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PubMed1984

Associations of subjective udder edema scores and descriptive trait codes for udder types.

Edema severity was scored by herd personnel in six North Carolina Holstein herds from 1 (none) to 5 (extremely severe). Cows (2612) were scored at calving and 1 and 2 wk postpartum. Total score was calculated as the sum of these three scores. Official Holstein-Friesian classification descriptive udder trait codes were available on a subset of the cows. All statistical analyses were within lactation and included adjustments for herd-year and age as well as classifier and stage of lactation where appropriate. Correlations between corresponding edema scores for first and second lactations were .18, .18, .19, and .20 for scores at calving, 1 wk, 2 wk, and for total score. Stepwise regression procedures showed that udder support codes were associated with a larger amount of variation of edema scores than for any other single mammary trait code. Fore and rear udder codes also were associated with significant variation of edema scores in some analyses. Prediction models showed edema was a significant predictor of subsequent udder support codes, although udder trait codes were not significant predictors of subsequent edema severity. It appeared that severe edema may be one of the causes of pendulous udders.

Animals↗
PubMed1991

A study of schizophrenic outpatients with the Defense Mechanism Test.

Intrapsychic defensive strategies are allegedly expressed on the Defense Mechanism Test through the presentation, at increasing tachistoscopic exposure times, of a picture in which a central figure is threatened by a peripheral person. Several types of perceptual alterations of the stimulus configuration are coded as defenses in the subjective reports. A number of test variables have already been shown to differentiate significantly between nonclinical controls and nonpsychotic psychiatric patients. In the present study, after a review of the pertinent percept-genetic literature, nonpsychotic patients (n = 57) were compared with a group of schizophrenic outpatients in the active phase (n = 21). As predicted, significantly more schizophrenics than controls were coded for projection and regression and for certain variants of these signs. Four subcodings of repression, three of isolation, the sign of reaction formation, and several variants of identification differentiated in the same direction. Reports in which the central figure was too old and changed from a correct to an incorrect sex attribution were highly characteristic of the schizophrenic sample. No defensive variable was significantly linked with nonpsychotic pathology. Two variants, one of regression and one of identification, allowed a correct diagnostic placement for all schizophrenics and for 82.4% of the nonpsychotic patients. The findings, besides being a further clinical validation of the Defense Mechanism Test, provide a preliminary distinction between high- and low-level defenses. It is suggested that they are congruent with an hierarchical model which implies inclusive nonreflexive relationships between classes of mental disorders.

Adult↗
PubMed1999

AIRE encodes a nuclear protein co-localizing with cytoskeletal filaments: altered sub-cellular distribution of mutants lacking the PHD zinc fingers.

The gene responsible for autoimmune polyendocrino-pathy candidiasis ectodermal dystrophy (APECED) recently has been positionally cloned to 21q22.3. This novel gene, AIRE, encodes for a predicted 57.7 kDa protein featuring two PHD-type zinc fingers shared by other proteins involved in chromatin-mediated tran-scriptional regulation. APECED is an autosomal recessive condition characterized by multiple polyendocrinopathies, and the typical triad of APECED symptoms includes hypoparathyroidism, primary adrenocortical failure and chronic mucocutaneous candidiasis. The aetiology of APECED is linked directly to mutations within the coding region of AIRE. These mutations are predicted to lead to truncated forms of the protein lacking at least one of the PHD zinc fingers. In this study, we have investigated the sub-cellular localization of AIRE expressed transiently in COS cells and fibroblasts. We found that AIRE has a dual nuclear and cytoplasmic localization. The wild-type protein is directed to speckled domains in the nucleus and also shows co-localization with cytoskeletal filaments. N-terminal AIRE fragments deleted for the PHD domain show altered nuclear localization, suggesting that the APECED mutations may elicit their primary effects in the nucleus.

Animals↗
PubMed1989

The role of stress on the language-independence and code-switching phenomena.

This investigation studies the extent to which stress affects the assumed functional separation of coordinate bilingual's linguistic organization. Spanish/English bilinguals were subjects in a GSR linguistic conditioning experiment using two intensities of buzzer sounds (stressful conditions) and two lists of words. One word for each list functioned as the conditioned stimulus. Generalization to semantically, phonemically, and unrelated words occurred in both languages and buzzer conditions. We found a differential impact of the buzzer on the functional separation of the languages, although not in the direction predicted. We concluded that stress produced code-switching, and hence, a primitivization of the subject's cognitive and linguistic functioning is assumed to have occurred. These findings are important in understanding the way stress affects the bilingual's languages at the linguistic and cognitive levels. They are also important in understanding the role of stress in language development and in the transfer of linguistic information.

