HCS-Neurons: identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening.

BACKGROUND: High-content screening (HCS) has become a powerful tool for drug discovery. However, the discovery of drugs targeting neurons is still hampered by the inability to accurately identify and quantify the phenotypic changes of multiple neurons in a single image (named multi-neuron image) of a high-content screen. Therefore, it is desirable to develop an automated image analysis method for analyzing multi-neuron images. RESULTS: We propose an automated analysis method with novel descriptors of neuromorphology features for analyzing HCS-based multi-neuron images, called HCS-neurons. To observe multiple phenotypic changes of neurons, we propose two kinds of descriptors which are neuron feature descriptor (NFD) of 13 neuromorphology features, e.g., neurite length, and generic feature descriptors (GFDs), e.g., Haralick texture. HCS-neurons can 1) automatically extract all quantitative phenotype features in both NFD and GFDs, 2) identify statistically significant phenotypic changes upon drug treatments using ANOVA and regression analysis, and 3) generate an accurate classifier to group neurons treated by different drug concentrations using support vector machine and an intelligent feature selection method. To evaluate HCS-neurons, we treated P19 neurons with nocodazole (a microtubule depolymerizing drug which has been shown to impair neurite development) at six concentrations ranging from 0 to 1000 ng/mL. The experimental results show that all the 13 features of NFD have statistically significant difference with respect to changes in various levels of nocodazole drug concentrations (NDC) and the phenotypic changes of neurites were consistent to the known effect of nocodazole in promoting neurite retraction. Three identified features, total neurite length, average neurite length, and average neurite area were able to achieve an independent test accuracy of 90.28% for the six-dosage classification problem. This NFD module and neuron image datasets are provided as a freely downloadable MatLab project at http://iclab.life.nctu.edu.tw/HCS-Neurons. CONCLUSIONS: Few automatic methods focus on analyzing multi-neuron images collected from HCS used in drug discovery. We provided an automatic HCS-based method for generating accurate classifiers to classify neurons based on their phenotypic changes upon drug treatments. The proposed HCS-neurons method is helpful in identifying and classifying chemical or biological molecules that alter the morphology of a group of neurons in HCS.

Can the neuropathic pain scale discriminate between non-neuropathic and neuropathic pain?

OBJECTIVES: 1) To determine if the neuropathic pain scale (NPS) can be used to classify chronic pain patients (CPPs) as having primarily neuropathic vs non-neuropathic pain, and furthermore; 2) to determine what, if any, cut-off score can be used to reliably make this determination. DESIGN: A total of 305 CPPs consecutive admissions to The Rosomoff Pain Center were administered the NPS and were assigned a diagnosis according to the physical examination and all available test results. CPPs with a diagnosis of chronic radiculopathy and spondylolysis/degenerative arthritis were segregated into two groups for the purposes of having a group representative of neuropathic pain (chronic radiculopathy) and non-neuropathic pain (spondylolysis/degenerative arthritis). Applying neuropathic pain criteria to each "of these two groups": a neuropathic pain "subtype" was identified within the chronic radiculopathy group; and, a non-neuropathic pain "subtype" was identified within the spondylolysis/degenerative arthritis group. This step was performed in order to assure that the CPPs selected for further analysis were truly representative of neuropathic and non-neuropathic pain. Discriminant function analysis was then employed to determine if NPS scoring could differentiate between these two "subtypes." Results from the discriminant function analysis model were utilized to derive an NPS cut-off score above which CPPs would be classified as having neuropathic pain. For the diagnoses of myofascial pain syndromes, spinal stenosis, epidural fibrosis, fibromyalgia, complex regional pain syndromes 1 and 2, and failed back surgery syndrome, a predicted NPS score was calculated and compared with the cut-off score. SETTING: Multidisciplinary pain facility. PATIENTS: Chronic pain patients. RESULTS: The NPS appeared to be able to separate CPPs into neuropathic pain vs non-neuropathic pain subtypes. The derived cut-off score from the model was 5.53. Myofascial pain syndrome and spinal stenosis had predictive scores lower than this cut-off score at 3.81 and 4.26, respectively. Epidural fibrosis, fibromyalgia, complex regional pain syndromes 1 and 2, and failed back surgery syndrome had predictive scores higher than the cut-off score at 6.15, 6.35, 6.87, 9.34, and 7.19, respectively. CONCLUSIONS: The NPS appears to be able to discriminate between neuropathic and non-neuropathic pain. A debate is currently raging as to whether diagnoses, such as fibromyalgia and complex regional pain syndrome 1, can be classified as neuropathic. Our NPS cut-off score results suggest that these diagnoses may have a neuropathic pain component. The reliability and validity of our NPS method will need to be tested further in other neuropathic pain models, such as diabetic peripheral neuropathic pain.

