bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Interactions Are Necessary for Translational Enhancement by Spleen Necrosis Virus RU5
Authors: Dangel Andrew W. , Hull Stacey , Roberts Tiffiney M. , Boris-Lawrie Kathleen 
Published: July 2002

ABSTRACT

The 5′ long terminal repeat of spleen necrosis virus (SNV) facilitates Rev/Rev-responsive element (RRE)-independent expression of intron-containing human immunodeficiency virus type 1 (HIV-1)
gag
. The SNV RU5 region, which corresponds to the 165-nucleotide 5′ RNA terminus, functions in a position- and orientation-dependent manner to enhance polysome association of intron-containing HIV-1
gag
RNA and also nonviral
luc
RNA. Evidence is mounting that association with nuclear factors during intron removal licenses mRNAs for nuclear export, efficient translation, and nonsense-mediated decay. This project addressed the relationship between the nuclear export pathway of SNV RU5-reporter RNA and translational enhancement. Results of RNA transfection experiments suggest that cytoplasmic proteins are insufficient for SNV RU5 translational enhancement of
gag
or
luc
RNA. Reporter gene assays, leptomycin B (LMB) sensitivity experiments, and RNase protection assays indicate that RU5
gag
RNA accesses a nuclear export pathway that is distinct from the LMB-inhibited leucine-rich nuclear export sequence-dependent CRM1 pathway, which is used by the HIV-1 RRE. As a unique tool with which to investigate the relationship between different RNA trafficking routes and translational enhancement, SNV RU5 and Rev/RRE were combined on a single
gag
RNA. We observed a less-than-synergistic effect on cytoplasmic mRNA utilization. Instead, Rev/RRE diverts RU5
gag
RNA to the CRM1-dependent, LMB-inhibited pathway and abrogates translational enhancement by SNV RU5. Our study is the first to show that a nuclear factor(s) directs SNV RU5-containing RNAs to a distinct export pathway that is not inhibited by LMB and programs the intron-containing transcript for translational enhancement.
Effects of Mutations in the Adenoviral E1B 55-Kilodalton Protein Coding Sequence on Viral Late mRNA Metabolism
Authors: Gonzalez Ramon A. , Flint S. J. 
Published: July 2002

ABSTRACT
The human subgroup C adenoviral E1B 55-kDa protein cooperates with the viral E4 Orf6 protein to induce selective export of viral, late mRNAs from the nucleus to the cytoplasm. Previous studies have suggested that such preferential transport of viral mRNA and the concomitant inhibition of export of cellular mRNAs are the result of viral colonization of specialized microenvironments within the nucleus. However, neither the molecular basis of this phenomenon nor the mechanism by which the E1B 55-kDa protein acts has been elucidated. We therefore examined viral late mRNA metabolism in HeLa cells infected with a series of mutant viruses that carry insertions at various positions in the E1B protein coding sequence (P. R. Yew, C. C. Kao, and A. J. Berk, Virology 179:795-805, 1990). All the mutations examined impaired cytoplasmic accumulation of viral L2 mRNAs and reduced L2 mRNA export efficiency. However, in most cases these defects could be ascribed to reduced E1B 55-kDa protein concentration or the unexpected failure of the altered E1B proteins to enter the nucleus efficiently. The latter property, the pleiotropic defects associated with all the mutations that impaired nuclear entry of the E1B protein, and consideration of its primary sequence suggest that these insertions result in misfolding of the protein. Insertion of four amino acids at residue 143 also inhibited viral mRNA export but resulted in increased rather than decreased accumulation of the E1B 55-kDa protein in the nucleus. This mutation specifically impaired the previously described association of the E1B protein with intranuclear structures that correspond to sites of adenoviral DNA replication and transcription (D. Ornelles and T. Shenk, J. Virol. 65:424-439, 1991) and the colocalization of the E1B and E4 Orf6 proteins. As this insertion has been shown to inhibit the interaction of the E1B with the E4 Orf6 protein in infected cell extracts (S. Rubenwolf, H. Schütt, M. Nevels, H. Wolf, and T. Dobner, J. Virol. 71:1115-1123, 1997), these phenotypes provide direct support for the hypothesis that selective viral mRNA export is determined by the functional organization of the infected cell nucleus.
Necropsies in African children: consent dilemmas for parents and guardians
Authors: Lishimpi K , Chintu C , Lucas S , Mudenda V , Kaluwaji J , Story A , Maswahu D , Bhat G , Nunn A J , Zumla A 
Published: July 2002

