cells. These studies demonstrate that adipocytes store retinoid and synthesize and secrete RBP, and suggest that rat adipocytes may be dynamically involved in retinoid storage and metabolism.

Itraconazole versus ketaconazole in the treatment of oral and oesophageal candidosis in patients infected with HIV

To determine the efficacy and toxicity of two systemically active antifungal agents in the treatment of buccal and oesophageal candidiasis 111 HIV-infected patients with microscopically-confirmed candidiasis were randomized to receive either 200 mg itraconazole once a day or 200 mg ketoconazole twice a day for 28 days in a double blind study. After 1 week of treatment, 75 and 82% of the patients on itraconazole and ketoconazole, respectively, had responded clinically. After 4 weeks of treatment, this had risen to 93% in each group. One patient discontinued itraconozole because of toxicity (rash), five patients discontinued ketaconazole (two nausea, two hepatotoxicity and one rash). Despite successful clinical and mycological clearance, 80% patients had a further episode of candidosis within the next 3 months.

Interaction of epsilon-globin cis-acting control elements with erythroid-specific regulatory macromolecules

We have used a competition assay to investigate the influence of erythroid-specific cellular factors on transcription from the human epsilon-globin major cap site promoter and the minor promoter located 200 base pairs (bp) upstream from the epsilon-globin cap site. In the human erythroid cell line K562, competition of the epsilon-globin major cap site promoter linked to the chloramphenicol acetyltransferase (CAT) gene (epsilon P-CAT) with the same promoter fragment linked to a neomycin resistance gene (epsilon P-NEO) leads to a reduction in CAT activity. This indicates the specific presence of K562 cells of factor(s) which interact with the 200-bp promoter fragment (isolated from the gene body or flanking sequences) to activate transcription from the epsilon-globin major cap site. Competition of the epsilon-globin major promoter (as epsilon P-CAT) with the upstream minor epsilon-globin promoter (as epsilon P2-NEO) also leads to a reduction in CAT activity, indicating that both promoters share erythroid-specific trans-acting factors. The reverse competition (epsilon P2-CAT with epsilon P-NEO) leads to an increase in CAT activity, suggesting that the existence of erythroid-specific factor(s) which repress transcription from the 200-bp-upstream epsilon-globin promoter.

A short, highly repetitive element in intron -1 of the human c-Ha-ras gene acts as a block to transcriptional readthrough by a viral promoter

We have identified a short, highly repetitive element within intron -1 of the human c-Ha-ras gene. This element was found to be transcribed in both orientations and to be homologous to heterogeneous nonpolyadenylated transcripts. The repetitive element blocked transcriptional readthrough from a strong upstream viral promoter but allowed unimpaired readthrough from the c-Has-ras promoter. We suggest that it may serve to prevent excessive transcription into the coding region of the gene under such circumstances as viral insertion.

Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element

The human epsilon-globin gene has a number of alternative transcription initiation sites which correspond with regions of DNase I hypersensitivity upstream of the canonical cap site. Transcripts originating from the promoters located -4.3/-4.5 and -1.48 kilobase pairs (kbp) and -900 and -200 base pairs (bp) upstream of the major epsilon-globin cap site can, at certain stages of erythroid differentiation, extend through the gene and are polyadenylated. The 350-bp PolIII transcripts, originating within the Alu repetitive element -2.2 kbp upstream of the cap site, extend in the opposite direction from the gene, are nonpolyadenylated, nucleus confined, and are detectable only in mature K562 cells or mature embryonic red blood cells where the epsilon-globin major cap site is maximally transcribed. Fragments containing the promoters located between -4.5 and -4.3 kbp upstream of the gene down regulate transcription from the epsilon-globin gene 20- to 30-fold in a transient expression assay in which both erythroid and nonerythroid cell lines were used. This occurs only when the direction of transcription from the -4.3/-4.5-kbp promoters is towards the gene, and we hypothesize that down regulation is caused by transcriptional interference. Fragments containing the Alu repetitive element -2.2 kbp upstream of the gene can overcome down regulation of the epsilon-globin gene by the -4.5-kbp element when interposed in the direct orientation between this element and the epsilon-globin gene.