Does smoking status affect multidisciplinary pain facility treatment outcome?

OBJECTIVES: Smoking may be a major problem in chronic low back pain (LBP) patients. The goal of this study was to determine whether smoking status affected multidisciplinary pain facility treatment outcome. DESIGN: As part of a grant study, chronic LBP patients identified themselves as either current smokers (N = 81) or current nonsmokers (N = 140), and were compared by chi-square for employment status at 1, 6, 12, and 24 months after multidisciplinary pain facility treatment. Smokers who were unemployed at each time interval were then compared with employed smokers for a large number of assessment scales and clinical variables of interest by chi-square or Student's t-test. The significant independent variables from these analyses were then utilized in a logistic regression to determine predictors for smoker nonemployment. SETTING: Pain facility. RESULTS: Current smokers were less likely to be employed at each follow-up time point. Pain levels over the previous 24 hours predicted employment status for current smokers at 1-, 12-, and 24-month follow-up, while worker compensation status predicted employment status at 6 months. CONCLUSIONS: Current smoking status appears to be associated with poorer treatment outcome after multidisciplinary pain facility treatment. Return to work within smokers is predicted by pain and worker compensation status. Pain facilities should target current smokers with significant perceived pain for close treatment monitoring in an attempt to improve treatment outcome.

Convergent host-parasite codon usage between honeybee and bee associated viral genomes.

By correlating the codon usage in four insects (the honeybee, red flour beetle, mosquito and fruit fly) with six honeybee host specific viruses, we found that the codon usage patterns of the bee viruses were strongly related to that of the honeybee and only weakly related to the red flour beetle. The insects shared varying degrees of codon usage similarity which roughly follow the known phylogenetic relatedness. All of the codon usage similarity can be described by relatedness-by-descent except for the high codon usage similarity between the honeybee and honeybee associated viruses. This evidence for the convergent evolution of the honeybee viruses toward the codon usage of the honeybee suggests that small host specific viral genomes have the freedom to quickly optimize codon usage to successfully parasitize their preferred host. The codon usage co-evolution of the six host specific honeybee viruses towards the codon usage of the honeybee described in this paper is the first evidence for codon usage correlation between an insect host and a single stranded RNA virus.

Are alcoholism treatments effective? The Project MATCH data.

BACKGROUND: Project MATCH was the largest and most expensive alcoholism treatment trial ever conducted. The results were disappointing. There were essentially no patient-treatment matches, and three very different treatments produced nearly identical outcomes. These results were interpreted post hoc as evidence that all three treatments were quite effective. We re-analyzed the data in order to estimate effectiveness in relation to quantity of treatment. METHODS: This was a secondary analysis of data from a multisite clinical trial of alcohol dependent volunteers (N = 1726) who received outpatient psychosocial therapy. Analyses were confined to the primary outcome variables, percent days abstinent (PDA) and drinks per drinking day (DDD). Overall tests between treatment outcome and treatment quantity were conducted. Next, three specific groups were highlighted. One group consisted of those who dropped out immediately; the second were those who dropped out after receiving only one therapy session, and the third were those who attended 12 therapy sessions. RESULTS: Overall, a median of only 3% of the drinking outcome at follow-up could be attributed to treatment. However this effect appeared to be present at week one before most of the treatment had been delivered. The zero treatment dropout group showed great improvement, achieving a mean of 72 percent days abstinent at follow-up. Effect size estimates showed that two-thirds to three-fourths of the improvement in the full treatment group was duplicated in the zero treatment group. Outcomes for the one session treatment group were worse than for the zero treatment group, suggesting a patient self selection effect. Nearly all the improvement in all groups had occurred by week one. The full treatment group had improved in PDA by 62% at week one, and the additional 11 therapy sessions added only another 4% improvement. CONCLUSION: The results suggest that current psychosocial treatments for alcoholism are not particularly effective. Untreated alcoholics in clinical trials show significant improvement. Most of the improvement which is interpreted as treatment effect is not due to treatment. Part of the remainder appears to be due to selection effects.

