The intracellular Ig fold: a robust protein scaffold for the engineering of molecular recognition

Protein scaffolds that support molecular recognition have multiple applications in biotechnology. Thus, protein frames with robust structural cores but adaptable surface loops are in continued demand. Recently, notable progress has been made in the characterization of Ig domains of intracellular origin--in particular, modular components of the titin myofilament. These Ig belong to the I(intermediate)-type, are remarkably stable, highly soluble and undemanding to produce in the cytoplasm of Escherichia coli. Using the Z1 domain from titin as representative, we show that the I-Ig fold tolerates the drastic diversification of its CD loop, constituting an effective peptide display system. We examine the stability of CD-loop-grafted Z1-peptide chimeras using differential scanning fluorimetry, Fourier transform infrared spectroscopy and nuclear magnetic resonance and demonstrate that the introduction of bioreactive affinity binders in this position does not compromise the structural integrity of the domain. Further, the binding efficiency of the exogenous peptide sequences in Z1 is analyzed using pull-down assays and isothermal titration calorimetry. We show that an internally grafted, affinity FLAG tag is functional within the context of the fold, interacting with the anti-FLAG M2 antibody in solution and in affinity gel. Together, these data reveal the potential of the intracellular Ig scaffold for targeted functionalization.

Accuracy of Recognition and Diagnosis of Comorbid Depression in the Nursing Home

A variety of research has documented high levels of depression among older adults in the health care setting. Additional research has shown that care providers in health care settings are not very effective at diagnosing comorbid depression.This is a troublesome finding since comorbid depression has been linked to a number of negative outcomes in older adults. Early results have indicated that comorbid depression may be associated with a number of unfavorable consequences ranging from impairments in physical functioning to increased mortality.The health care setting with arguably the highest rate of physical impairment is the nursing home and it is the nursing home where the effects of comorbid depression may be most costly. Therefore, the current analysis uses data from the Institutional Population Component of the NationalMedical Expenditure Survey (US Department of Health and Human Services, 1990) to explore rates of both recognized and unrecognized comorbid depression in the nursing home setting. Using a constructed proxy variable representative of the DSM-III-R diagnosis of depression, results indicate that approximately 8.1% of nursing home residents have an unrecognized potential comorbid depression.

Post-translational signal peptide cleavage controls differential epitope recognition in the QP-rich domain of recombinant Theileria parva PIM

The presence of the schizont stage of the obligate intracellular parasites Theileria parva or T. annulata in the cytoplasm of an infected leukocyte results in host cell transformation via a mechanism that has not yet been elucidated. Proteins, secreted by the schizont, or expressed on its surface, are of interest as they can interact with host cell molecules that regulate host cell proliferation and/or survival. The major schizont surface protein is the polymorphic immunodominant molecule, PIM, which contains a large glutamine- and proline-rich domain (QP-rd) that protrudes into the host cell cytoplasm. Analyzing QP-rd generated by in vitro transcription/translation, we found that the signal peptide was efficiently cleaved post-translationally upon addition of T cell lysate or canine pancreatic microsomes, whereas signal peptide cleavage of a control protein only occurred cotranslationally and in the presence of microsomal membranes. The QP-rd of PIM migrated anomalously in SDS-PAGE and removal of the 19 amino acids corresponding to the predicted signal peptide caused a decrease in apparent molecular mass of 24kDa. The molecule was analyzed using monoclonal antibodies that recognize a set of previously defined PIM epitopes. Depending on the presence or the absence of the signal peptide, two conformational states could be demonstrated that are differentially recognized, with N-terminal epitopes becoming readily accessible upon signal peptide removal, and C-terminal epitopes becoming masked. Similar observations were made when the QP-rd of PIM was expressed in bacteria. Our observations could also be of relevance to other schizont proteins. A recent analysis of the proteomes of T. parva and T. annulata revealed the presence of a large family of potentially secreted proteins, characterized by the presence of large stretches of amino acids that are also particularly rich in QP-residues.

Offline grammar-based recognition of handwritten sentences

This paper proposes a sequential coupling of a Hidden Markov Model (HMM) recognizer for offline handwritten English sentences with a probabilistic bottom-up chart parser using Stochastic Context-Free Grammars (SCFG) extracted from a text corpus. Based on extensive experiments, we conclude that syntax analysis helps to improve recognition rates significantly.

