Classification Using Generalized Partial Least Squares

The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in which to study various aspects of gene functions but they also present challenge of analyzing data with large number of covariates and few samples. As an integral part of machine learning, classification of samples into two or more categories is almost always of interest to scientists. In this paper, we address the question of classification in this setting by extending partial least squares (PLS), a popular dimension reduction tool in chemometrics, in the context of generalized linear regression based on a previous approach, Iteratively ReWeighted Partial Least Squares, i.e. IRWPLS (Marx, 1996). We compare our results with two-stage PLS (Nguyen and Rocke, 2002A; Nguyen and Rocke, 2002B) and other classifiers. We show that by phrasing the problem in a generalized linear model setting and by applying bias correction to the likelihood to avoid (quasi)separation, we often get lower classification error rates.

[HIV-associated thrombocytopenia]

Thrombocytopenia is a relatively frequent hematological complication of HIV (human immunodeficiency virus) infection. The incidence of thrombocytopenia in a cohort of 359 homo- or bisexual men with HIV infection was 3%, while it was 9% in a cohort of 321 HIV positive persons with a history of intravenous drug abuse. We followed 42 thrombocytopenic patients prospectively to study the clinical significance of thrombocytopenia in these patients. Thrombocytopenia was significantly more severe in intravenous drug abusers than in homo- or bisexual men: 52% of the drug abusers had thrombocyte counts below 10,000/mm3, compared with only 9% of the homo- or bisexual men. Symptoms of bleeding, almost always harmless skin or mucosal bleeding, were found in 45% of patients with a history of intravenous drug abuse and in 18% of the homo- or bisexual men. Life-threatening bleeding episodes did not occur during a median observation period of approximately one year. Prednisone was the most commonly used drug in symptomatic thrombocytopenia and had demonstrable effect only while being administered. After medication was stopped the thrombocyte counts usually fell to pretreatment values. Our findings suggest that therapy of HIV-associated thrombocytopenia should be reserved for severely symptomatic patients, particularly since this symptom of HIV infection rarely causes serious complications and we do not know the influence of drugs such as corticosteroids on the progression rate of HIV-infection.

Low extracellular (ECF) glucose affects the neurochemical profile in severe head-injured patients

Glucose (Gluc) is the main energy source for the brain. After severe head-injury energy demand is massively increased and supply is often decreased. In pilot microdialysis studies, many patients with severe head-injury had undetectable glucose concentrations, probably reflecting changes in metabolism and/or reduced supply. We therefore investigated whether patients with low ECF glucose (criterion: < 50 microM for > or = 5 hrs), LOWgluc, differ from patients with higher glucose levels (NORMALgluc) We also tested the interrelationships between other parameters such as lactate, glutamate, K+, brain O2 and CO2, ICP, CPP, and CBF in these two groups. We found that patients with low ECF glucose, LOWgluc, have significantly lower lactate concentrations than patients with "normal" glucose, NORMALgluc, levels do. Spearman correlations between glucose and most other parameters were similar in both patient groups. However, glutamate correlated positively with glucose, lactate, brain CO2 and negatively with brain O2 in the NORMALgluc patient group, whereas glutamate did not significantly correlate with any of these parameters in the LOWgluc group. There was also no correlation between outcome and the dialysate glucose. The results indicate that low ECF glucose is almost always present in severe head-injury. Moreover, the lack of correlation between low glucose and outcome, however, suggests that other energy substrates, such as lactate, are important after TBI.

Infiltrating Lobular Carcinoma of the Breast: Systemic Treatment

Invasive lobular carcinoma (ILC) is the second most common type of breast cancer after invasive ductal carcinoma (IDC). It is characterized by unique clinical, biological and molecular properties. ILC is almost always positive for the estrogen receptor and is typically of a lower grade compared with IDC. We have reviewed selected literature on preoperative (neoadjuvant) and adjuvant systemic therapy of breast cancer focusing on the differential therapy of ILC. Despite the importance of this type of breast cancer, information about its specific treatment is sparse, in particular with regard to adjuvant systemic chemotherapy. ILC has significantly lower rates of response to neoadjuvant chemotherapy compared with IDC; however, the low chemosensitivity seems not to result in a survival disadvantage. Adjuvant hormonal therapy studies do not distinguish between ILC and IDC. Thus, recommendations about endocrine therapies are made using the same criteria as for IDC.

