bluuebunny/crossref_metadata_2025_split huggingface dataset:
A page allocation strategy for multiprogramming systems
Authors: Chamberlin Donald D. , Fulier Samuel H. , Liu Leonard Y. 
Published: October 2004

In a multiprogramming, virtual-memory computing system, many processes compete simultaneously for system resources, which include CPU's, main memory page frames, and the transmission capacity of the paging drum. (We define a “process” here as a program with its own virtual memory, requiring an allocation of real memory and a CPU in order to execute). This paper studies ways of allocating resources to processes in order to maximize throughput in systems which are not CPU-bound.
As is customary, we define the multiprogramming “set” (MPS) as the set of processes eligible for allocation of resources at any given time. Each process in the MPS is allocated a certain number of page frames and allowed to execute, interrupted periodically by page faults. A process remains in the MPS until it finishes or exhausts its “time slice”, at which time it is demoted. We assume the existence of two resource managers within the operating system: The Paging Manager and the Scheduler. The function of the Paging Manager is to control the size of the MPS, and to allocate main storage page frames among those processes in the MPS. The function of the Scheduler is to assign time-slice lengths to the various processes, and to define a promotion order among those processes not currently in the MPS. The Scheduler must ensure that system responsiveness is adequate, while the Paging Manager is primarily concerned with throughput. This paper studies possible strategies for the Paging Manager. A strategy for the Scheduler is proposed in (2).
Polynomial complete scheduling problems
Authors: Ullman J. D. 
Published: October 2004

We show that the problem of finding an optimal schedule for a set of jobs is polynomial complete even in the following two restricted cases.
(1) All jobs require one time unit.
(2) All jobs require one or two time units, and there are only two processors.
As a consequence, the general preemptive scheduling problem is also polynomial complete.
These results are tantamount to showing that the scheduling problems mentioned are intractable.
Real-time packet video over satellite channels
Authors: Cohen Danny 
Published: October 2004

The paper describes major issues and problems in the use of packet satellite channels for real-time video images and suggests some solutions. The DARPA Wide Band Communication Network provides the testbed for this activity.
The main idea in this paper is the automatic online tradeoff between the quality and the dynamics of the communicated images in order to optimally adapt to the changes of the channel performance and of the scene to be communicated.
The paper discusses the problems of real-time packet video, suggests several techniques to cope with them, and describes some new approaches to the encoding of real-time video communication. The paper describes in more detail several encoding schemes based on this approach, using the 2-dimensional Discrete Cosine Transform (DCT).
Section-C describes issues which are arise in the application of packet satellite channels for real-time video communication. Section-D discusses a general approach which addresses these issues. Section-E describes a general methodology for signal coding and compression, and Section-F describes a scheme for the communication of video images using DCT of the raw images in an absolute way, unlike the four differential schemes which are described in Section-G. Section-H describes a scheme which self-corrects the accumulated quantization errors introduced by the encoding and compression. Such errors are totally eliminated for static images.
Controlling window protocols for time-constrained communication in a multiple access environment
Authors: Kurose James F. , Schwartz Mischa , Yemini Yechiam 
Published: October 2004

For many time-constrained communication applications, such as packetized voice, a critical performance measure is the percentage of messages which are transmitted within a given amount of time after their arrival at a sending station. We examine the use of a group random access protocol based on time windows for achieving time-constrained communication in a multiple access environment. First, we formulate a policy for controlling protocol operation in order to minimize the percentage of messages with waiting times greater than some given bound. A semi-Markov decision model is then developed for protocol operation and three of the four optimal control elements of this policy are then determined.
Although the semi-Markov decision model can also be used to obtain performance results, the procedure is too computationally expensive to be of practical use. Thus, an alternate performance model based on a centralized queueing system with impatient customers is developed. Protocol performance under the optimal elements of the control policy shows significant improvements over cases in which the protocol is not controlled in this manner. Simulation results are also presented to corroborate the analytic results.
Access and communication controls in an accounting information system
Authors: Rushinek Avi , Rushinek Sara F. 
Published: October 2004

This paper involves the exploration of two very important security controls in a computerized accounting information system: (1) access controls, and (2) communication controls. The various specific access and communication controls are examined, analyzing their roles in an accounting information system's computer network.
The growing use of computers in the accounting information systems of the business environment, along with the presence of growing computer fraud, necessitate managements to implement stricter access and communication controls.
Resource management in a distributed system
Authors: Yudkin Mark 
Published: October 2004