The rationale for a spine registry

In the discussion about the rationale for spine registries, two basic questions have to be answered. The first one deals with the value of orthopaedic registries per se, considering them as observational studies and comparing the evidence they generate with that of randomised controlled trials. The second question asks if the need for registries in spine surgery is similar to that in the arthroplasty sector. The widely held view that randomised controlled trials are the 'gold standard' for evaluation and that observational methods have little or no value ignores the limitations of randomised trials. They may prove unnecessary, inappropriate, impossible, or inadequate. In addition, the external validity and hence the ability to make generalisations about the results of randomised trials is often low. Therefore, the false conflict between those who advocate randomised trials in all situations and those who believe observational data provide sufficient evidence needs to be replaced with mutual recognition of their complementary roles. The fact that many surgical techniques or technologies were introduced into the field of spine surgery without randomised trials or prospective cohort comparisons makes obvious an even increased need for spine registries compared to joint arthroplasty. An essential methodological prerequisite for a registry is a common terminology for reporting results and a sophisticated technology that networks all participants so that one central data pool is created and accessed. Recognising this need, the Spine Society of Europe has researched and developed Spine Tango, the first European spine registry, which can be accessed under www.eurospine.org.

Application and comparison of classification algorithms for recognition of Alzheimer's disease in electrical brain activity (EEG)

The early detection of subjects with probable Alzheimer's disease (AD) is crucial for effective appliance of treatment strategies. Here we explored the ability of a multitude of linear and non-linear classification algorithms to discriminate between the electroencephalograms (EEGs) of patients with varying degree of AD and their age-matched control subjects. Absolute and relative spectral power, distribution of spectral power, and measures of spatial synchronization were calculated from recordings of resting eyes-closed continuous EEGs of 45 healthy controls, 116 patients with mild AD and 81 patients with moderate AD, recruited in two different centers (Stockholm, New York). The applied classification algorithms were: principal component linear discriminant analysis (PC LDA), partial least squares LDA (PLS LDA), principal component logistic regression (PC LR), partial least squares logistic regression (PLS LR), bagging, random forest, support vector machines (SVM) and feed-forward neural network. Based on 10-fold cross-validation runs it could be demonstrated that even tough modern computer-intensive classification algorithms such as random forests, SVM and neural networks show a slight superiority, more classical classification algorithms performed nearly equally well. Using random forests classification a considerable sensitivity of up to 85% and a specificity of 78%, respectively for the test of even only mild AD patients has been reached, whereas for the comparison of moderate AD vs. controls, using SVM and neural networks, values of 89% and 88% for sensitivity and specificity were achieved. Such a remarkable performance proves the value of these classification algorithms for clinical diagnostics.

False positive dipstick for urinary blood in childhood

BACKGROUND: In view of the obvious practical advantages, the most common test for hematuria is currently a reagent strip. METHODS: A standardized microscopic examination of the sediment was performed in 20 asymptomatic children referred for evaluation of chronic isolated microhematuria detected by means of a reagent strip. RESULTS: In 6 of the 20 children the microscopic examination failed to confirm the result of the dipstick test. CONCLUSIONS: Confirmation for the presence of hematuria by microscopy is the most important step in children with a positive dipstick for urinary blood.

The syndromology of anorectal malformations revisited: from patterns of associated malformations to the recognition of syndromes

ackground: Although the frequency of associated malformation is high, the incidence of inheritable syndromes is widely underestimated in children with anorectal malformation (ARM). Data sources: OMIM database, patient records and charts of the Department of Pediatric Surgery, Johannes Gutenberg-University, Mainz, Germany. Methods: We analyzed all associations, sequences and syndromes listed in the OMIM database that can be accompanied by ARM. A large cohort of children born with ARM was then retrospectively investigated as to the type of ARM, presence of additional malformations and possible categorization as a syndrome, sequence or association. For this process a syndrome finder was developed and employed. This simplistic tool allows for a rapid first check of possible syndromes before a more complex analysis is started using the OMIM database and consulting specialists. Results: Among 317 children with ARM, associated malformations were present in 77.7% of 127 children with high ARM, in 68.7% of 32 with intermediate ARM, and in 25.3% of 158 with a low type ARM. Three or more organ systems were involved in 29.1% children with high type ARM and 25% with intermediate ARM and 8.2% with a low type ARM. An association of the vertebral anal tracheo-esophageal renal (VATER) and vertebral anal cardiac tracheo-esophageal renal limb (VACTERL) type was found in a total of 35 patients. Before analysis, 11 syndromes and 35 associations which were not clear previously in this patient cohort were described. In other 17 patients, 14 syndromes and 3 associations were identified. Conclusions: The high number of only retrospectively identified syndromes suggests that a routine search is necessary in every patient with ARM and additional malformations.