Nervous system dysfunction in Henoch-Schonlein syndrome: systematic review of the literature

OBJECTIVE: CNS or peripheral nervous system dysfunction sometimes occurs in Henoch-Schönlein patients. METHODS: We review all Henoch-Schönlein cases published after 1969 with CNS dysfunction without severe hypertension and neuroimaging studies (n = 35), cranial or peripheral neuropathy (n = 15), both CNS and peripheral nervous system dysfunction without severe hypertension (n = 2) or nervous system dysfunction with severe hypertension (n = 2). Forty-four of the 54 patients were <20 years of age. RESULTS: In patients with CNS dysfunction without or with severe hypertension the following presentations were observed in decreasing order of frequency: altered level of consciousness, convulsions, focal neurological deficits, visual abnormalities and verbal disability. Imaging studies disclosed the following lesions: vascular lesions almost always involving two or more vessels, intracerebral haemorrhage, posterior subcortical oedema, diffuse brain oedema and thrombosis of the superior sagittal sinus. Following lesions were noted in the subjects with cranial or peripheral neuropathy without severe hypertension: peroneal neuropathy, peripheral facial palsy, Guillain-Barré syndrome, brachial plexopathy, posterior tibial nerve neuropathy, femoral neuropathy, ulnar neuropathy and mononeuritis multiplex. Persisting signs of either CNS (n = 9) or peripheral (n = 1) nervous system dysfunction were sometimes reported. CONCLUSIONS: In Henoch-Schönlein syndrome, signs of nervous system dysfunction are uncommon but clinically relevant. This review helps clinicians managing Henoch-Schönlein syndrome with nervous system dysfunction.

Vaccination of cystic fibrosis patients against Pseudomonas aeruginosa reduces the proportion of patients infected and delays time to infection

INTRODUCTION: Cystic fibrosis (CF) almost always leads to chronic airway infection with Pseudomonas aeruginosa. Despite advances in antibiotic therapy, after chronic infection rapid deterioration in lung function occurs, increasing morbidity and mortality. Prevention of infection by vaccination is desirable, but earlier trials produced disappointing results. The promising short term immunogenicity and safety of a new P. aeruginosa vaccine prompted us to evaluate its long term efficacy. We conducted a 10-year retrospective analysis of outcomes in a group of vaccinated patients. MATERIALS AND METHODS: In 1989-1990, 30 young children with CF, mean age 7 years, with no prior history of infection with P. aeruginosa, were vaccinated against P. aeruginosa with a polyvalent conjugate vaccine. We report the follow-up of 26 of these patients from 1989 to 2001. The patients were given yearly vaccine boosters. Comparisons were made with a CF patient control group matched for gender, age and, where possible, genetic mutation. Vaccinated patients and controls were attending a single CF clinic and received the same clinical management throughout the study period. Main outcomes were time to infection, proportion of patients infected, development of P. aeruginosa mucoid phenotype, lung function and body weight. RESULTS: The time to infection with P. aeruginosa was longer in the vaccination group than in the control group, and fewer vaccinated patients than controls became chronically infected (32% versus 72%; P < 0.001). The proportion of mucoid infections was higher in the control group (44%) than in the vaccinated group (25%). Patients >/=18 years of age at the end of the study had a lower mean forced expiratory volume at 1 s (FEV1) than did those 13-17 years of age, but this difference was small in the vaccinated group (73.6% versus 83.7%) compared with the controls (48.0% versus 78.7%). In the >/=18 year age category the mean FEV1% at 10 years was 73.6% (vaccinated) and 48.0% (controls) (P < 0.05). In the vaccinated group only 11 (44%) of 25 patients were underweight at the 10-year follow-up compared with 18 (72%) of 25 at the beginning of the study. In the control group 17 (68%) of 25 patients were underweight at 10-year follow-up compared with 16 (64%) of 25 at the beginning of the study. CONCLUSION: Regular vaccination of young CF patients for a period of 10 years with a polyvalent conjugate vaccine reduced the frequency of chronic infection with P. aeruginosa. This was associated with better preservation of lung function. Vaccinated patients gained more weight during the study period, a possible indication of an improved overall health status.

