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PubMed2026

PepGen: conditional generation of peptides for MHC binding.

MOTIVATION: Peptide-MHC II binding drives adaptive immunity, yet discovery of novel binder peptides remains challenging due to open binding grooves of MHC-II that accommodate variable-length peptides. While discriminative models perform well, they are unfeasible for generation via enumeration due to vast peptide space (2013≈8×1016 for peptides of length 13 amino acids). Generative AI approaches could accelerate binder design to enable vaccines targeted to particular MHC-II alleles or optimize other peptide chemical properties. RESULTS: We introduce PepGen, the first protein language model for MHC II peptide generation building on Generalized Language Modeling. PepGen conditions on alleles, arbitrary partial peptides including putative TCR-interacting motifs, and continuous binding affinity. Across multiple benchmarks including infilling and de novo generation, PepGen outperformed frequency sampling, Gibbs clustering, and autoregressive baselines. Adjusted log-probabilities enable good classification performance. Experimental validation confirmed that the SARS-CoV-2 peptide TEGALNTPKDHIGTR binding the HLA-DQA101:03-DQB106:03 allele can be redesigned to bind the HLA-DQA101:02-DQB105:02 allele. PepGen generated three putative TCR-motif-preserving binders gaining up to 70% of original MFI. Overall, PepGen provides scalable, motif-constrained MHC II peptide redesign and de novo generation, validated through thorough benchmarks and functional assays. AVAILABILITY AND IMPLEMENTATION: Code and Data are available at https://github.com/DaniTheOrange/PepGen.

Peptides↗

PubMed2006

A neuroscientist-consumer alliance to transform mental health care.

The field of mental health has long suffered from a lack of convergence of disciplines that deal with the mind, the brain, and behavior. This mind-brain dualism has been particularly detrimental for consumers and their families who daily face stigma and discrimination. The understanding of the brain and its dysfunctions has benefited from the study of the human genome and, in particular, of the mutations and variations in its code. This analysis permits a better understanding of the biological basis of mental disease and will soon inform a generation of new diagnostic tools and individualized pharmacological therapies. A biological perspective on mental illness will be complemented by the analysis of the social factors influencing people's behavior and their impact on brain biology and gene function. Neurobiology has progressed to a level for which the knowledge that is generated, even if still colored with uncertainty, could represent a catalyst for the creation of an alliance between neuroscientists and consumers. This partnership has the potential to benefit both parties but will require some concrete steps that might be outside of the usual courses of action for both consumers and scientists. It is by building collaborations based on personal contact and information sharing that a transformation of the mental health care system can occur.

Community Participation↗

PubMed1998

Homology-dependent gene silencing in Paramecium.

Microinjection at high copy number of plasmids containing only the coding region of a gene into the Paramecium somatic macronucleus led to a marked reduction in the expression of the corresponding endogenous gene(s). The silencing effect, which is stably maintained throughout vegetative growth, has been observed for all Paramecium genes examined so far: a single-copy gene (ND7), as well as members of multigene families (centrin genes and trichocyst matrix protein genes) in which all closely related paralogous genes appeared to be affected. This phenomenon may be related to posttranscriptional gene silencing in transgenic plants and quelling in Neurospora and allows the efficient creation of specific mutant phenotypes thus providing a potentially powerful tool to study gene function in Paramecium. For the two multigene families that encode proteins that coassemble to build up complex subcellular structures the analysis presented herein provides the first experimental evidence that the members of these gene families are not functionally redundant.

Animals↗

PubMed2000

Computational fluid dynamics as a method for assessing fume cupboard performance.

A commercially available computational fluid dynamic (CFD) software program, specific for HVAC systems, was used to study the performance of an aerodynamic fume cupboard. The numerical results showed good qualitative agreement with physical measurements giving confidence in the CFD model to simulate and predict overall fume cupboard performance. However, there were some quantitative differences specifically around 'aerodynamic' features that could not be accurately simulated by the software code. The CFD model was clearly able to demonstrate differences in performance between good and bad cupboard designs, and show the importance of using rear baffles and lipfoils. It also showed the importance of good design features when a 'worker' was standing against the front edge or when there were draughts in front of the aperture. The computer model was used to simulate the gas tracer containment test method described in BS 7258 (1994) [Laboratory Fume Cupboards], and had a much greater sensitivity than the recommended physical measuring instruments. The results given in this paper demonstrate the potential for using a commercially available software package for the optimisation of fume cupboard design and testing. It also indicates the economy of using CFD compared with building a prototype and testing a model.