Adolescent↗
PubMed1994

A family of defensin-like genes codes for diverse cysteine-rich peptides in mouse Paneth cells.

Cryptdins constitute a diverse population of defensins in Paneth cells of intestinal crypts. In mice, certain intestinal mRNAs, termed "CRSIC" and "CRS4C," are considered to be cryptdin-related sequences, because their prepro-coding sequences are 94% identical to those of cryptdin-1 mRNA; however, their predicted products, which are cationic, cysteine-rich peptides are not defensins (A. J. Ouellette and J. C. Lualdi, J. Biol. Chem. 265: 9831-9837, 1990). Here we describe several mouse small intestinal mRNAs and genes that code for CRS4C prepropeptides. The 10-kDa deduced CRS4C proteins consist of a prepro sequence, potential monobasic or dibasic peptide cleavage sites, a predicted 3.7-kDa peptide that contains 7 [C]-[X]-[Y] repeats, and a C(N/K)CNPK carboxyl-terminal consensus sequence. In situ hybridization experiments showed that CRS4C mRNAs are found in Paneth cells of adult small bowel. The CRS4C genes closely resemble cryptdin genes, having a two-exon structure with highly conserved transcription start sites, intron-exon junctions, and a single intron of approximately 550 bp. Like the cryptdin genes, exon 1 of CRS4C genes consists of 5' untranslated sequences (UTS) and the prepro-coding region, and exon 2 codes for the predicted mature peptide and 3' UTS. Despite the similarity of first exons in CRS4C and cryptdin genes, their introns exhibit very little homology, and their second exons code for unrelated peptides. Analysis of introns suggests that the ancestral cryptdin and CRS4C genes may have diverged from a common ancestor in the distant past and expanded only recently. We speculate that the cryptdin/CRS genes evolved so that prepro regions encoded by exon 1 were conserved to allow the varied peptides coded by exon 2 to be directed into Paneth cell secretory granules.

Amino Acid Sequence↗
PubMed2000

Solh, the mouse homologue of the Drosophila melanogaster small optic lobes gene: organization, chromosomal mapping, and localization of gene product to the olfactory bulb.

The Drosophila melanogaster small optic lobes gene (sol) is required for normal development of the neuropiles of the medulla and lobula complexes of the adult optic lobes. The predicted protein products of sol and its human homologue SOLH contain zinc-finger-like repeats, a calpain-like protease domain, and a C-terminal domain of unknown function. Long-distance PCR was used to amplify genomic DNA for Solh, the mouse homologue of sol, following the identification of mouse Solh expressed sequence tags. The nucleotide sequence of the Solh coding region (6.0 kb) was determined. The predicted Solh protein of 1095 amino acid residues shows 89% identity (93% similarity) to the human homologue. Solh was localized by in situ hybridization to band A3.3 on mouse Chromosome 17, in a region of maintained homology with human 16p13.3. Antipeptide antibodies were prepared and verified by demonstration of specific reactivity with recombinant human SOLH protein prepared by in vitro transcription/translation and expression in insect cells using the baculovirus system. The antibodies were used to show that the Solh protein localizes to the olfactory bulb in mouse and rat brain, suggesting that it could have an analogous role in development of sensory system neurons in Drosophila and in mammals.

Amino Acid Sequence↗
PubMed2000

Uncertainty in compartmental models for hazardous materials - a case study.

Performing uncertainty analysis on compartmental models is the main topic of this article. Elements of the methodology developed during a joint CEC/USNRC accident consequence code uncertainty analysis are introduced. The uncertainty is quantified using structured expert judgment. Experts are queried about physically observable quantities. Many code input parameters of the accident consequence codes are not physically observable but are used to predict observable quantities. Therefore, a probabilistic inversion technique was developed which 'transfers' the uncertainty from the physically observable quantities to the code input parameters. The probabilistic inversion technique is illustrated using the compartmental model of systemic retention of Sr in the human body. The article is concluded with a discussion on capturing uncertainty via compartmental models.

Hazardous Substances↗
PubMed2006

Predicting odorant quality perceptions from multidimensional scaling of olfactory bulb glomerular activity patterns.