[The comatose child]

The child who presents with acute coma runs a high risk of cardiopulmonary insufficiency, direct brain injury or even cerebral herniation. The case-management of such child requires a coma-specific emergent evaluation, immediate treatment of any hypoxicischemic insults and of the underlying cause. The coma-specific examination includes performance of child-adapted Glasgow Coma Score, the evaluation of brain stem functions such as pupillary response to light, cough- and gag reflex, and determination of all vital signs including body temperature. Treatment of hypoxicischemic insults includes control of airways and ventilation in patient with coma defined as GCS <8; liberal treatment of impaired cardiovascular states with isotonic fluids such as 0.9% sodium chloride; and treatment of cerebral herniation with head elevation, mannitol, hypertonic sodium chlorid fluids, steroids and hyperventilation. Immediately treatable causes are hypoglycemia, meningitis/encephalitis, opioid overdose and status epilepticus. Exclusion of rapidly progressive intracranial lesions almost always requires referral to the tertiary centre with head CT-scan facilities. Finally, an extensive etiology search of the stable coma is performed by looking for disease or trauma of the brain, for metabolic causes, for intoxications and for cardiopulmonary problems.

Did John really promise Mary to leave?

This paper contrasts finite and non-finite complement constructions containing the matrix verb promise. Using data from the British National Corpus, I show that when no explicit mention is made of the promissee the non-finite form of complement is overwhelmingly preferred to its finite counterparts. The exact opposite is the case when the promissee is mentioned between the matrix verb and the complement clause. In addition, the promiser in the x promise y to infinitive construction is almost always pronominal. I suggest that these two facts, the dispreference for the to infinitive form of complement when the promissee is mentioned and the pronominal encoding of the promiser in such cases, are both related to the very rarity of this form of construction in English. Data is adduced showing that another rare construction, the so-called possessive -ing construction, also occurs with a disproportionate number of pronominal subjects. It is suggested that the preference for pronominal subjects in these constructions may be related to a wish to reduce the overall processing complexity of the predications in question.

Equine cytochrome P450 2B6--genomic identification, expression and functional characterization with ketamine

Ketamine is an anesthetic and analgesic regularly used in veterinary patients. As ketamine is almost always administered in combination with other drugs, interactions between ketamine and other drugs bear the risk of either adverse effects or diminished efficacy. Since cytochrome P450 enzymes (CYPs) play a pivotal role in the phase I metabolism of the majority of all marketed drugs, drug-drug interactions often occur at the active site of these enzymes. CYPs have been thoroughly examined in humans and laboratory animals, but little is known about equine CYPs. The characterization of equine CYPs is essential for a better understanding of drug metabolism in horses. We report annotation, cloning and heterologous expression of the equine CYP2B6 in V79 Chinese hamster fibroblasts. After computational annotation of all CYP2B genes, the coding sequence (CDS) of equine CYP2B6 was amplified by RT-PCR from horse liver total RNA and revealed an amino acid sequence identity of 77% and a similarity of 93.7% to its human ortholog. A non-synonymous variant c.226G>A in exon 2 of the equine CYP2B6 was detected in 97 horses. The mutant A-allele showed an allele frequency of 82%. Two further variants in exon 3 were detected in one and two horses of this group, respectively. Transfected V79 cells were incubated with racemic ketamine and norketamine as probe substrates to determine metabolic activity. The recombinant equine CYP2B6 N-demethylated ketamine to norketamine and produced metabolites of norketamine, such as hydroxylated norketamines and 5,6-dehydronorketamine. V(max) for S-/and R-norketamine formation was 0.49 and 0.45nmol/h/mg cellular protein and K(m) was 3.41 and 2.66μM, respectively. The N-demethylation of S-/R-ketamine was inhibited concentration-dependently with clopidogrel showing an IC(50) of 5.63 and 6.26μM, respectively. The functional importance of the recorded genetic variants remains to be explored. Equine CYP2B6 was determined to be a CYP enzyme involved in ketamine and norketamine metabolism, thus confirming results from inhibition studies with horse liver microsomes. Clopidogrel seems to be a feasible inhibitor for equine CYP2B6. The specificity still needs to be established with other single equine CYPs. Heterologous expression of single equine CYP enzymes opens new possibilities to substantially improve the understanding of drug metabolism and drug interactions in horses.

