Program for the visualization and interactive study of molecules on a calligraphic display system

Mops is a computer program for the visualization and interactive analysis of crystallographic and molecular structures on a calligraphic PS 300 display system. This system allows the interactive display of bond lengths, bond angles and torsion angles with colour coding of atom types as well as crystalline packing interactions. Mops is also capable of easily drawing a chosen image on the screen using the Ortep program. This facility allows the very fast preparation of slides or illustrations.     

Comparison of computer modelling and X-ray results of the binding of a pyrazole derivative to liver alcohol dehydrogenase

The binding to liver alcohol dehydrogenase of the inhibitor 2,4-(4-pyrazolyl)-butylisothiourea has been studied both by modelling experiments using computer graphics with interactive energy minimization and by X-ray crystallographic structure determination. For the modelling experiments, we used the program system TOM, which was developed in our laboratory as an extension of the program FRODO. Different strategies for using computer graphics with interactive energy minimization were tested. Two essentially different binding modes were found. One of these was favoured from energy minimizations using a potential energy function which was the sum of a Coulomb interaction term and two different van der Waals' interaction terms for non-bonded and torsional interactions. This binding mode was close to the crystallographic observed structure. The results show that flexibility of both ligand and receptor side-chains as well as main-chain conformations are important for docking to the active site of liver alcohol dehydrogenase.     

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions. Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrange-multiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded beta-ribbon into an approximate beta-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and (2) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed.     

Computer-aided prediction of RNA secondary structures.

A brief survey of computer algorithms that have been developed to generate predictions of the secondary structures of RNA molecules is presented. Two particular methods are described in some detail. The first utilizes a thermodynamic energy minimization algorithm that takes into account the likelihood that short-range folding tends to be favored over long-range interactions. The second utilizes an interactive computer graphic modelling algorithm that enables the user to consider thermodynamic criteria as well as structural data obtained by nuclease susceptibility, chemical reactivity and phylogenetic studies. Examples of structures for prokaryotic 16S and 23S ribosomal RNAs, several eukaryotic 5S ribosomal RNAs and rabbit beta-globin messenger RNA are presented as case studies in order to describe the two techniques. Anm argument is made for integrating the two approaches presented in this paper, enabling the user to generate proposed structures using thermodynamic criteria, allowing interactive refinement of these structures through the application of experimentally derived data.     

An automated laboratory control system: collection and analysis of behavioral and electro-physiological data.

A system of man-machine interactive PDP-11 assembly language programs is described which presents stimuli to a subject and records and analyzes behavioral and evoked potential data. The system was designed for researchers with no knowledge of computer programming and enables the user to create complicated sequences of stimulus presentations ("trials") and sequences of successive trials ("runs"), with no new programming required. The system is written for DEC.s DECLAB 11/40 system.     

Computers in health-sciences education. An application to electrocardiography

Aspects of a computer-based education (CBE) are described. Recent developments in the use of computer in health-sciences education are highlighted. An interactive computer system ( CALE ) has been developed to provide individualised instruction and testing for biomedical and medical sciences students. CALE is a system for computer assisted learning of electrocardiography which consists of an organizer program and few subprograms . The system has a self-instruction mode which is equivalent to lecturing . Moreover, review questions are supplied either in multiple choice questions ( MCQ ) and/or matched questions and answers ( MQA ) forms. Furthermore, the system can stimulate normal as well as abnormal electrocardiograms. A statistical program is included to evaluate the performance of the students while using the CALE -system. A comment file is created so that the users can register their comments about the CALE and the difficulties they have faced in using the system. CALE is easy to use and requires no knowledge of programming. The feedback obtained from the students currently using the system is encouraging. CALE is written in Data General FORTRAN 5.     

Interactive computer supported tumor registry in the state of Rhode Island.

A new interactive computerized tumor registry has been established for the state of Rhode Island. The registry is implemented with new data base software which features a pagination scheme with rapid retrieval of non-coded variable data. The types of data stored are discussed as well as the computer system and methods of data entry storage and retrieval.     

Role of heterotypic tissue interactions in deer pedicle and first antler formation-revealed via a membrane insertion approach

Heterotypic tissue interactions play an indispensable role in organ generation and regeneration. In contrast to the classic examples of tissue interactions prevailing in the formation of tetrapod limbs or pectoral fins that can only take place when the interactive tissues are in intimate contacts, the interactions in deer antler formation are novel in that the inducer and the responder are separated by a distance of 1-2 mm. This feature offers a unique opportunity to explore the mechanism underlying tissue interactions by permitting membrane insertion between the two interactive tissues. Four experiments were conducted in this study. The results showed that the impermeable membranes inhibited antler formation. In contrast, the permeable membrane (0.45 microm in pore size) substantially slowed pedicle growth and antler initiation but did not stop them. Interestingly, the impermeable membrane/sheath only slightly retarded antler elongation. Overall, our results demonstrate that interactions between the two interactive tissues, antlerogenic tissue and the overlying skin, are indispensable for first antler initiation and are achieved through diffusible molecules rather than direct physical contact. As the heterotypic tissue interactions are only required during antler initiation but not elongation, they must be transient in nature, and thus differ from those operating in limb/fin formation that can only be sustained by continuous interactions. A system in which organ development is achieved only through transient tissue interactions must be novel, if not completely unique. Understanding this system will undoubtedly enrich the knowledge in the field of tissue interactions and organogenesis.     

