In the current study, momentary time sampling (MTS) and partial-interval recording (PIR) were compared to continuous-duration recording of stereotypy and to the frequency of self-injury during a treatment analysis to determine whether the recording method affected data interpretation. Five previously conducted treatment analysis data sets were analyzed by creating separate graphic displays for each measurement method (duration or frequency, MTS, and PIR). An expert panel interview and structured criterion visual inspection were used to evaluate treatment effects across measurement methods. Results showed that treatment analysis interpretations based on both discontinuous recording methods often matched those based on frequency or duration recording; however, interpretations based on MTS were slightly more likely to match those based on duration and those based on PIR were slightly more likely to match those based on frequency.
measurement; momentary time sampling; partial-interval recording
Paired immunoglobulin-like receptors of activating (PIR-A) and inhibitory (PIR-B) isoforms are expressed by many hematopoietic cells including B lymphocytes and myeloid cells. To determine the functional roles of PIR-A and PIR-B in primary bacterial infection, PIR-B-deficient (PIR-B-/-) and wild-type (WT) control mice were injected intravenously with an attenuated strain of Salmonella enterica Typhimurium (WB335). PIR-B-/- mice were found to be more susceptible to Salmonella infection than WT mice as evidenced by high mortality rate, high bacterial loads in the liver and spleen, and a failure to clear bacteria from the circulation. While blood levels of major cytokines and Salmonella-specific antibodies were mostly comparable in the two groups of mice, distinct patterns of inflammatory lesions were found in their livers at 7- to 14-d post-infection: diffuse spreading along the sinusoids in PIR-B-/- mice versus nodular restricted localization in WT mice. PIR-B-/- mice have more inflammatory cells in the liver but fewer B cells and CD8+ T cells in the spleen than WT mice at 14-d post-infection. PIR-B-/- bone marrow-derived macrophages (BMMφ) failed to control intracellular replication of Salmonella in vitro, in part due to inefficient phagosomal oxidant production, when compared with WT BMMφ. PIR-B-/- BMMφ also produced more nitrite and TNFα upon exposure to Salmonella than WT BMMφ. These findings suggest that the disruption of PIR-A and PIR-B balance affects their regulatory roles in host defense to bacterial infection.
This study examined the percentage time estimates of momentary time sampling against the real time obtained with handheld computers in a natural setting. Twenty-two concurrent observations were conducted in elementary schools by one observer who used 15-s momentary time sampling and a second who used a handheld computer. Results for the six behaviors showed a close correspondence between the momentary time sampling percentage observation intervals and the real time percentage observation time, although 15-s momentary time sampling tended not to sample low-frequency short-duration behaviors. The results confirmed laboratory findings that short-interval momentary time sampling estimates percentage time accurately for a wide range of behavior frequencies and durations, and suggested that observers using momentary time sampling in a natural setting are able to obtain accurate data.
time sample; methodology; naturalistic observations
Walking speed and activity are important measures of functional ability in the elderly. Our earlier studies have suggested that continuous monitoring may allow us to detect changes in walking speed that are also predictive of cognitive changes. We evaluated the use of passive infrared (PIR) sensors for measuring walking speed in the home on an ongoing basis. In comparisons with gait mat estimates (ground truth) and the results of a timed walk test (the clinical gold standard) in 18 subjects, we found that the clinical measure overestimated typical walking speed, and the PIR sensor estimations of walking speed were highly correlated to actual gait speed. Examination of in-home walking patterns from more than 100,000 walking speed samples for these subjects suggested that we can accurately assess walking speed in the home. We discuss the potential of this approach for continuous assessment.
A person manufactured his in-seat behavior for 15, 30-min sessions so that there were three blocks of five sessions where the behavior occurred 20%, 50%, and 80% of the time. Whole interval, partial interval, and momentary time-sample measures of the behavior were taken and compared to the continuous measure of the behavior i.e., per cent of time the behavior occurred. For interval time sampling, the difference between the continuous and sample measures i.e., measurement error, was: (1) extensive, (2) unidirectional, (3) a function of the time per response, and (4) inconsistent across changes in the continuous measure. A procedural analysis demonstrated that the frequency and duration of behavior are confounded in interval time sampling. Momentary time sampling was found to be superior to interval time sampling in estimating the duration a behavior occurs.