Detecting offsets in GPS time series: first results from the Detection of Offsets in GPS Experiment

The accuracy of Global Positioning System (GPS) time series is degraded by the presence of offsets. To assess the effectiveness of methods that detect and remove these offsets, we designed and managed the Detection of Offsets in GPS Experiment. We simulated time series that mimicked realistic GPS data consisting of a velocity component, offsets, white and flicker noises (1/f spectrum noises) composed in an additive model. The data set was made available to the GPS analysis community without revealing the offsets, and several groups conducted blind tests with a range of detection approaches. The results show that, at present, manual methods (where offsets are hand picked) almost always give better results than automated or semi‒automated methods (two automated methods give quite similar velocity bias as the best manual solutions). For instance, the fifth percentile range (5% to 95%) in velocity bias for automated approaches is equal to 4.2 mm/year (most commonly ±0.4 mm/yr from the truth), whereas it is equal to 1.8 mm/yr for the manual solutions (most commonly 0.2 mm/yr from the truth). The magnitude of offsets detectable by manual solutions is smaller than for automated solutions, with the smallest detectable offset for the best manual and automatic solutions equal to 5 mm and 8 mm, respectively. Assuming the simulated time series noise levels are representative of real GPS time series, robust geophysical interpretation of individual site velocities lower than 0.2–0.4 mm/yr is therefore certainly not robust, although a limit of nearer 1 mm/yr would be a more conservative choice. Further work to improve offset detection in GPS coordinates time series is required before we can routinely interpret sub‒mm/yr velocities for single GPS stations.

Adult-onset mastocytosis in the skin is highly suggestive of systemic mastocytosis

Adult-onset urticaria pigmentosa/mastocytosis in the skin almost always persists throughout life. The prevalence of systemic mastocytosis in such patients is not precisely known. Bone marrow biopsies from 59 patients with mastocytosis in the skin and all available skin biopsies (n=27) were subjected to a meticulous cytological, histological, immunohistochemical, and molecular analysis for the presence of WHO-defined diagnostic criteria for systemic mastocytosis: compact mast cell infiltrates (major criterion); atypical mast cell morphology, KIT D816V, abnormal expression of CD25 by mast cells, and serum tryptase levels >20 ng/ml (minor criteria). Systemic mastocytosis is diagnosed when the major diagnostic criterion plus one minor criterion or at least three minor criteria are fulfilled. Systemic mastocytosis was confirmed in 57 patients (97%) by the diagnosis of compact mast cell infiltrates plus at least one minor diagnostic criterion (n=42, 71%) or at least three minor diagnostic criteria (n=15, 25%). In two patients, only two minor diagnostic criteria were detectable, insufficient for the diagnosis of systemic mastocytosis. By the use of highly sensitive molecular methods, including the analysis of microdissected mast cells, KIT D816V was found in all 58 bone marrow biopsies investigated for it but only in 74% (20/27) of the skin biopsies. It is important to state that even in cases with insufficient diagnostic criteria for systemic mastocytosis, KIT D816V-positive mast cells were detected in the bone marrow. This study demonstrates, for the first time, that almost all patients with adult-onset mastocytosis in the skin, in fact, have systemic mastocytosis with cutaneous involvement.