Odorants and their perceptions differ along multiple dimensions, requiring that a critical examination of any putative neural code directly assess the multidimensional nature of the encoding process. Previous work has examined simple, systematic odorant differences that, regardless of coding strategy, would be expected to produce simple, systematic predictions in neural and behavioral responses. In the present study, an odorant identification confusion matrix task that extracts precise quality relationships across odorants was used to determine whether spatially specific glomerular activity patterns predict perceptual quality relationships for odorants that cannot easily be classified a priori along a single chemical dimension. Multidimensional scaling (MDS) analysis of odorant pattern similarity measures derived from the comparison of [14C]-2-deoxyglucose glomerular activity pattern data yielded a two-dimensional odorant activity space that was highly significantly predictive of similarly obtained odorant perceptual spaces, uniformly across animals. These results strongly support the relevance of global spatial patterns in the olfactory bulb to the encoding of odor quality.

Animals↗
PubMed2006

STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.

MOTIVATION: Alignment of RNA has a wide range of applications, for example in phylogeny inference, consensus structure prediction and homology searches. Yet aligning structural or non-coding RNAs (ncRNAs) correctly is notoriously difficult as these RNA sequences may evolve by compensatory mutations, which maintain base pairing but destroy sequence homology. Ideally, alignment programs would take RNA structure into account. The Sankoff algorithm for the simultaneous solution of RNA structure prediction and RNA sequence alignment was proposed 20 years ago but suffers from its exponential complexity. A number of programs implement lightweight versions of the Sankoff algorithm by restricting its application to a limited type of structure and/or only pairwise alignment. Thus, despite recent advances, the proper alignment of multiple structural RNA sequences remains a problem. RESULTS: Here we present StrAl, a heuristic method for alignment of ncRNA that reduces sequence-structure alignment to a two-dimensional problem similar to standard multiple sequence alignment. The scoring function takes into account sequence similarity as well as up- and downstream pairing probability. To test the robustness of the algorithm and the performance of the program, we scored alignments produced by StrAl against a large set of published reference alignments. The quality of alignments predicted by StrAl is far better than that obtained by standard sequence alignment programs, especially when sequence homologies drop below approximately 65%; nevertheless StrAl's runtime is comparable to that of ClustalW.

Algorithms↗
PubMed1994

Eye movement behaviour viewing colour-coded and monochrome avionic displays.

This paper reports on two experiments in which subjects' eye movement behaviour was monitored while they searched for target information in colour coded and monochrome horizontal situation indicator (HSI) displays. The first experiment required subjects to locate and report alphanumeric information associated with the active waypoint on the displayed flightpath. Initial fixations in the display were more accurately directed to the target information when it was redundantly colour coded compared with when it was coded by shape and relative positional codes. Fewer fixations and a shorter time were required to locate the colour coded target and verbally report the relevant information. The time advantage of colour coded displays compared with monochrome displays was greatest for visually cluttered displays. In the second study there was no advantage of a coloured display when the task was to count all the displayed waypoint symbols on the flight path. The lack of any benefit for colour coding was a result of waypoint symbols having strong positional predictability due to their relationship to the displayed flightpath in both the colour and monochrome displays. The implication from these results is that colour coded information confers an advantage over a spatial code for targets at unknown spatial location but less benefit when target location can be predicted by other visual cues.

Aerospace Medicine↗
PubMed2004

EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches.

EGPred is a Web-based server that combines ab initio methods and similarity searches to predict genes, particularly exon regions, with high accuracy. The EGPred program proceeds in the following steps: (1) an initial BLASTX search of genomic sequence against the RefSeq database is used to identify protein hits with an E-value <1; (2) a second BLASTX search of genomic sequence against the hits from the previous run with relaxed parameters (E-values <10) helps to retrieve all probable coding exon regions; (3) a BLASTN search of genomic sequence against the intron database is then used to detect probable intron regions; (4) the probable intron and exon regions are compared to filter/remove wrong exons; (5) the NNSPLICE program is then used to reassign splicing signal site positions in the remaining probable coding exons; and (6) finally ab initio predictions are combined with exons derived from the fifth step based on the relative strength of start/stop and splice signal sites as obtained from ab initio and similarity search. The combination method increases the exon level performance of five different ab initio programs by 4%-10% when evaluated on the HMR195 data set. Similar improvement is observed when ab initio programs are evaluated on the Burset/Guigo data set. Finally, EGPred is demonstrated on an approximately 95-Mbp fragment of human chromosome 13. The list of predicted genes from this analysis are available in the supplementary material. The EGPred program is computationally intensive due to multiple BLAST runs during each analysis. The EGPred server is available at http://www.imtech.res.in/raghava/egpred/.

Algorithms↗
PubMed1993

Dynamics of the hippocampal ensemble code for space.

