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At least 19 recordsLinked to original sources
PubMed1992

Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions.

A recently developed procedure to predict backbone structure from the amino acid sequence [Rooman, M., Kocher, J. P., & Wodak, S. (1991) J. Mol. Biol, 221, 961-979] is fine tuned to identify protein segments, of length 5-15 residues, that adopt well-defined conformations in the absence of tertiary interactions. These segments are obtained by requiring that their predicted lowest energy structures have a sizable energy gap relative to other computed conformations. Applying this procedure to 69 proteins of known structure, we find that regions with largest energy gaps--those having highly preferred conformations--are also the most accurately predicted ones. On the basis of previous findings that such regions correlate well with sites that become structured early during folding, our approach provides the means of identifying such sites in proteins without prior knowledge of the tertiary structure. Furthermore, when predictions are performed so as to ignore the influence of residues flanking each segment along the sequence, a situation akin to excising the considered peptide from the rest of the chain, they offer the possibility of identifying protein segments liable to adopt well-defined conformations on their own. The described approach should have useful applications in experimental and theoretical investigations of protein folding and stability, and aid in designing peptide drugs and vaccines.

Amino Acid Sequence↗
PubMed1992

Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins.

It is investigated whether protein segments predicted to have a well-defined conformational preference in the absence of tertiary interactions are conserved in families of homologous proteins. The prediction method follows the procedures of Rooman, M., Kocher, J.-P., and Wodak, S. (preceding paper in this issue). It uses a knowledge-based force field that incorporates only local interactions along the sequence and identifies segments whose lowest energy structure displays a sizable energy gap relative to other computed conformations. In 13 of the protein families and subfamilies considered that are sufficiently homologous to have similar 3D structures, at least one region is consistently predicted as having the same preferred conformation in virtually all family members. These regions are between 4 and 26 residues long. They are often located at chain ends and correspond primarily to segments of secondary structure heavily involved in interactions with the rest of the protein, suggesting that they could act as nuclei around which other parts of the structure would assemble. Experimental data on early folding intermediates or on protein fragments with appreciable structure in aqueous solution are available for more than half of the protein families. Comparison of our results with these data is quite favorable. They reveal that each of the experimentally identified early formed, or independently stable, substructures harbors at least one of the segments consistently predicted as having a preferred conformation by our procedure. The implications of our findings for the conservation of folding pathways in homologous proteins are discussed.

Adenylate Kinase↗
PubMed2025

Large Language Model and Knowledge Graph-Driven AJCC Staging of Prostate Cancer Using Pathology Reports.

Background/Objectives: To develop an automated American Joint Committee on Cancer (AJCC) staging system for radical prostatectomy pathology reports using large language model-based information extraction and knowledge graph validation. Methods: Pathology reports from 152 radical prostatectomy patients were used. Five additional parameters (Prostate-specific antigen (PSA) level, metastasis stage (M-stage), extraprostatic extension, seminal vesicle invasion, and perineural invasion) were extracted using GPT-4.1 with zero-shot prompting. A knowledge graph was constructed to model pathological relationships and implement rule-based AJCC staging with consistency validation. Information extraction performance was evaluated using a local open-source large language model (LLM) (Mistral-Small-3.2-24B-Instruct) across 16 parameters. The LLM-extracted information was integrated into the knowledge graph for automated AJCC staging classification and data consistency validation. The developed system was further validated using pathology reports from 88 radical prostatectomy patients in The Cancer Genome Atlas (TCGA) dataset. Results: Information extraction achieved an accuracy of 0.973 and an F1-score of 0.986 on the internal dataset, and 0.938 and 0.968, respectively, on external validation. AJCC staging classification showed macro-averaged F1-scores of 0.930 and 0.833 for the internal and external datasets, respectively. Knowledge graph-based validation detected data inconsistencies in 5 of 150 cases (3.3%). Conclusions: This study demonstrates the feasibility of automated AJCC staging through the integration of large language model information extraction and knowledge graph-based validation. The resulting system enables privacy-protected clinical decision support for cancer staging applications with extensibility to broader oncologic domains.

artificial intelligence↗
PubMedDate not supplied

Extraction of information from CT scans at different energies.

The image displayed in computed tomography is a scaled representation of attenuation coefficients within the patient's body. A number of authors have presented methods by which additional information (such as electron density, effective atomic number, and extrapolated attenuation coefficients for therapy applications) can be extracted from CT scans carried out at different energies. In the present paper, the dual-energy method described by Rutherford has been used to produce complete images of effective atomic number and electron density of a known phantom (the AAPM phantom) in order to investigate the usefulness of applying this method to current commercial scanners.

Tomography, X-Ray Computed↗
PubMed1976

The extraction of information from visual persistence.