Classifying and mapping the urban transition in Vietnam

The urban transition almost always involves wrenching social adjustment as small agricultural communities are forced to adjust rapidly to industrial ways of life. Large-scale in-migration of young people, usually from poor regions, creates enormous demand and expectations for community and social services. One immediate problem planners face in approaching this challenge is how to define, differentiate, and map what is rural, urban, and transitional (i.e., peri-urban). This project established an urban classification for Vietnam by using national census and remote sensing data to identify and map the smallest administrative units for which data are collected as rural, peri-urban, urban, or urban core. We used both natural and human factors in the quantitative model: income from agriculture, land under agriculture and forests, houses with modern sanitation, and the Normalized Difference Vegetation Index. Model results suggest that in 2006, 71% of Vietnam's 10,891 communes were rural, 18% peri-urban, 3% urban, and 4% urban core. Of the communes our model classified as peri-urban, 61% were classified by the Vietnamese government as rural. More than 7% of Vietnam's land area can be classified as peri-urban and approximately 13% of its population (more than 11 million people) lives in peri-urban areas. We identified and mapped three types of peri-urban places: communes in the periphery of large towns and cities; communes along highways; and communes associated with provincial administration or home to industrial, energy, or natural resources projects (e.g., mining). We validated this classification based on ground observations, analyses of multi-temporal night-time lights data, and an examination of road networks. The model provides a method for rapidly assessing the rural–urban nature of places to assist planners in identifying rural areas undergoing rapid change with accompanying needs for investments in building, sanitation, road infrastructure, and government institutions.

A Logical Descriptor for Regular Languages via Stone Duality

In this paper we introduce a class of descriptors for regular languages arising from an application of the Stone duality between finite Boolean algebras and finite sets. These descriptors, called classical fortresses, are object specified in classical propositional logic and capable to accept exactly regular languages. To prove this, we show that the languages accepted by classical fortresses and deterministic finite automata coincide. Classical fortresses, besides being propositional descriptors for regular languages, also turn out to be an efficient tool for providing alternative and intuitive proofs for the closure properties of regular languages.

Der allergische Notfall: Adrenalin das Mittel der Wahl bei der Anaphylaxie

Although allergic emergencies do not occur every day, they are as unpredictable as the course of the reaction, and require rapid treatment. Anaphylaxis is a life-threatening general reaction that usually manifests within a few minutes after a known or potential antigen contact. While sole cutaneous symptoms are not sufficient to diagnose anaphylaxis, an episode of acute bronchospasm or hypotension in rare cases may be the only symptom. Almost always two or more organ systems are affected and usually the skin and/or mucous membranes are involved. Epinephrine (adrenaline) is the most important and effective drug in the treatment of anaphylaxis. Since there is no absolute contraindication, epinephrine should be administered intramuscularly at the first signs of anaphylaxis. However, there is a gap between the international treatment guidelines and the daily practice in the treatment of acute allergic, particularly anaphylactic, reactions. This is due not least to the fact that anaphylaxis, the most severe form of allergy, is not sufficiently clear or uniformly defined. After a systemic allergic reaction, all patients should be equipped with emergency medications, appropriately instructed obtain a complete allergy work-up.

Investigating the potential of reported cattle mortality data in Switzerland for syndromic surveillance

Systems for the identification and registration of cattle have gradually been receiving attention for use in syndromic surveillance, a relatively recent approach for the early detection of infectious disease outbreaks. Real or near real-time monitoring of deaths or stillbirths reported to these systems offer an opportunity to detect temporal or spatial clusters of increased mortality that could be caused by an infectious disease epidemic. In Switzerland, such data are recorded in the "Tierverkehrsdatenbank" (TVD). To investigate the potential of the Swiss TVD for syndromic surveillance, 3 years of data (2009-2011) were assessed in terms of data quality, including timeliness of reporting and completeness of geographic data. Two time-series consisting of reported on-farm deaths and stillbirths were retrospectively analysed to define and quantify the temporal patterns that result from non-health related factors. Geographic data were almost always present in the TVD data; often at different spatial scales. On-farm deaths were reported to the database by farmers in a timely fashion; stillbirths were less timely. Timeliness and geographic coverage are two important features of disease surveillance systems, highlighting the suitability of the TVD for use in a syndromic surveillance system. Both time series exhibited different temporal patterns that were associated with non-health related factors. To avoid false positive signals, these patterns need to be removed from the data or accounted for in some way before applying aberration detection algorithms in real-time. Evaluating mortality data reported to systems for the identification and registration of cattle is of value for comparing national data systems and as a first step towards a European-wide early detection system for emerging and re-emerging cattle diseases.