time sampling; partial interval; whole interval; momentary; measurement error
Fifty-one human glycosyltransferases were expressed in Saccharomyces cerevisiae as immobilized enzymes and were assayed for enzymatic activities. The stem and catalytic regions of sialyl-, fucosyl-, galactosyl-, N-acetylgalactosaminyl-, and N-acetylglucosaminyltransferases were fused with yeast cell wall Pir proteins, which anchor glycosyltransferases at the yeast cell wall glucan. More than 75% of expressed recombinant glycosyltransferases retained their enzymatic activities in the yeast cell wall fraction and will be used as a human glycosyltransferase library. In increasing the enzymatic activities of immobilized glycosyltransferases, several approaches were found to be effective. Additional expression of yeast protein disulfide isomerase increased the expression levels and activities of polypeptide N-acetylgalactosaminyltransferases and other glycosyltransferases. PIR3 and/or PIR4 was more effective than PIR1 as a cell wall anchor when the Pir-glycosyltransferase fusions were expressed under the control of the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter. Oligosaccharides such as Lewis x, Lewis y, and H antigen were successfully synthesized using this immobilized glycosyltransferase library, indicating that the Pir-fused glycosyltransferases are useful for the production of various human oligosaccharides.
This study investigates whether motion density maps based on passive infrared (PIR) motion sensors and the average time out and average density per hour measures of the density map are sensitive enough to detect changes in mental health over time.
Within the sensor network, data are logged from PIR motion sensors which capture motion events as people move around the home. If there is continuous motion, the sensor will generate events at 7 second intervals. If the resident is less active, events will be generated less frequently. A web application displays the data as activity density maps showing events per hour with hours on the vertical axis and progressive days on the horizontal axis. Color and intensity provide textural indications of time spent away from home and activity level. Texture features from the co-occurrence matrix are used to capture the periodicity pattern of the activity (including homogeneity, local variation, and entropy) and are combined with the average motion density per hour and the average time away from home. The similarity of two different density maps is represented by a number that is computed in feature space as the distance from one map to the other, or a measure of dis-similarity. Employing a retrospective approach, density maps were compared with health assessment information (Geriatric Depression Scale, Mini Mental State Exam, and Short Form Health Survey -12) to determine congruence between activity pattern changes and the health information20. A case by case study method, analyzed the density maps of 5 individuals with identified mental health issues. These density maps were reviewed along with the averages of time out of apartment per day per hour and average density per hour for hours at home and mental health assessment scores to determine if there were activity changes and if activity patterns reflected changes in mental health conditions.
Results & Discussion
The motion density maps show visual changes in the client’s activity, including circadian rhythm, time away from home, and general activity level (sedentary vs. puttering). The measures are sensitive enough, yielding averages of time out of apartment and average density per hour for hours at home that indicate significant change. There is evidence of congruence with health assessment scores. This pilot study demonstrates that density maps can be used as a tool for early illness detection. The results indicate that sensor technology has the potential to augment traditional health care assessments and care coordination.
passive sensors; early illness detection; technology and mental illness; motion density mapping
Continuous and time-sample measures of the in-seat behavior of a secretary were obtained. Measurement error, i.e., the extent to which the sample measures deviated from the continuous measure, was a function of the frequency of the sample measurements and the criterion used to score an example of the behavior. If the behavior had to be exhibited throughout the observational interval (whole-interval time sampling), there was a consistent underestimate of the continuous measure. If the behavior had to be exhibited only briefly within the observational interval (partial-interval time sampling), there was a consistent overestimate of the continuous measure. And, if the behavior had to be exhibited at the end of the observational interval (momentary time sampling), overestimations and underestimations of the continuous measure occurred about equally often. As expected, the more frequently the sample measures were made the closer was the agreement between the sample and continuous measures. Two conclusions concerning measurement error in interval time sampling were made. The first was that the error will be a function of the mean time per response. The second is that this error will not be consistent across experimental conditions.
time sampling; whole interval; partial interval; momentary; measurement error; continuous versus time-sample recording
Using sequential analysis, the authors examined how therapists' actions related to the verbal disclosure and defensive patterns that followed therapists' interventions within a single therapy hour for 20 patients. At the same time, a new measure, the Psychodynamic Intervention Rating Scale (PIRS), was tested for reliability and construct validity. Results indicated that therapists fit their styles of intervention to patients' levels of distress and functioning. Within the session, patient's emotional elaboration was followed by therapist's defense interpretation, followed by more patient emotional elaboration. Patient elaboration of significance was followed by more transference interpretation, followed by more patient elaboration of significance. Noninterpretive interventions were followed by patient's disclosure of facts, not emotion. Both interpretive intervention process sequences and therapist's use of support predicted posttreatment symptom reduction. The PIRS was shown to have satisfactory reliability and construct validity. (The Journal of Psychotherapy Practice and Research 1999; 8:40–54)
Pirin (PIR) is a highly conserved nuclear protein originally isolated as an interactor of NFI/CTF1 transcription/replication factor. It is a member of the functionally diverse cupin superfamily and its activity has been linked to different biological and molecular processes, such as regulation of transcription, apoptosis, stress response and enzymatic processes. Although its precise role in these functions has not yet been defined, PIR expression is known to be deregulated in several human malignancies.
