bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Herpes Simplex Virus Type 1 U
S
11 Protein Interacts with Protein Kinase R in Infected Cells and Requires a 30-Amino-Acid Sequence Adjacent to a Kinase Substrate Domain
Authors: Cassady Kevin A. , Gross Martin 
Published: July 2002

ABSTRACT

The herpes simplex virus type 1 γ
1
34.5 gene product precludes the host-mediated protein shutoff response induced by activated protein kinase R (PKR). Earlier studies demonstrated that recombinant viruses lacking the γ
1
34.5 gene (Δγ
1
34.5) developed secondary mutations that allowed earlier U
S
11 expression and enabled continued protein synthesis. Further, in vitro studies demonstrated that a recombinant expressed U
S
11 protein binds PKR, blocks the phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF-2α) by activated PKR, and, if provided prior to PKR activation, precluded PKR autophosphorylation. The present study furthers the hypothesis that early U
S
11 production precludes PKR-mediated host protein shutoff by demonstrating that (i) U
S
11 and PKR interact in the context of viral infection, (ii) this interaction is RNA dependent and requires a 30-amino-acid domain (amino acids 91 to 121) in the carboxyl domain of the U
S
11 protein, (iii) the proteins biochemically colocalize in the S100 ribosomal fraction, and (iv) there is a PKR substrate domain immediately adjacent to the binding domain. The results suggest that the U
S
11 interaction with PKR at the ribosome is RNA dependent and that the U
S
11 protein contains a substrate domain with homology to eIF-2α in close proximity to an essential binding domain.
Pathogenesis of Herpes Simplex Virus Type 2 Virion Host Shutoff (vhs) Mutants
Authors: Smith Tracy J. , Morrison Lynda A. , Leib David A. 
Published: July 2002

ABSTRACTDuring lytic infection, the virion host shutoff (vhs) protein mediates the rapid degradation of mRNA and the shutoff of host protein synthesis. In vivo, herpes simplex virus type 1 (HSV-1) mutants lackingvhsactivity are profoundly attenuated. Homologs ofvhsexist in all of the neurotropic herpesviruses, and the goal of this study was to determine the virulence of HSV-2 mutants lacking vhs. Two HSV-2 recombinants were used in this study: 333-vhsB, which has alacZcassette inserted into the N terminus ofvhs, and 333d41, which has a 939-bp deletion invhs. As expected, both 333-vhsB and 333d41 failed to induce the cellular RNA degradation characteristic of HSV. Corneal, vaginal, and intracerebral routes of infection were used to study pathogenesis. Both viruses grew to significantly lower titers in the corneas, trigeminal ganglia, vaginas, dorsal root ganglia, spinal cords, and brains of mice than wild-type and rescue viruses, with a correspondingly reduced induction of disease. Both viruses, however, reactivated efficiently from explanted trigeminal ganglia, showing thatvhsis dispensable for reactivation. The lethality of 333d41 following peripheral infection of mice, however, was significantly higher than that of 333-vhsB, suggesting that some of the attenuation of 333-vhsB may be due to the presence of alacZcassette in thevhslocus. Taken together, these data show thatvhsrepresents an important determinant of HSV-2 pathogenesis and have implications for the design of HSV-2 recombinants and vaccines.
Identification of Human Herpesvirus 6 Latency-Associated Transcripts
Authors: Kondo Kazuhiro , Shimada Kazuya , Sashihara Junji , Tanaka-Taya Keiko , Yamanishi Koichi 
Published: July 2002

ABSTRACT
Four kinds of latency-associated transcripts of human herpesvirus 6 were identified which were detected only in latently infected cells. Although they were oriented in the same direction as the immediate-early 1 and 2 (IE1/IE2) genes and shared their protein-coding region with IE1/IE2, their transcription start sites and exon(s) were latency associated.
Self reported symptoms and inhibition of acetylcholinesterase activity among Kenyan agricultural workers
Authors: Ohayo-Mitoko Grace J A , Kromhout Hans , Simwa James M , Boleij Jan S M , Heederik Dick 
Published: July 2002