Air Pollution, Indoor↗

PubMed1992

Genes for polyketide secondary metabolic pathways in microorganisms and plants.

Recent advances in molecular genetics have led to the isolation, sequencing and functional analysis of genes encoding synthases that catalyse the formation of several classes of polyketides. The structures of the genes and their protein products differ strikingly in the various examples. For Streptomyces aromatic polyketides, exemplified by granaticin and tetracenomycin, the synthases correspond to Type II (bacterial and plant) fatty acid synthases in consisting of distinct proteins for such processes as condensation, acyl carrier function and ketoreduction. In contrast, for actinomycete macrolides such as erythromycin, similar catalytic functions are performed by a set of multifunctional proteins resembling Type I (animal) fatty acid synthases, but with every step in chain-building being catalysed by a different enzymic domain. Penicillium patulum has a simple Type I synthase for 6-methylsalicylic acid. For plant chalcones and stilbenes, a single small polypeptide acts as a condensing enzyme for carbon chain-building and may be unrelated to any of the other polyketide and fatty acid synthases. Thus, although these systems share a common general mechanism of chain assembly, they must differ in the ways that synthase 'programming' has evolved to determine chain length, choice of chain starter and extender units, and handling of successive keto groups during chain assembly, and so control the great diversity of possible chemical products.

Actinomycetaceae↗

PubMed2006

Description of the cardiac movement using hexagonal image structures.

The most notable characteristic of the heart is its movement. Detection of dynamic information describing cardiac movement such as amplitude, speed and acceleration facilitates interpretation of normal and abnormal function. In recent years, the Omni-directional M-mode Echocardiography System (OMES) has been developed as a process that builds moving information from a sequence of echocardiography image frames. OMES detects cardiac movement through construction and analysis of Position-Time Grey Waveform (PTGW) images on some feature points of the boundaries of the ventricles. Image edge detection plays an important role in determining the feature boundary points and their moving directions as the basis for extraction of PTGW images--Spiral Architecture (SA) has proved efficient for image edge detection. SA is a hexagonal image structure in which an image is represented as a collection of hexagonal pixels. There are two operations called spiral addition and spiral multiplication defined on SA. They correspond to image translation and rotation, respectively. In this paper, we perform ventricle boundary detection based on SA using various defined chain codes. The gradient direction of each boundary point is determined at the same time. PTGW images at each boundary point are obtained through a series of spiral additions according to the directions of boundary points. Unlike the OMES system, our new approach is no longer affected by the translation movement of the heart. As its result, three curves representing the amplitude, speed and acceleration of cardiac movement can be easily drawn from the PTGW images obtained. Our approach is more efficient and accurate than OMES, and our results contain a more robust and complete description of cardiac motion.

Algorithms↗

PubMed1995

Analysis of consensus sequence patterns in Giardia cytoskeleton gene promoters.

Protein-coding genes in the ancient eukaryote Giardia lamblia lack typical promoter consensus elements. We have analysed the immediate 5' flanking sequences of seven genes of related function (structural cytoskeleton proteins) to identify shared DNA motifs that might have a role in transcription initiation. Transcription start sites for five genes have been determined previously. Genomic mapping and mRNA primer extension experiments demonstrate additionally that the genes for beta-giardin and median body protein are (i) present as single copies in the genome, (ii) transcribed with very short 5' leader sequences. Two search algorithms designed to extract conserved motifs from either aligned or non-aligned sequences independently discovered three sites constituting a common pattern in all seven promoters. Sites were optimally aligned using weight matrix building trials to achieve the maximum 'information content'. Profiling the information content of best alignments defines the extent of the homologies as: a 9 bp box (initiator) at the start site and upstream 18 and 6 bp boxes. The initiator is the most highly conserved element and contains a universal Py-A-Pu motif at which transcription starts. We show that the best matrices can be combined in a search pattern that correctly locates transcription start sites in genomic DNA sequences.

Algorithms↗

PubMedDate not supplied

Age and gender as determinants of stress exposure, generation, and reactions in youngsters: a transactional perspective.