We performed immunohistochemical analysis of PIR expression in primary samples from normal human tissues and tumors and identified a dislocation of PIR to the cytoplasm in a subset of melanomas, and a positive correlation between cytoplasmic PIR levels and melanoma progression. PIR localization was subsequently analyzed in vitro in melanoma cell lines through a high content immunofluorescence based approach (ImmunoCell-Array).
The high consistency between in vivo and in vitro results obtained by immunohistochemistry and ImmunoCell-Array provides a validation of the potential of ImmunoCell-Array technology for the rapid screening of putative biological markers, and suggests that cytoplasmic localization of PIR may represent a characteristic of melanoma progression.
Fatigue in chronic fatigue syndrome (CFS) is usually assessed with retrospective measures rather than real-time momentary symptom assessments. In this study, the authors hypothesized that in participants with CFS, discrepancies between recalled and momentary fatigue would be related to catastrophizing, anxiety, and depression and to variability of momentary fatigue. They also expected that catastrophizing, anxiety, and depression would be associated with momentary fatigue. The authors asked 53 adults with CFS to carry electronic diaries for 3 weeks and record their experiences of momentary fatigue. The authors assessed participants' fatigue recall with weekly ratings and administered questionnaires for catastrophizing, depression, and anxiety. Recall discrepancy was significantly related to the variability of momentary fatigue. In addition, catastrophizing, depression, and momentary fatigue were all significantly related to recall discrepancy. Catastrophizing, depression, anxiety, and momentary negative affect were all significantly associated with momentary fatigue. The findings suggest that momentary fatigue in patients with CFS is related to modifiable psychological factors.
affect; chronic fatigue syndrome; fatigue; measurement; pain
Objectives—To investigate relations between physical and psychosocial environmental problems in schools, as perceived by school principals, and injuries among pupils.
Method—Proportionate injury ratios (PIRs) were computed for 77 public sector Swedish schools (33 248 pupils), and divided into four classes based on types of environmental problems reported. Sports related injuries, injuries during recesses, and violence related injuries were considered.
Results—The schools reporting psychosocial problems (9.1% of schools and 7.3% of pupils) had more injuries than expected by chance than all types of injuries aggregated (PIR = 1.92; 95% confidence interval (CI) 1.64 to 2.27), and in the case of sports related injuries (PIR = 1.79; 95% CI 1.37 to 2.34) and injuries due to physical violence (PIR = 2.20; 95% CI 1.33 to 3.65). There were no significant excess risks of injuries for schools facing physical problems or a combination of physical and psychosocial problems.
Conclusions—Psychosocial problems may exacerbate the risk of intentional and unintentional injuries among pupils. The results offer a reminder that school environment must be planned as part of any assessment of youth safety.
Individuals differ in their adjustment to stressful life events, with some exhibiting impaired functioning, including depression, while others exhibit impressive resilience. The present study examined the hypothesis that the ability to deploy a particularly adaptive type of emotion regulation—cognitive reappraisal—may be a protective factor. It expands upon existing research in three ways. First, participants’ ability to use reappraisal (cognitive reappraisal ability: CRA) was measured by using a behavioral challenge that assessed changes in experiential and physiological domains, rather than questionnaires. Second, all participants had been exposed to one or more recent stressful life events, a context in which emotion regulation may be particularly important. Third, a community sample of 78 women aged 20 to 60 was recruited, as opposed to undergraduates. Results indicate that, at low levels of stress, participants’ CRA was not associated with depressive symptoms. However, at high levels of stress, women with high CRA exhibited less depressive symptoms than those with low CRA, suggesting that CRA may be an important moderator of the link between stress and depressive symptoms.
stress; depression; emotion regulation ability; psychophysiology
Objective: The Veterans Health Administration's patient incident reporting system was established to obtain comprehensive data on adverse events that affect patients and to act as a harbinger for risk management. It maintains a dataset of tort claims that are made against Veterans Administration's employees acting within the scope of employment. In an effort to understand the thoroughness of reporting, we examined the relationship between tort claims and patient incident reports (PIRs).