OBJECTIVESThis study was part of the East African pesticides project. The general objective was to assess health hazards posed by handling, storage, and use of pesticides, on agricultural estates and small farms with a view to developing strategies for prevention and control of pesticide poisoning. The aim of this paper is to describe the prevalence of symptoms in this population, to relate levels of inhibition to reported symptoms and evaluate at which levels of inhibition symptoms become increased.METHODSComplete data were available for 256 exposed subjects and 152 controls from four regions in Kenya. A structured questionnaire on symptoms experienced at the time of interview was given to all subjects and controls. Information was also obtained on sex, age, main occupation, and level of education. Symptoms reported during the high exposure period, were initially clustered in broader symptom categories from reference literature on health effects of pesticides that inhibit cholinesterase (organophosphate and carbamate). Prevalence ratios were estimated for symptoms with changes in cholinesterase activity in serum.RESULTSSymptom prevalence in exposed subjects was higher during the high exposure period than the low exposure period, although these differences were not significant. Interestingly, a clear and significant change in symptoms prevalence was found in the controls with a higher prevalence in the low exposure period. Analysis of the relation between cholinesterase inhibition and symptoms showed that prevalence ratios were significantly >1 for respiratory, eye, and central nervous system symptoms for workers with >30% inhibition. Similar results were found for analyses with the actual level of acetylcholinesterase activity.CONCLUSIONThe results suggest the presence of a relation between exposure and acetylcholinesterase inhibition, acetylcholinesterase activity, and respiratory, eye, and central nervous system symptoms. Increased symptom prevalence was found at acetylcholinesterase activities generally considered to be non-adverse.
Serial perfusion brain tomographic scans detect reversible focal ischaemia in Rasmussen's encephalitis
Authors: Vinjamuri Sobhan , Leach J P , Hart I K 
Published: July 2002

Summary
A 39-year-old man with advanced adult-onset Rasmussen's encephalitis was treated with prednisolone and long-term, high-dose, human intravenous immunoglobulin. A pretreatment, semiquantitative interictal brain perfusion single photon emission computed tomography (SPECT) scan using 99Tcm HMPAO (hexamethylene propylene amine oxime) showed hypoperfusion in the clinically affected right frontal, parietal and temporal lobes and contralateral perfusion defects. A second scan 8 months later revealed significant improvements (more than two standard deviations) in perfusion of the right frontal and temporal lobes despite serial magnetic resonance imaging evidence of permanent brain damage. This was associated with useful recovery of the patient's physical and cognitive function. We conclude that serial perfusion brain SPECT scanning is a useful method to demonstrate improvement in patients with Rasmussen's encephalitis in response to therapy.
Audit of the investigation of iron deficiency anaemia in a district general hospital, with sample guidelines for future practice
Authors: Willoughby J M T , Laitner S M 
Published: July 2002

Abstract
Iron deficiency anaemia commonly presents in patients who are asymptomatic. In the absence of published guidelines the search for a cause in such cases is frequently uncoordinated, and risks delay in the diagnosis of pathologies requiring urgent attention. This audit was undertaken to determine how thoroughly patients referred to the gastrointestinal unit in a district general hospital between 1990 and 1995 had been investigated, and to draw up guidelines for future practice on the basis of its results. From the case notes of 334 patients examined endoscopically for anaemia 126 were identified as having both proved iron deficiency and a lack of clinical pointers to its cause. The percentage and details of diagnoses made during initial study and a median follow up period of 28 months were ascertained, together with the certified diagnoses of patients who had died. A cause of iron deficiency was identified in 48 (38%) of patients, 22 with cancer. Ten others received a diagnosis during follow up, of whom three died from the condition to which their anaemia had been attributed. Death certificates supplied diagnoses of potential relevance in three further cases. The main gaps in endoscopic coverage consisted of omitting duodenal biopsy or colonoscopy after negative upper gastrointestinal endoscopy. Moreover, diagnosis of certain extraintestinal pathologies, including cancers, was sometimes delayed for lack of liaison between gastroenterologists and other specialists. These and other points have been addressed in the guidelines now proposed.
Peritoneal encapsulation: a preoperative diagnosis is possible
Authors: Naraynsingh V , Maharaj D , Singh M , Ramdass M J 
Published: July 2002