BACKGROUNDNecropsy examination provides a good index of the accuracy of clinical diagnosis and the quality of treatment, but its use in sub-Saharan Africa is limited.AIMSTo identify the main reasons for parents'/guardians' refusal of consent for necropsy and to explore the issues affecting their decision.METHODSA sequential necropsy study of Zambian children between 2 months and 15 years dying of respiratory disease. When the parent/guardian refused permission for necropsy, the main reason given was recorded, after encouragement to express their specific concerns in their own words.RESULTSParents/guardians of 891 of 1181 children (75.4%) refused to give permission, and 290 (24.6%) consented. Of those who refused, 43% did so on the grounds that it would be a “waste of time,” as the diagnosis should have been made in life and the findings would now be of no benefit to them. More than one quarter of those who refused did so because a death certificate had already been issued and arrangements to transport the body had been made and could not be delayed. Traditional beliefs that ancestral spirits forbade the mutilation of dead bodies were cited by 77 (8.6%). Other reasons included the child not being their own or that they must seek permission from other family members who were not available (6%). Religious beliefs were not a major cause of refusal.CONCLUSIONSIt is possible to achieve a rate of necropsy consent sufficient to undertake valuable clinical pathology studies on children in sub-Saharan Africa. The wide range of reasons cited for refusal points to the diverse and complex interaction of social and cultural factors affecting attitudes to necropsy examination. Medical staff need training and support to improve the uptake of clinical pathology services.Key messagesWorldwide necropsy rates are declining in both adults and childrenEven in conditions where trained counsellors and rapid access to necropsy examination exist, rates of consent remain lowIn Zambia, necropsy examination of children is most commonly perceived by parents/guardians as a waste of time and an inconvenience to arrangements for burial
Delayed union stress fractures of the anterior tibia: conservative management
Authors: Batt M E , Kemp S , Kerslake R 
Published: July 2002

Introduction—A conservative method of treating four delayed union stress fractures of the anterior mid-tibia is described, with an illustrative case history.Methods—Once diagnosed each of the patients was treated in a pneumatic lower leg brace with modified rest. The mean (range) age of the patients was 28 (24–32) years and all were involved in professional or amateur sports. The mean (range) duration of symptoms before diagnosis and definitive treatment of the four fractures was 9 (3–14) months.Results—Use of this technique avoided the need for surgery in this group of patients and allowed return to unrestricted activity an average of 12 months from presentation.Conclusion—The treatment is cost effective and avoids the often uncertain results and morbidity associated with surgery for these difficult stress fractures.
Abnormal regulation of the oestrogen receptor in benign breast lesions
Authors: Shoker B S , Jarvis C , Clarke R B , Anderson E , Munro C , Davies M P A , Sibson D R , Sloane J P 
Published: July 2002

Background—In normal breast tissue the oestrogen receptor (ER) and the proliferation associated antigen Ki67 are negatively associated, indicating that ER+ cells are non-dividing, or that the receptor is downregulated as cells enter cycle. This relation is completely or partially lost in many ER+ breast cancers and in in situ proliferations associated with an increased cancer risk, where coexpression of the two markers is often found.Aims—To determine whether similar changes can be identified in other risk associated breast lesions.Patients/Methods—Paraffin wax blocks from 12 cases of lactational change, 21 apocrine metaplasias, 22 duct ectasias, 20 sclerosing adenosis, 20 fibroadenomas, 19 phyllodes tumours, 20 radial scars, 21 papillomas (15 solitary and six multiple), 15 gynaecomastias, and nine postmortem male breast tissues were retrieved. Immunohistochemistry was used to determine the expression of ER and dual labelling immunofluorescence was used to detect cells expressing both ER and Ki67.Results—Increased numbers of ER+ cells were seen in sclerosing adenosis, radial scars, papillomas, fibroadenomas, and phyllodes tumours but not in apocrine cysts (where no ER+ cells were detected) or duct ectasia (where normal numbers were found). As in the normal breast, the proportion of ER+ cells increased with age in all lesions with the exception of fibroadenomas. Coexpression of ER and Ki67 was found in an increased proportion of cells of all risk associated lesions studied. ER+ cells were less likely to be dividing than ER− cells in all cases, although this was significant only for sclerosing adenosis. The data on sclerosing adenosis, radial scars, papillomas, and fibroadenomas are comparable with those reported previously in hyperplasia of usual type, whereas those in duct ectasia are similar to those of the normal breast. The findings in all lesions, however, differed from those in ductal carcinoma in situ, where proportions of ER+ and ER+/Ki67+ cells are higher and the relation between ER+ cell numbers and age is lost. Thus, the nature and degree of dysregulation of ER in benign breast lesions is broadly in accordance with the degree of risk of developing breast cancer with which they are associated. In gynaecomastia, the proportions of ER+ and ER+/Ki67+ cells were comparable with those seen in benign female breast lesions, but changes with age were not observed. However, the changes in gynaecomastia were similar to those seen in normal male breast.Conclusion—These findings are in keeping with the contention that the dissociation of ER and Ki67 expression is a very early change in the pathway to many breast cancers. However, this change might only have preneoplastic importance in the hormonal milieu of the female breast.
Abstract description of pointer data structures
Authors: Hummel Joseph , Hendren Laurie J. , Nicolau Alexandru 
Published: July 2002

