A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies

BACKGROUND

RNA sequencing combined with machine learning techniques has provided a modern approach to the molecular classification of cancer. Class predictors, reflecting the disease class, can be constructed for known tissue types using the gene expression measurements extracted from cancer patients. One challenge of current cancer predictors is that they often have suboptimal performance estimates when integrating molecular datasets generated from different labs. Often, the quality of the data is variable, procured differently, and contains unwanted noise hampering the ability of a predictive model to extract useful information. Data preprocessing methods can be applied in attempts to reduce these systematic variations and harmonize the datasets before they are used to build a machine learning model for resolving tissue of origins.

RESULTS

We aimed to investigate the impact of data preprocessing steps-focusing on normalization, batch effect correction, and data scaling-through trial and comparison. Our goal was to improve the cross-study predictions of tissue of origin for common cancers on large-scale RNA-Seq datasets derived from thousands of patients and over a dozen tumor types. The results showed that the choice of data preprocessing operations affected the performance of the associated classifier models constructed for tissue of origin predictions in cancer.

CONCLUSION

By using TCGA as a training set and applying data preprocessing methods, we demonstrated that batch effect correction improved performance measured by weighted F1-score in resolving tissue of origin against an independent GTEx test dataset. On the other hand, the use of data preprocessing operations worsened classification performance when the independent test dataset was aggregated from separate studies in ICGC and GEO. Therefore, based on our findings with these publicly available large-scale RNA-Seq datasets, the application of data preprocessing techniques to a machine learning pipeline is not always appropriate.

Training machine learning potentials for reactive systems: A Colab tutorial on basic models

In the last several years, there has been a surge in the development of machine learning potential (MLP) models for describing molecular systems. We are interested in a particular area of this field - the training of system-specific MLPs for reactive systems - with the goal of using these MLPs to accelerate free energy simulations of chemical and enzyme reactions. To help new members in our labs become familiar with the basic techniques, we have put together a self-guided Colab tutorial (https://cc-ats.github.io/mlp_tutorial/), which we expect to be also useful to other young researchers in the community. Our tutorial begins with the introduction of simple feedforward neural network (FNN) and kernel-based (using Gaussian process regression, GPR) models by fitting the two-dimensional Müller-Brown potential. Subsequently, two simple descriptors are presented for extracting features of molecular systems: symmetry functions (including the ANI variant) and embedding neural networks (such as DeepPot-SE). Lastly, these features will be fed into FNN and GPR models to reproduce the energies and forces for the molecular configurations in a Claisen rearrangement reaction.

Preclinical Evaluation of Novel Positron Emission Tomography (PET) Probes for Imaging Leucine-Rich Repeat Kinase 2 (LRRK2)

Parkinson's disease (PD) is one of the most highly debilitating neurodegenerative disorders, which affects millions of people worldwide, and leucine-rich repeat kinase 2 (LRRK2) mutations have been involved in the pathogenesis of PD. Developing a potent LRRK2 positron emission tomography (PET) tracer would allow for in vivo visualization of LRRK2 distribution and expression in PD patients. In this work, we present the facile synthesis of two potent and selective LRRK2 radioligands [11C]3 ([11C]PF-06447475) and [18F]4 ([18F]PF-06455943). Both radioligands exhibited favorable brain uptake and specific bindings in rodent autoradiography and PET imaging studies. More importantly, [18F]4 demonstrated significantly higher brain uptake in the transgenic LRRK2-G2019S mutant and lipopolysaccharide (LPS)-injected mouse models. This work may serve as a roadmap for the future design of potent LRRK2 PET tracers.

In vivo three-dimensional brain imaging with chemiluminescence probes in Alzheimer's disease models

Optical three-dimensional (3D) molecular imaging is highly desirable for providing precise distribution of the target-of-interest in disease models. However, such 3D imaging is still far from wide applications in biomedical research; 3D brain optical molecular imaging, in particular, has rarely been reported. In this report, we designed chemiluminescence probes with high quantum yields, relatively long emission wavelengths, and high signal-to-noise ratios to fulfill the requirements for 3D brain imaging in vivo. With assistance from density-function theory (DFT) computation, we designed ADLumin-Xs by locking up the rotation of the double bond via fusing the furan ring to the phenyl ring. Our results showed that ADLumin-5 had a high quantum yield of chemiluminescence and could bind to amyloid beta (Aβ). Remarkably, ADLumin-5's radiance intensity in brain areas could reach 4 × 107 photon/s/cm2/sr, which is probably 100-fold higher than most chemiluminescence probes for in vivo imaging. Because of its strong emission, we demonstrated that ADLumin-5 could be used for in vivo 3D brain imaging in transgenic mouse models of Alzheimer's disease.

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.

RAS-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome-associated cardiac hypertrophy

RIT1 is a RAS guanosine triphosphatase (GTPase) that regulates different aspects of signal transduction and is mutated in lung cancer, leukemia, and in the germline of individuals with Noonan syndrome. Pathogenic RIT1 proteins promote mitogen-activated protein kinase (MAPK) hyperactivation; however, this mechanism remains poorly understood. Here, we show that RAF kinases are direct effectors of membrane-bound mutant RIT1 necessary for MAPK activation. We identify critical residues in RIT1 that facilitate interaction with membrane lipids and show that these are necessary for association with RAF kinases and MAPK activation. Although mutant RIT1 binds to RAF kinases directly, it fails to activate MAPK signaling in the absence of classical RAS proteins. Consistent with aberrant RAF/MAPK activation as a driver of disease, we show that pathway inhibition alleviates cardiac hypertrophy in a mouse model of RIT1 mutant Noonan syndrome. These data shed light on the function of pathogenic RIT1 and identify avenues for therapeutic intervention.