In the Cambridge Distributed System, developed at the Computer Laboratory. Cambridge, terminals, machines and peripherals are separated by a ring network. A problem that arises is the establishment and control of suitable connexions between the individual components, so that users may use machines, machines may use peripherals or other machines, etc. in a secure manner.
This paper describes an experimental mechanism used to control the connexions and provide security in our particular system. The solution is not restricted to the Cambridge ring, although a different architecture may suggest alternative solutions more suited to its specific features. Some possibilities are discussed.
Uniform access to Internet directory services
Authors: Comer D. , Droms R. E. 
Published: October 2004

As networks and internetworks of computers expand in size and scope, discovery and location of resources becomes a primary function of the networked computing environment. Static tables describing network resources have been replaced by dynamic directory services, such as X.500 and the Internet Domain Name System. These dynamic directory services provide more timely and accurate information about network resources than static tables.
A wide variety of services address various components of the resource discovery and location problem. These services can be loosely classified as either low-level protocols or high-level services. Low-level protocols, such as RARP and ICMP, are simple delivery protocols and provide limited information; high-level services, such as the Internet Domain Name System and X.500, use complex delivery protocols to answer complex queries. Neither class of directory service is appropriate in all situations. Low-level services are too restrictive in the type of queries and information they support, while high-level services may be too expensive for some low-function networks.
Multiplexing issues in communication system design
Authors: Feldmeier C. C. 
Published: October 2004

This paper considers some of the multiplexing issues in communication system design by examining overall system issues. In particular, we distinguish physical multiplexing of resources from logical multiplexing of streams. Both physical-resource multiplexing and logical multiplexing determine the service that can be provided by a communication system. We also discuss two issues affected by logical multiplexing - flow control and the relationship between control and data streams of a connection.We conclude that the granularity of physical resource sharing must be fine enough to meet the jitter and latency constraints of demanding applications. Also, high speed communication systems should restrict their logical multiplexing to layer 3.
Adrenal cortex: scalpels, syringes, and separatory funnels
Authors: Akana Susan F. 
Published: October 2004

This essay looks at the historical significance of three APS classic papers that are freely available online: Houssay BA and Lewis JT. The relative importance to life of cortex and medulla of the adrenal glands. Am J Physiol 64: 512—521, 1923 ( http://ajplegacy.physiology.org/cgi/reprint/64/3/512 ). Marine D and Baumann EJ. Duration of life after suprarenalectomy in cats and attempts to prolong it by injections of solutions containing sodium salts, glucose and glycerol. Am J Physiol 81: 86—100, 1927 ( http://ajplegacy.physiology.org/cgi/reprint/81/1/86 ). Swingle WW and Pfiffner JJ. Studies on the adrenal cortex. I. The effect of a lipid fraction upon the life-span of adrenalectomized cats. Am J Physiol 96: 153—163, 1931 ( http://ajplegacy.physiology.org/cgi/reprint/96/1/153 ).
Berne's adenosine hypothesis of coronary blood flow control
Authors: Feigl Eric O. 
Published: October 2004

This essay looks at the historical significance of an APS classic paper that is freely available online: Berne RM. Cardiac nucleotides in hypoxia: possible role in regulation of coronary blood flow. Am J Physiol 204: 317–322, 1963 ( http://ajplegacy.physiology.org/cgi/reprint/204/2/317 ).
Two classic papers in acid-base physiology: contributions of R. F. Pitts, R. S. Alexander, and W. D. Lotspeich
Authors: Giebisch Gerhard 
Published: October 2004

This essay looks at the historical significance of two APS classic papers that are freely available online:Pitts RF and Alexander RS. The nature of the renal tubular mechanism for acidifying the urine. Am J Physiol 144: 239—254, 1945 ( http://ajplegacy.physiology.org/cgi/reprint/144/2/239 ).Pitts RF and Lotspeich WD. Bicarbonate and the renal regulation of acid base balance. Am J Physiol 147: 138—154, 1946 ( http://ajplegacy.physiology.org/cgi/reprint/147/1/138 ).
Ca-induced Ca release: lessons regarding cell models
Authors: Harder David R. 
Published: October 2004

This essay looks at the historical significance of an APS classic paper that is freely available online: Fabiato A. Calcium-induced release of calcium from the cardiac sarcoplasmic reticulum. Am J Physiol Cell Physiol 245: C1–C14, 1983 ( http://ajpcell.physiology.org/cgi/reprint/245/1/C1 ).
Nature vs. nurture: can exercise really alter fiber type composition in human skeletal muscle?
Authors: Ingalls Christopher P. 
Published: October 2004

