A domain-agnostic approach for characterization of lifelong learning systems

Despite the advancement of machine learning techniques in recent years, state-of-the-art systems lack robustness to "real world" events, where the input distributions and tasks encountered by the deployed systems will not be limited to the original training context, and systems will instead need to adapt to novel distributions and tasks while deployed. This critical gap may be addressed through the development of "Lifelong Learning" systems that are capable of (1) Continuous Learning, (2) Transfer and Adaptation, and (3) Scalability. Unfortunately, efforts to improve these capabilities are typically treated as distinct areas of research that are assessed independently, without regard to the impact of each separate capability on other aspects of the system. We instead propose a holistic approach, using a suite of metrics and an evaluation framework to assess Lifelong Learning in a principled way that is agnostic to specific domains or system techniques. Through five case studies, we show that this suite of metrics can inform the development of varied and complex Lifelong Learning systems. We highlight how the proposed suite of metrics quantifies performance trade-offs present during Lifelong Learning system development - both the widely discussed Stability-Plasticity dilemma and the newly proposed relationship between Sample Efficient and Robust Learning. Further, we make recommendations for the formulation and use of metrics to guide the continuing development of Lifelong Learning systems and assess their progress in the future.

Search for Tensor, Vector, and Scalar Polarizations in the Stochastic Gravitational-Wave Background

The detection of gravitational waves with Advanced LIGO and Advanced Virgo has enabled novel tests of general relativity, including direct study of the polarization of gravitational waves. While general relativity allows for only two tensor gravitational-wave polarizations, general metric theories can additionally predict two vector and two scalar polarizations. The polarization of gravitational waves is encoded in the spectral shape of the stochastic gravitational-wave background, formed by the superposition of cosmological and individually unresolved astrophysical sources. Using data recorded by Advanced LIGO during its first observing run, we search for a stochastic background of generically polarized gravitational waves. We find no evidence for a background of any polarization, and place the first direct bounds on the contributions of vector and scalar polarizations to the stochastic background. Under log-uniform priors for the energy in each polarization, we limit the energy densities of tensor, vector, and scalar modes at 95% credibility to Ω_{0}^{T}<5.58×10^{-8}, Ω_{0}^{V}<6.35×10^{-8}, and Ω_{0}^{S}<1.08×10^{-7} at a reference frequency f_{0}=25  Hz.

GW170817: Implications for the Stochastic Gravitational-Wave Background from Compact Binary Coalescences

The LIGO Scientific and Virgo Collaborations have announced the event GW170817, the first detection of gravitational waves from the coalescence of two neutron stars. The merger rate of binary neutron stars estimated from this event suggests that distant, unresolvable binary neutron stars create a significant astrophysical stochastic gravitational-wave background. The binary neutron star component will add to the contribution from binary black holes, increasing the amplitude of the total astrophysical background relative to previous expectations. In the Advanced LIGO-Virgo frequency band most sensitive to stochastic backgrounds (near 25 Hz), we predict a total astrophysical background with amplitude Ω_{GW}(f=25  Hz)=1.8_{-1.3}^{+2.7}×10^{-9} with 90% confidence, compared with Ω_{GW}(f=25  Hz)=1.1_{-0.7}^{+1.2}×10^{-9} from binary black holes alone. Assuming the most probable rate for compact binary mergers, we find that the total background may be detectable with a signal-to-noise-ratio of 3 after 40 months of total observation time, based on the expected timeline for Advanced LIGO and Virgo to reach their design sensitivity.

First Search for Nontensorial Gravitational Waves from Known Pulsars

We present results from the first directed search for nontensorial gravitational waves. While general relativity allows for tensorial (plus and cross) modes only, a generic metric theory may, in principle, predict waves with up to six different polarizations. This analysis is sensitive to continuous signals of scalar, vector, or tensor polarizations, and does not rely on any specific theory of gravity. After searching data from the first observation run of the advanced LIGO detectors for signals at twice the rotational frequency of 200 known pulsars, we find no evidence of gravitational waves of any polarization. We report the first upper limits for scalar and vector strains, finding values comparable in magnitude to previously published limits for tensor strain. Our results may be translated into constraints on specific alternative theories of gravity.