Abstract
Peritoneal encapsulation is an exceedingly rare developmental abnormality in which the small intestine is encased in an accessory peritoneal sac between the omentum and mesocolon. Two clinical signs associated with the dense fibrous layer encapsulating the intestine are described. The first is a fixed, asymmetrical distension of the abdomen, which does not vary with peristaltic activity due to the unvarying position of the fibrous capsule. The second is the difference in the consistency of the abdominal wall to palpation. The flat area is firm, due to the dense fibrous capsule and the distended area soft, due to the thin walled distended small intestine with no overlying fibrous layer.
FIBRE BUNDLE FORMULATION OF NONRELATIVISTIC QUANTUM MECHANICS V: INTERPRETATION, SUMMARY AND DISCUSSION
Authors: ILIEV BOZHIDAR Z. 
Published: July 2002

We propose a new systematic fibre bundle formulation of nonrelativistic quantum mechanics. The new form of the theory is equivalent to the usual one and is in harmony with the modern trends in theoretical physics and potentially admits new generalizations in different directions. In it the Hilbert space of a quantum system (from conventional quantum mechanics) is replaced with an appropriate Hilbert bundle of states and a pure state of the system is described by a lifting of paths or section along paths in this bundle. The evolution of a pure state is determined through the bundle (analog of the) Schrödinger equation. Now the dynamical variables and density operator are described via liftings of paths or morphisms along paths in suitable bundles. The mentioned quantities are connected by a number of relations derived in this work. This is the fifth, closing, part of our investigation. We briefly discuss the observer's role in the theory and different realizations of the space–time model used as a base space in the bundle approach to quantum mechanics. The exact conditions for the equivalence of Hilbert bundle and Hilbert space formulations of the theory are pointed out. A table of comparison between both descriptions of nonrelativistic quantum mechanics is presented. We discuss some principal moments of the Hilbert bundle description and show that as a scheme it is more general than the Hilbert space one. Different directions for further research are pointed out.
THE LINEAR BOLTZMANN EQUATION FOR LONG-RANGE FORCES: A DERIVATION FROM PARTICLE SYSTEMS
Authors: DESVILLETTES L. , PULVIRENTI M. 
Published: July 2002

In this paper we consider a particle moving in a random distribution of obstacles. Each obstacle generates an inverse power law potential εs/|x|s, where ε is a small parameter and s>2. Such a rescaled potential is truncated at distance εγ-1, where γ∈] 0, 1[ is suitably large. We also assume that the scatterer density is diverging as ε-d+1, where d is the dimension of the physical space. We prove that, as ε→0 (the Boltzmann–Grad limit), the probability density of a test particle converges to a solution of the linear (uncutoff) Boltzmann equation with the cross-section relative to the potential V(x)=|x|-s.
INVARIANTS OF KNOT DIAGRAMS AND RELATIONS AMONG REIDEMEISTER MOVES
Authors: ÖSTLUND OLOF-PETTER 
Published: July 2002

In this paper a classification of Reidemeister moves, which is the most refined, is introduced. In particular, this classification distinguishes some Ω3-moves that only differ in how the three strands that are involved in the move are ordered on the knot. To transform knot diagrams of isotopic knots into each other one must in general use Ω3-moves of at least two different classes. To show this, knot diagram invariants that jump only under Ω3-moves are introduced. Knot diagrams of isotopic knots can be connected by a sequence of Reidemeister moves of only six, out of the total of 24, classes. This result can be applied in knot theory to simplify proofs of invariance of diagrammatical knot invariants. In particular, a criterion for a function on Gauss diagrams to define a knot invariant is presented.
RNA In Silico The Computational Biology of RNA Secondary Structures
Authors: Flamm Chirstoph , Hofacker Ivo L. , Stadler Peter F. 
Published: July 2002