This essay looks at the historical significance of two APS classic papers that are freely available online:Gollnick PD, Armstrong RB, Saubert CW IV, Piehl K, and Saltin B. Enzyme activity and fiber composition in skeletal muscle of untrained and trained men. J Appl Physiol 33: 312—319, 1972 ( http://jap.physiology.org/cgi/reprint/33/3/312 ).Gollnick PD, Armstrong RB, Saltin B, Saubert CW IV, Sembrowich WL, and Shepherd RE. Effect of training on enzyme activity and fiber composition of human skeletal muscle. J Appl Physiol 34: 107—111, 1973 ( http://jap.physiology.org/cgi/reprint/34/1/107 ).
Hypothalamic control of body temperature: insights from the past
Authors: Mack Gary W. 
Published: October 2004

This essay looks at the historical significance of three APS classic papers that are freely available online: Hammel HT, Hardy JD, and Fusco MM. Thermoregulatory responses to hypothalamic cooling in unanesthetized dogs. Am J Physiol 198: 481—486, 1960 ( http://ajplegacy.physiology.org/cgi/reprint/198/3/481 ). Hammel HT, Jackson DC, Stolwijk JAJ, Hardy JD, and Strømme SB. Temperature regulation by hypothalamic proportional control with an adjustable set point. J Appl Physiol 18: 1146—1154, 1963 ( http://jap.physiology.org/cgi/reprint/18/6/1146 ). Hellstrøm B and Hammel HT. Some characteristics of temperature regulation in the unanesthetized dog. Am J Physiol 213: 547—556, 1967 ( http://ajplegacy.physiology.org/cgi/reprint/213/2/547 ).
Eugene M. Landis and the physiology of the microcirculation
Authors: Renkin E. M. 
Published: October 2004

This essay looks at the historical significance of two APS classic papers that are freely available online: Landis EM. The capillary pressure in frog mesentery as determined by micro-injection methods. Am J Physiol 75: 548–570, 1926 ( http://ajplegacy.physiology.org/cgi/reprint/75/3/548 ). Landis EM. Micro-injection studies of capillary permeability. II. The relation between capillary pressure and the rate at which fluid passes through the walls of single capillaries. Am J Physiol 82: 217–238, 1927 ( http://ajplegacy.physiology.org/cgi/reprint/82/2/217 ).
Experimental validation of the countercurrent model of urinary concentration
Authors: Schafer James A. 
Published: October 2004

This essay looks at the historical significance of four APS classic papers that are freely available online:Jolliffe N, Shannon JA, and Smith HW. The excretion of urine in the dog. III. The use of non-metabolized sugars in the measurement of the glomerular filtrate. Am J Physiol 100: 301—312, 1932 ( http://ajplegacy.physiology.org/cgi/reprint/100/2/301 ).Shannon JA. The excretion of inulin by the dog. Am J Physiol 112: 405—413, 1935 ( http://ajplegacy.physiology.org/cgi/reprint/112/3/405 ).Shannon JA and Fisher S. The renal tubular reabsorption of glucose in the normal dog. Am J Physiol 122: 765—774, 1938 ( http://ajplegacy.physiology.org/cgi/reprint/122/3/765 ).Shannon JA, Farber S, and Troast L. The measurement of glucose Tm in the normal dog. Am J Physiol 133: 752—761, 1941 ( http://ajplegacy.physiology.org/cgi/reprint/133/3/752 ).
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries
Authors: Keime Céline , Damiola Francesca , Mouchiroud Dominique , Duret Laurent , Gandrillon Olivier 
Published: October 2004

Abstract
Background
Serial Analysis of Gene Expression (SAGE) is a method of large-scale gene expression analysis that has the potential to generate the full list of mRNAs present within a cell population at a given time and their frequency. An essential step in SAGE library analysis is the unambiguous assignment of each 14 bp tag to the transcript from which it was derived. This process, called tag-to-gene mapping, represents a step that has to be improved in the analysis of SAGE libraries. Indeed, the existing web sites providing correspondence between tags and transcripts do not concern all species for which numerous EST and cDNA have already been sequenced.

Results
This is the reason why we designed and implemented a freely available tool called Identitag for tag identification that can be used in any species for which transcript sequences are available. Identitag is based on a relational database structure in order to allow rapid and easy storage and updating of data and, most importantly, in order to be able to precisely define identification parameters. This structure can be seen like three interconnected modules : the first one stores virtual tags extracted from a given list of transcript sequences, the second stores experimental tags observed in SAGE experiments, and the third allows the annotation of the transcript sequences used for virtual tag extraction. It therefore connects an observed tag to a virtual tag and to the sequence it comes from, and then to its functional annotation when available. Databases made from different species can be connected according to orthology relationship thus allowing the comparison of SAGE libraries between species. We successfully used Identitag to identify tags from our chicken SAGE libraries and for chicken to human SAGE tags interspecies comparison. Identitag sources are freely available on http://pbil.univ-lyon1.fr/software/identitag/ web site.