GW170817: Observation of Gravitational Waves from a Binary Neutron Star Inspiral

On August 17, 2017 at 12∶41:04 UTC the Advanced LIGO and Advanced Virgo gravitational-wave detectors made their first observation of a binary neutron star inspiral. The signal, GW170817, was detected with a combined signal-to-noise ratio of 32.4 and a false-alarm-rate estimate of less than one per 8.0×10^{4}  years. We infer the component masses of the binary to be between 0.86 and 2.26  M_{⊙}, in agreement with masses of known neutron stars. Restricting the component spins to the range inferred in binary neutron stars, we find the component masses to be in the range 1.17-1.60  M_{⊙}, with the total mass of the system 2.74_{-0.01}^{+0.04}M_{⊙}. The source was localized within a sky region of 28  deg^{2} (90% probability) and had a luminosity distance of 40_{-14}^{+8}  Mpc, the closest and most precisely localized gravitational-wave signal yet. The association with the γ-ray burst GRB 170817A, detected by Fermi-GBM 1.7 s after the coalescence, corroborates the hypothesis of a neutron star merger and provides the first direct evidence of a link between these mergers and short γ-ray bursts. Subsequent identification of transient counterparts across the electromagnetic spectrum in the same location further supports the interpretation of this event as a neutron star merger. This unprecedented joint gravitational and electromagnetic observation provides insight into astrophysics, dense matter, gravitation, and cosmology.

GW170814: A Three-Detector Observation of Gravitational Waves from a Binary Black Hole Coalescence

On August 14, 2017 at 10∶30:43 UTC, the Advanced Virgo detector and the two Advanced LIGO detectors coherently observed a transient gravitational-wave signal produced by the coalescence of two stellar mass black holes, with a false-alarm rate of ≲1 in 27 000 years. The signal was observed with a three-detector network matched-filter signal-to-noise ratio of 18. The inferred masses of the initial black holes are 30.5_{-3.0}^{+5.7}M_{⊙} and 25.3_{-4.2}^{+2.8}M_{⊙} (at the 90% credible level). The luminosity distance of the source is 540_{-210}^{+130}  Mpc, corresponding to a redshift of z=0.11_{-0.04}^{+0.03}. A network of three detectors improves the sky localization of the source, reducing the area of the 90% credible region from 1160   deg^{2} using only the two LIGO detectors to 60  deg^{2} using all three detectors. For the first time, we can test the nature of gravitational-wave polarizations from the antenna response of the LIGO-Virgo network, thus enabling a new class of phenomenological tests of gravity.

GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2

We describe the observation of GW170104, a gravitational-wave signal produced by the coalescence of a pair of stellar-mass black holes. The signal was measured on January 4, 2017 at 10∶11:58.6 UTC by the twin advanced detectors of the Laser Interferometer Gravitational-Wave Observatory during their second observing run, with a network signal-to-noise ratio of 13 and a false alarm rate less than 1 in 70 000 years. The inferred component black hole masses are 31.2_{-6.0}^{+8.4}M_{⊙} and 19.4_{-5.9}^{+5.3}M_{⊙} (at the 90% credible level). The black hole spins are best constrained through measurement of the effective inspiral spin parameter, a mass-weighted combination of the spin components perpendicular to the orbital plane, χ_{eff}=-0.12_{-0.30}^{+0.21}. This result implies that spin configurations with both component spins positively aligned with the orbital angular momentum are disfavored. The source luminosity distance is 880_{-390}^{+450}  Mpc corresponding to a redshift of z=0.18_{-0.07}^{+0.08}. We constrain the magnitude of modifications to the gravitational-wave dispersion relation and perform null tests of general relativity. Assuming that gravitons are dispersed in vacuum like massive particles, we bound the graviton mass to m_{g}≤7.7×10^{-23}  eV/c^{2}. In all cases, we find that GW170104 is consistent with general relativity.

Chemoradiotherapy with Brachytherapy or Electron Therapy Boost for Locally Advanced Squamous Cell Carcinoma of the Anus-Reducing the Colostomy Rate

Purpose

The aim of this study is to determine overall survival, disease-specific survival and stoma-free survival after treatment of squamous cell carcinoma of the anus with chemoradiotherapy followed by brachytherapy or electron boost in a recent cohort of patients.

Methods

Fifty-two patients (median age 62 years) were treated with radical chemoradiotherapy (mitomycin C, infusional 5-fluorouracil concurrently with conformal radical radiotherapy 45 Gy in 25 fractions over 5 weeks) followed by a radiotherapy boost between 1 December 2000 and 30 April 2011. Follow-up was to 30 November 2014. Thirty-six patients received a boost (15–20 Gy) over 2 days with ¹⁹²Ir needle brachytherapy for anal canal tumours, and 16 patients received electron beam therapy (20 Gy in 10 fractions in 2 weeks) for anal margin tumours. A defunctioning stoma was only created prior to chemoradiotherapy for fistula or severe anal pain.

Results

The overall survival for the 36 patients treated with chemoradiotherapy followed by brachytherapy was 75 % (95 % CI, 61–89) at 5 years, the disease-specific survival was 91 % (95 % CI, 81–101 %), and the stoma-free survival was 97 % (95 % CI, 91–103 %) all at 5 years. For the 16 patients treated with an electron boost for anal margin tumours, the 5-year overall survival, disease-specific survival and stoma-free survival were 68 % (95 % CI, 44–92 %), 78 % (95 % CI, 56–100 %) and 80 % (95 % CI, 60–100 %), respectively.