In Vivo Three-dimensional Brain Imaging with Chemiluminescence Probes in Alzheimer's Disease Models

Optical three-dimensional (3D) molecular imaging is highly desirable for providing precise distribution of the target-of-interest in disease models. However, such 3D imaging is still far from wide applications in biomedical research; 3D brain optical molecular imaging, in particular, has rarely been reported. In this report, we designed chemiluminescence probes with high quantum yields (QY), relatively long emission wavelengths, and high signal-to-noise ratios (SNRs) to fulfill the requirements for 3D brain imaging in vivo. With assistance from density-function theory (DFT) computation, we designed ADLumin-Xs by locking up the rotation of the double-bond via fusing the furan ring to the phenyl ring. Our results showed that ADLumin-5 had a high quantum yield of chemiluminescence and could bind to amyloid beta (Aβ). Remarkably, ADLumin-5's radiance intensity in brain areas could reach 4×107 photon/s/cm2/sr, which is probably 100-fold higher than most chemiluminescence probes for in vivo imaging. Because of its strong emission, we demonstrated that ADLumin-5 could be used for in vivo 3D brain imaging in transgenic mouse models of Alzheimer's disease (AD).

Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations

Inspired by the recent work from Noé and coworkers on the development of machine learning based implicit solvent model for the simulation of solvated peptides [Chen et al., J. Chem. Phys., 2021, 155, 084101], here we report another investigation of the possibility of using machine learning (ML) techniques to "derive" an implicit solvent model directly from explicit solvent molecular dynamics (MD) simulations. For alanine dipeptide, a machine learning potential (MLP) based on the DeepPot-SE representation of the molecule was trained to capture its interactions with its average solvent environment configuration (ASEC). The predicted forces on the solute deviated only by an RMSD of 0.4 kcal mol-1 Å-1 from the reference values, and the MLP-based free energy surface differed from that obtained from explicit solvent MD simulations by an RMSD of less than 0.9 kcal mol-1. Our MLP training protocol could also accurately reproduce combined quantum mechanical molecular mechanical (QM/MM) forces on the quantum mechanical (QM) solute in ASEC environment, thus enabling the development of accurate ML-based implicit solvent models for ab initio-QM MD simulations. Such ML-based implicit solvent models for QM calculations are cost-effective in both the training stage, where the use of ASEC reduces the number of data points to be labelled, and the inference stage, where the MLP can be evaluated at a relatively small additional cost on top of the QM calculation of the solute.

Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian

Molecular dynamics (MD) simulations employing ab initio quantum mechanical and molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the high computational cost associated with the ai-QM calculations remains a theoretical challenge for their routine application. Here, we present a modified protocol of the multiple time step (MTS) method for accelerating ai-QM/MM MD simulations of condensed-phase reactions. Within a previous MTS protocol [Nam J. Chem. Theory Comput. 2014, 10, 4175], reference forces are evaluated using a low-level (semiempirical QM/MM) Hamiltonian and employed at inner time steps to propagate the nuclear motions. Correction forces, which arise from the force differences between high-level (ai-QM/MM) and low-level Hamiltonians, are applied at outer time steps, where the MTS algorithm allows the time-reversible integration of the correction forces. To increase the outer step size, which is bound by the highest-frequency component in the correction forces, the semiempirical QM Hamiltonian is recalibrated in this work to minimize the magnitude of the correction forces. The remaining high-frequency modes, which are mainly bond stretches involving hydrogen atoms, are then removed from the correction forces. When combined with a Langevin or SIN(R) thermostat, the modified MTS-QM/MM scheme remains robust with an up to 8 (with Langevin) or 10 fs (with SIN(R)) outer time step (with 1 fs inner time steps) for the chorismate mutase system. This leads to an over 5-fold speedup over standard ai-QM/MM simulations, without sacrificing the accuracy in the predicted free energy profile of the reaction.

The seventh international RASopathies symposium: Pathways to a cure-expanding knowledge, enhancing research, and therapeutic discovery

RASopathies are a group of genetic disorders that are caused by genes that affect the canonical Ras/mitogen-activated protein kinase (MAPK) signaling pathway. Despite tremendous progress in understanding the molecular consequences of these genetic anomalies, little movement has been made in translating these findings to the clinic. This year, the seventh International RASopathies Symposium focused on expanding the research knowledge that we have gained over the years to enhance new discoveries in the field, ones that we hope can lead to effective therapeutic treatments. Indeed, for the first time, research efforts are finally being translated to the clinic, with compassionate use of Ras/MAPK pathway inhibitors for the treatment of RASopathies. This biannual meeting, organized by the RASopathies Network, brought together basic scientists, clinicians, clinician scientists, patients, advocates, and their families, as well as representatives from pharmaceutical companies and the National Institutes of Health. A history of RASopathy gene discovery, identification of new disease genes, and the latest research, both at the bench and in the clinic, were discussed.

Epitope alteration by small molecules and applications in drug discovery

Small molecules and antibodies are normally considered separately in drug discovery, except in the case of covalent conjugates. We unexpectedly discovered several small molecules that could inhibit or enhance antibody–epitope interactions which opens new possibilities in drug discovery and therapeutic modulation of auto-antibodies. We first discovered a small molecule, CRANAD-17, that enhanced the binding of an antibody to amyloid beta (Aβ), one of the major hallmarks of Alzheimer's disease, by stable triplex formation. Next, we found several small molecules that altered antibody–epitope interactions of tau and PD-L1 proteins, demonstrating the generality of this phenomenon. We report a new screening technology for ligand discovery, screening platform based on epitope alteration for drug discovery (SPEED), which is label-free for both the antibody and small molecule. SPEED, applied to an Aβ antibody, led to the discovery of a small molecule, GNF5837, that inhibits Aβ aggregation and another, obatoclax, that binds Aβ plaques and can serve as a fluorescent reporter in brain slices of AD mice. We also found a small molecule that altered the binding between Aβ and auto-antibodies from AD patient serum. SPEED reveals the sensitivity of antibody–epitope interactions to perturbation by small molecules and will have multiple applications in biotechnology and drug discovery.

A screening platform based on epitope alteration for drug discovery (SPEED).