Correlation between patterns of DNase I-hypersensitive sites and upstream promoter activity of the human epsilon-globin gene at different stages of erythroid development

DNA 5' to the human epsilon-globin gene exhibits unique patterns of DNase I-hypersensitive sites (DHS) in three human erythroleukemic cell lines which represent the embryonic (K562), fetal (HEL), and adult (KMOE) stages of erythroid development. We have mapped 10 epsilon-globin DHS in K562 cells, in which the epsilon-globin gene is maximally active. Major sites are located -11.7, -10.5, -6.5, -2.2 kilobase pairs (kbp) and -200 base pairs (bp) upstream of the gene and directly over the major cap site. Minor sites are located -5.5, -4.5, and -1.48 kbp and -900 bp upstream of the cap site. In HEL cells, in which the epsilon-globin gene is expressed at extremely low levels, the -11.7-, -10.5-, -5.5-, -4.5-, and -2.2-kbp DHS are no longer detectable; the -200-bp site is approximately 300-fold less sensitive to DNase I; and the -1.48-kbp, -900-bp, and major cap site DHS are 3- to 4-fold less sensitive. Only the DHS located -6.5 kbp relative to the major cap site is detectable at all three stages of erythroid development, including KMOE cells in which epsilon-globin synthesis is undetectable. We suggest that this site may be implicated in maintaining the entire beta-globin cluster in an active chromatin conformation. The five DHS downstream of the -6.5-kbp element possess associated promoters. Thus two distinct types of DHS exist--promoter positive and promoter negative. In HEL cells, all the upstream promoters are inactivated, although the -1.48-kbp and -900- and -200-bp DHS are still present. This suggests that the maintenance of DHS and regulation of their associated promoters occur by independent mechanisms. The inactivation of the upstream promoters in HEL cells while the major cap site remains active represents a unique pattern of expression and suggests that HEL cells possess regulatory factors which specifically down regulate the epsilon-globin upstream promoters.

c-Ha-ras gene bidirectional promoter expressed in vitro: location and regulation

Increased transcriptional activity of the c-Ha-ras gene product is correlated with induction of several important human tumor types. For this reason, we have investigated the nature of the c-Ha-ras promoter and the factors that regulate its expression. Using S1 and primer extension analysis of c-Ha-ras RNA from EJ cells, we have identified 18 initiation sites within an upstream exon (exon -1) whose 3' end (the donor splice site [D]) is located 1,105 base pairs (bp) upstream of the ATG codon. The furthest-upstream initiation site is located -191 bp relative to D, and the furthest downstream is located -16 bp relative to D. Transient expression assays, in which a series of mutants spanning this region were ligated to a promoterless chloramphenicol acetyltransferase vector, functionally confirmed the position and extent of this promoter. Mutational analysis further located a 47-bp element located between -243 and -196 relative to D that up-regulated transcriptional activity of the promoter region by 20- to 40-fold. This region contained both a GC box known to bind SP1 and a CCAAT box. Insertion of a simian virus 40 enhancer 5' to the promoter up-regulated transcription from each initiation site by approximately 10- to 20-fold. We have also localized, both by chloramphenicol acetyltransferase assay and by S1 analysis, a strong promoter operating in the direction opposite that of the gene and originating immediately 5' to the 47-bp regulatory region. The reverse promoter was found to have nine initiation sites between -248 and -278 relative to D.

Phenobarbital treatment and major depressive disorder in children with epilepsy

The prevalence and severity of psychopathology in 15 epileptic patients treated with phenobarbital and 24 patients treated with carbamazepine were compared. The groups were similar across a wide range of demographic, seizure-related, and family-environmental variables. Patients treated with phenobarbital, when compared with those treated with carbamazepine, showed a much higher prevalence of major depressive disorder (40% v 4%, P = .02), and suicidal ideation (47% v 4%, P = .005) as determined by semistructured psychiatric interviews. The differential prevalence of depression between medication groups was only noted in those with a family history of a major affective disorder among first-degree relatives. Family discord and number of stressful life events were also associated with depression in this cohort. Patients treated with phenobarbital should be closely monitored for depression, and alternative treatments should probably be sought for patients with newly diagnoses epilepsy and a personal or family history of an affective disorder. The clinical and research implications of these findings are discussed.