Methods: Using social security and record numbers, we matched 8260 tort claims and 32 207 PIRs from fiscal years 1993–2000. Tort claims and PIRs were considered to be related if the recorded dates of incident were within 1 month of each other. Descriptive statistics, odds ratios, and two sample t tests with unequal variances were used to determine the relationship between PIRs and tort claims.
Results: 4.15% of claims had a related PIR. Claim payment (either settlement or judgment for plaintiff) was more likely when associated with a PIR (OR 3.62; 95% CI 2.87 to 4.60). Payment was most likely for medication errors (OR 8.37; 95% CI 2.05 to 73.25) and least likely for suicides (OR 0.25; 95% CI 0.11 to 0.55).
Conclusions: Although few tort claims had a related PIR, if a PIR was present the tort claim was more likely to result in a payment; moreover, the payment was likely to be higher. Underreporting of patient incidents that developed into tort claims was evident. Our findings suggest that, in the Veterans Health Administration, there is a higher propensity to both report and settle PIRs with bad outcomes.
Pyrethroids are neurotoxic pesticides that interact with membrane bound ion channels in neurons and disrupt nerve function. The purpose of this study was to characterize and explore changes in gene expression that occur in the rat frontal cortex, an area of CNS affected by pyrethroids, following an acute low-dose exposure.
Rats were acutely exposed to either deltamethrin (0.3 – 3 mg/kg) or permethrin (1 – 100 mg/kg) followed by collection of cortical tissue at 6 hours. The doses used range from those that cause minimal signs of intoxication at the behavioral level to doses well below apparent no effect levels in the whole animal. A statistical framework based on parallel linear (SAM) and isotonic regression (PIR) methods identified 95 and 53 probe sets as dose-responsive. The PIR analysis was most sensitive for detecting transcripts with changes in expression at the NOAEL dose. A sub-set of genes (Camk1g, Ddc, Gpd3, c-fos and Egr1) was then confirmed by qRT-PCR and examined in a time course study. Changes in mRNA levels were typically less than 3-fold in magnitude across all components of the study. The responses observed are consistent with pyrethroids producing increased neuronal excitation in the cortex following a low-dose in vivo exposure. In addition, Significance Analysis of Function and Expression (SAFE) identified significantly enriched gene categories common for both pyrethroids, including some relating to branching morphogenesis. Exposure of primary cortical cell cultures to both compounds resulted in an increase (~25%) in the number of neurite branch points, supporting the results of the SAFE analysis.
In the present study, pyrethroids induced changes in gene expression in the frontal cortex near the threshold for decreases in ambulatory motor activity in vivo. The penalized regression methods performed similarly in detecting dose-dependent changes in gene transcription. Finally, SAFE analysis of gene expression data identified branching morphogenesis as a biological process sensitive to pyrethroids and subsequent in vitro experiments confirmed this predicted effect. The novel findings regarding pyrethroid effects on branching morphogenesis indicate these compounds may act as developmental neurotoxicants that affect normal neuronal morphology.
Many neurons display post-inhibitory rebound (PIR), in which neurons display enhanced excitability following inhibition. PIR can strongly influence the timing of spikes on rebound from an inhibitory input. We studied PIR in the Lateral Pyloric (LP) neuron, part of the stomatogastric ganglion of the crab Cancer borealis. The LP neuron is part of the pyloric network, a central pattern generator that normally oscillates with a period of ~ 1 s. We used the dynamic clamp to create artificial rhythmic synaptic inputs of various periods and duty cycles in the LP neuron. Surprisingly, we found that the strength of PIR increased slowly over multiple cycles of synaptic input. Moreover, this increased excitability persisted for 10–20 s after the rhythmic inhibition was removed. These effects are considerably slower than the rhythmic activity typically observed in LP. Thus this slow postinhibitory rebound allows the neuron to adjust its level of excitability to the average level of inhibition over many cycles, and is another example of an intrinsic “short-term memory” mechanism.