Imaging Autotaxin In Vivo with 18F-Labeled Positron Emission Tomography Ligands

Autotaxin (ATX) is a secreted phosphodiesterase that has been implicated in a remarkably wide array of pathologies, especially in fibrosis and cancer. While ATX inhibitors have entered the clinical arena, a validated probe for positron emission tomography (PET) is currently lacking. With the aim to develop a suitable ATX-targeted PET radioligand, we have synthesized a focused library of fluorinated imidazo[1,2-a]pyridine derivatives, determined their inhibition constants, and confirmed their binding mode by crystallographic analysis. Based on their promising in vitro properties, compounds 9c, 9f, 9h, and 9j were radiofluorinated. Also, a deuterated analog of [¹⁸F]9j, designated as [¹⁸F]ATX-1905 ([¹⁸F]20), was designed and proved to be highly stable against in vivo radiodefluorination compared with [¹⁸F]9c, [¹⁸F]9f, [¹⁸F]9h, and [¹⁸F]9j. These results along with in vitro and in vivo studies toward ATX in a mouse model of LPS-induced liver injury suggest that [¹⁸F]ATX-1905 is a suitable PET probe for the non-invasive quantification of ATX.

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions

Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate MLPs for enzymatic reactions. Here we report a protocol for performing machine-learning-assisted free energy simulation of solution-phase and enzyme reactions at the ab initio quantum-mechanical/molecular-mechanical (ai-QM/MM) level of accuracy. Within our protocol, the MLP is built to reproduce the ai-QM/MM energy and forces on both QM (reactive) and MM (solvent/enzyme) atoms. As an alternative strategy, a delta machine learning potential (ΔMLP) is trained to reproduce the differences between the ai-QM/MM and semiempirical (se) QM/MM energies and forces. To account for the effect of the condensed-phase environment in both MLP and ΔMLP, the DeePMD representation of a molecular system is extended to incorporate the external electrostatic potential and field on each QM atom. Using the Menshutkin and chorismate mutase reactions as examples, we show that the developed MLP and ΔMLP reproduce the ai-QM/MM energy and forces with errors that on average are less than 1.0 kcal/mol and 1.0 kcal mol^-1 Å^-1, respectively, for representative configurations along the reaction pathway. For both reactions, MLP/ΔMLP-based simulations yielded free energy profiles that differed by less than 1.0 kcal/mol from the reference ai-QM/MM results at only a fraction of the computational cost.

Identification and Development of a New Positron Emission Tomography Ligand 4-(2-Fluoro-4-[11C]methoxyphenyl)-5-((1-methyl-1H-pyrazol-3-yl)methoxy)picolinamide for Imaging Metabotropic Glutamate Receptor Subtype 2 (mGlu2)

Metabotropic glutamate receptor 2 (mGlu₂) is a known target for treating several central nervous system (CNS) disorders. To develop a viable positron emission tomography (PET) ligand for mGlu₂, we identified new candidates 5a-i that are potent negative allosteric modulators (NAMs) of mGlu₂. Among these candidates, 4-(2-fluoro-4-methoxyphenyl)-5-((1-methyl-1H-pyrazol-3-yl)methoxy)picolinamide (5i, also named as [¹¹C]MG2-1812) exhibited high potency, high subtype selectivity, and favorable lipophilicity. Compound 5i was labeled with positron-emitting carbon-11 (¹¹C) to obtain [¹¹C]5i in high radiochemical yield and high molar activity by O-[¹¹C]methylation of the phenol precursor 12 with [¹¹C]CH₃I. In vitro autoradiography with [¹¹C]5i showed heterogeneous radioactive accumulation in the brain tissue sections, ranked in the order: cortex > striatum > hippocampus > cerebellum ≫ thalamus > pons. PET study of [¹¹C]5i indicated in vivo specific binding of mGlu₂ in the rat brain. Based on the [¹¹C]5i scaffold, further optimization for new candidates is underway to identify a more suitable ligand for imaging mGlu₂.

Synthesis and preliminary studies of 11C-labeled tetrahydro-1,7-naphthyridine-2-carboxamides for PET imaging of metabotropic glutamate receptor 2

Selective modulation of metabotropic glutamate receptor 2 (mGlu2) represents a novel therapeutic approach for treating brain disorders, including schizophrenia, depression, Parkinson's disease (PD), Alzheimer's disease (AD), drug abuse and addiction. Imaging mGlu2 using positron emission tomography (PET) would allow for in vivo quantification under physiological and pathological conditions and facilitate drug discovery by enabling target engagement studies. In this paper, we aimed to develop a novel specific radioligand derived from negative allosteric modulators (NAMs) for PET imaging of mGlu2. Methods. A focused small molecule library of mGlu2 NAMs with tetrahydro naphthyridine scaffold was synthesized for pharmacology and physicochemical evaluation. GIRK dose-response assays and CNS panel binding selectivity assays were performed to study the affinity and selectivity of mGlu2 NAMs, among which compounds 14a and 14b were selected as PET ligand candidates. Autoradiography in SD rat brain sections was used to confirm the in vitro binding specificity and selectivity of [11C]14a and [11C]14b towards mGlu2. In vivo binding specificity was then studied by PET imaging. Whole body biodistribution study and radiometabolite analysis were conducted to demonstrate the pharmacokinetic properties of [11C]14b as most promising PET mGlu2 PET ligand. Results. mGlu2 NAMs 14a-14g were synthesized in 14%-20% yields in five steps. NAMs 14a and 14b were selected to be the most promising ligands due to their high affinity in GIRK dose-response assays. [11C]14a and [11C]14b displayed similar heterogeneous distribution by autoradiography, consistent with mGlu2 expression in the brain. While PET imaging study showed good brain permeability for both tracers, compound [11C]14b demonstrated superior binding specificity compared to [11C]14a. Further radiometabolite analysis of [11C]14b showed excellent stability in the brain. Conclusions. Compound 14b exhibited high affinity and excellent subtype selectivity, which was then evaluated by in vitro autoradiography and in vivo PET imaging study after labeling with carbon-11. Ligand [11C]14b, which we named [11C]MG2-1904, demonstrated high brain uptake and excellent in vitro/in vivo specific binding towards mGlu2 with high metabolic stability in the brain. As proof-of-concept, our preliminary work demonstrated a successful example of visualizing mGlu2in vivo derived from NAMs, which represents a promising chemotype for further development and optimization aimed for clinical translation.