The present study used a contextual and transactional approach to examine age and gender differences in the experience and consequences of life stress in clinic-referred preadolescents and adolescents. Eighty-eight youngsters and their parents completed the Child Episodic Life Stress Interview, a detailed semistructured interview assessing the occurrence of stressful events in multiple life domains. Interviews were coded using a contextual threat rating method to determine event stressfulness and dependence. Youngsters also completed the Children's Depression Inventory and the Revised Child Manifest Anxiety Scale to assess self-reported symptoms of depression and anxiety. Consistent with predictions, age- and gender-related patterns of life stress varied across the type and context of stressors. Most notably, adolescent girls experienced the highest levels of interpersonal stress, especially stress and conflict that they generated within parent-child and peer relationships. Preadolescent girls experienced the highest levels of independent stress and conflict in the family context. Adolescent boys experienced the highest levels of noninterpersonal stress associated with self-generated events. Girls demonstrated particular vulnerability to depressive responses to dependent stress. The results build on and extend previous theory and research on age and gender differences in close relationships and stress, and illustrate the value of more refined conceptual models and more sophisticated methodologies in child life stress research.

Adaptation, Psychological↗

PubMed1997

Evaluating standardized coding and classification systems for clinical practice: a critical review of the nursing literature in the United States.

Developers of healthcare information systems are challenged by the difficulty of meeting the simultaneous goals of 1) capturing and electronically representing the broad array of data related to healthcare with sufficient expressibility to provide adequate documentation of the patient encounter, and 2) utilizing standardized coding and classification systems to facilitate linkages among computer-based systems. The evaluation studies to date have primarily focused on matching actual clinical data with terms in the recognized classification systems. These studies have provided evidence that the classification systems are relatively domain complete for categorizing patient problems and nursing interventions. Although several of the published criteria for evaluation relate to structure, it is noteworthy that this has not yet been a major focus of study in nursing. There are several areas of critical need that must be addressed. First, additional work is needed to develop and refine a standardized set of atomic-level terms relevant to nursing, including those for assessments, problems, and activities. Second, knowledge representations must be developed to support the building of complex concepts from atomic-level data.

Classification↗

PubMed2005

Preliminary shielding assessment for the 100 MeV proton linac (KOMAC).

The Proton Engineering Frontier Project is building the Korea Multipurpose Accelerator Complex facilities from 2002 to 2012, which consists of a high-current 100 MeV proton linear accelerator and various beam-lines. This paper provides a preliminary estimate of the shielding required for the 20 mA proton linac and the beam-dump. For an accurate information on secondary neutron production from the guiding magnet and primary heat sink of the beam dump, proton-induced 63Cu and 65Cu cross section data were evaluated and applied to shielding calculations. The required thickness of the concrete was assessed by a simple line-of-sight model for the lateral shielding of the beam-line and the full shielding of the beam dump. Monte Carlo simulations were also performed using the MCNPX code to obtain the source term and attenuation coefficients for the three-dimensional lateral shielding model of the beam-line.

Computer Simulation↗

PubMed2000

Typologies of the cultural position of drinking.

OBJECTIVE: Typologies of the cultural position of drinking from the social science literature are reviewed. METHOD: The article reviews significant studies and literature on the topic. RESULTS: Starting in the 1940s, two research traditions considered variations in the cultural position of drinking as explanations of rates of drinking problems. A "holocultural" tradition coded and analyzed ethnographic data on tribal and village societies, starting in the 1940s, with each study identifying a different social dimension as crucial. A "sociocultural" tradition distinguished abstinent cultures from prescriptive cultures, in which drinking was integrated with daily life, and expected, but drunkenness was prohibited. These types were implicitly contrasted with American drinking, which was variously characterized. Other dimensional and typological approaches in the literature are considered, including a little-known Jellinek typology. Problems with the widely used distinction between "wetter" and "drier" (or "temperance") cultures are discussed. CONCLUSIONS: Four ideal types of the cultural position of drinking can be readily distinguished: abstinent societies, constrained ritual drinking, banalized drinking and fiesta drunkenness. A large residual category remains, however, and a dimensional approach to typology building may be more fruitful. Two basic dimensions are proposed--regularity of drinking and extent of drunkenness--and further dimensions are described that may be added to fit the requirements of the particular study.

Alcohol Drinking↗

PubMed2001

Mimos: a description framework for exchanging medical image processing results.

Image processing plays increasingly important role in using medical images, both for routine as for research purposes, due to the growing interest in functional studies (PET, MR, etc.). Unfortunately, there exist nearly as many formats for data and results coding as image processing procedures. If Dicom presently supports a kind of structured reporting of image studies, it does not take into account the semantics of the image handling domain. This can impede the exchange and the interpretation of processing results. In order to facilitate the use of image processing results, we have designed a framework for representing image processing results. This framework, whose principle is called an "ontology" in the literature, extends the formalism, which we have used in our previous work on image databases. It permits a systematic representation of the entities and information involved in the processing, that is not only input data, command parameters, output data, but also software and hardware descriptions, and relationships between these different parameters. Consequently, this framework allows the building of standardized documents, which can be exchanged amongst various users. As the framework is based on a formal grammar, documents can be encoded using XML. They are thus compatible with Internet / Intranet technology. In this paper, the main characteristics of the framework are presented and illustrated. We also discuss implementation issues in order to be able to integrate documents, and correlated images, handling these with a classical Web browser.