Conclusions

A very low stoma formation rate can be obtained with radical chemoradiotherapy followed by a brachytherapy boost for squamous cell carcinoma of the anal canal but not with an electron boost for anal margin tumours.

Adult neurogenesis and neurite outgrowth are impaired in LRRK2 G2019S mice

The generation and maturation of adult neural stem/progenitor cells are impaired in many neurodegenerative diseases, among them is Parkinson's disease (PD). In mammals, including humans, adult neurogenesis is a lifelong feature of cellular brain plasticity in the hippocampal dentate gyrus (DG) and in the subventricular zone (SVZ)/olfactory bulb system. Hyposmia, depression, and anxiety are early non-motor symptoms in PD. There are parallels between brain regions associated with non-motor symptoms in PD and neurogenic regions. In autosomal dominant PD, mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are frequent. LRRK2 homologs in non-vertebrate systems play an important role in chemotaxis, cell polarity, and neurite arborization. We investigated adult neurogenesis and the neurite development of new neurons in the DG and SVZ/olfactory bulb system in bacterial artificial chromosome (BAC) human Lrrk2 G2019S transgenic mice. We report that mutant human Lrrk2 is highly expressed in the hippocampus in the DG and the SVZ of adult Lrrk2 G2019S mice. Proliferation of newly generated cells is significantly decreased and survival of newly generated neurons in the DG and olfactory bulb is also severely impaired. In addition, after stereotactic injection of a GFP retrovirus, newly generated neurons in the DG of Lrrk2 G2019S mice exhibited reduced dendritic arborization and fewer spines. This loss in mature, developed spines might point towards a decrease in synaptic connectivity. Interestingly, physical activity partially reverses the decrease in neuroblasts observed in Lrrk2 G2010S mice. These data further support a role for Lrrk2 in neuronal morphogenesis and provide new insights into the role of Lrrk2 in adult neurogenesis.

The CTP:phosphocholine cytidylyltransferase encoded by the licC gene of Streptococcus pneumoniae: cloning, expression, purification, and characterization

Streptococcus pneumoniae is a member of a small group of bacteria that display phosphocholine on the cell surface, covalently attached to the sugar groups of teichoic acid and lipoteichoic acid. The putative pathway for this phosphocholine decoration is, in its first two enzymes, functionally similar to the CDP-choline pathway used for phosphatidylcholine biosynthesis in eukaryotes. We show that the licC gene encodes a functional CTP:phosphocholine cytidylyltransferase (CCT). The enzyme has been expressed and purified to homogeneity. Assay conditions were optimized, particularly with respect to linearity with time, pH, Mg(2+), and ammonium sulfate concentration. The pure enzyme has K(M) values of 890+/-240 microM for CTP, and 390+/-170 microM for phosphocholine. The k(cat) is 17.5+/-4.0 s(-1). S. pneumoniae CTP:phosphocholine cytidylyltransferase (SpCCT) is specific for CTP or dCTP as the nucleotide substrate. SpCCT is strongly inhibited by Ca(2+). The IC(50) values for recombinant and native SpCCT are 0.32+/-0.04 and 0.27+/-0.03 mM respectively. The enzyme is also inhibited by all other tested divalent cations, including Mg(2+) at high concentrations. The cloning and expression of this enzyme sets the stage for design of inhibitors as possible antipneumococcal drugs.

Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity

The dimeric enzyme CTP:glycerol-3-phosphate cytidylyltransferase (GCT) displays strong negative cooperativity between the first and second binding of its substrate, CTP. Using NMR to study the allosteric mechanism of this enzyme, we observe widespread chemical shift changes for the individual CTP binding steps. Mapping these changes onto the molecular structure allowed the formulation of a detailed model of allosteric conformational change. Upon the second step of ligand binding, NMR experiments indicate an extensive loss of conformational exchange broadening of the backbone resonances of GCT. This suggests that a fraction of the free energy of negative cooperativity is entropic in origin.