Synthesis and preliminary evaluation of 4-hydroxy-6-(3-[11C]methoxyphenethyl)pyridazin-3(2H)-one, a 11C-labeled d-amino acid oxidase (DAAO) inhibitor for PET imaging

Selective DAAO inhibitors have demonstrated promising therapeutic effects in clinical studies, including clinically alleviating symptoms of schizophrenic patients and ameliorating cognitive function in Alzheimer's patients with early phase. Herein we report the synthesis and preliminary evaluation of a ¹¹C-labeled positron emission tomography ligand based on a DAAO inhibitor, DAO-1903 (8). ¹¹C-Isotopologue of 8 was prepared in high radiochemical yield with high radiochemical purity (>99%) and high molar activity (>37 GBq/µmol). In vitro autoradiography studies indicated that the ligand possessed high in vitro specific binding to DAAO, while in vivo dynamic PET studies demonstrated that [¹¹C]8 failed to cross the blood-brain barrier possibly due to moderate brain efflux mechanism. Further chemical scaffold optimization is necessary to overcome limited brain permeability and improve specific binding.

The molecular functions of RIT1 and its contribution to human disease

RIT1 is a member of the Ras family of GTPases that direct broad cellular physiological responses through tightly controlled signaling networks. The canonical Ras GTPases are well-defined regulators of the RAF/MEK/ERK pathway and mutations in these are pathogenic in cancer and a class of developmental disorders termed RASopathies. Emerging clinical evidences have now demonstrated a role for RIT1 in RASopathies, namely Noonan syndrome, and various cancers including lung adenocarcinoma and myeloid malignancies. While RIT1 has been mostly described in the context of neuronal differentiation and survival, the mechanisms underlying aberrant RIT1-mediated signaling remain elusive. Here, we will review efforts undertaken to characterize the biochemical and functional properties of the RIT1 GTPase at the molecular, cellular, and organismal level, as well as provide a phenotypic overview of different human conditions caused by RIT1 mutations. Deeper understanding of RIT1 biological function and insight to its pathogenic mechanisms are imperative to developing effective therapeutic interventions for patients with RIT1-mutant Noonan syndrome and cancer.

Turn-on chemiluminescence probes and dual-amplification of signal for detection of amyloid beta species in vivo

Turn-on fluorescence imaging is routinely studied; however, turn-on chemiluminescence has been rarely explored for in vivo imaging. Herein, we report the design and validation of chemiluminescence probe ADLumin-1 as a turn-on probe for amyloid beta (Aβ) species. Two-photon imaging indicates that ADLumin-1 can efficiently cross the blood-brain barrier and provides excellent contrast for Aβ plaques and cerebral amyloid angiopathy. In vivo brain imaging shows that the chemiluminescence signal of ADLumin-1 from 5-month-old transgenic 5xFAD mice is 1.80-fold higher than that from the age-matched wild-type mice. Moreover, we demonstrate that it is feasible to further dually-amplify signal via chemiluminescence resonance energy transfer (DAS-CRET) using two non-conjugated smart probes (ADLumin-1 and CRANAD-3) in solutions, brain homogenates, and in vivo whole brain imaging. Our results show that DAS-CRET can provide a 2.25-fold margin between 5-month-old 5xFAD mice and wild type mice. We believe that our strategy could be extended to other aggregating-prone proteins.

Genetic deletion of Urocortin 3 does not prevent functional maturation of beta cells

There is great interest in generating functionally mature beta cells from stem cells, as loss of functional beta cell mass contributes to the pathophysiology of diabetes. Identifying markers of beta cell maturity is therefore very helpful for distinguishing stem cells that have been successfully differentiated into fully mature beta cells from stem cells that did not. Urocortin 3 (UCN3) is a peptide hormone whose expression is associated with the acquisition of functional maturity in beta cells. The onset of its expression occurs after other beta cell maturity markers are already expressed and its loss marks the beginning of beta cell dedifferentiation. Its expression pattern is therefore tightly correlated with beta cell maturity. While this makes UCN3 an excellent marker of beta cell maturity, it is not established whether UCN3 is required for beta cell maturation. Here, we compared gene expression and function of beta cells from Ucn3-null mice relative to WT mice to determine whether beta cells are functionally mature in the absence of UCN3. Our results show that genetic deletion of Ucn3 does not cause a loss of beta cell maturity or an increase in beta cell dedifferentiation. Furthermore, virgin beta cells, first identified as insulin-expressing, UCN3-negative beta cells, can still be detected at the islet periphery in Ucn3-null mice. Beta cells from Ucn3-null mice also exhibit normal calcium response when exposed to high glucose. Collectively, these observations indicate that UCN3 is an excellent mature beta cell marker that is nevertheless not necessary for beta cell maturation.

Are long-term psychiatric patients causing more crisis consultations outside office hours in mental health care?

BACKGROUND

As well as an improvement in community services, the de-institutionalization of patients receiving long-term psychiatric care can lead to marginally staffed mental health services, more homelessness, rising admission rates and more people in prison cells. It is assumed that an imbalance between community and hospital care for chronic patients puts pressure on crisis services.

AIMS

In this study, the central question is whether patients receiving long-term psychiatric care in Amsterdam do indeed put pressure on the city's emergency mental health services. We compare the pressure exerted by this group with the pressure resulting from the use of these services by all registered patients.

METHODS

Data were taken from the client registration systems of three mental health organizations in Amsterdam in the period from 2000 to 2004. Inclusion criteria for long-term psychiatric patients were age above 19 years and uninterrupted receipt of mental health care for a minimum of two successive years.

RESULTS

Annually, 6%-8% of all non-long-term patients experienced a crisis outside office hours in the period under investigation; this was 4%-6% for long-term patients. The non-long-term patients accounted for 83% of crisis contacts outside office hours over the entire study period, with long-term patients accounting for 17%.

CONCLUSIONS

The assumption that crises are more prevalent in long-term patients in the community seems to be an example of stigmatization rather than an observation based on fact.

Prevalence and risk factors for recurrence of depression five years after short term psychodynamic therapy

BACKGROUND

Follow-up research concerning the efficacy of treatment for depression is scarce and varies widely in clinical and methodological terms. Aim was to conduct a five-year follow-up study of recurrence of depression after short supportive Psychodynamic Treatment (PDT) alone or in combination with pharmacotherapy.