RNA secondary structure prediction using conditional random fields model.

Non-coding RNAs (ncRNAs) have important biological functions in living cells dependent on their conserved secondary structures. Here, we focus on computational RNA secondary structure prediction by exploring primary sequences and complementary base pair interactions using the Conditional Random Fields (CRFs) model, which treats RNA prediction as a sequence labelling problem. Proposing suitable feature extraction from known RNA secondary structures, we developed a feature extraction based on natural RNA's loop and stem characteristics. Our CRFs models can predict the secondary structures of the test RNAs with optimal F-score prediction between 56.61 and 98.20% for different RNA families.

Prediction of the disulphide bonding state of cysteines in proteins using conditional random fields.

The formation of disulphide bonds between cysteines plays a major role in protein folding, structure, function and evolution. Many computational approaches have been used to predict the disulphide bonding state ofcysteines. In our work, we developed a novel method based on Conditional Random Fields (CRFs) to predict the disulphide bonding state from protein primary sequence, predicted secondary structures and predicted relative solvent accessibilities (all-state information). Our experiments obtain 84% accuracy, 88% precision and 94% recall, using all-state information. However, our results show essentially identical results when using protein sequence and predicted relative solvent accessibilities in the absence of secondary structure.

Synonymous codon usage bias dependent on local nucleotide context in the class Deinococci.

To study the evolution of mutation biased synonymous codon usage, we examined nucleotide co-occurrence patterns in the Deinococcus radiodurans, D. geothermalis, and Thermus thermophilus genomes for nucleotide replacement dependent on the surrounding nucleotide context. Nucleotides on the third codon site were found to be strongly correlated with nucleotide sites at most six nucleotides away in all three species, where abundance patterns were dependent on whether two nucleotides share the same purine(R)/pyrimidine(Y) status. In the class Deinococci adjacent third site nucleotides were strongly correlated, where NNR|NNR and NNY|NNY codon pairs were overabundant while NNR|NNY and NNY|NNR codon pairs were underabundant. By far the largest deviations in all three species occur for NN(YR)|(YR)NN codon pairs. In the Thermus species, the NNY|YNN and NNR|RNN codon pairs were overabundant versus the underabundant NNY|RNN and NNR|YNN codon pairs, whereas in the Deinococcus species the opposite over-/underabundance relationship held for adjacent (GC) bases. We also observed a weaker overabundance of NNR|NRN and NNY|NYN codon pairs versus the underabundant NNR|NYN and NNY|NRN codon pairs. The perfect purine/pyrimidine symmetry of each of these cases, plus the lack of significant deviations for nucleotide pairs on other length scales up to 20 codons apart demonstrates that a pervasive pattern of nucleotide replacement dependent on local nucleotide context, and not codon bias, has occurred in these species. This nucleotide replacement has led to modified synonymous codon usage within the class Deinococci that affects which codons are positioned at particular codon sites dependent on the local nucleotide context.

The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome.

Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine [A] or thyamine [T]) versus strong (guanine [G] or cytosine [C]) status, to nucleotides on the first codon site which are dependent on their purine (A/G) versus pyrimidine (C/T) status. In particular, for adjacent third and first site nucleotides, weak-pyrimidine and strong-purine nucleotide combinations occur much more frequently than the underabundant weak-purine and strong-pyrimidine nucleotide combinations. Since a similar effect is also found in the noncoding regions, but is present for all adjacent nucleotides, this coding effect is most likely due to a genome-wide context-dependent mutation error correcting mechanism in combination with selective constraints on adjacent first and second nucleotide pairs within codons. The position-dependent relationship of synonymous codon usage is evidence for a novel form of codon position bias which utilizes the redundancy in the genetic code to minimize the effect of nucleotide mutations within coding regions.

Variables associated with current smoking status in chronic pain patients.