Seven-letter targets were flashed for 50 msec and followed by either a blank adapting field (persisting representation of the stimulus fully available) or a series of continuous cycles of target and mask until the cumulative duration of the target matched the estimated duration of visual persistence (stimulus physically present for same interval as representation). The reportability of information from the targets in the latter case was only 50% that in the former. The interpretation is that visual persistence is an active, continuously operating process rather than a passive neural copy of the stimulus.

Form Perception↗
PubMed1978

Binaural detection at high frequencies with time-delayed waveforms.

Recent research has demonstrated that the binaural system can utilize ongoing interaural time differences for lateralization at high frequencies as well as at low frequencies. The requirement is that the signal be complex so that the time difference appears as a delay in the envelope of the waveform at one ear. Reported here are several masking experiments that examine detection performance with time-delayed signals or maskers. In the first experiment, the signal was a 50-Hz band of noise centered at 4000 Hz that was time delayed by different amounts on different blocks of trials; the masker was similar band of noise, presented diotically. Large masking-level differences (MLDs) were obtained for some values of time delay, but the MLDs did not increase monotonically within time delay as they should were envelope time delay the basis for detection performance. Subsequent experiments in which the masker was time delayed and the signal was a diotic, high-frequency tone, revealed that detectability follows the autocorrelation function, and that MLDs as large as 24 dB can be obtained at 4000 Hz at time delays corresponding to negative values in the autocorrelation function. Examination of the signal-plus masker waveforms in these conditions reveals that ongoing interaural differences in level and cycle-by-cycle time exist in those conditions that yield MLDs. Since the time differences are small by usual standards, the basis for detection performance in these conditions appears to be the ongoing interaural level differences. In a final experiment, lateralization performance was measured for a time-delayed, complex waveform in the presence of maskers of various intensities. The results show that subjects are able to extract information about the time delay in the envelope even when the signal is added to a masker of equal intensity or greater. Thus, at the small signal-to-noise ratios used in our detection experiments, extraction of envelope time information was impossible, but also unnecessary, for detection was accomplished on the basis of another cue--most likely the ongoing interaural level differences.

Auditory Perception↗
PubMed1992

Melanoma incidence and trends in the Nelson-Marlborough area of New Zealand.

AIMS: To determine the recent incidence of melanoma in the Nelson-Marlborough area of New Zealand and to compare this with a formerly determined incidence from the same area and with published incidences and trends elsewhere in New Zealand and Queensland. METHODS: All histopathology reports for the region were examined retrospectively each four weeks and relevant information extracted. In cases of doubt, pathologists were consulted and cases reviewed. Population, demographic and weather information was obtained from statistical records. RESULTS: These showed a doubling of the incidence since the previous survey with a reduction in female incidence. There was marked reduction in the incidence in the age groups 20-39 with an increase in those over 60 years. The number of superficial more easily cured lesions were almost doubled with marked reduction in the more sinister thicker and nodular lesions. CONCLUSIONS: The incidence of melanoma in the region is increasing at a rate comparable with other areas but with significant reductions in the incidence of thicker and more advanced melanoma as well as a decreased incidence in those under 40 years of age. The incidence in Nelson-Marlborough still remains very high but is slightly less than that shown for the Tauranga district over a similar period.

Adult↗
PubMed1992

Human HPRT mutant database: software for data entry and retrieval.

We have developed a computer database containing information on over 1,000 human hypoxanthine guanine phosphoribosyl transferase (HPRT) mutants. Both published and unpublished data are present. The database itself is maintained in a dBASE format (.DBF) and we provide a set of programs to examine and extract information from the database. A program to input information into the database is also supplied. The database and programs are available directly from us or via remote FTP (file transfer protocol) using BITNET/INTERNET. All programs require an IBM-compatible computer, the MS-DOS operating system (version 3.3 or greater), and a hard disk with about 5 megabytes of free disk space. The purpose of the database is 1) to allow investigators to contribute their HPRT mutants directly to the database in a standardized fashion, and 2) to allow access to the entire database with a set of programs that allows manipulation and extraction of data. For example, using our programs it is possible to i) order the database by base pair position, ii) examine only information regarding mutagenesis by a particular agent, iii) search for a particular author, iv) create a report which contains selected portions of the database, the report can be printed or saved as a file. The database will be updated every several months and distributed.

Databases, Bibliographic↗
PubMed1976

Effects of stimulus information and stimulus duration on amplitude and habituation of the electrodermal orienting response.

This study was designed to investigate the effects of stimulus information and stimulus duration on the skin conductance response (SCR) component of the orienting response (OR). Three levels of stimulus information were combined with two levels of stimulus duration in a 3 X 2 independent groups factorial design (N = 90). On the basis of Sokolov's (1966) theory, it was hypothesized that: (a) high information stimuli would elicit larger initial SCR'S than would stimuli of low information, (B) high-information stimuli would evoke more SCRs throughout a habituation series than would low-information stimuli, and (c) high-information stimuli would require more presentations to reach a habituation criterion than would stimuli of low information. It was also hypothesized that (d) long-duration stimuli would require fewer presentations to reach a habituation criterion and result in a faster rate of habituation than would stimuli of short duration. The stimuli consisted of black and white chequered patterns containing 12, 26 or 60 bits of information. Stimulus duration was either 0.5 or 4.5 sec, and each subject received 20 presentations at randomly ordered intervals of 20, 25, 30 and 35 sec. The results provided support for hypotheses (b), (c) and (d), but not for hypothesis (a). These results support the view that OR habituation can be conceptualized as a process of information extraction.