METHODS

Patients who had been treated five years previously for major depressive disorder in a randomised control trial comparing short supportive PDT alone or in combination with pharmacotherapy, were traced. Patients who completed treatment were included. Recurrent episodes in the past five years were identified using CIDI. Severity of symptoms after five years was measured with the Hamilton Rating Scale for Depression and sub-scales Depression, Anxiety and Somatisation of the self-report Symptom Checklist 90.

RESULTS

52 (37%) patients of the original sample were localised. 42% had suffered from one or more recurrences during the follow-up period. There was no significant difference between the group who had received psychotherapy and the group who had received combined therapy during the acute phase. Young women and patients with more residual depressive symptoms and less somatic symptoms directly after treatment, were more at risk for recurrence.

LIMITATIONS

Relatively small study population. Furthermore it was not known if patients received other treatment during the follow-up period.

CONCLUSIONS

The long-term efficacy of PDT (with or without antidepressants) seemed to be comparable with other psychotherapies for depression. But the high recurrence rate urges us to shift the focus of depression treatment to improving long-term outcome and to the prevention of recurrence, in particular for young women and patients with residual symptoms of depression.

FlhA, a component of the flagellum assembly apparatus of Pseudomonas aeruginosa, plays a role in internalization by corneal epithelial cells

Pseudomonas aeruginosa invades various epithelial cell types in vitro and in vivo. The P. aeruginosa genome possesses a gene (flhA) which encodes a protein that is believed to be part of the export apparatus for flagellum assembly and which is homologous to invA of Salmonella spp. Because invA is required for invasion of Salmonella spp., a role for flhA in P. aeruginosa invasion was explored using cultured rabbit corneal epithelial cells. An flhA mutant of P. aeruginosa strain PAO1 was constructed and was shown to be nonmotile. Complementation with flhA in trans restored motility. Corneal cells were infected for 3 h with the wild type (PAO1), the flhA mutant, the flhA mutant complemented with flhA in trans, an flhA mutant containing the plasmid vector control, or an fliC mutant (nonmotile mutant control). Invasion was quantified by amikacin exclusion assays. Both the flhA and the fliC mutants invaded at a lower level than the wild-type strain did, suggesting that both fliC and flhA played roles in invasion. However, loss of motility was not sufficient to explain the reduced invasion by flhA mutants, since centrifugation of bacteria onto cells did not restore invasion to wild-type levels. Unexpectedly, the flhA mutant adhered significantly better to corneal epithelial cells than wild-type bacteria or the fliC mutant did. The percentage of adherent bacteria that invaded was reduced by approximately 80% for the flhA mutant and approximately 50% for the fliC mutant, showing that only part of the role of flhA in invasion involves fliC. Invasion was restored by complementing the flhA mutant with flhA in trans but not by the plasmid vector control. Intracellular survival assays, in which intracellular bacteria were enumerated after continued incubation in the presence of antibiotics, showed that although flhA and fliC mutants had a reduced capacity for epithelial cell entry, they were not defective in their ability to survive within those cells after entry. These results suggest that the flagellum assembly type III secretion system plays a role in P. aeruginosa invasion of epithelial cells. Since the flhA mutants were not defective in their ability to adhere to corneal epithelial cells, to retain viability at the cell surface, or to survive inside epithelial cells after entry, the role of flhA in invasion of epithelial cells is likely to occur during the process of bacterial internalization.

Ocular surface epithelia express mRNA for human beta defensin-2

Human skin, lung and trachea produce human beta defensin-2 (hBD-2), an inducible, transcriptionally regulated antibiotic peptide with activity against gram negative bacteria, which may explain the unusual resistance of these tissues to infection. Since an intact corneal epithelium is also highly resistant to infection, we examined whether human ocular surface epithelia might produce hBD-2. Conjunctival epithelial cells were obtained from a human cadaver eye, while corneal epithelial cells were obtained from both a cadaver eye and the eye of a living human patient. Using reverse transcription-polymerase chain reaction and custom primers for hBD-2, a 257 bp sequence was amplified from both human corneal and conjunctival epithelial cell cDNA, and the amino acid sequence of this DNA band was computer-matched with the known gene sequence of hBD-2 available through GenBank (Z71389). To determine whether bacterial by-products upregulate hBD-2 mRNA expression, we stimulated confluent SV 40-immortalized human corneal epithelial cells with bacterial culture supernatant prepared from either wild-type P. aeruginosa strain PAO1 or two different lipopolysaccharide (LPS) mutants of PAO1. Both of these mutants, strains AK1012 and PAO1 algC::tet, are deficient in phosphomannomutase activity which is required for the synthesis of both a complete polysaccharide core and the O side chain structures of the LPS molecule. Neither of these mutations affects the lipid A portion of LPS. Cells treated with P. aeruginosa wild-type PAO1 bacterial culture supernatant demonstrated strong upregulation of hBD-2 mRNA expression, whereas cells stimulated with culture supernatant produced by either of the LPS mutants showed little or no change in hBD-2 gene expression. LPS extracted from the bacterial culture supernatant was used to demonstrate that upregulation of hBD-2 is caused by LPS. Genistein blocked this upregulation suggesting that protein tyrosine kinase activity is involved. Thus, both human corneal and conjunctival epithelium express mRNA for hBD-2, and this expression is upregulated by bacterial LPS. Data obtained from LPS mutants suggest that lipid A, which is responsible for initiating a number of the pathophysiological manifestations induced by endotoxin in mammals, is not required. Stimulation of endogenous hBD-2 production via the active portion of LPS might have therapeutic potential.

Prospective study of toxigenic Clostridium difficile in children given amoxicillin/clavulanate for otitis media

OBJECTIVE

Evaluate antibiotic-associated diarrhea and toxigenic Clostridium difficile in stool specimens obtained from children before and after 10 days of amoxicillin/clavulanate for otitis media.

DESIGN

Children, 12 to 47 months of age, treated with amoxicillin/clavulanate for otitis media in an outpatient setting were enrolled. Stool specimens were obtained at enrollment, when diarrhea occurred and at the end of therapy. All stool specimens were tested for C. difficile toxins A and B by enzyme immunoassay.