Ensemble recordings of 73 to 148 rat hippocampal neurons were used to predict accurately the animals' movement through their environment, which confirms that the hippocampus transmits an ensemble code for location. In a novel space, the ensemble code was initially less robust but improved rapidly with exploration. During this period, the activity of many inhibitory cells was suppressed, which suggests that new spatial information creates conditions in the hippocampal circuitry that are conducive to the synaptic modification presumed to be involved in learning. Development of a new population code for a novel environment did not substantially alter the code for a familiar one, which suggests that the interference between the two spatial representations was very small. The parallel recording methods outlined here make possible the study of the dynamics of neuronal interactions during unique behavioral events.

Animals↗
PubMed1996

Using severity measures to predict the likelihood of death for pneumonia inpatients.

OBJECTIVE: To see whether predictions of patients, likelihood of dying in-hospital differed among severity methods. DESIGN: Retrospective cohort. PATIENTS: 18,016 persons 18 years of age and older managed medically for pneumonia; 1,732 (9.6%) in-hospital deaths. METHODS: Probability of death was calculated for each patient using logistic regression with age, age squared, sex, and each of five severity measures as the independent variables: 1) admission MedisGroups probability of death scores; 2) scores based on 17 admission physiologic variables; 3) Disease Staging's probability of mortality model; the Severity Score of Patient Management Categories (PMCs); 4) and the All Patient Refined Diagnosis-Related Groups (APR-DRGs). Patients were ranked by calculated probability of death; 5) rankings were compared across severity methods. Frequencies of 14 clinical findings considered poor prognostic indicators in pneumonia were examined for patients ranked differently by different methods. RESULTS: MedisGroups and the physiology score predicted a similar likelihood of death for 89.2% of patients. In contrast, the three code-based severity methods rated over 25% of patients differently by predicted likelihood of death when compared with the rankings of the two clinical data-based methods [MedisGroups and the physiology score]. MedisGroups and the physiology score demonstrated better clinical credibility than the three severity methods based on discharge abstract data. CONCLUSIONS: Some pairs of severity measures ranked over 25% of patients very differently by predicted probability of death. Results of outcomes studies may vary depending on which severity method is used for risk adjustment.

Adolescent↗
PubMed2004

Proportional odds ratio model for comparison of diagnostic tests in meta-analysis.

BACKGROUND: Consider a meta-analysis where a 'head-to-head' comparison of diagnostic tests for a disease of interest is intended. Assume there are two or more tests available for the disease, where each test has been studied in one or more papers. Some of the papers may have studied more than one test, hence the results are not independent. Also the collection of tests studied may change from one paper to the other, hence incomplete matched groups. METHODS: We propose a model, the proportional odds ratio (POR) model, which makes no assumptions about the shape of ORp, a baseline function capturing the way OR changes across papers. The POR model does not assume homogeneity of ORs, but merely specifies a relationship between the ORs of the two tests. One may expand the domain of the POR model to cover dependent studies, multiple outcomes, multiple thresholds, multi-category or continuous tests, and individual-level data. RESULTS: In the paper we demonstrate how to formulate the model for a few real examples, and how to use widely available or popular statistical software (like SAS, R or S-Plus, and Stata) to fit the models, and estimate the discrimination accuracy of tests. Furthermore, we provide code for converting ORs into other measures of test performance like predictive values, post-test probabilities, and likelihood ratios, under mild conditions. Also we provide code to convert numerical results into graphical ones, like forest plots, heterogeneous ROC curves, and post test probability difference graphs. CONCLUSIONS: The flexibility of POR model, coupled with ease with which it can be estimated in familiar software, suits the daily practice of meta-analysis and improves clinical decision-making.

Data Interpretation, Statistical↗
PubMed2005

Transcriptional analysis of the ylaABCD operon of Bacillus subtilis encoding a sigma factor of extracytoplasmic function family.