The laboratory animal management system--an animal housing management data-processing system]

The Laboratory Animal Management System (LAMS) is a flexible, multi-purpose animal house management tool. It has a decentralized structure and was developed using UNIFACE and Oracle-database software. The multiuser LAMS system runs on a Micro-Vax computer and can be accessed from several workstations. LAMS has been designed to manage the following functions: animal study details; animal procurement; book keeping and follow-up; amendments; update of data; inquiries; statistics and numerous additional tasks. LAMS is a user-friendly interactive system which does not allow input of incorrect data and can be operated by staff with very little computer experience. The system fully complies with German legal requirements and is becoming an increasingly important tool for routine management of animal house facilities and animal experimentation.     

A program system for interactive measurements on digitized cell images.

Using a high precision image scanner and a PDP-8/F minicomputer, we have developed a program system for interactive measurements on microscopic images. By giving simple keyboard commands, the operator can run the image scanner and manipulate the digitized images. The interface between the operator and the microscope-computer system is a Tektronix 4010 graphic terminal. The system allows objects to be isolated and parameters to be calculated from each object, e.g., parameters characterizing shape of the object, irregularity in light transmission over the object, area, integrated light transmission, etc. Objects are isolated and parameters are calculated under complete operator control using interactive computer graphics technique. Calculated parameters may be stored in dedicated data records, which are stored in files for later statistical analysis. The system also includes a statistical evaluation part. Technically, the system consists of a command scanner, which translates commands into internal representation, a parser, which checks the syntax of the commands, and an interpreter, which executes the commands. The system is designed so that new commands can be added easily.     

Computer tools for the analysis of schooling

Synopsis Quantification of fish school structure is difficult because of: (1) the large amount of positional data that must be recorded, (2) the fact that schools are moving, and (3) the fact that schools are threedimensional. Computer tools for addressing these problems include x,y digitizing devices interfaced to computers and interactive computer graphics systems. General computer algorithms now exist for 3-D reconstruction of schools given any two 2-D views such as photographs.Our computerized film analyzer, the Galatea system, is described in detail. This system allows for rapid, accurate input of multiple points which can be followed through each frame in a film sequence. Its software packages perform 3-D reconstructions, analyze undulatory motion, and do extensive statistical tests.     

Microcomputer programs for DNA sequence analysis.

Computer programs are described which allow (a) analysis of DNA sequences to be performed on a laboratory microcomputer or (b) transfer of DNA sequences between a laboratory microcomputer and another computer system, such as a DNA library. The sequence analysis programs are interactive, do not require prior experience with computers and in many other respects resemble programs which have been written for larger computer systems (1-7). The user enters sequence data into a text file, accesses this file with the programs, and is then able to (a) search for restriction enzyme sites or other specified sequences, (b) translate in one or more reading frames in one or both directions in order to find open reading frames, or (c) determine codon usage in the sequence in one or more given reading frames. The results are given in table format and a restriction map is generated. The modem program permits collection of large amounts of data from a sequence library into a permanent file on the microcomputer disc system, or transfer of laboratory data in the reverse direction to a remote computer system.     

噪声和高温对机体健康影响的复合效应

当今社会随着经济和科技的发展,多种有害职业因素往往共同存在于同一岗位。复合因素对机体健康影响的相互作用包括四种情况:协同作用、相加作用、拮抗作用和无关作用。噪声和高温作为有害的职业因素常存在于同一岗位,那么噪声复合高温对机体健康会产生怎样的影响,这两种环境因素是否存在复合效应?文献报道不一。噪声和高温联合对听觉系统、心血管系统、神经系统的影响可能表现为协同、相加、拮抗和无关作用,对呼吸系统的影响表现为拮抗作用,目前,研究结果不一致主要原因是实验条件和暴露方法的不一致。我们认为将来的研究热点集中在噪声和高温联合产生复合效应的条件及剂量反应关系研究、机制及防治措施研究,噪声和高温联合对其他系统如消化、免疫系统是否存在复合效应也值得深入研究。     

Behaviour and social organization in a colony of the Damaraland mole-rat Cryptomys damarensis

This paper reports qualitative and quantitative behavioural studies of the social mole-rat C. damarensis . The behaviours were subdivided into four major categories: nest, maintenance, interactive and auto-behaviours. Social interactions and behavioural types were analysed by sex, age category and caste. The nest area is a focal point in the burrow system with individuals spending more than 70% of the day there. Many of the interactive behaviours occurred there and the mole-rats showed definite preferences with regard to which individuals they rested next to or avoided.
The Damaraland mole-rat colonies show some division of labour, into frequent and infrequent worker groups; these castes differed significantly in the amount of both digging and soil movement undertaken.     