RESULTS

Seventy-six children who had stool specimens collected at enrollment and after therapy were included in the analysis. None had C. difficile toxin in stool specimens at enrollment. Six (27%) of 22 children with diarrhea, and 4 (7%) of 54 children without diarrhea had C. difficile toxin present at completion of therapy (P = 0.03).

CONCLUSION

Toxigenic C. difficile was identified in 13% of children at the conclusion of amoxicillin/clavulanate therapy with a significantly higher frequency in children with diarrhea.

Outbreaks of astrovirus gastroenteritis in day care centers

OBJECTIVE

This study evaluated astrovirus as a cause of diarrhea outbreaks among infants and toddlers in day care centers.

DESIGN

Stool specimens were collected weekly during four periods (from January 1986 through December 1991) from children 6 to 30 months of age who were enrolled in prospective studies of diarrhea in day care centers. All diarrheal stool specimens were tested for bacterial enteropathogens, rotavirus, enteric adenovirus, and Giardia lamblia. A total of 1365 stool specimens from 70 outbreaks in which no etiologic agent was identified and from another 11 outbreaks with a known cause were tested for astrovirus, by means of a monoclonal antibody-based enzyme immunoassay. Confirmatory testing was performed by reverse transcriptase-polymerase chain reaction with primers designed to produce an 89 base-pair product.

RESULTS

Astrovirus was detected in 6 (7%) of the 81 outbreaks. Of 217 children tested, 73 (34%) were infected with astrovirus; infections in 35 (48%) were symptomatic and in 38 (52%) asymptomatic. The six outbreaks lasted 11 to 44 days (median 22 days). Astrovirus excretion was detected for a duration of 2 to 30 days, with excretion occurring from 1 to 8 days (median 2 days) before diarrhea began to 1 to 20 days (median 2 days) after diarrhea ceased. Younger children (< or = 12 months) were at greater risk than older children (p = 0.011) of becoming infected with astrovirus during an outbreak and were more likely (p = 0.015) to have symptoms when infected. Of 24 specimens with astrovirus by enzyme immunoassay, 20 (83%) were confirmed to have the virus by reverse transcriptase-polymerase chain reaction.

CONCLUSION

Astrovirus was an important cause of outbreaks of diarrhea among children attending day care centers, more frequently infected younger children, and often produced asymptomatic infections.

Evaluation of the molecular epidemiology of an outbreak of multiply resistant Shigella sonnei in a day-care center by using pulsed-field gel electrophoresis and plasmid DNA analysis

Outbreaks of diarrhea in child day-care centers (DCC) are common. This study was undertaken to evaluate the molecular epidemiology of an outbreak of diarrhea due to Shigella sonnei. This outbreak involved 25 of 52 (48%) DCC children and 14 of 132 (11%) teachers and household contacts. S. sonnei isolates from nine children and five contacts were characterized by antimicrobial susceptibility, plasmid content, plasmid DNA restriction fragment pattern, and pulsed-field gel electrophoresis (PFGE) of total genomic DNA; 33 isolates from Houston, Tex., Chicago, Ill., and Mexico City, Mexico, also were studied. All outbreak isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole and shared five to six plasmids ranging from 3.3 to 70 MDa. A total of 8 of 12 temporally associated nonoutbreak Houston isolates had plasmid profiles and restriction fragment patterns similar to those of the outbreak strain, despite possessing different antibiotic susceptibility patterns. PFGE demonstrated identical DNA patterns among outbreak isolates and similar or identical patterns among temporally associated sporadic Houston isolates with plasmid profiles similar to that of the outbreak strain. All other nonoutbreak strains from Houston, Chicago, and Mexico had plasmid profiles, restriction fragment patterns, and PFGE patterns different from those of the outbreak strain. DCC outbreak isolates could be distinguished from most sporadic isolates by antimicrobial susceptibility testing, but plasmid analysis and PFGE could not differentiate common-source isolates from sporadic isolates in the same location during the same time period, indicating that isolates present in the community were genetically similar to those producing outbreaks in the DCC.

Diarrhea associated with Aeromonas species in children in day care centers

Outbreaks of diarrhea caused by enteropathogens have been reported in day care centers (DCC), but Aeromonas species have not been implicated. This study evaluated 381 children involved in 51 outbreaks in four DCC to determine the association of Aeromonas species with diarrhea and to characterize the isolates. The organism was identified in two outbreaks of diarrhea. In one, Aeromonas species were isolated from 6 (24%) of 25 children and in the other from 5 (21%) of 24 children. Seven other Aeromonas strains from children in DCC were studied. Fourteen (78%) of 18 were Aeromonas caviae and 15 were from children with diarrhea. Of the isolates, 75% did not have plasmids detected; all others had unique plasmid patterns. All strains had different DNA content. Twenty-two control isolates of Aeromonas from children with diarrhea in Mexico and Dallas had different chromosomal DNA patterns. Most Aeromonas infections were associated with symptoms. Chromosomal DNA patterns differentiated Aeromonas strains better than did plasmid DNA patterns. The outbreaks of diarrhea were unusual in that several different Aeromonas genospecies were involved in each outbreak.

Intermediate resistance of Streptococcus pneumoniae to penicillin in children in day-care centers

This study was performed to determine the prevalence, serotypes and antibiotic susceptibility patterns of penicillin-resistant Streptococcus pneumoniae in children younger than 3 years of age in day-care centers in Houston, TX. Nasopharyngeal cultures were obtained on two occasions, in March and May, 1989, from 140 children in 4 day-care centers. All penicillin-resistant S. pneumoniae organisms isolated in this study had minimum inhibitory concentrations to penicillin of between 0.1 and 0.5 microgram/ml and were thus intermediately resistant. No highly resistant S. pneumoniae (minimum inhibitory concentration > or = 1.0 microgram/ml) was isolated in this study. Nasal carriage of S. pneumoniae occurred in 39% of children; carriage of intermediately resistant S. pneumoniae occurred in 4% of children. Of the 39% of children who carried S. pneumoniae, 11% carried intermediately resistant strains. In one day-care center with a prior history of intermediately resistant S. pneumoniae (Center 1), the prevalence of intermediate penicillin resistance was significantly (P = 0.047) higher than in the other three centers. Among children surveyed twice 15% of Center 1 children carried an intermediately penicillin-resistant strain at least once, whereas in the other centers 3% of children carried an intermediately resistant strain at least once. Sixty-two percent of intermediately penicillin-resistant strains were resistant to multiple antibiotics and all were serotype 14. Intermediately penicillin-resistant S. pneumoniae isolates were prevalent among young children in day-care centers in Houston and may persist in some day-care centers and become endemic.