The ylaABCD operon of Bacillus subtilis contains four predicted ORFs in the order ylaA, ylaB, ylaC and ylaD, where ylaC is assumed to code for a sigma factor of the extracytoplasmic function (ECF) family. Predicted YlaD may function as the anti-YlaC factor as it has an oxidative stress sensing domain similar to that of the RsrA, which is the anti-sigma factor of SigR, an ECF sigma of Streptomyces coelicolor. Northern blot analysis of the ylaABCD operon revealed two transcriptional products resulting from a distal promoter upstream of ylaA and from an internal promoter located at the first codon of ylaC. Both transcription start sites were determine by primer extension and 5'-RACE PCR. The transcription from the distal promoter was initiated by over-expression of YlaC on a multi-copy plasmid and depended on YlaC. DNA sequences of the -35 and -10 regions were similar to those recognized by other ECF sigmas of B. subtilis. On the other hand the transcription from the internal promoter was induced by oxidative stress and depended on Spx, which is an oxidative stress responding factor interacting with the alpha subunit of RNA polymerase core enzyme. The latter transcription depended possibly on SigA. We could not detect translation of YlaC from this transcript. Experiments with ylaD-disruption or co-overexpression of ylaD with ylaC suggested that YlaD functions as the anti-YlaC factor. Although YlaD has an oxidative stress sensing domain, oxidative stress did not induce the whole ylaABCD operon.

Bacillus subtilis↗
PubMed1989

The c1 genes of P1 and P7.

The c1 genes of the heteroimmune phages P1 and P7 were sequenced and their products were compared. P7c1 expression was correlated with the translation in vitro of a protein whose predicted molecular weight (33,000 daltons) is indistinguishable from that of the P1c1 repressor. The c1 regions from both P1 and P7 were found to contain open reading frames capable of coding for a 283-amino acid protein whose predicted secondary structure lacks the helix-turn-helix motif commonly associated with repressor proteins. Two P1c1 amber mutations were localized to the 283-amino acid open reading frame. The P1c1 and P7c1 sequences were found to differ at only 18 positions, all but two of which alter the third position of the affected codon and do not alter the amino acid sequence of the protein. Plasmids expressing the c1 gene from either phage cause the repression of transcription from a cloned promoter situated upstream of P1c1.

Amino Acid Sequence↗
PubMed1994

Sequencing and characterization of the sdaC gene and identification of the sdaCB operon in Escherichia coli K12.

We describe here the regulatory and coding region, and DNA sequence, for a newly recognized gene, sdaC, which codes for a hydrophobic protein with several predicted membrane-spanning domains. sdaC and sdaB form a single operon, with 57 bp between the end of sdaC and the start of sdaB. Expression of the sdaCB operon is regulated mainly by catabolite repression, but is also slightly sensitive to regulation by leucine-responsive regulatory protein. Cells carrying sdaC on a multicopy plasmid have increased L-serine transport capacity, insensitive to threonine, suggesting that sdaC might code for a recently described highly specific serine transporter [Kayahara, T., Thelen, P., Ogawa, W., Inaba, K., Tsuda, M., Goldberg, E. B. & Tsuchiya, T. (1992) J. Bacteriol. 174, 7482-7485].

Amino Acid Sequence↗
PubMed2003

Ability of Medicaid claims data to identify incident cases of breast cancer in the Ohio Medicaid population.

BACKGROUND: The use of Medicaid data to study cancer-related outcomes would be highly desirable. However, the accuracy of Medicaid claims data in the identification of incident cases of breast cancer is unknown. OBJECTIVES: (1) To estimate the sensitivity of Medicaid claims data for case ascertainment of breast cancer, and (2) to determine the positive predictive value (PPV) of diagnostic and procedure codes retrieved from Medicaid claims, using the Ohio Cancer Incidence Surveillance System (OCISS) as the gold standard. METHODS: The study used the linked OCISS and Medicaid enrollment files, 1997-1998 (n = 1,648). The claims search yielded 2,635 incident cases, of which 1,132 were also identified through the OCISS-Medicaid files. Sensitivity and PPV of Medicaid data were calculated in subgroups of the population. RESULTS: The overall sensitivity was 68.7 percent, but varied greatly across the subgroups of the population. It was lower among women enrolled in Medicaid only for part of the study year than those enrolled in Medicaid for 12 months of the study year (56.7 percent and 78.0 percent respectively, p < 0.0001), and lower among those who are dual Medicare-Medicaid eligible compared to those not participating in the Medicare program (63.1 percent and 78.6 percent respectively, p < 0.0001). The overall PPV was 43.0 percent, increasing up to 86.6 percent in the presence of procedure codes indicating the presence of mastectomy and lumpectomy, in addition to that of breast cancer diagnosis. CONCLUSIONS: The sensitivity of Medicaid claims for case ascertainment of breast cancer is somewhat low, but improves considerably when accounting for women enrolled in Medicaid for the entire duration of the study year. The PPV is poor due to a high rate of false positives. The higher PPV obtained in the presence of procedure codes, in addition to diagnosis codes, will help researchers to correctly identify incident cases of breast cancer using Medicaid claims data.

Adult↗