Conclusions
Identitag is a flexible and powerful tool for tag identification in any single species and for interspecies comparison of SAGE libraries. It opens the way to comparative transcriptomic analysis, an emerging branch of biology.
Tools for loading MEDLINE into a local relational database
Authors: Oliver Diane E , Bhalotia Gaurav , Schwartz Ariel S , Altman Russ B , Hearst Marti A 
Published: October 2004

Abstract
Background
Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers.

Results
We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated.

Conclusions
Relational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at http://biotext.berkeley.edu.
Extreme conservation of noncoding DNA near HoxD complex of vertebrates
Authors: Sabarinadh Chilaka , Subramanian Subbaya , Tripathi Anshuman , Mishra Rakesh K 
Published: October 2004

Abstract
Background
Homeotic gene complexes determine the anterior-posterior body axis in animals. The expression pattern and function of hox genes along this axis is colinear with the order in which they are organized in the complex. This 'chromosomal organization and functional correspondence' is conserved in all bilaterians investigated. Genomic sequences covering the HoxD complex from several vertebrate species are now available. This offers a comparative genomics approach to identify conserved regions linked to this complex. Although the molecular basis of 'colinearity' of Hox complexes is not yet understood, it is possible that there are control elements within or in the proximity of these complexes that establish and maintain the expression patterns of hox genes in a coordinated fashion.

Results
We have compared DNA sequence flanking the HoxD complex of several primate, rodent and fish species. This analysis revealed an unprecedented conservation of non-coding DNA sequences adjacent to the HoxD complex from fish to human. Stretches of hundreds of base pairs in a 7 kb region, upstream of HoxD complex, show 100% conservation across the vertebrate species. Using PCR primers from the human sequence, these conserved regions could be amplified from other vertebrate species, including other mammals, birds, reptiles, amphibians and fish. Our analysis of these sequences also indicates that starting from the conserved core regions, more sequences have been added on and maintained during evolution from fish to human.

Conclusion
Such a high degree of conservation in the core regions of this 7 kb DNA, where no variation occurred during ~500 million years of evolution, suggests critical function for these sequences. We suggest that such sequences are likely to provide molecular handle to gain insight into the evolution and mechanism of regulation of associated gene complexes.
Branched-chain amino acid aminotransferase and methionine formation in Mycobacterium tuberculosis
Authors: Venos Erik S , Knodel Marvin H , Radford Cynthia L , Berger Bradley J 
Published: October 2004

Abstract
Background
Tuberculosis remains a major world-wide health threat which demands the discovery and characterisation of new drug targets in order to develop future antimycobacterials. The regeneration of methionine consumed during polyamine biosynthesis is an important pathway present in many microorganisms. The final step of this pathway, the conversion of ketomethiobutyrate to methionine, can be performed by aspartate, tyrosine, or branched-chain amino acid aminotransferases depending on the particular species examined.

Results
The gene encoding for branched-chain amino acid aminotransferase in Mycobacterium tuberculosis H37Rv has been cloned, expressed, and characterised. The enzyme was found to be a member of the aminotransferase IIIa subfamily, and closely related to the corresponding aminotransferase in Bacillus subtilis, but not to that found in B. anthracis or B. cereus. The amino donor preference for the formation of methionine from ketomethiobutyrate was for isoleucine, leucine, valine, glutamate, and phenylalanine. The enzyme catalysed branched-chain amino acid and ketomethiobutyrate transamination with a Km of 1.77 – 7.44 mM and a Vmax of 2.17 – 5.70 μmol/min/mg protein, and transamination of ketoglutarate with a Km of 5.79 – 6.95 mM and a Vmax of 11.82 – 14.35 μmol/min/mg protein. Aminooxy compounds were examined as potential enzyme inhibitors, with O-benzylhydroxylamine, O-t-butylhydroxylamine, carboxymethoxylamine, and O-allylhydroxylamine yielding mixed-type inhibition with Ki values of 8.20 – 21.61 μM. These same compounds were examined as antimycobacterial agents against M. tuberculosis and a lower biohazard M. marinum model system, and were found to completely prevent cell growth. O-Allylhydroxylamine was the most effective growth inhibitor with an MIC of 78 μM against M. marinum and one of 156 μM against M. tuberculosis.

Conclusion
Methionine formation from ketomethiobutyrate is catalysed by a branched-chain amino acid aminotransferase in M. tuberculosis. This enzyme can be inhibited by selected aminooxy compounds, which also have effectiveness in preventing cell growth in culture. These compounds represent a starting point for the synthesis of branched-chain aminotransferase inhibitors with higher activity and lower toxicity.