OBJECTIVES: Smokers may report more pain and may be at greater risk for psychiatric comorbidity. Smoking may be a major problem in chronic pain patients (CPPs). The goal of this study was to determine if pain and psychiatric comorbidity are associated with smoking status in CPPs. DESIGN: As part of a return-to-work grant study CPPs who could potentially return to work identified themselves as either current smokers (N=81) or nonsmokers (N=140). These two groups were compared on a large number of demographic, function, pain, disability, behavior, and psychiatric diagnoses variables gathered at admission into the grant study. The incidence of smoking was tested with either the student's t-test or chi-square to detect differences in continuous and categorical variables, respectively. Logistic regression was utilized to determine the predictive variables for smoking status by inputting significant independent variables (P<0.01) from the prior analyses. SETTING: Pain facility. RESULTS: Five variables were found to explain 38.8% of the variance for smoking status. These were education; race (Caucasian); cups of coffee per day; a diagnosis of current alcohol abuse/dependence; and personality disorder. CONCLUSIONS: Smoking status in CPPs is associated with some variables that are similar for smoking in the general and psychiatric populations (education, race, alcoholism). However, a number of variables expected to be relevant (e.g., mood disorders) were not associated with smoking status in CPPs. These results may not be generalizable to all CPPs as they are derived from CPPs who are return-to-work candidates.

Relationships between functional capacity measures and baseline psychological measures in chronic pain patients.

The extent to which baseline psychological measures, pain, and compensation status are related to admission and posttreatment functional capacity and employment outcome was investigated. Four pass/fail functional capacity tests based on the DOT (Dictionary of Occupational Titles) classification system and previously shown to be predictive of treatment outcome in chronic pain patients were analyzed in relation to baseline measures of depression, state and trait anxiety, and perceived stress. Statistical tests of all measures with employment level at admission to treatment, 1 month follow-up and at long-term follow-up were also performed. The results showed that pain level and/or compensation status were the primary predictors of functional capacity and employment status at follow-up. Admission functional capacity measures were also predictors of employment outcome. Depression scores at admission predicted some admission functional capacity results, however, psychological scores were not as significantly related to discharge functional capacity tests. One functional capacity test, the crouching test, was an independent predictor of short- and long-term employment outcome. Trait anxiety was the only psychological factor that was independently predictive of long-term employment outcome. In conclusion, these results suggest that psychological variables are related to measures of functional capacity measured at admission. However, psychological measures at admission are not good predictors of later functional capacity measures. Functional capacity measures are important predictors of follow-up employment outcome, but return to work cannot be predicted without taking pain into account.

Does the conscious exaggeration scale detect deception within patients with chronic pain alleged to have secondary gain?

OBJECTIVES: The illness behavior questionnaire (IBQ) is a test battery developed by Pilowsky to detect what he has termed abnormal illness behavior, which includes malingering. The IBQ has been widely utilized in patients with chronic pain (PWCP). Clayer developed a 21-item scale out of the IBQ, which he termed the conscious exaggeration (CE) scale. He proposed that the CE scale could detect conscious deception, i.e., malingering. The purpose of the present study is to test the CE scale in PWCP alleged to have secondary gain and thereby at greater risk for poor pain treatment outcome. It was postulated that the CE scale should generate scores in these groups significantly different from a comparison group and should predict treatment outcome in the secondary gain groups. DESIGN: A total of 96 PWCP completed the CE scale at admission and after completion of a 1-month pain facility treatment regimen. Other relevant pain variables, such as pain, depression, and anxiety, were measured and the data collected at admission and treatment completion. Work status was determined at 1, 3, 6, 12, 18, 24, and 30 months posttreatment. PWCP secondary gain subgroups (Workers' Compensation patients, patients in litigation, patients having a lawyer) were compared to the comparison group (no secondary gain factors) for treatment CE scale change scores. In order to control for the effects of pain, an analysis of covariance with pain level statistically removed was performed on admission and discharge CE scores utilizing the above patient subgroups. Pearson product correlations were utilized to determine the relationships between CE scores and psychological variables. Stepwise regression analyses were utilized to predict return to work with the CE scale score as a potential predictor. SETTING: Pain facility. PATIENTS: PWCP treated for 1 month in a pain facility. RESULTS: Overall, the analyses did not support the main hypothesis. For example, CE scale scores did not predict return to work. There was a significant degree of correlation between the variables of pain, depression, anxiety, and CE scale scores. CONCLUSIONS: PWCP characterized by the alleged secondary gain variables of Workers' compensation status, litigation, and having a lawyer did not differentially respond to the CE scale versus the comparison group. The CE scale, therefore, does not appear to be a valid instrument for identifying exaggeration in PWCP.