Adolescent↗
PubMedDate not supplied

From experimental units to unique experiments: chronobiologic pilots complement large trials.

The timing of treatment affects outcome. For mapping multi-frequency rhythm spectra first to optimize chronochemotherapy, 1000 marker determinations on the subject are more informative than a few determinations on each of hundreds of patients. N-of-6 subgroups should follow, with one subject assigned to each of 6 marker rhythm stages, 60 (e.g. 4 hours on a 24-hour scale) apart. Once the time structure has been mapped, minimal sampling requirements determined, and guidelines for treatment established, the information gained from chronobiologic n-of-1 and n-of-6 test pilot designs can be built cost-effectively into randomized controlled trials to benefit large patient populations. Sequential tests combined with marker rhythmometry and cosinor analysis on single test subjects, small groups and eventually on each patient are powerful tools that can extract information otherwise unattainable even at great cost and bring the P-value from publications to the patients.

Antineoplastic Agents↗
PubMed2026

The reporting and handling of missing data in genetic epidemiological studies of mental health in childhood and adolescence: A systematic review.

BACKGROUND: Genetic epidemiological analyses of child and adolescent mental health often use data from prospective longitudinal cohorts. Missingness due to selective attrition is therefore an important potential source of bias in such analyses. Informatively reporting on missingness and taking appropriate steps to handle it in analyses can mitigate this potential bias. Here, we aim to systematically assess how researchers report and address missingness in genetic epidemiological studies of child and adolescent mental health-related outcomes using cohort data. METHODS: We systematically searched the Ovid Medline database for studies published between August 2012 and August 2025, reporting polygenic score, genome-wide association, or Mendelian randomization analyses, of data on children or adolescents participating in cohort studies. We extracted information from eligible studies based on criteria adapted from the strengthening and reporting of observational studies in epidemiology (STROBE) guidelines. RESULTS: A total of 133 eligible studies were included, of which 125 (93.98%) reported the number of complete cases in all waves, while 84 (63.16%) detailed the amount of missingness on all key variables. Most studies used complete case analysis, while 39 studies explicitly reported applying other methods to handle missingness, with multiple imputation (n = 20, 15.04%) being the most common, followed by full information maximum likelihood 10 (8.1%). Only 18 studies (13.53%) reported an assumed missing mechanism along with the method used to address missingness. Full reporting of both the extent and handling of missingness at the item level was rare, occurring in only 5 (3.76%) and 15 (11.28%) studies, respectively, among the 123 studies that used multi-item instruments. CONCLUSION: Best practice recommendations for reporting on missing data handling emphasize the importance of detailing the proportion of missingness, types of mechanisms underpinning missingness, and details of approaches used. Based on this review, these recommendations for proper reporting of missing data are rarely followed in full.

children and adolescents↗
PubMed1977

Kinetics of Na+-dependent D-glucose transport.

The kinetic parameters of the Na+-dependent glucose transport system have been determined in isolated membrane vesicles for D-glucose, Na+, and phlorhizin. The D-glucose flux measurements were carried out by the equilibrium exchange procedure at constant external and internal Na+ concentrations and zero potential. Equations were developed to extract information about Km and Vmax from uptake measurements into a vesicle population that is heterogeneous with respect to size (surface to volume ratio). The Km for D-glucose was 14 mM and independent of the Na+-concentration, while the Vmax was strongly Na+-dependent and increased 15-fold between 1 and 100 mM Na+. The Km of Na+ for activation of the Vmax was 18 mM. The calculated KI values for phlorhizin were 2.7 and 1.9 micrometer when determined under active and equilibrating D-glucose flux conditions, respectively.

Animals↗
PubMed1979

A model for processing of movement in the visual system.

Processing of spatio-temporal information in the human visual system has been investigated thoroughly during the past decade, but is still far from being properly understood. Moreover, the theory of separation of information by means of sustained and transient channels already at the retinal level is not satisfactory, as experimental results indicate that these two types of channels span a continuum of temporal characteristics. It is however obvious, that the process of pattern recognition and velocity perception calls for their separation at some level of the hierarchy. In this communication, we extend our model of three-dimensional spatio-temporal frequency expansion in the visual system (Gafni and Zeevi, 1977) to show how velocity-information extraction channels, sensitive to direction and velocity exclusively, can be formed by simple summation of signals from well-defined sets of channels representing points in the frequency space. Correspondence of these channels to characteristics of the cortical neurons is discussed.

Depth Perception↗