Negative cooperativity of substrate binding but not enzyme activity in wild-type and mutant forms of CTP:glycerol-3-phosphate cytidylyltransferase

CTP:glycerol-3-phosphate cytidylyltransferase (GCT) catalyzes the synthesis of CDP-glycerol for teichoic acid biosynthesis in certain Gram-positive bacteria. This enzyme is a model for a cytidylyltransferase family that includes the enzymes that synthesize CDP-choline and CDP-ethanolamine for phosphatidylcholine and phosphatidylethanolamine biosynthesis. We have used quenching of intrinsic tryptophan fluorescence to measure binding affinities of substrates to the GCT from Bacillus subtilis. Binding of either CTP or glycerol-3-phosphate to GCT was biphasic, with two binding constants of about 0.1-0.3 and 20-40 microm for each substrate. The stoichiometry of binding was 2 molecules of substrate/enzyme dimer, so the two binding constants represented distinctly different affinities of the enzyme for the first and second molecule of each substrate. The biphasic nature of binding was observed with the wild-type GCT as well as with several mutants with altered Km or kcat values. This negative cooperativity of binding was also seen when a catalytically defective mutant was saturated with two molecules of CTP and then titrated with glycerol-3-phosphate. Despite the pronounced negative cooperativity of substrate binding, negative cooperativity of enzyme activity was not observed. These data support a mechanism in which catalysis occurs only when the enzyme is fully loaded with 2 molecules of each substrate/enzyme dimer.

A comparison of CAL with a conventional method of delivery of cell biology to undergraduate nursing students using an experimental design

This paper describes the development and evaluation of a series of computer assisted learning (CAL) packages on cell biology produced for an undergraduate nursing course. The CAL packages were based on the material originally delivered in Kindermann's slide practical classes. The decision to convert this teaching material into CAL packages was taken for a number of reasons, but mainly in response to student evaluations and lack of equipment and staff resources needed to adequately deliver the sessions. Student feedback showed that CAL was preferred to the slide classes. Two studies were carried out to compare the CAL method of delivery with the conventional method using an experimental design. Students taught using CAL felt more confident that they would be able to use the material they had learnt if required as a basis for future work. The distributions rating 'how necessary was the contribution of a teacher in the session' were skewed towards the 'essential' end of the scale for the slide group but towards the 'unnecessary' end for the CAL group. Learning effectiveness was not compromised by the introduction of CAL, even though this meant that no lecturer was on hand to deal with questions.

Cloning and characterization of a lipid-activated CTP:phosphocholine cytidylyltransferase from Caenorhabditis elegans: identification of a 21-residue segment critical for lipid activation

The genome of the nematode Caenorhabditis elegans contains several genes that appear to encode proteins similar to CTP:phosphocholine cytidylyltransferase (CCT). We have isolated a 1044-nucleotide cDNA clone from a C. elegans cDNA library that encodes the 347-amino acid version of CCT that is most similar to previously-identified CCTs. Native and His-tagged forms were expressed and purified using a baculovirus expression system. The enzyme was maximally activated by 5 microM phosphatidylcholine:oleate (50:50) vesicles with a k(cat) value in the presence of lipid 37-fold greater than the k(cat) value in the absence of lipid. To localize the region of C. elegans CCT critical for lipid activation, a series of C-terminal truncation mutants was analyzed. CCT truncated after amino acids 225 or 245 was quite active in the absence of lipids and not further activated in the presence of lipids, supporting the concept that the lipid-activation segment is inhibitory to catalysis in the absence of lipids. CCT truncated after amino acids 266, 281, or 319 was activated by lipid similar to wild-type enzyme. Kinetic analysis in the absence of lipid revealed the lipid-independent CCT truncated after amino acid 245 to have a k(cat) value 15-fold greater than either full-length CCT or CCT truncated after amino acid 266. We conclude that elements critical for activation of C. elegans CCT by lipids are contained within amino acids 246-266, that this region is inhibitory in the absence of lipids, and that the inhibition is relieved by the association of the enzyme with lipid.

Cruising on the Internet highway

This study evaluated differences in sexual behavior and risk for sexually transmitted diseases (STDs) among men who have sex with men (MSM) who met their partners on-line and those who did not. A self-administered questionnaire on sexual behavior was offered to a convenience sample of patients seeking public STD services. Thirty-two percent of MSM patients reported meeting a sexual partner over the Internet in the past year. MSM with on-line partners were younger, more likely to report sex with an HIV-positive person in the last year, and more likely to report casual partners in the last year compared with MSM with only off-line partners. HIV-negative MSM with on-line partners were more likely than HIV-negative MSM with only off-line partners to have received money or drugs for sex in the past year and to report sex with an HIV-positive partner in the past year. Although meeting partners on the Internet was common and associated with increased risk for STDs in MSM, it also presents new untapped opportunities for on-line health promotion and disease prevention.

Fleeting foreskins: the misclassification of male circumcision status

BACKGROUND

Errors in the classification of male circumcision status could bias studies linking infection to lack of circumcision.

GOAL

To determine the frequency and factors associated with the reproducibility of reporting circumcision status.

STUDY DESIGN

Secondary analysis of data using logistic regression modeling from a multicenter randomized controlled trial was performed.