Even though impressive progress has been made in the area of optimizing and parallelizing array-based programs, the application of similar techniques to programs using pointer data structures has remained difficult. Unlike arrays which have a small number of well-defined properties, pointers can be used to implement a wide variety of structures which exhibit a much larger set of properties. The diversity of these structures implies that programs with pointer data structures cannot be effectively analyzed by traditional optimizing and parallelizing compilers.In this paper we present a new approach that leads to the improved analysis and transformation of programs with recursively defined pointer data structures. Our approach is based on a mechanism for the Abstract Description of Data Structures (ADDS). ADDS is a simple extension to existing imperative languages that allows the programmer to explicitly describe the important properties of a large class of data structures. These abstract descriptions may be used by the compiler to achieve more accurate program analysis in the presence of pointers, which in turn enables and improves the application of numerous optimizing and parallelizing transformations. We present ADDS by describing various data structures; we discuss how such descriptions can be used to improve analysis and debugging; and we supply three important transformations enabled by ADDS.
Processor allocation strategies for multiprocessor database machines
Authors: Boral Haran , DeWitt David J. 
Published: July 2002

In this paper four alternative strategies for assigning processors to queries in multiprocessor database machines are described and evaluated. The results demonstrate that SIMD database machines are indeed a poor design when their performance is compared with that of the three MIMD strategies presented.
Also introduced is the application of data-flow machine techniques to the processing of relational algebra queries. A strategy that employs data-flow techniques is shown to be superior to the other strategies described by several experiments. Furthermore, if the data-flow query processing strategy is employed, the results indicate that a two-level storage hierarchy (in which relations are paged between a shared data cache and mass storage) does not have a significant impact on performance.
Digital Computer System for Dynamic Analysis of Speech and Sound Feedback Mechanisms
Authors: Smith K. U. , Ansell S. D. , Koehler J. , Servos G. H. 
Published: July 2002

The aim of the research reported is to put the laboratory application of closed-loop digital computer systems to experimental control and analysis in biology and behavioral science on a formal basis, using special concepts of programming to quantitatively control different parameters of variation in sensory feedback of specific response systems. The theory is unconventional in that the computer and the techniques of closed-loop programming are designed to control time delays, space displacements, kinetic modulations, and informational and symbolic transformations in the sensory feedback that is generated by movements and/or physiological actions of the living subject.
The present experiment illustrates application of the system and the methods of closed-loop perturbation programming to study of delayed auditory feedback of speech. The subject's speech is transduced, amplified, converted by an analog-to-digital converter, programmed for delays, deconverted by a digital-to-analog converter, filtered, amplified, and then used to activate protected earphones on the speaker's ears. The computer is also used to introduce many special perturbation of the auditory feedback of speech in real time.
An Online Display for the Study of Approximating Functions
Authors: Conn Richard W. , von Holdt Richard E. 
Published: July 2002

The method of least squares is often used to determine the arbitrary constants in an empirical formula or approximating function. If such a function is not linear in its unknowns, approximate values must first be obtained. Typically they are obtained graphically or as the result of physical supposition or similar experiment. This paper describes a program written to find first approximations for certain oscilloscope traces by: (1) displaying the trace on a cathode-ray tube (CRT) and, (2) imposing upon it a computer generated curve which (3) employs parameters arbitrarily supplied by an operator in a quest for visual coincidence.
While the technique proved successful in this application, a greater value may lie in its having indicated a mechanism for further automation. In its present form the method might best be utilized as a tool for studying the behavior of selected approximating functions.
A Database Management System for the Federal Courts
Authors: Buchanan Jack R. , Fennell Richard D. , Samet Hanan 
Published: July 2002

A judicial systems laboratory has been established and several large-scale information management systems projects have been undertaken within the Federal Judicial Center in Washington, D.C. The newness of the court application area, together with the experimental nature of the initial prototypes, required that the system building tools be as flexible and efficient as possible for effective software design and development. The size of the databases, the expected transaction volumes, and the long-term value of the court records required a data manipulation system capable of providing high performance and integrity. The resulting design criteria, the programming capabilities developed, and their use in system construction are described herein. This database programming facility has been especially designed as a technical management tool for the database administrator, while providing the applications programmer with a flexible database software interface for high productivity.
Specifically, a network-type database management system using SAIL as the data manipulation host language is described. Generic data manipulation verb formats using SAIL's macro facilities and dynamic data structuring facilities allowing in-core database representations have been developed to achieve a level of flexibility not usually attained in conventional database systems.
An application of FORMAC
Authors: Neidleman L. D. 
Published: July 2002