Detection of rotaviruses in the day care environment by reverse transcriptase polymerase chain reaction

Group A rotavirus is an important cause of morbidity among infants and toddlers in day care centers. Transmission by the fecal-oral route is well established, but fomites and environmental surfaces may also play an important role in transmission. A highly sensitive polymerase chain reaction (PCR) assay was used to detect rotavirus RNA in day care environments. Areas sampled included floors, diaper change areas, toy balls, and other surfaces. In two centers undergoing outbreaks of rotavirus, 7 (39%) of 18 toy balls had detectable rotavirus as did 8 (21%) of 39 swabs from environmental surfaces. By comparison, only 1 (5%) of 21 toy balls and 1 (2%) of 44 environmental surface swabs had detectable rotavirus in centers without rotavirus outbreaks (P = .0001). Thus, rotaviruses are highly prevalent in day care centers during outbreaks of diarrhea. The monitoring of environments by sensitive nucleic acid amplification techniques may lead to strategies for the diminution of disease transmission within the day care environment.

Outbreaks of human enteric adenovirus types 40 and 41 in Houston day care centers

OBJECTIVE

Human enteric adenovirus (EAd) types 40 and 41 cause diarrhea in young children, but little is known about their association with outbreaks of diarrhea in the child care setting. This study evaluated EAd as a cause of outbreaks of diarrhea among infants and toddlers in day care centers.

DESIGN

Stool specimens were collected weekly regardless of symptoms during four periods from January 1986 to April 1991, from children 6 to 24 months of age enrolled in prospective studies of diarrhea in day care centers. All diarrhea stool specimens were tested for bacterial enteropathogens, rotavirus, and Giardia lamblia. A total of 131 outbreaks occurred during the study. No etiologic agent was identified in 77 outbreaks. Stool specimens from 75 of these 77 outbreaks and from another 21 outbreaks of diarrhea with a known cause were evaluated for EAd with a monoclonal antibody-based enzyme immunoassay.

RESULTS

A total of 4402 stool specimens from 613 children from these 96 outbreaks was tested for EAd. The virus was detected in specimens collected during 10 outbreaks, 3 of which occurred in 1986, 3 in 1988, 1 in 1989, 1 in 1990, and 2 in 1991. Of 249 children, 94 (38%) in these 10 EAd outbreaks were infected with EAd. In 51 children (54%) the infection was symptomatic and in 43 (46%) it was asymptomatic. Outbreaks lasted 7 to 44 days (mean 24.5 days). Duration of EAd excretion ranged from 1 to 14 days (mean 3.9 days), with excretion occurring from 7 days (mean 2.6) before diarrhea began to 11 days (mean 5.3 days) after diarrhea stopped.

CONCLUSION

Enteric adenovirus types 40 and 41 are an important cause of outbreaks of diarrhea among children attending day care centers, often involve children in more than one room, and frequently produce asymptomatic infection.

Comparative inactivation of isepamicin, amikacin, and gentamicin by nine beta-lactams and two beta-lactamase inhibitors, cilastatin and heparin

This study was undertaken to compare the susceptibility to inactivation of isepamicin with amikacin and gentamicin when exposed to different beta-lactams, beta-lactamase inhibitors, and heparin. The aminoglycosides (5, 10, 20, and 50 micrograms/ml) were incubated in human serum with ampicillin, azlocillin, aztreonam, carbenicillin, ceftazidime, piperacillin, and ticarcillin (100 and 600 micrograms/ml) and with clavulanate, cilastatin, 1:1 imipenemcilastatin, oxacillin, and sulbactam (20 and 120 micrograms/ml) for 48 h at 37 degrees C. Aminoglycoside concentrations were measured by fluorescence polarization immunoassay (FPI) after 0, 8, and 48 h of incubation and by radial diffusion bioassay after 48 h of incubation. Each of the three aminoglycosides was also added to whole blood containing either heparin (100 U/ml) or 0.5% EDTA as a control and assayed after 6 h by FPI. The degree of inactivation of isepamicin by the beta-lactams was significantly less than that by amikacin (P less than 0.003) and gentamicin (P less than 0.0002) when determined by bioassay. Piperacillin, carbenicillin, and azlocillin produced the greatest amount of inactivation, and cilastatin and oxacillin produced the least. A similar pattern was observed when the degree of inactivation was measured by FPI. A significant difference in the degree of inactivation was noted between isepamicin and gentamicin (P less than 0.003 at 8 h and P less than 0.006 at 48 h) but not between isepamicin and amikacin (P greater than 0.7 at 8 h and P greater than 0.08 at 48 h). Aminoglycoside determinations by FPI were not influenced by the presence of heparin. In summary, isepamicin was found to be at least as stable as amikacin against inactivation by beta-lactam compounds and beta-lactamase inhibitors. Heparin (100 U/ml) did not influence aminoglycoside determinations by FPI.

The effect of diaper type and overclothing on fecal contamination in day-care centers

Fecal coliform contamination of environmental surfaces and hands in the day-care center is common. This study evaluated the effect of two diaper types on fecal contamination. Ten rooms in four day-care centers containing 141 children were studied in a prospective, randomized, crossover study. A total of 2946 samples were cultured during the 9-week study. Fecal coliforms were isolated from 307 inanimate objects (15%), 73 toy balls (46%), and 131 hands (17%). The number of contaminated inanimate objects was significantly less in rooms where paper diapers were worn when compared with that in rooms where double cloth diapers with plastic overpants were worn and in rooms where clothes were worn over diapers. Inanimate object cultures had more contamination in rooms in which diarrhea had occurred. Containment of feces by overclothes and diaper type may be important in decreasing transmission of enteric pathogens in day-care environments.