Image Processing, Computer-Assisted↗

PubMed2003

External cause-specific summaries of occupational fatal injuries. Part I: an analysis of rates.

BACKGROUND: Industries and occupations vary with respect to the incidence of fatal injuries and their causes. METHODS: Fatalities from the National Traumatic Occupational Fatality database (years 1983-1994) serve as the basis for examining external cause of death code specific rates. Industries and occupations are compared with respect to rate and frequency of fatal injuries. In addition, external causes of injury (E-codes) are examined across all industries and occupations as well as within industries and occupations to evaluate which events would be identified by frequency ordered comparisons versus injury rate ordered comparisons. RESULTS: Machinery, electric current, homicide, falls, and transportation-related events are identified by high frequency and rate of occurrence. CONCLUSIONS: The external cause categories of homicide, machinery-related, motor-vehicle-related, electric current, and falls, account for over one-half of all occupational fatal injuries. Targeted interventions in homicide may be especially warranted in sales and service occupations and in the retail trade and services industries. In addition, younger workers might be targeted for special interventions designed to identify hazardous practices, procedures, and solutions to reduce fatalities associated with electrocution or falls from buildings.

Accidental Falls↗

PubMed2006

What are the key attributes of primary care for patients? Building a conceptual 'map' of patient preferences.

BACKGROUND: Responding to the preferences of patients is a key focus of current health policy and is especially important in primary care. Responding effectively to patient preferences requires a clear understanding of the way in which patients assess primary care services. OBJECTIVE: This study was designed to provide a 'map' of the content and structure of the key attributes of patient preferences concerning primary care. DESIGN: The development of the 'map' used secondary research methods. Electronic databases were searched for published conceptual reviews of patient preferences, which were used to develop a basic 'map' through content analysis. A search for recently published primary empirical studies of patient preferences was conducted to extend and develop the 'map'. The 'map' was tested by taking a random sample of patient assessment instruments and categorizing the item content. RESULTS: Seven major categories and multiple subcategories were described. The major categories were access, technical care, interpersonal care, patient-centredness, continuity, outcomes, and hotel aspects of care. The coverage of these attributes in a selection of patient assessment instruments varied widely, and the coding of a proportion of items in the patient assessment instruments according to the 'map' was problematic. CONCLUSIONS: The conceptual 'map' can be used to plan comprehensive assessment of patient preferences in primary care. It also raises many theoretical issues concerning the nature of attributes and their interrelationships. The implications for the measurement of patient preferences are discussed.

Continuity of Patient Care↗

PubMed2002

Stop, look, listen, and think? What young children really do when crossing the road.

This study sought to provide basic information about children's behaviour in realistic traffic situations. Most literature in this area has focused on children's knowledge about road safety or has assessed their behaviour in simulated traffic environments. However, until more is known about what children actually do in traffic environments, our ability to identify the important elements for inclusion in educational programmes remains limited. Fifty-six children, aged 5-6 years, took part in a 'treasure trail' activity in which they were confronted with two road crossings, one at a T-junction with a moving car and the other between parked cars. Children's performance was videotaped and coded for relevant behaviours such as stopping at the kerb, looking for traffic, direction of gaze, and style of crossing (i.e. walking vs. running). Results revealed that performance was extremely poor. Sixty percent of the children failed to stop before proceeding from the kerb onto the road. Looking for oncoming traffic was exhibited by no more than 41% of the sample, dropping to as low as 7% in some instances. When looking did occur, it was initially as likely to be in the inappropriate direction (i.e. to the left) as in the appropriate direction (i.e. to the right). Consideration of individual performance revealed the existence of individual differences within the sample; such differences were relatively stable across the two road crossings. These findings, based on controlled naturalistic tasks and detailed observational methods, build on earlier studies that are generally able to provide only estimated rates of children's behaviour.

Accidents, Traffic↗

PubMed1982

A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A.