RESULTS

At follow-up assessment, 15.6% of clinician reports on circumcision status disagreed with baseline reports. Disagreement was more common if both clinicians were women than if both were men (odds ratio [OR], 2.8; 95% CI, 1.9-4.1). As compared with whites reported as circumcised (4%, 19/532 visits), the highest disagreement involved uncircumcised Hispanic (OR, 3.3; 95% CI, 1.7-6.3), white (OR, 12.2; 95% CI, 5.8-25.6), or black (OR, 17.1; 95% CI, 10.4-27.9) men.

CONCLUSIONS

This is one study among a small number of studies examining the reproducibility of clinician-reported circumcision status by comparing multiple clinical examinations of the same patient. The magnitude of the misclassification discovered could bias results and indicates the need for greater accuracy in reporting circumcision status in future studies.

Determinants of persistent and recurrent Chlamydia trachomatis infection in young women: results of a multicenter cohort study

BACKGROUND

Sequelae of genital Chlamydia trachomatis infection in women are more strongly linked to repeat infections than to initial ones, and persistent or subsequent infections foster continued transmission.

OBJECTIVE

To identify factors associated with persistent and recurrent chlamydial infection in young women that might influence prevention strategies.

METHODS

Teenage and young adult women with uncomplicated C trachomatis infection attending reproductive health, sexually transmitted disease, and adolescent medicine clinics in five US cities were recruited to a cohort study. Persistent or recurrent chlamydial infection was detected by ligase chain reaction (LCR) testing of urine 1 month and 4 months after treatment.

RESULTS

Among 1,194 women treated for chlamydial infection, 792 (66.4%) returned for the first follow-up visit, 50 (6.3 %) of whom had positive LCR results. At that visit, women who resumed sex since treatment were more likely to have chlamydial infection (relative risk [RR], 2.0; 95% CI, 1.03-3.9), as were those who did not complete treatment (RR, 3.4; 95% CI, 1.6-7.3). Among women who tested negative for C trachomatis at the first follow-up visit, 36 (7.1%) of 505 had positive results by LCR at the second follow-up visit. Reinfection at this visit was not clearly associated with having a new sex partner or other sexual behavior risks; new infection was likely due to resumption of sex with untreated partners. Overall, 13.4% of women had persistent infection or became reinfected after a median of 4.3 months, a rate of 33 infections per 1,000 person months.

CONCLUSIONS

Persistent or recurrent infection is very common in young women with chlamydial infection. Improved strategies are needed to assure treatment of women's male sex partners. Rescreening, or retesting of women for chlamydial infection a few months after treatment, also is recommended as a routine chlamydia prevention strategy.

Purification and kinetic characterization of CTP:phosphocholine cytidylyltransferase from Saccharomyces cerevisiae

CTP:phosphocholine cytidylyltransferase (CCT) regulates the biosynthesis of phosphatidylcholine in mammalian cells. In order to understand the mechanism by which this enzyme controls phosphatidylcholine synthesis, we have initiated studies of CCT from the model genetic system, the yeast Saccharomyces cerevisiae. The yeast CCT gene was isolated from genomic DNA using the polymerase chain reaction and was found to encode tyrosine at position 192 instead of histidine, as originally reported. Levels of expression of yeast CCT activity in Escherichia coli or in the yeast, Pichia pastoris, were somewhat low. Expression of yeast CCT in a baculovirus system as a 6x-His-tag fusion protein was higher and was used to purify yeast CCT by a procedure that included delipidation. Kinetic characterization revealed that yeast CCT was activated approximately 20-fold by 20 microM phosphatidylcholine:oleate vesicles, a level 5-fold lower than that necessary for maximal activation of rat CCT. The k(cat) value was 31.3 s(-1) in the presence of lipid and 1.5 s(-1) in the absence of lipid. The K(m) values for the substrates CTP and phosphocholine did not change significantly upon activation by lipids; K(m) values in the presence of lipid were 0.80 mM for phosphocholine and 1.4 mM for CTP while K(m) values in the absence of lipid were 1.2 mM for phosphocholine and 0.8 mM for CTP. Activation of yeast CCT, therefore, appears to be due to an increase in the k(cat) value upon lipid binding.

Circumcision and STD in the United States: cross sectional and cohort analyses

BACKGROUND

Male circumcision status has been shown to be associated with sexually transmitted disease (STD) acquisition in some, but not all, studies. Most studies have been cross sectional.

OBJECTIVES

We examined the association between circumcision status and the prevalence and incidence of gonorrhoea, chlamydia, and syphilis.

METHODS

We analysed cross sectional and cohort study data from a multicentre controlled trial in the United States. Between July 1993 and September 1996, 2021 men visiting public inner city STD clinics in the United States were examined by a clinician at enrolment and 1456 were examined at follow up visits 6 and 12 months later. At each visit, men had laboratory tests for gonorrhoea, chlamydia, and syphilis and were examined for circumcision status. We used multiple logistic regression to compare STD risk among circumcised and uncircumcised men adjusted for potentially confounding factors.