The Influence of Social Norms upon Behavioral Expressions of Implicit and Explicit Weight-Related Stigma in an Interactive Game

This research explored the roles of social influence and stigma-related attitudes in how people behaved toward an overweight female in an interactive computer game. Photographs were used to manipulate whether one of the players in the game was overweight or average weight. We found that both explicit and implicit anti-fat attitudes influenced interactions with an overweight player, but only when other players ostracized the overweight player, not when they included her. Under conditions of ostracism, explicit attitudes were better predictors of more controllable behaviors, while implicit attitudes were better predictors of more automatic behaviors.     

Interaction matters: Bottom-up driver interdependencies alter the projected response of phytoplankton communities to climate change

Phytoplankton growth is controlled by multiple environmental drivers, which are all modified by climate change. While numerous experimental studies identify interactive effects between drivers, large-scale ocean biogeochemistry models mostly account for growth responses to each driver separately and leave the results of these experimental multiple-driver studies largely unused. Here, we amend phytoplankton growth functions in a biogeochemical model by dual-driver interactions (CO₂ and temperature, CO₂ and light), based on data of a published meta-analysis on multiple-driver laboratory experiments. The effect of this parametrization on phytoplankton biomass and community composition is tested using present-day and future high-emission (SSP5-8.5) climate forcing. While the projected decrease in future total global phytoplankton biomass in simulations with driver interactions is similar to that in control simulations without driver interactions (5%–6%), interactive driver effects are group-specific. Globally, diatom biomass decreases more with interactive effects compared with the control simulation (−8.1% with interactions vs. no change without interactions). Small-phytoplankton biomass, by contrast, decreases less with on-going climate change when the model accounts for driver interactions (−5.0% vs. −9.0%). The response of global coccolithophore biomass to future climate conditions is even reversed when interactions are considered (+33.2% instead of −10.8%). Regionally, the largest difference in the future phytoplankton community composition between the simulations with and without driver interactions is detected in the Southern Ocean, where diatom biomass decreases (−7.5%) instead of increases (+14.5%), raising the share of small phytoplankton and coccolithophores of total phytoplankton biomass. Hence, interactive effects impact the phytoplankton community structure and related biogeochemical fluxes in a future ocean. Our approach is a first step to integrate the mechanistic understanding of interacting driver effects on phytoplankton growth gained by numerous laboratory experiments into a global ocean biogeochemistry model, aiming toward more realistic future projections of phytoplankton biomass and community composition.     

互作基因定位方法的研究和计算机软件的开发

质量性状中存在6种可能的基因互作类型, 即互补、重叠、累加、显性上位、隐性上位和抑制。在遗传研究中, 有时会遇到互作基因定位的问题, 但至今未见有关互作基因定位方法和计算机软件的系统的研究报道。文章给出了基于极大似然估计的互作基因定位方法及相应的计算机软件(IGMapping 1.0)。计算机模拟表明, 此方法可以无偏地估计一个共显性标记与一个互作基因之间的重组率或连锁距离。     

Mean geometry of the thiopeptide unit and conformational features of dithiopeptides and polythiopeptides

The mean geometry of the thiopeptide [Ca-N-C(=S)-Ca] unit has been derived from an analysis of X-ray crystal structure data, as well as MM2 and Gaussian 80/82 calculations. The conformational flexibilities of dithiopeptides with glycl- and alanyl-side chains have been investigated by molecular mechanics. Minimum energy conformations were examined using interactive computer graphics molecular modeling techniques. Alanyl-dithiopeptide substitution within an oligopeptide results in considerable restriction of conformational freedom whereas the effect is minimal for glycyl-dithiopeptide substitution. Polyglycyl-thiopeptide adopts a left-handed three or fourfold or right-handed threefold helical structure with favorable interchain C = S...H-N hydrogen bond interactions. A poly-L-alanyl-thiopeptide prefers a left-handed threefold poly-L-proline-like helical structure.     

A model for simulating cognate recognition and response in the immune system.

We have constructed a model of the immune system that focuses on the clonotypic cell types and their interactions with other cells, and with antigens and antibodies. We carry out simulations of the humoral immune system based on a generalized cellular automaton implementation of the model. We propose using computer simulation as a tool for doing experiments in machine, in the computer, as an adjunct to the usual in vivo and in vitro techniques. These experiments would not be intended to replace the usual biological experiments since, in the foreseeable future, a complete enough computer model capable of reliably simulating the whole immune would not be possible. However a model simulating areas of interest could be used for extensively testing ideas to help in the design of the critical biological experiments. Our present model concentrates on the cellular interactions and is quite adept at testing the importance and effects of cellular interactions with other cells, antigens and antibodies. The implementation is quite general and unrestricted allowing most other immune system components to be added with relative ease when desired.