stomatogastric; pylorus; central pattern generator; slow; channel; memory
The Protein Information Resource (PIR) recently joined the European Bioinformatics Institute (EBI) and Swiss Institute of Bioinformatics (SIB) to establish UniProt -- the Universal Protein Resource -- which now unifies the PIR, Swiss-Prot and TrEMBL databases. The PIRSF (SuperFamily) classification system is central to the PIR/UniProt functional annotation of proteins, providing classifications of whole proteins into a network structure to reflect their evolutionary relationships. Data integration and associative studies of protein family, function and structure are supported by the iProClass database, which offers value-added descriptions of all UniProt proteins with highly informative links to more than 50 other databases. The PIR system allows consistent, rich and accurate protein annotation for all investigators.
protein web sites; protein family; functional annotation
PIR-A and PIR-B, paired immunoglobulin-like receptors encoded, respectively, by multiple Pira genes and a single Pirb gene in mice, are relatives of the human natural killer (NK) and Fc receptors. Monoclonal and polyclonal antibodies produced against a recombinant PIR protein identified cell surface glycoproteins of ∼85 and ∼120 kD on B cells, granulocytes, and macrophages. A disulfide-linked homodimer associated with the cell surface PIR molecules was identified as the Fc receptor common γ (FcRγc) chain. Whereas PIR-B fibroblast transfectants expressed cell surface molecules of ∼120 kD, PIR-A transfectants expressed the ∼85-kD molecules exclusively intracellularly; PIR-A and FcRγc cotransfectants expressed the PIR-A/ FcRγc complex on their cell surface. Correspondingly, PIR-B was normally expressed on the cell surface of splenocytes from FcRγc−/− mice whereas PIR-A was not. Cell surface levels of PIR molecules on myeloid and B lineage cells increased with cellular differentiation and activation. Dendritic cells, monocytes/macrophages, and mast cells expressed the PIR molecules in varying levels, but T cells and NK cells did not. These experiments define the coordinate cellular expression of PIR-B, an inhibitory receptor, and PIR-A, an activating receptor; demonstrate the requirement of FcRγc chain association for cell surface PIR-A expression; and suggest that the level of FcRγc chain expression could differentially affect the PIR-A/PIR-B equilibrium in different cell lineages.
Fc receptor γ chain; activating receptor; inhibitory receptor; dendritic cells; innate immunity
The pir multigene family, found in the genomes of Plasmodium vivax, P. knowlesi and the rodent malaria species, encode variant antigens that could be targets of the immune response. Individual parasites of the rodent malaria Plasmodium yoelii, selected by micromanipulation, transcribe only 1 to 3 different pir (yir) suggesting tight transcriptional control at the level of individual cells. Using microarray and quantitative RT-PCR, we show that despite this very restricted transcription in a single cell, many yir genes are transcribed throughout the intra-erythrocytic asexual cycle. The timing and level of transcription differs between genes, with some being more highly transcribed in ring and trophozoite stages, whereas others are more highly transcribed in schizonts. Infection of immunodeficient mice with single infected erythrocytes results in populations of parasites each with transcriptional profiles different from that of the parent parasite population and from each other. This drift away from the original ‘set’ of transcribed genes does not appear to follow a preset pattern and “epigenetic memory” of the yir transcribed in the parent parasite can be rapidly lost. Thus, regulation of pir gene transcription may be different from that of the well-characterised multigene family, var, of Plasmodium falciparum.
Three pairs of pigeons were trained to peck at two keys presented simultaneoulsy in discrete trials with intertrial intervals of 1, 22, or 120 sec. Left-key responses incremented the probability of reinforcement for the first right-key response and, conversely, right-key responses incremented the probability of reinforcement for the first left-key response. In terms of relative response rates, it was found that all birds' choices were described by a momentary maximizing strategy, but this fact was not reflected in the detailed sequential statistics for birds with the longer (22 or 120 sec) intertrial intervals. It was hypothesized that choice behavior, in general, may be accurately described by a momentary maximizing sequence, but that prior failures to demonstrate this were due to “errors” in executing the momentary maximizing sequence. These misappropriated responses, which are hypothesized to be randomly distributed among the responses defining the momentary maximizing sequence, caused successive choices to appear to be statistically independent when, in fact, they were not.