RESULTS

Uncircumcised men were significantly more likely than circumcised men to have gonorrhoea in the multivariate analyses, adjusted for age, race, and site, in both the cross sectional (odds ratio (OR), 1.3; 95% confidence interval (CI), 0.9 to 1.7) and in the cohort analysis (OR, 1.6; 95% CI, 1.0 to 2.6). There was no association between lack of circumcision and chlamydia in either the cross sectional (OR, 1.0; 95% CI 0.7-1.4) or the cohort analysis (OR, 0.9; 95% CI 0.5-1.5). The magnitude of association between lack of circumcision and syphilis was similar in the cross sectional (OR, 1.4; 95% CI 0.6 to 3.3) and cohort analysis (OR, 1.5; 95% CI 0.4 to 6.1).

CONCLUSION

Uncircumcised men in the United States may be at increased risk for gonorrhoea and syphilis, but chlamydia risk appears similar in circumcised and uncircumcised men. Our results suggest that risk estimates from cross sectional studies would be similar to cohort findings.

A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis

BACKGROUND

The formation of critical intermediates in the biosynthesis of lipids and complex carbohydrates is carried out by cytidylyltransferases, which utilize CTP to form activated CDP-alcohols or CMP-acid sugars plus inorganic pyrophosphate. Several cytidylyltransferases are related and constitute a conserved family of enzymes. The eukaryotic members of the family are complex enzymes with multiple regulatory regions or repeated catalytic domains, whereas the bacterial enzyme, CTP:glycerol-3-phosphate cytidylyltransferase (GCT), contains only the catalytic domain. Thus, GCT provides an excellent model for the study of catalysis by the eukaryotic cytidylyltransferases.

RESULTS

The crystal structure of GCT from Bacillus subtilis has been determined by multiwavelength anomalous diffraction using a mercury derivative and refined to 2.0 A resolution (R(factor) 0.196; R(free) 0.255). GCT is a homodimer; each monomer comprises an alpha/beta fold with a central 3-2-1-4-5 parallel beta sheet. Additional helices and loops extending from the alpha/beta core form a bowl that binds substrates. CTP, bound at each active site of the homodimer, interacts with the conserved (14)HXGH and (113)RTXGISTT motifs. The dimer interface incorporates part of a third motif, (63)RYVDEVI, and includes hydrophobic residues adjoining the HXGH sequence.

CONCLUSIONS

Structure superpositions relate GCT to the catalytic domains from class I aminoacyl-tRNA synthetases, and thus expand the tRNA synthetase family of folds to include the catalytic domains of the family of cytidylyltransferases. GCT and aminoacyl-tRNA synthetases catalyze analogous reactions, bind nucleotides in similar U-shaped conformations, and depend on histidines from analogous HXGH motifs for activity. The structural and other similarities support proposals that GCT, like the synthetases, catalyzes nucleotidyl transfer by stabilizing a pentavalent transition state at the alpha-phosphate of CTP.

Resection and permanent I-125 brachytherapy without whole brain irradiation for solitary brain metastasis from non-small cell lung carcinoma

We assessed a treatment plan of local therapy (resection and placement of permanent low dose-rate I-125 seeds) without whole brain irradiation in 15 patients with solitary brain metastasis (SBM) from primary non-small cell lung cancer between January, 1991 and May, 1996. Thirteen lesions were confirmed as solitary by MRI scan, and 2 patients had CT scan only. With median follow up of 14 months, 3 patients remain alive at 6, 33, and 62 months post-resection. Median survival is 14 months for all patients and 26 months for patients with SBM as the only site of disease. Five tumors failed in the brain: 2 solitary recurrences adjacent to the site of SBM, 2 multiple metastases outside the primary site, and 1 multiple recurrence including the primary site. No failures were seen with SBM <2.5 cm. Only 2 of 13 patients with SBM confirmed with MRI experienced relapses elsewhere in the brain. Recurrence rates both adjacent and outside the area of the initial brain lesion are similar to studies employing resection plus whole brain irradiation (WBI), and the patient is spared the acute and potential late toxicity of WBI. This approach may be considered for selected patients with solitary brain metastases (SBMs), although further experience with larger patient numbers is needed.