RNA secondary structures provide a unique computer model for investigating the most important aspects of structural and evolutionary biology. The existence of efficient algorithms for solving the folding problem, i.e., for predicting the secondary structure given only the sequence, allows the construction of realistic computer simulations. The notion of a "landscape" underlies both the structure formation (folding) and the (in vitro) evolution of RNA. Evolutionary adaptation may be seen as hill climbing process on a fitness landscape which is determined by the phenotype of the RNA molecule (within the model this is its secondary structure) and the selection constraints acting on the molecules. We find that a substantial fraction of point mutations do not change an RNA secondary structure. On the other hand, a comparable fraction of mutations leads to very different structures. This interplay of smoothness and ruggedness (or robustness and sensitivity) is a generic feature of both RNA and protein sequence-structure maps. Its consequences, "shape space covering" and "neutral networks" are inherited by the fitness landscapes and determine the dynamics of RNA evolution. Punctuated equilibria at phenotype level and a diffusion like evolution of the underlying genotypes are a characteristics feature of such models. As a practical application of these theoretical findings we have designed an algorithm that finds conserved (and therefore potentially functional substructures of RNA virus genomes from spares data sets. The folding dynamics of particular RNA molecule can also be studied successfully based on secondary structure. Given an RNA sequence, we consider the energy landscape formed by all possible conformations (secondary structures). A straight formward implementation of the Metropolis algorithm is sufficient to produce a quite realistic folding kinetics, allowing to identify meta-stable states and folding pathways. Just as in the protein case there are good and bad folders which can be distinguished by the properties of their landscapes.
Coevolutionary Learning and the Design of Complex Systems
Authors: Juillé Hugues , Pollack Jordan B. 
Published: July 2002

Complex systems composed of a large number of loosely coupled entities, with no central coordination offer a number of attractive properties like scalability, robustness or massively distributed computation. However, designing such complex systems presents some challenging issues that are difficult to tackle with traditional top-down engineering methodologies. Coevolutionary learning, which involves the embedding of adaptive learning agents in a fitness environment that dynamically responds to their progress, is proposed as a paradigm to explore a space of complex system designs. It is argued that coevolution offers a flexible framework for the implementation of search heuristics that can efficiently exploit some of the structural properties exhibited by such state spaces. However, several drawbacks have to be overcome in order for coevolutionary learning to achieve continuous progress in the long term. This paper presents some of those problems and introduces a new strategy based on the concept of an "ideal" trainer to address them. This presentation is illustrated with a case study: the discovery of cellular automata rules to implement a classification task. The application of the "ideal" trainer paradigm to that problem resulted in a significant improvement over previously known best rules for this task.
Adaptable concurrency control for atomic data types
Authors: Atkins M. S. , Coady M. Y. 
Published: July 2002

In many distributed systems concurrent access is required to a shared object, where abstract object servers may incorporate type-specific properties to define consistency requirements. Each operation and its outcome is treated as an event, and conflicts may occur between different event types. Hence concurrency control and synchronization are required at the granularity of conflicting event types. With such a fine granularity of locking, the occurrence of conflicts is likely to be lower than with whole-object locking, so optimistic techniques become more attractive.
This work describes the design, implementation, and performance of servers for a shared atomic object, a semiqueue, where each server employs either pessimistic or optimistic locking techniques on each conflicting event type. We compare the performance of a purely optimistic server, a purely pessimistic server, and a hybrid server which treats certain event types optimistically and others pessimistically, to demonstrate the most appropriate environment for using pessimistic, optimistic, or hybrid control. We show that the advantages of low overhead on optimistic locking at low conflict levels is offset at higher conflict levels by the wasted work done by aborted transactions.
To achieve optimum performance over the whole range of conflict levels, an adaptable server is required, whereby the treatment of conflicting event types can be changed dynamically between optimistic and pessimistic, according to various criteria depending on the expected frequency of conflict.
We describe our implementations of adaptable servers which may allocate concurrency control strategy on the basis of state information, the history of conflicts encountered, or by using preset transaction priorities.
We show that the adaptable servers perform almost as well as the best of the purely optimistic, pessimistic, or hybrid servers under the whole range of conflict levels, showing the versatility and efficiency of the dynamic servers.
Finally we outline a general design methodology for implementing adaptable concurrency control in servers for atomic objects, illustrated using an atomic shared B-tree.
File-system development with stackable layers
Authors: Heidemann John S. , Popek Gerald J. 
Published: July 2002