A pilot study has been conducted to validate the Breath Motion Detecting System (BMDS), a new concept using Passive Infrared (PIR) technology for a contactless detection of respiratory movements. The primary objective of the study was to show if movements detected during sleep by the BMDS were indeed related to breathing. This medical device is not intended to measure the respiratory rate, but in a second step, it will be able to detect pathological central apnea in adults. One hundred and sixty-nine adult patients underwent a full polysomnography in which each respiratory movement was recorded concomitantly through the BMDS. Curves obtained by the BMDS were compared to those of thoracic movements recorded by classical piezoelectric belts and of pressure obtained with nasal cannula. The correlations between the PIR sensors were highly indicative of respiratory movement detection. Since PIR sensors are sensitive only to the exemplification of the rib cage, they did not detect obstructive apnea. Unfortunately, only a few patients in the studied population had a central apnea. Moreover as our sleep laboratory was equipped only with piezoelectric bands, the central apnea respiratory effort data are not a validated signal to be used during sleep recordings. The data recorded by the BMDS demonstrate the ability of the PIR technology to detect respiratory movements in adults. The concept is practical, inexpensive and safe for the patient. Further studies with respiratory inductive plethysmography are needed to investigate the potential of BMDS to detect central apneas.
Respiration monitoring; PIR technology; Apnea; Noncontact monitoring
Low socioeconomic status (SES) is associated with mortality in several populations. SES measures, such as education and income, may operate through different pathways. However, the independent effect of each measure mutually adjusting for the effect of other SES measures is not clear. The association between poverty-income ratio (PIR) and education and all-cause mortality among 15,646 adults, aged >20 years, who participated in the Third National Health and Nutrition Examination Survey in the USA, was examined. The lower PIR quartiles and less than high school education were positively associated with all-cause mortality in initial models adjusting for the demographic, lifestyle and clinical risk factors. After additional adjustment for education, the lower PIR quartiles were still significantly associated with all-cause mortality. The multivariable odds ratio (OR) [95% confidence interval (CI)] of all-cause mortality comparing the lowest to the highest quartile of PIR was 2.11 (1.52-2.95, p trend≤0.0001). In contrast, after additional adjustment for income, education was no longer associated with all-cause mortality [multivariable OR (95% CI) of all-cause mortality comparing less than high school to more than high school education was 1.05 (0.85-1.31, p trend=0.57)]. The results suggest that income may be a stronger predictor of mortality than education, and narrowing the income differentials may reduce the health disparities.
Education; Income; Inequality; Mortality; Risk factors; Socioeconomic conditions; United States
Increased serum phosphate is associated with adverse health outcomes. High intake of inexpensive processed and fast foods is common in impoverished communities and is linked with excessive dietary phosphorus intake and elevated serum phosphate concentrations in chronic kidney disease patients. We examined the impact of socioeconomic status on dietary phosphorus intake and serum phosphate concentrations in the general population.
14,261 adult participants in the Third National Health and Nutrition Examination Survey.
Predictors and Outcomes
Poverty to income ratio (PIR; family income indexed to the federal poverty level) was the primary index of socioeconomic status. Serum phosphate was the primary outcome variable.
Although estimated phosphorus intake decreased with decreasing quartiles of PIR (P < 0.001), serum phosphate was inversely associated with PIR (P = 0.003). The relationship between lower PIR and higher serum phosphate remained significant after adjustment for demographic, laboratory, and dietary intake characteristics (P = 0.02). Compared to participants in the highest PIR quartile (income >300% of the federal poverty level), participants in the lowest quartile (income < the federal poverty level) had more than twice the odds of hyperphosphatemia (≥4.4 mg/dl) in unadjusted and multivariable-adjusted logistic regression analyses (OR 2.2, 95%CI 1.5, 3.2).
Although lower income was associated with decreased estimated phosphorus intake, increasing poverty was independently linked with increased serum phosphate and higher likelihood of hyperphosphatemia. These findings may indicate that conventional dietary instruments underestimate phosphorus intake, especially among impoverished individuals. Further studies are needed to explore these possibilities.
Phosphate; Poverty; Nutrition
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases).
In vivo protein structures and protein-protein interactions are critical to the function of proteins in biological systems. As a complementary approach to traditional protein interaction identification methods, cross-linking strategies are beginning to provide additional data on protein and protein complex topological features. Previously, photocleavable protein interaction reporter (pcPIR) technology was demonstrated by cross-linking pure proteins and protein complexes and the use of ultraviolet light to cleave or release cross-linked peptides to enable identification. In the present report, the pcPIR strategy is applied to E. coli cells and in vivo protein interactions and topologies are measured. More than 1600 labeled peptides from E. coli were identified, indicating many protein sites react with pcPIR in vivo. From those labeled sites, 53 in vivo inter-cross-linked peptide pairs were identified and manually validated. Approximately half of the interactions have been reported using other techniques, although detailed structures exist for very few. Three proteins or protein complexes with detailed crystallography structures are compared to the cross-linking results obtained from in vivo application of pcPIR technology.