Enzymatic and cellular characterization of a catalytic fragment of CTP:phosphocholine cytidylyltransferase alpha

To probe the mechanism of lipid activation of CTP:phosphocholine cytidylyltransferase (CCTalpha), we have characterized a catalytic fragment of the enzyme that lacks the membrane-binding segment. The kinetic properties of the purified fragment, CCTalpha236, were characterized, as well as the effects of expressing the fragment in cultured cells. CCTalpha236 was truncated after residue 236, which corresponds to the end of the highly conserved catalytic domain. The activity of purified CCTalpha236 was independent of lipids and about 50-fold higher than the activity of wild-type CCTalpha assayed in the absence of lipids, supporting a model in which the membrane-binding segment functions as an inhibitor of the catalytic domain. The kcat/Km values for CCTalpha236 were only slightly lower than those for lipid-activated CCTalpha. The importance of the membrane-binding segment in vivo was tested by expression of CCTalpha236 in CHO58 cells, a cell line that is temperature-sensitive for growth and CCTalpha activity. Expression of wild-type CCTalpha in these cells complemented the defective growth phenotype when the cells were cultured in complete or delipidated fetal bovine serum. Expression of CCTalpha236, however, did not complement the growth phenotype in the absence of serum lipids. These cells were capable of making phosphatidylcholine in the delipidated medium, so the inability of the cells to grow was not due to defective phosphatidylcholine synthesis. Supplementation of the delipidated medium with an unsaturated fatty acid allowed growth of CHO58 cells expressing CCTalpha236. These results indicate that the membrane-binding segment of CCTalpha has an important role in cellular lipid metabolism.

CTP:phosphocholine cytidylyltransferase: insights into regulatory mechanisms and novel functions

A key regulatory enzyme in phosphatidylcholine biosynthesis, CTP:cholinephosphate cytidylyltransferase (CCT), catalyzes the formation of CDP-choline. This review discusses the essential features of CCT and addresses intriguing new insights into the catalytic and regulatory properties of this complex enzyme. Characterization of a lipid-binding segment in rat CCT is described and the role of lipids in CCT activation is discussed. An analysis of the phosphorylation domain is presented and possible physiological rationales for reversible phosphorylation of CCT are discussed. The nuclear localization of CCT is examined in the context of multiple CCT isoforms, as is recent evidence establishing a potential link between CCT activity and vesicular transport.

Interactions among pathways for phosphatidylcholine metabolism, CTP synthesis and secretion through the Golgi apparatus

Phosphatidylcholine is the major phospholipid in eukaryotic cells. It serves as a structural component of cell membranes and a reservoir of several lipid messengers. Recent studies in yeast and mammalian systems have revealed interrelationships between the two pathways of phosphatidylcholine metabolism, and between these pathways and those for CTP synthesis and secretion via the Golgi. These processes involve the regulation of the CDP-choline and phosphatidylethanolamine-methylation pathways of phosphatidylcholine synthesis, CTP synthetase, phospholipase D and the phospholipid-transfer protein Sec14p.

Effects of neonatal capsaicin administration on the numbers and volumes of neurons in left and right T10 dorsal root ganglia in the rat

The long-term effects of neonatal capsaicin were studied in left and right dorsal root ganglia (T10) from control and capsaicin-treated groups of Wistar rats. At 12 hours post partum, 5 females per group were injected subcutaneously with capsaicin or vehicle solution and killed at 6 months of age. Tissues were perfusion-fixed, embedded in resin and serially sectioned. A Nissl stain was used to distinguish between A and B neurons and systematic random sampling schemes were employed to obtain stereological estimates of numbers of neurons and mean volumes of their perikarya. Numbers were calculated from ganglion volumes (estimated via the Cavalieri principle) and neuron packing densities (estimated using physical disectors). Mean perikaryal volumes were calculated from packing densities and volume densities (estimated by point counting). Data were analysed to isolate main and interaction effects of neuron subtype, laterality and treatment. There was no evidence of lateral asymmetry or interaction effects. Control ganglia contained 3320 (coefficient of variation, CV, 8%) neurons. Most (73%) were B cells with a mean volume of 13,100 microm(3) (CV 17%) of which the nucleus accounted for 1,800 microm(3) (CV 18%). About 22% were A cells with a mean volume of 79,800 microm(3) (CV 24%) and a nucleus of 6,100 microm(3) (CV 26%). After capsaicin, over half the original population of cells was destroyed and B cell loss was significantly greater than that of A cells (about 80% of all cells lost were B cells). The mean size of A cells was greater after capsaicin due to selective loss of smaller cells and a greater volume of cytoplasm. B cell perikaryal volume was not affected but nuclear volume declined. The findings show that capsaicin destruction of peripheral sensory neurons is bilaterally symmetrical. In general, smaller neurons are selectively destroyed but this operates differently in A and B cells. It is size-dependent in A cells but size-independent (possibly random) in B cells.