Environmental contamination in child day-care centers

Enteropathogens associated with outbreaks of diarrhea in day-care centers are spread by the fecal-oral route through contaminated hands or environmental objects. This prospective study was undertaken to determine the prevalence of fecal coliform contamination in day care. Ten rooms in six centers housing 121 children less than 2 years of age were studied for 13 weeks (February to May 1988). Inanimate objects (n = 1,275), toy balls (n = 724), and hands (n = 954) were cultured 1-3 times per week. Fecal coliform contamination was common and was greater (p less than 0.05) for objects, toy balls, and hands of children in toddler compared with infant rooms. In five rooms in which clothes were worn over diapers, there was a significantly lower prevalence of fecal coliform contamination of toy balls (p less than 0.005), inanimate objects (p less than 0.05), and hands (p less than 0.001) when compared with rooms in which overclothes were not worn. Occurrence of diarrhea was significantly associated with increased contamination of hands (p = 0.001). Stool and environmental isolates from individual rooms had the same plasmid patterns, which were unique to each center. In summary, fecal coliform contamination of environmental objects and hands of children and caregivers in day-care centers is common; toy balls can serve as sentinels of contamination; fecal coliform contamination can be significantly decreased by use of overclothes; and Escherichia coli strains from stool showed the same plasmid patterns.

Human milk secretory immunoglobulin A to Shigella virulence plasmid-coded antigens

Although antibodies to the lipopolysaccharide antigens of Shigella have been demonstrated in human milk, such antibodies do not explain the putative protective effect of breast-feeding against symptomatic Shigella infection. Shigella species do not share related lipopolysaccharides, but they do possess closely related virulence plasmids that code for the proteins essential for cell invasion. We therefore sought to determine the frequency, amount, and duration of excretion of human milk antibodies to these shared virulence plasmid-associated antigens in populations of different rates of Shigella infection frequency (Mexico City, high; Houston, low). Such antibodies were present in the milk of virtually all the Mexican women but also were present in a large proportion of milk samples from the women living in Houston. The amounts of these antibodies were highest in colostrum but after 2 weeks of lactation fell to stable levels. The frequency and persistence of these antibodies in the milk of the women from Houston suggest that the memory and drive for secretion of these antibodies is extremely long lived.

Invasive disease due to multiply resistant Streptococcus pneumoniae in a Houston, Tex, day-care center

Two toddlers who attended the same day-care center were hospitalized hours apart with sepsis and meningitis due to a multiply resistant Streptococcus pneumoniae. We determined the prevalence of multiply resistant S pneumoniae respiratory carriage and disease in infants, toddlers, and staff in the day-care center and in household contacts. The nasopharynges of 82 (96%) of 85 day-care center children, 26 (90%) of 29 day-care center staff, and 28 (90%) of 31 family members were cultured. Streptococcus pneumoniae grew from 29 (35%) of the 82 cultured day-care center children. Ten (34%) of the S pneumoniae isolates were resistant to sulfamethoxazole-trimethoprim, oxacillin, and tetracycline and were relatively resistant to penicillin (minimum inhibitory concentration, 0.5 mg/L). All were serotype 14 and had the same antibiotic resistance pattern. Treatment of 97% of the day-care center children and staff with rifampin (10 mg/kg twice daily for 2 days) resulted in 70% reduction in positive nasopharyngeal cultures for S pneumoniae. No additional disease due to multiply resistant S pneumoniae was identified in the day-care center during a 9-month follow-up period. This report documents that an outbreak of multiply resistant invasive S pneumoniae occurred in a day-care center setting; that nasopharyngeal colonization of exposed children was common; and that rifampin treatment of 2 days only partially eradicated the organism from colonized individuals.

Longitudinal study of Giardia lamblia infection in a day care center population

An enzyme-linked immunosorbent assay was used to detect Giardia lamblia in stool specimens collected during a 15-month longitudinal study of diarrhea in 82 children 1 to 24 months old attending a day care center (DCC) in Houston. A total of 2727 stool specimens were collected on a weekly basis from the DCC children and were evaluated for rotavirus and Giardia. For DCC children who developed diarrhea stool specimens were also cultured for bacterial enteropathogens. During the 15-month study period, 48 episodes of Giardia infection were detected in 27 of 82 (33%) DCC children, compared with 57 episodes of rotavirus detected in 37 (45%) of these same DCC children. The duration of Giardia excretion was 2.0 +/- 1.5 weeks (mean +/- SD). Only 6 (7%) of the 82 DCC children, or 6 of the 27 (22%) with infection, developed symptoms attributable to Giardia. Ten of the 27 (37%) DCC children infected with Giardia had 2 or more episodes of infection. Giardia was identified in the DCC in all months except June. Two Giardia outbreaks occurred in 1 of the 6 DCC rooms under study. One outbreak was associated with overcrowding. Neither outbreak was associated with the introduction of a new Giardia-positive child into the involved room. In this study Giardia infection occurred commonly in the DCC throughout the year, was rarely associated with illness and was not associated with introduction of asymptomatic carriers into the DCC rooms.

Adipocyte precursor cells in obese and nonobese humans

Adipose precursors isolated from the stromal-vascular fraction of omental and subcutaneous adipose tissue, from defined hyperplastic obese and nonobese human adults were cultured in order to measure and compare replication rates. After multiplication to confluence these cells were also cultured in an enriched viscous suspension medium to optimize the expression of these cells to adipocytes, allowing an estimation of the number of cells having the ability to express an adipocyte phenotype. No difference in replication rate was seen between obese and nonobese donors or when adipocyte precursors from different depots were compared. When cells were allowed to develop fully in the enriched medium, approximately 6.5% of the original inoculated cell population exhibited an adipocyte morphology. Thus, these results suggest that environmental rather than genetic factors may be responsible for the hyperplasia seen in certain massively obese humans. Furthermore, the results indicate that fat-free cells found within the stromal-vascular fraction of adipose tissue have the ability to develop into adipocytes. However, it is suggested that the relatively low yield in obtaining fully differentiated fat cells under these conditions may be due to the heterogeneity of adipose related cells within the original stromal-vascular fraction from which these cultures were initially derived.