C-peptide, which contains the 13 NH2-terminal residues of RNase A, shows partial helix formation in water at low temperature (1 degree C, pH 5, 0.1 M NaCl), as judged by CD spectra; the helix is formed intramolecularly [Brown, J. E. & Klee, W. A. (1971) Biochemistry 10, 470-476]. We find that helix stability depends strongly on pH: both a protonated histidine (residue 12) and a deprotonated glutamate (residue 9 or 2 or both) are required for optimal stability. This information, together with model building, suggests that the salt bridge Glu-9- ... His-12+ stabilizes the helix. Formation of the helix is enthalpy driven [van't Hoff delta H, - 16Kcal/mol (1 cal = 4.18 J)] and the helix is not observed above 30 degrees C. Proton NMR data indicate that several side chains adopt specific conformations as the helix is formed. These results have two implications for the mechanism of protein folding. First, they indicate that short alpha-helices, stabilized by specific side-chain interactions within the helix, can be stable enough in water to function as folding intermediates. Second, they suggest that similar experiments with peptides of controlled amino acid sequence could be used to catalogue the intrahelix interactions that stabilize or destabilize alpha-helices in aqueous solution. These data might provide the code relating amino acid sequence to the locations of alpha-helices in proteins.

Chromatography, High Pressure Liquid↗

PubMed1989

Health hazards from fine asbestos dusts. An analysis of 70,656 occupational preventive medical investigations from 1973 to the end of 1986.

For the period from 1973 to the end of 1986, 70,656 data sets on occupational preventive medical examinations in employees exposed occupationally to asbestos dust (G 1.2) were made available to us by the Central Registry for Employees Exposed to Asbestos Dust (ZAS). On the basis of this data, an analysis of asbestosis risk was to be made in relation to specific areas of work, taking into consideration the beginning and duration of exposure. Proceedings for declaratory appraisal in accordance with occupational disease no. 4103 were instituted in 1760 cases in the report period. In accordance with the character of the available data, the X-ray findings in the lungs were available from the persons investigated as parameters of possible asbestosis risk on the basis of coding consistent with the International Pneumoconiosis Classification (ILO U/C 1971 and/or ILO 1980 West Germany). The major result of the statistical analyses on the mainframe macrocomputer of the University of Erlangen-Nuremberg was that the relatively highest risk of asbestosis was present in persons whose exposure began before 1955. On the other hand, with increasing duration of exposure, an unequivocal rise of the asbestosis risk could not be detected on the basis of the overall population. In relation to the individual fields of work, the relatively highest risk of asbestosis was shown to be in the asbestos textile and paper industry, as well as in the asbestos cement industry. No detectable risk of asbestosis was present in the fields of mining, traffic and health service and for women in the industrial sectors of building material, gas and water, catering trade, building, commerce as well as banking and insurance. Accordingly, it can be assumed that certain fields of work are or were exposed to such a small extent or not at all that a risk of asbestosis which is relevant in terms of occupational medicine is no longer to be assumed or was not to be assumed. This applies above all to certain work in the frictional coating (brake lining) and asbestos paper industry. Furthermore, the analysis of the data material did not provide any unequivocal indications that inhalative smoking habits have a negative effect on the risk of asbestosis. In principle, it can be stated that the occupational preventive medical investigations according to G 1.2 are effective.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗

PubMed2006

Combinatorial epigenetics, "junk DNA", and the evolution of complex organisms.

At certain evolutionary junctures, two or more mutations participating in the build-up of a new complex function may be required to become available simultaneously in the same individuals. How could this happen in higher organisms whose populations are small compared to those of microbes, and in which chances of combined nearly simultaneous highly specific favorable mutations are correspondingly low? The question can in principle be answered for regulatory evolution, one of the basic processes of evolutionary change. A combined resetting of transcription rates in several genes could occur in the same individual. It is proposed that, in eukaryotes, changes in epigenetic trends and epigenetically transforming encounters between alternative chromatin structures could arise frequently enough so as to render probable particular conjunctions of changed transcription rates. Such conjunctions could involve mutational changes with low specificity requirements in gene-associated regions of non-protein-coding sequences. The effects of such mutations, notably when they determine the use of histone variants and covalent modifications of histones, can be among those that migrate along chromatin. Changes in chromatin structure are often cellularly inheritable over at least a limited number of generations of cells, and of individuals when the germ line is involved. SINEs and LINEs, which have been considered "junk DNA", are among the repeat sequences that would appear liable to have teleregulatory effects on the function of a nearby promoter, through changes in their numbers and distribution. There may also be present preexisting unstably inheritable epigenetic trends leading to cellular variegation, trends endemic in a cell population based on DNA sequences previously established in the neighborhood. Either way, epigenetically conditioned teleregulatory trends may display only limited penetrance. The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal "gene kissing". The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes ("epimutations") with effects at a distance would then perdure over the number of generations required for "assimilation" of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of "junk DNA", through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.

Animals↗