Expression of superoxide dismutase messenger RNA in adult rat brain cholinergic neurons

Superoxide dismutase (SOD) protects cells exposed to an excess of the free radical nitric oxide, by preventing the formation of peroxynitrite. Certain central cholinergic neurons express constitutive nitric oxide synthase (nNOS), and presumably they are at risk from peroxynitrite intoxication. Immunocytochemistry for choline acetyltransferase (ChAT) was combined with in situ hybridization histochemistry (ISHH) to examine whether brain cholinergic populations differ with respect to their expression of the messenger RNA molecules (mRNAs) for the manganese-dependent (Mn-SOD) and copper/zinc-dependent superoxide dismutases (Cu /Zn-SOD). The cholinergic neurons located in the reticular formation of the upper brainstem (the laterodorsal tegmental nucleus [LDTN] and the pedunculopontine nucleus [PPN]) were found to express relatively high levels of Mn-SOD mRNA, whereas cholinergic neurons located in the basal forebrain (substantia innominata [SI], diagonal band [DB], medial septum [MS], and the nucleus basalis magnocellularis [nBM]), and the striatal cholinergic interneurons expressed low to intermediate levels of Mn-SOD mRNA. The rank order of median Mn-SOD mRNA density per cholinergic cell was LDTN > PPN > SI > striatum = nBM = DB > MS. This is similar to the rank order of nNOS mRNA densities in the cholinergic cells in these regions (R = 0.9, p < 0.02). The rank order of Cu/Zn-SOD mRNA levels in cholinergic populations (DB > LDTN = PPN =MS > SI = nBM = striatum) was not correlated with nNOS mRNA (R = 0.29, P > 0.05). Thus, for cholinergic neurons, Mn-SOD may be important for protection from NO-related oxidative stress.

Bilateral acute retinal necrosis caused by cytomegalovirus in an immunocompromised patient

PURPOSE

To report a case of bilateral acute retinal necrosis caused by cytomegalovirus.

METHODS

A diagnostic vitrectomy was performed on a patient with non-Hodgkin lymphoma who presented with a bilateral, rapidly progressing necrotizing retinitis and uveitis.

RESULTS

Immunohistochemical studies and polymerase chain reaction disclosed cytomegalovirus as the cause of retinitis. The patient was treated with intravitreal and intravenous ganciclovir.

CONCLUSIONS

Although rare, cytomegalovirus may lead to an appearance identical to acute retinal necrosis and should be considered among the viral etiologies of this syndrome.

Efficacy of risk-reduction counseling to prevent human immunodeficiency virus and sexually transmitted diseases: a randomized controlled trial. Project RESPECT Study Group

CONTEXT

The efficacy of counseling to prevent infection with the human immunodeficiency virus (HIV) and other sexually transmitted diseases (STDs) has not been definitively shown.

OBJECTIVE

To compare the effects of 2 interactive HIV/STD counseling interventions with didactic prevention messages typical of current practice.

DESIGN

Multicenter randomized controlled trial (Project RESPECT), with participants assigned to 1 of 3 individual face-to-face interventions.

SETTING

Five public STD clinics (Baltimore, Md; Denver, Colo; Long Beach, Calif; Newark, NJ; and San Francisco, Calif) between July 1993 and September 1996.

PARTICIPANTS

A total of 5758 heterosexual, HIV-negative patients aged 14 years or older who came for STD examinations.

INTERVENTIONS

Arm 1 received enhanced counseling, 4 interactive theory-based sessions. Arm 2 received brief counseling, 2 interactive risk-reduction sessions. Arms 3 and 4 each received 2 brief didactic messages typical of current care. Arms 1, 2, and 3 were actively followed up after enrollment with questionnaires at 3, 6, 9, and 12 months and STD tests at 6 and 12 months. An intent-to-treat analysis was used to compare interventions.

MAIN OUTCOME MEASURES

Self-reported condom use and new diagnoses of STDs (gonorrhea, chlamydia, syphilis, HIV) defined by laboratory tests.

RESULTS

At the 3- and 6-month follow-up visits, self-reported 100% condom use was higher (P<.05) in both the enhanced counseling and brief counseling arms compared with participants in the didactic messages arm. Through the 6-month interval, 30% fewer participants had new STDs in both the enhanced counseling (7.2%; P= .002) and brief counseling (7.3%; P= .005) arms compared with those in the didactic messages arm (10.4%). Through the 12-month study, 20% fewer participants in each counseling intervention had new STDs compared with those in the didactic messages arm (P = .008). Consistently at each of the 5 study sites, STD incidence was lower in the counseling intervention arms than in the didactic messages intervention arm. Reduction of STD was similar for men and women and greater for adolescents and persons with an STD diagnosed at enrollment.

CONCLUSIONS

Short counseling interventions using personalized risk reduction plans can increase condom use and prevent new STDs. Effective counseling can be conducted even in busy public clinics.