Filing services have experienced a number of innovations in recent years, but many of these promising ideas have failed to enter into broad use. One reason is that current filing environments present several barriers to new development. For example, file systems today typically stand alone instead of building on the work of others, and support of new filing services often requires changes that invalidate existing work.
Stackable file-system design addresses these issues in several ways. Complex filing services are constructed from layer “building blocks,” each of which may be provided by independent parties. There are no syntactic constraints to layer order, and layers can occupy different address spaces, allowing very flexible layer configuration. Independent layer evolution and development are supported by an extensible interface bounding each layer.
This paper discusses stackable layering in detail and presents design techniques it enables. We describe an implementation providing these facilities that exhibits very high performance. By lowering barriers to new filing design, stackable layering offers the potential of broad third-party file-system development not feasible today.
Generality in artificial intelligence
Authors: McCarthy John 
Published: July 2002

My 1971 Turing Award Lecture was entitled "Generality in Artificial Intelligence." The topic turned out to have been overambitious in that I discovered I was unable to put my thoughts on the subject in a satisfactory written form at that time. It would have been better to have reviewed my previous work rather than attempt something new, but such was not my custom at that time.
I am grateful to ACM for the opportunity to try again. Unfortunately for our science, although perhaps fortunately for this project, the problem of generality in artificial intelligence (AI) is almost as unsolved as ever, although we now have many ideas not available in 1971. This paper relies heavily on such ideas, but it is far from a full 1987 survey of approaches for achieving generality. Ideas are therefore discussed at a length proportional to my familiarity with them rather than according to some objective criterion.
It was obvious in 1971 and even in 1958 that AI programs suffered from a lack of generality. It is still obvious; there are many more details. The first gross symptom is that a small addition to the idea of a program often involves a complete rewrite beginning with the data structures. Some progress has been made in modularizing data structures, but small modifications of the search strategies are even less likely to be accomplished without rewriting.
Another symptom is no one knows how to make a general database of commonsense knowledge that could be used by any program that needed the knowledge. Along with other information, such a database would contain what a robot would need to know about the effects of moving objects around, what a person can be expected to know about his family, and the facts about buying and selling. This does not depend on whether the knowledge is to be expressed in a logical language or in some other formalism. When we take the logic approach to AI, lack of generality shows up in that the axioms we devise to express commonsense knowledge are too restricted in their applicability for a general commonsense database. In my opinion, getting a language for expressing general commonsense knowledge for inclusion in a general database is the key problem of generality in AI.
Here are some ideas for achieving generality proposed both before and after 1971. I repeat my disclaimer of comprehensiveness.
Partial-match retrieval using indexed descriptor files
Authors: Pfaltz John L. , Berman William J. , Cagley Edgar M. 
Published: July 2002

In this paper we describe a practical method of partial-match retrieval in very large data files. A binary code word, called a descriptor, is associated with each record of the file. These record descriptors are then used to form a derived descriptor for a block of several records, which will serve as an index for the block as a whole; hence, the name “indexed descriptor files.”
First the structure of these files is described and a simple, efficient retrieval algorithm is presented. Then its expected behavior, in terms of storage accesses, is analyzed in detail. Two different file creation procedures are sketched, and a number of ways in which the file organization can be “tuned” to a particular application are suggested.