A nonlinear circuit analysis problem is stated and the way in which it was solved using FORMAC is indicated. The solution of the problem using FORMAC was notable since several other methods that were tried failed. The problem is straightforward (although untenable by hand) but nevertheless involved an elaborate use of the FORMAC language. The program was fairly large and utilized practically every command. In particular, it made extensive use of the PART command. Several tricks were necessary in order to circumvent some of the shortcomings of the FORMAC system.
This paper is more concerned with the use of programming techniques in FORMAC than with the actual engineering problem, although readers may be interested in the problem because it is stated in a general (mathematical) sense and could be of interest in areas other than circuit analysis.
A general business-oriented language based on decision expressions
Authors: Lombardi Lionello A. 
Published: July 2002

The structure of a digital computer programming language which covers a wide class of business and file processing applications is presented. Such a structure, based on identifying and incorporating into a compiler the aspects common to all processes of such class, permits writing extremely compact programs, even for comparatively complex applications, in terms of tables of control expressions which express only information characteristic of the particular application. Furthermore, local changes of a process (e.g. changes affecting only one of the output files involved) can be effected by local modifications in the program (e.g. modification of only one entry of the tables). This structure also allows for inexpensive preparation of loading-speed compilers which translate the source programs into efficient machine codes.
The approach adopted here departs from conventional mechanical language design philosophies. It stresses the structural analysis of the class of processes to be represented in the languages, as opposed to emphasizing formal (i.e., contents-independent) syntactical definitions. It relies exclusively on nonprocedural representation of processes as sets (tables) of relations between data and results (there are no control statements such as GO TO, etc.), instead of using procedure descriptions (which are one-to-one translations of flowcharts). Here an invariant pattern of procedure is identified as characteristic of the class of all batch file processes.
Effects of job loading policies for multiprogramming systems in processing a job stream
Authors: Kameda Hisao 
Published: July 2002

The scheduling of jobs for multiprogramming systems includes the selection of jobs to be loaded into memory (job loading policy or memory schedule) and the scheduling for CPU processing (CPU schedule). There has been a successful empirical claim for the optimal CPU schedule; its optimality has been proved in a Markovian model of job-stream processing that uses the first-come-first-loaded (FCFL) job loading policy. We extend this model to gain insight into the effects of job loading policies.
The model studied consists of an input stream of jobs of two classes and a multiple-resource system (the model of a multiprogramming system) with a stack for waiting jobs. The system consists of a finite amount of memory and a cyclic queue of a single (CPU) server station and a multiple (I/O) server station. The values of parameters describing each class of jobs are distinct except the mean I/O service time and the amount of memory required. The estimate of the maximum processing capacity (throughput bound) of the system is obtained and is shown to be achieved by the combination of the empirically claimed optimal CPU schedule and a job loading policy whereby the set of jobs in memory is kept to be (nearly) balanced with respect to the job stream. Furthermore, we show that the job loading policies independent of the system status have no improvement over the FCFL policy.
Our investigation, supported by numerical calculations, suggests that much more care may be needed in implementing the job loading policy that aims at the optimal processing capacity than in implementing the optimal CPU schedule. This agrees with what has been conjectured on the basis of empirical studies.
An algebra for structured office documents
Authors: Güting Ralf Hartmut , Zicari Roberto , Choy David M. 
Published: July 2002

We describe a data model for structured office information objects, which we generically call “documents,” and a practically useful algebraic language for the retrieval and manipulation of such objects. Documents are viewed as hierarchical structures; their layout (presentation) aspect is to be treated separately. The syntax and semantics of the language are defined precisely in terms of the formal model, an extended relational algebra.The proposed approach has several new features, some of which are particularly useful for the management of office information. The data model is based on nested sequences of tuples rather than nested relations. Therefore, sorting and sequence operations and the explicit handling of duplicates can be described by the model. Furthermore, this is the first model based on a many-sorted instead of a one-sorted algebra, which means that atomic data values as well as nested structures are objects of the algebra. As a consequence, arithmetic operations, aggregate functions, and so forth can be treated inside the model and need not be introduced as query language extensions to the model. Many-sorted algebra also allows arbitrary algebra expressions (with Boolean result) to be admitted as selection or join conditions and the results of arbitrary expressions to be embedded into tuples. In contrast to other formal models, this algebra can be used directly as a rich query language for office documents with precisely defined semantics.